Article

Determination of Phenotype Associated SNPs in the MC1R Gene*

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Abstract

Prediction of physical appearance based on genetic analysis is a very attractive prospect for forensic investigations. Recent studies have proved that there is a significant association between some genetic variants of the melanocortin 1 receptor (MC1R) gene and red hair color. The present study focuses on the potential forensic applicability of variation within this pigment-related gene. Sequencing of the complete MC1R gene was performed on a group of red-haired individuals and controls with different pigmentation. A major role in determination of red hair color is played by two MC1R variants—C451T and C478T. The optimized minisequencing assay for genotyping of the above positions and three other important red hair-related MC1R polymorphisms, C252A, G425A, and G880C was successfully applied to analyze typical forensic specimens. Determination of a homozygous or heterozygous combination can be a good predictor of both red hair color and fair skin of a subject.

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... The idea, also known as forensic DNA phenotyping (FDP) assumes description of the physical appearance of an unknown felon or decomposed body based on genotypic data of highly predictive DNA polymorphisms, usually single nucleotide polymorphisms (SNPs) [12,13]. The identification of the important role of the HERC2-OCA2 gene complex for eye colour determination [14][15][16][17][18], as well as the MC1R gene for hair colour determination [19][20][21][22][23], were found to be particularly significant for prediction [17,23]. Information about the variation in several pigmentation genes allowed the development of the first forensic prediction models and assays [17,[23][24][25][26][27][28][29][30]. ...
... DNA from the study sample was extracted using the NucleoSpin 1 Tissue extraction kit (Macherey-Nagel GmbH & Co. KG, Germany) as previously described [38]. The study involved 37 SNP positions and one insertion-deletion polymorphism located in 13 selected genes including SLC45A2, IRF4, EXOC2, TYRP1, TPCN2, TYR, KITLG, SLC24A4, OCA2, HERC2, MC1R, ASIP and VDR, which have been associated with pigmentation characteristics in many previous studies [14][15][16][17][18][19][20][21][22][23]25,[38][39][40][41][42][43][44][45][46][47][48][49]. The VDR gene was the only non-pigmentation gene included in the study due to its hypothesized possible interaction with pigmentation genes [50]. ...
... The same approach was used in the case of low penetrance variants. Such a categorization takes into account the impact of compound heterozygosity on the phenotype and has already been used in several previous studies [20][21][22][23]38]. The multivariate association testing performed also considered analysis of haplotypes (with the frequency exceeding 1%) reconstructed with PHASE v. 2.1 (http://www.stat.washington.edu/stephens/software.html) for pairs of SNPs located closely on a single chromosome. ...
Article
The role of epistatic effects in the determination of complex traits is often underlined but its significance in the prediction of pigmentation phenotypes has not been evaluated so far. The prediction of pigmentation from genetic data can be useful in forensic science to describe the physical appearance of an unknown offender, victim, or missing person who cannot be identified via conventional DNA profiling. Available forensic DNA prediction systems enable the reliable prediction of several eye and hair colour categories. However, there is still space for improvement. Here we verified the association of 38 candidate DNA polymorphisms from 13 genes and explored the extent to which interactions between them may be involved in human pigmentation and their impact on forensic DNA prediction in particular. The model-building set included 718 Polish samples and the model-verification set included 307 independent Polish samples and additional 72 samples from Japan. In total, 29 significant SNP-SNP interactions were found with 5 of them showing an effect on phenotype prediction. For predicting green eye colour, interactions between HERC2 rs12913832 and OCA2 rs1800407 as well as TYRP1 rs1408799 raised the prediction accuracy expressed by AUC from 0.667 to 0.697 and increased the prediction sensitivity by >3%. Interaction between MC1R ‘R’ variants and VDR rs731236 increased the sensitivity for light skin by >1% and by almost 3% for dark skin colour prediction. Interactions between VDR rs1544410 and TYR rs1042602 as well as between MC1R ‘R’ variants and HERC2 rs12913832 provided an increase in red/non-red hair prediction accuracy from an AUC of 0.902 to 0.930. Our results thus underline epistasis as a common phenomenon in human pigmentation genetics and demonstrate that considering SNP-SNP interactions in forensic DNA phenotyping has little impact on eye, hair and skin colour prediction.
... W ramach kilku zespołów badawczych opracowano szereg oznaczeń typu multipleks na bazie autosomalnych SNP, przeznaczonych między innymi do analizy pochodzenia przodków [8], identyfikacji [22] oraz badań fenotypowych [23]. Na przykład w konsorcjum SNPforID (www.snpforid.org) ...
... Na przykład w konsorcjum SNPforID (www.snpforid.org) powstała metoda typowania SNP do identyfikacji człowieka, która umożliwia amplifikację 52 SNP z minimalnych ilości genomowego DNA [13][14][15][16][17][18][19][20][21][22][23][24]. Wszystkie loci SNP amplifikowano w ramach jednej reakcji PCR, a SNP analizowano przy wykorzystaniu dwóch reakcji wydłużania łańcucha o jedną zasadę (single base extension -SBE) oraz elektroforezy kapilarnej. ...
... Various autosomal SNP multiplexes have been developed by some working groups, for different applications: ancestry determination [8], human identification [22], and phenotypic studies [23]. The SNPforID consortium (www.snpforid.org) ...
Article
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Some emerging technologies are used as strategies for the analyses of single nucleotide polymorphisms (SNPs) that have attracted much interest in recent years, applied to various scientific areas. They have been extensively used as markers to identify genes that underlie complex diseases and also to realize the potential of pharmacogenomics in relation to different drug responses. Additionally, SNPs have been shown to be very useful in forensic genetics resolving all kinds of legal problems, namely crime cases, disaster victim identification and paternity and kinship investigation testing. The low mutation rate of SNPs, makes these markers very suitable for relationship testing. In the great majority of the cases, analyses with the widely used sets of STR markers provide powerful statistical evidence but some of them remain with ambiguous results. Those include cases with complex pedigrees or cases with some problems, like mutations, that are inherent to the use of STRs. At this time several forensic laboratories are using SNPs especially to complement the study of STRs in some of their casework cases. This paper intends to analyze some of our casework examples and to providea data update on the joint use of STRs and autosomal SNPs in the evaluation and kinship calculation, one of the strategies currently used for this purpose, namely reviewing and comparing results published by various working groups.
... Three of the 11 variable positions: N29insa, D294H and y152ocH (variants strongly predisposing to reddish hair colour) were non-polymorphic in the population sample, which is associated with a very low incidence of these variants in Poland (in the southern Polish population from 1.3-2.5%) and the relative- The most common polymorphic changes in the group of redheads were r151c and r160w, with an incidence of about 28%. in the red-haired people from the northern Polish population, in contrast to the southern Polish population [5], a relatively large number (about 13%) of heterozygous r/wild type and recessive homozygous r/r were observed. one of the possible explanations could be the small number of red haired persons studied. ...
... The role of this variant in the determination of the rHc phenotype in the northern Polish population is small because of the low frequency of occurrence (small sample population). a similar observation was also made for the population of southern Poland [5]. ...
... Four of them (one with reddish blond hair) were simple heterozygotes for these variants (one person 151/0 and 3 persons 160/0). This result is consistent with the assumptions that only 10-20% of red-haired people have a combination of one consensus allele and one recessive variant of the Mc1r gene [5,18]. They may probably have a whole range of hair colours from blond through red to black. ...
Article
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Prediction of appearance based on genetic analysis is a very attractive prospect for forensic science. That is why trends towards researching those areas of DNA that are or may be highly associated with the phenotypic appearance of a person (pigmentation of the skin, hair and eye colour, height or body type) are more and more clearly visible in forensic genetics. It has been known for over 15 years that red hair colour is mainly related to variability in the gene of melanocortin receptor I. However, there have been no studies on the polymorphism of this gene in the northern Polish population. This paper presents a polymorphism study of the MC1R gene in a population of 100 persons of both sexes from this area. Hairs were analyzed by optical microscopy, assessing their morphological characteristics. DNA was isolated from mouth swabs and hair roots using the organic method. DNA was amplified using primers that are complementary to the genes of MC1R and amelogenin in multiplex PCR reactions. PCR products were minisequenced using appropriate primers. Eighteen people out of 95 had reddish hair colour. The relationship between SNP polymorphisms and the occurrence of reddish hair colour was examined.
... MC1R proved to be the most significant gene in red hair colour determination. These observations are in accordance with previous studies of the MC1R gene's involvement in pigmentary phenotype variation where the two variants also greatly contributed to red hair colour determination regardless of the geographical ancestry of the studied population (Beaumont et al., 2007;Box et al., 1997;Branicki et al., 2007;Flanagan et al., 2000;Sulem et al., 2007;Valenzuela et al., 2010). There were a number of other SNPs within MC1R that seemed distinctive of the red-haired group, as their penetrance for this colour category reached 100% in our study (rs200616835:C>G, rs11547464:G>A). ...
... As regards c.488G>A (p.(Arg163Gln)), other researchers (Box et al., 1997;Flanagan et al., 2000) who have had similar observations, considered it to be correlated with geographical and ethnic descent rather than with visible pigmentary traits and generally designated it as an r allele of low (Branicki et al., 2007;Branicki et al., 2011) or of no significance (Mengel-From et al., 2009). The c.252C>A (p.(Asp84Glu)) substitution is somewhat controversial, since it has been previously reported to diminish the receptor's functional ability (Beaumont et al., 2007) and to be characteristic of red-haired people (Branicki et al., 2007;Valverde et al., 1995). ...
... As regards c.488G>A (p.(Arg163Gln)), other researchers (Box et al., 1997;Flanagan et al., 2000) who have had similar observations, considered it to be correlated with geographical and ethnic descent rather than with visible pigmentary traits and generally designated it as an r allele of low (Branicki et al., 2007;Branicki et al., 2011) or of no significance (Mengel-From et al., 2009). The c.252C>A (p.(Asp84Glu)) substitution is somewhat controversial, since it has been previously reported to diminish the receptor's functional ability (Beaumont et al., 2007) and to be characteristic of red-haired people (Branicki et al., 2007;Valverde et al., 1995). What supports our lack of association of this allele is the fact that we have only found a heterozygous state in the checked individuals, thus, we were not able to predict what the hair phenotype would look like in variant homozygous people. ...
Article
Twenty-two variants (single nucleotide polymorphisms – SNPs) of the genes involved in hair pigmentation (OCA2, HERC2, MC1R, SLC24A5, SLC45A2, TPCN2, TYR, TYRP1) were genotyped in a group of 186 Polish participants, representing a range of hair colours (45 red, 64 blond, 77 dark). A genotype-phenotype association analysis was performed. Using z-statistics we identified three variants highly associated with different hair colour categories (rs12913832:A > G in HERC2, rs1805007:T > C and rs1805008:C > T in MC1R). Two variants: rs1800401:C > T in OCA2 and rs16891982:C > G in SLC45A2 showed a high probability of a relation with hair colour, although that probability did not exceed the threshold of statistical significance after applying the Bonferroni correction. We created and validated mathematical logistic regression models in order to test the usefulness of the sets of polymorphisms for hair colour prediction in the Polish population. We subjected four models to stratified cross-validation. The first model consisted of three polymorphisms that proved to be important in the associative analysis. The second model included, apart from the mentioned polymorphisms, additionally rs16891982:C > G in SLC45A. The third model included, apart from the variants relevant in the associating analysis, rs1800401:C > T in OCA. The fourth model consisted of the set of polymorphisms from the first model supplemented with rs16891982:C > G in SLC45A and rs1800401:C > T in OCA. The validation of our models has shown that the inclusion of rs16891982:C > G in SLC45A and rs1800401:C > T in OCA increases the prediction of red hair in comparison with the algorithm including only rs12913832:A > G in HERC2, rs1805007:T > C and rs1805008:C > T in MC1R. The model consisting of all the five above-mentioned genetic variants has shown good prediction accuracies, expressed by the area under the curve (AUC) of the receiver operating characteristics: 0.84 for the red-haired, 0.82 for the dark-haired and 0.71 for the blond-haired. A genotype-phenotype association analysis brought results similar to those in other studies and confirmed the role of rs16891982:C > G, rs12913832:A > G, rs1805007:T > C and rs1805008:C > T in hair colour determination in the Polish population. Our study demonstrated for the first time the possibility of a share of the rs1800401:C > T SNP in the OCA2 gene in hair colour determination. Including this single nucleotide polymorphism in the actual hair colour predicting models would improve their predictive accuracy.
... One pair (namely, rs12931267 and rs1805007) represent variants from different, but neighbouring genes (FANCA and MC1R, respectively). For further analyses polymorphic DNA variants within the MC1R gene were divided into two subgroups and assigned according to their penetrance as high-penetrance MC1R R (rs1805006, rs11547464, rs1805007, rs1805008, and rs1805009) and low-penetrance MC1R r (rs1805005, rs2228479, rs1110400 and rs885479), as applied in many previous papers [23][24][25][26][27][28]. Nine rare SNP markers were excluded at the level of statistical analyses (monomorphic in our dataset: rs1800414 in OCA2 and rs3212355, rs312262906, rs201326893 in MC1R gene or minor allele frequency < 1%: rs74653330, rs121918166, rs1448484 in OCA2, rs6119471 in ASIP and rs1426654 in SLC24A5 genes). ...
... These results are in line with the red hair colour phenotype distribution in carriers of MC1R variants. In the Polish population R/R genotype was observed in 98.3% red (or red-blond) while R/0 in 15.4% individuals and other phenotypic effects (like red facial hair) of single R or even r variants could have been noticed in some individuals [23]. The dosage and pleiotropic effects of the MC1R variants have also been reported in other populations [e.g. ...
Article
Freckles or ephelides are hyperpigmented spots observed on skin surface mainly in European and Asian populations. Easy recognition and external visibility make prediction of ephelides, the potentially useful target in the field of forensic DNA phenotyping. Prediction of freckles would be a step forward in sketching the physical appearance of unknown perpetrators or decomposed cadavers for the forensic DNA intelligence purposes. Freckles are especially common in people with pale skin and red hair and therefore it is expected that predisposition to freckles may partially share the genetic background with other pigmentation traits. The first proposed freckle prediction model was developed based on investigation that involved variation of MC1R and 8 SNPs from 7 genes in a Spanish cohort [19]. In this study we examined 113 DNA variants from 46 genes previously associated with human pigmentation traits and assessed their impact on freckles presence in a group of 960 individuals from Poland. Nineteen DNA variants revealed associations with the freckle phenotype and the study also revealed that females have ∼1.8 higher odds of freckles presence comparing to males (p-value = 9.5 × 10-5). Two alternative prediction models were developed using regression methods. A simplified binomial 12-variable model predicts the presence of ephelides with cross-validated AUC = 0.752. A multinomial 14-variable model predicts one of three categories - non-freckled, medium freckled and heavily freckled. The two extreme categories, non-freckled and heavily freckled were predicted with moderately high accuracy of cross-validated AUC = 0.754 and 0.792, respectively. Prediction accuracy of the intermediate category was lower, AUC = 0.657. The study presents novel DNA models for prediction of freckles that can be used in forensic investigations and emphasizes significance of pigmentation genes and sex in predictive DNA analysis of freckles.
... We also tested MC1R variants in pairwise comparisons for all available hair colour phenotypes to determine their possible contribution to colours other than red. In addition to the associations with darker hair and skin for rs1805005 and rs2228479 mentioned above, prior publications have reported weak association for rs1805005 with blonde hair in [9,73,11]. However, our results show that compared to red hair, the predictive power of MC1R variants for other hair colours is very weak (Figure 4) and could not be reliably used for the purposes of identifying a missing individual's phenotype. ...
... However, our results show that compared to red hair, the predictive power of MC1R variants for other hair colours is very weak (Figure 4) and could not be reliably used for the purposes of identifying a missing individual's phenotype. The higher AUROC for light-dark hair colour models compared to light-light and dark-dark could be explained by some overlap Table 5, the first two [27,11] relied on exclusively MC1R variants and contingency tables for red hair colour prediction. While their precision of 96 and 97.5%, respectively, for R homozygous or compound heterozygous genotypes predicting red hair is high, it is notable that their sample was enriched for redhaired individuals (27% and 41%, respectively) and not representative of the general population (2-5%). ...
Article
Full-text available
Genetic variation in melanocortin-1 receptor (MC1R) is a known contributor to disease-free red hair in humans. Three loss-of-function single-nucleotide variants (rs1805007, rs1805008, and rs1805009) have been established as strongly correlated with red hair. The contribution of other loss-of-function MC1R variants (in particular rs1805005, rs2228479, and rs885479) and the extent to which other genetic loci are involved in red hair colour is less well understood. Here, we used the U.K. Biobank cohort to capture a comprehensive list of MC1R variants contributing to red hair colour. We report a correlation with red hair for both strong-effect variants (rs1805007, rs1805008, and rs1805009) and weak-effect variants (rs1805005, rs2228479, and rs885479) and show that their coefficients differ by two orders of magnitude. On the haplotype level, both strong- and weak-effect variants contribute to the red hair phenotype, but when considered individually, weak-effect variants show a reverse, negative association with red hair. The reversal of association direction in the single-variant analysis is facilitated by a distinguishing structure of MC1R, in which loss-of-function variants are never found to co-occur on the same haplotype. The other previously reported hair colour genes’ variants do not substantially improve the MC1R red hair colour predictive model. Our best model for predicting red versus other hair colours yields an unparalleled AUROC of 0.96 using only MC1R variants. In summary, we present a comprehensive statistically-derived characterisation of the role of MC1R variants in red hair colour and offer a powerful, economical, and parsimonious model that achieves unsurpassed performance.
... Atualmente, o gene do MC1-R é considerado um dos maiores marcadores de susceptibilidade a neoplasias malignas cutâneas, já que variantes gênicas estão associadas, com risco aumentado, para melano-ma e cânceres de pele não-melanoma. 17,30,34,[42][43][44] Outros estudos demonstraram que efélides e lentigos solares são distintos tipos de lesões pigmentadas, pois apresentam diferenças marcantes, nas suas etiologias, porém, variantes gênicas do MC1-R são um fator necessário para o desenvolvimento de efélides, quando desempenham um papel menos importante no caso dos lentigos. 3,30,45,46 Variação relacionada ao gene MC1-R é excepcionalmente alta entre caucasianos e tem um significante impacto no fenótipo pigmentar deste grupo étnico. ...
... Cabelos vermelhos (ruivos) têm sido relacionados a alguns alelos, mas recentes estudos indicam que os mesmos genótipos podem expressar diferentes cores de cabelos, dependendo da população estudada. 3,44 MC1-R está expresso, abundantemente, em células de melanoma humano e de ratos e em níveis significativamente mais baixos em melanócitos de ratos. Mais recentemente, foi demonstrado em glândulas normais da pele humana e folículos capilares, bem como em malformações e neoplasmas da pele. ...
Article
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Melasma é uma dermatose comum que cursa com alteração da cor da pele normal, resultante da hiperatividade melanocítica focal epidérmica de clones de melanócitos hiperfuncionantes, com consequente hiperpigmentação melânica induzida, principalmente, pela radiação ultravioleta. Clinicamente, caracteriza-se por manchas acastanhadas, localizadas preferencialmente na face, embora possa acometer também região cervical, torácica anterior e membros superiores.Mulheres em período fértil e de fototipos intermediários representam as populações mais acometidas. Grande parte de sua fisiopatogenia permanece desconhecida, havendo relação com fatores genéticos, hormonais, uso de medicamentos, cosméticos, endocrinopatias e fotoexposição. Os autores discutem os principais elementos relacionados à pigmentação da pele e ao desenvolvimento do melasma.Melasma is a common dermatosis that involves changes in normal skin pigmentation, resulting from the hyperactivity of epidermal melanocytes. The consequent hyperpigmentation is mostly induced by ultraviolet radiation. Clinically, melasma is characterized by light to dark brown macules that usually occur on the face, although they can also affect the cervical and anterior thoracic regions and upper members.Fertile age women and those with intermediate skin phototypes are most likely to develop melasma. Most of its physiopathogenics is not yet fully understood, but there is a relation with genetic and hormonal factors, drugs and cosmetics use, endocrinopathies and sun exposure. The authors discuss the main aspects associated with skin pigmentation and the development of melasma.
... However, a large portion of heritability, for many phenotypes, still remains unknown and is often attributed to rare or low effect size variants, structural variation and/or epistatic interactions [11][12][13]. Notably, whole genome analyses have increased our knowledge on the genetics of hair colour and has led to the prediction of this trait beyond red hair colour, which was previously well understood as variation in the MC1R gene [14][15][16]. Several methods have been proposed for hair colour prediction using DNA variants [17][18][19]. ...
... In two cases compound heterozygosity was noted, once with two low-penetrance variants and the other a high-penetrance and low-penetrance MC1R allele was observed. Our previous study has shown that these genotypes may sporadically produce red hair colour and in some very rare cases, subjects with two consensus MC1R alleles may also have red hair [15]. No individuals with phenotypic black hair colour were reported within the studied group of children. ...
... Melanoma-derived IL-1b and its downstream intermediates are biologically active as autocrine and paracrine factors, markedly enhancing synthesis of IL-1 in melanoma cells, and mediating macrophage recruitment and angiogenesis in vitro [20]. IL-1b has also been shown to maintain survival and proliferation of melanoma and host stromal cells including macrophages and immune suppressor cells in vivo [5,12,34,[39][40][41]. IL-1b thus promotes tumor cell invasion and metastasis [11,[30][31][32][33]. ...
... Tumor microenvironment contains both tumor cells and stromal cells (such as macrophages and myeloid-derived cells). Tumor-associated macrophages have several tumor-promoting functions and are considered to be key regulators of the link between inflammation and cancer [39][40][41]. Myeloid-derived suppressor cells (MDSCs) recruit T regulatory cells to downregulate immune surveillance and antitumor immunity, thereby facilitating tumor growth [5,12,34]. ...
Article
The inflammasome is a multi-protein complex that mediates immune responses to microbial, host, and environmental signals. When active, inflammasomes regulate caspase-1 activation and IL-1β secretion. There is a strong link between inflammation and cancer, and IL-1β is one of the major molecules involved in both of these disease processes. Here we review the role of inflammasomes in regulating IL-1β secretion, and the impact of this pathway on cancer pathogenesis, with a focus on melanoma. This represents an exciting new area of research, and could potentially result in new targets for melanoma therapeutics in the future.
... O gene MC1R localiza-se no braço longo do cromossomo 16 e é responsável por codificar o receptor de melanocortina 1 (MC1R) acoplado à proteína G, presente na membrana dos melanócitos [36]. É um gene altamente polimórfico e que possui efeito pleiotrópico (expressa uma multiplicidade de efeitos fenotípicos) [37]. ...
Article
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A fenotipagem forense pelo DNA se apresenta como uma abordagem promissora para suprir lacunas na busca de pessoas desconhecidas, em investigações criminais, e na identificação de vítimas de catástrofes e de pessoas desaparecidas. Essa metodologia permite a previsão individual de características externamente visíveis (CEVs) a partir de análises com SNPs informativos de fenótipos. Entre esses SNPs, os mais bem descritos são aqueles relacionados com as características de pigmentação, como cor dos olhos, pele e cabelo. Estudos vêm demonstrando o elevado poder de predição dessas CEVs, apresentando resultados satisfatórios na predição da cor de íris castanha e azul e cabelo ruivo, enquanto para as demais ainda são necessárias mais pesquisas para predizer com precisão esses fenótipos. Embora seja muito promissora, a aplicação prática da fenotipagem forense pelo DNA levanta diversas questões de ordem ética e legal. No Brasil, avanços ainda precisam acontecer, uma vez que a população brasileira é heterogênea e grande parte dos marcadores descritos é relacionada às populações europeias. Neste sentido, o Brasil já conta com a Rede Integrada de Bancos de Perfis Genéticos (RIBPG), a qual visa compartilhar e comparar os perfis genéticos entre os bancos do país. Em um futuro próximo essa metodologia estará apta a integrar às rotinas forenses, com grande aplicabilidade e confiabilidade.
... As an individual ages, DNA is impacted by a general hypomethylation, especially in repetitive elements of the genome, as well as localized hypermethylation in specific regions, such as promoter-associated CpG islands (Jung and Pfeifer, 2015;Zampieri et al., 2015). In recent years, multiple epigenetic studies have reported a high number of CpG positions with methylation levels that are highly correlated with age (Bocklandt et al., 2011;Hannum et al., 2013;Rakyan et al., 2010), and this has allowed the development of several age prediction tests using DNA methylation estimation. ...
Chapter
Phenotypic markers are genetic and epigenetic polymorphisms bearing information about either intrinsic or extrinsic features of a human being. Inference of the characteristics from DNA is useful from a forensic point of view, since they can contribute to a molecular portrait of the donor of a biological sample found at a crime scene. Externally visible characteristics are represented by visually discernible characters associated with the physical appearance of a human being. A person's biogeographical origin is an intrinsic characteristic that can be indicated by the genetically inherited population markers originating from their ancestors. Although forensic individual age estimation was initially approached by the assessment of bones and teeth, this was followed by tests of biomolecules which experience gradual alterations during a lifespan. As an individual age, DNA is impacted by a general hypomethylation, especially in repetitive elements of the genome, as well as localized hypermethylation in specific regions, such as promoter‐associated CpG islands.
... Looking across populations of all hair colors, we did not find rs2228479 to be significant by ANOVA. Additionally, Flanagan et al. (2000) and Branicki et al. (2007) found that rs1805007 (R151G) in combination with rs1805008 (R160W) to be associated with red hair color. Moreover, found both of these SNPs to be associated with hair color in Icelandic and Dutch populations. ...
... Branicki et al. in the year 2007 sequenced the MC1R gene in more than 180 individuals with hair color variations which included 40 red-haired ones and 36 blond hair individual. They, thus, developed red hair prediction assay on the basis of 5 MC1R DNA variants (Branicki et al. 2007). Sulem et al. (2007) in the year 2007 started a GWAS on pigmentation and published the first DNA prediction assay for hair colors belonging to all category. ...
... The genome-wide association study (GWAS), a linkage analysis and candidate gene study, has been used to identify genetic variants influencing such EVCs. Variations in the MC1R gene have been associated with red hair [11]. The red hair prediction method, based on a combination of nonsynonymous SNPs in MC1R, was already developed for forensic science more than 10 years ago [12], and its accuracy was 84% in the prediction of red-haired individuals. ...
Article
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The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population.
... This is due to limited genetic complexity coupled with limited environmental impact that has led to accumulative success in exploring the genetic basis of eye and hair colour via candidate gene and genome-wide association studies [17][18][19][20][21][22]. From these association studies, highly predictive eye and hair colour DNA markers have been identified [23][24][25][26][27][28][29][30][31][32][33]. ...
Article
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Background DNA analysis of ancient skeletal remains is invaluable in evolutionary biology for exploring the history of species, including humans. Contemporary human bones and teeth, however, are relevant in forensic DNA analyses that deal with the identification of perpetrators, missing persons, disaster victims or family relationships. They may also provide useful information towards unravelling controversies that surround famous historical individuals. Retrieving information about a deceased person’s externally visible characteristics can be informative in both types of DNA analyses. Recently, we demonstrated that human eye and hair colour can be reliably predicted from DNA using the HIrisPlex system. Here we test the feasibility of the novel HIrisPlex system at establishing eye and hair colour of deceased individuals from skeletal remains of various post-mortem time ranges and storage conditions. Methods Twenty-one teeth between 1 and approximately 800 years of age and 5 contemporary bones were subjected to DNA extraction using standard organic protocol followed by analysis using the HIrisPlex system. Results Twenty-three out of 26 bone DNA extracts yielded the full 24 SNP HIrisPlex profile, therefore successfully allowing model-based eye and hair colour prediction. HIrisPlex analysis of a tooth from the Polish general Władysław Sikorski (1881 to 1943) revealed blue eye colour and blond hair colour, which was positively verified from reliable documentation. The partial profiles collected in the remaining three cases (two contemporary samples and a 14th century sample) were sufficient for eye colour prediction. Conclusions Overall, we demonstrate that the HIrisPlex system is suitable, sufficiently sensitive and robust to successfully predict eye and hair colour from ancient and contemporary skeletal remains. Our findings, therefore, highlight the HIrisPlex system as a promising tool in future routine forensic casework involving skeletal remains, including ancient DNA studies, for the prediction of eye and hair colour of deceased individuals.
... From the 105 Slovenian samples we eliminated only one person, this being the only person with red hair in our population (0.9% of the Slovenian population). This low frequency of red hair color was expected for the general Slovenian population and additionally confirmed that red haired individuals were more prevalent in the Baltic region and Northern Europe populations (28). ...
Article
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Aim To analyze two phenotype characteristics – eye and hair color – using single-nucleotide polymorphisms (SNPs) and evaluate their prediction accuracy in Slovenian population. Methods Twelve SNPs (OCA2 – rs1667394, rs7170989, rs1800407, rs7495174; HERC2 – rs1129038, rs12913832; MC1R – rs1805005, rs1805008; TYR – rs1393350; SLC45A2 – rs16891982, rs26722; SLC24A5 – rs1426654) were used for the development of a single multiplex assay. The single multiplex assay was based on SNaPshot chemistry and capillary electrophoresis. In order to evaluate the accuracy of the prediction of eye and hair color, we used the logistic regression model and the Bayesian network model, and compared the parameters of both. Results The new single multiplex assay displayed high levels of genotyping sensitivity with complete profiles generated from as little as 62 pg of DNA. Based on a prior evaluation of all SNPs in a single multiplex, we focused on the five most statistically significant in our population in order to investigate the predictive value. The two prediction models performed reliably without prior ancestry information, and revealed very good accuracy for both eye and hair color. Both models determined the highest predictive value for rs12913832 (P < 0.0001), while the other four SNPs (rs1393350, rs1800407, rs1805008, and rs7495174) showed additional association for color prediction. Conclusion We developed a sensitive and reliable single multiplex genotyping assay. More samples from different populations should be analyzed before this assay could be used as one of the supplemental tools in tracing unknown individuals in more complicated crime investigations.
... For the other categories (i.e. blond versus non-blond, brown versus non-brown and black versus non-black), we used a total set of 1134 individuals representing the 80% model-building subset but now omitting the red hair individuals from the analyses due to their rare DNA variants and the fact that red hair is not a continuous colour but more a combined MC1R mutation effect on colour change [47,51]. As the probability values shown suggest, the results for hair colour variation from blond via brown to black (without red) are consistent with our previous findings [35] in several DNA variants, i.e. rs12913832 (HERC2) and rs12203592 (IRF4) with high statistical support (P 10 À6 to 10 À16 ) in the present enlarged dataset considering Poland, Ireland and Greece. ...
Article
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Recently, the field of predicting phenotypes of externally visible characteristics (EVCs) from DNA genotypes with the final aim of concentrating police investigations to find persons completely unknown to investigating authorities, also referred to as Forensic DNA Phenotyping (FDP), has started to become established in forensic biology. We previously developed and forensically validated the IrisPlex system for accurate prediction of blue and brown eye colour from DNA, and recently showed that all major hair colour categories are predictable from carefully selected DNA markers. Here, we introduce the newly developed HIrisPlex system, which is capable of simultaneously predicting both hair and eye colour from DNA. HIrisPlex consists of a single multiplex assay targeting 24 eye and hair colour predictive DNA variants including all 6 IrisPlex SNPs, as well as two prediction models, a newly developed model for hair colour categories and shade, and the previously developed IrisPlex model for eye colour. The HIrisPlex assay was designed to cope with low amounts of template DNA, as well as degraded DNA, and preliminary sensitivity testing revealed full DNA profiles down to 63pg input DNA. The power of the HIrisPlex system to predict hair colour was assessed in 1551 individuals from three different parts of Europe showing different hair colour frequencies. Using a 20% subset of individuals, while 80% were used for model building, the individual-based prediction accuracies employing a prediction-guided approach were 69.5% for blond, 78.5% for brown, 80% for red and 87.5% for black hair colour on average. Results from HIrisPlex analysis on worldwide DNA samples imply that HIrisPlex hair colour prediction is reliable independent of bio-geographic ancestry (similar to previous IrisPlex findings for eye colour). We furthermore demonstrate that it is possible to infer with a prediction accuracy of >86% if a brown-eyed, black-haired individual is of non-European (excluding regions nearby Europe) versus European (including nearby regions) bio-geographic origin solely from the strength of HIrisPlex eye and hair colour probabilities, which can provide extra intelligence for future forensic applications. The HIrisPlex system introduced here, including a single multiplex test assay, an interactive tool and prediction guide, and recommendations for reporting final outcomes, represents the first tool for simultaneously establishing categorical eye and hair colour of a person from DNA. The practical forensic application of the HIrisPlex system is expected to benefit cases where other avenues of investigation, including STR profiling, provide no leads on who the unknown crime scene sample donor or the unknown missing person might be.
... In a forensic era where intelligence information regarding an individual's physical appearance can be retrieved from DNA material [1][2][3], the accurate determination of chronological age from crime scene samples has the potential to significantly aid forensic investigations towards identifying and finding unknown individuals. In the majority of the forensic cases where intact skeletal remains are available, age determination can be conducted successfully by anthropological measurements and calculations as well as cross-referencing with medical records. ...
Presentation
Placing forensic traces in time is an important factor in forensic sciences, and this can greatly contribute to the chronological reconstruction of past events. The temporal aspects of trace serve the three main purposes of forensic sciences as: information to help investigators; evidence for presentation in court; and in support of a more proactive policing framework such as in intelligence-led approaches. The length of time that traces, objects, and corpses have lain in situ at a place, can directly or indirectly, contribute to the dating of an event. While most researches have been generally confined to one type of trace or problem, the issues are clearly comparable and can generally be addressed using the same approaches. Thus, a multidisciplinary approach is commended rather than confinement to single class of evidence. This review aims to provide an overview of dating methods that have been used or considered. Evidence obtained from questioned documents, bloodstains, fingermarks, gunshot residues, pollen, spores, plants, and fungi, will be considered. The approaches used in different fields will be compared and contrasted, and a transversal approach is commended.
... The MC1R gene has got the broadest literature documentation among all the pigmentation determining genetic factors in man. Its polymorphism (rs1805007) in the form of homozygote of the more rare (T) allele is by far the best predictor of red hair color (Sturm et al. 2001;Sturm et al. 2003;Duffy et al. 2004;Beaumont et al. 2007;Branicki et al. 2007;Branicki et al. 2011;Han et al. 2008;Brudnik et al. 2009;Siewierska 2012) and of light skin (Sturm et al. 2003, Beaumont et al. 2007Brudnik et al. 2009), what results from a decreased ability of its protein product to activate the cAMP cascade and, in consequence, from a weaker stimulation of the melanogenesis pathway (Sturm et al. 2001;Sturm et al. 2003;Beaumont et al. 2007). In effect, the TT genotype of the above-mentioned polymorphism carries the highest risk for melanoma among all the variants of the gene (Raimondi et al. 2008;Brudnik et al. 2009;Nan et al. 2009;Nan et al. 2011;Gerstenblith et al. 2010;Stefanaki et al. 2013). ...
Article
Background: Human pigmentation, similarly as many other biological features, changes in the course of postnatal ontogenesis, while in case of hair, pigmentation changes are more distinctive than in the skin or the iris. It is therefore extremely important to identify the genes involved in the constitution of human pigmentation features at various stages of ontogenesis. Results of this type of analyses are of high practical significance in forensic study because they enable to create mathematical tools, allowing for prediction of the pigmentation phenotype, based on DNA studies. Aim: The objective of the investigation was finding out whether the genes, associated with pigmentation of adult subjects, differentiated in any way the newly forming pigmentation phenotype in Polish prepubertal children. Material and methods: The study encompassed Polish children, aged 7 to 10 years, without any abnormalities in skin or hair pigmentation. A total of 245 children were examined. Constitutive skin pigmentation according to skin melanin index (SMI) was evaluated, using a dermaspectrometer, and classified into three groups based on the reference values of 25 and 75 percentile for Polish children. Hair colors were evaluated by means of the descriptive Fischer-Saller scale and classified by a division of color variants (as accepted in that scale) (light blonde, blonde, dark blonde, brown and dark brown). In saliva samples, collected from the children, five (5) single nucleotide polymorphisms were identified: SNPs: rs1800401 (OCA2-15q11.2-q12), rs35264875 (TPCN2-11q13.3), rs16891982 (SLC45A2-5p13.2), rs12913832 (HERC2-15q13) and rs1805007 (MC1R-16q24.3). An association between each allele of verified genotype and skin and hair color phenotypes was assessed, using the z-statistic and associated p-value. The quality of classifiers was evaluated by 10-fold stratified cross-validation and was characterized by the area under the receiver operating characteristic curve (AUC). Results: Light skin pigmentation phenotype (SMI<25 percentile) was associated with rs1805007 (MC1R) (allelic OR=3.95; 95% Cl:1.20–12.99; p=0.0235), while the dark shade of the skin (SMI>75 percentile) with rs16891982 (SLC45A2) (allelic OR =14.37; 95% Cl: 1.78–115.88; p=0.0123). The probability of dark hair (brown and dark brown) in childhood was increased by T rs12913832 allele (HERC2) (OR=3.63); 95% Cl: 2.25–5.85; p < 0.0001) and dependent on it – rs1800401 (OCA2) (OR=6.31; 95% Cl: 1.74–22.91; p=0.0051). Other SNPs were not significantly associated with skin and hair color but improved prediction of these features. Conclusions: From the five gene polymorphisms analysed in Polish children the strongest correlation with hair color has the rs12913832 (HERC2) and with skin color – rs16891982 (SLC45A2). Therefore, the above-mentioned polymorphisms may be used as components of potential models, used to predict pigmentation features in European origin children in prepubertal age. To improve predictive value of the potential scoring model for hair color, the following should be additionally included: rs1800401 (OCA2), rs35264875 (TPCN2) and rs1805007 (MC1R), while for skin color: rs12913832 (HERC2) and rs1805007 (MC1R).
... Individual age estimation is a major key factor in forensic science analysis which can provide very useful information applicable to crime investigations. Age estimation in forensic science was initially based on various morphological approaches or radiographic investigations [1]. Later, molecular approaches came into practice for age estimation [2,3]. ...
Article
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Forensic age estimation can be used to gain information relevant to criminal and anthropological investigations. Forensic dentistry involves the processing, review, evaluation and presentation of dental evidence with the purpose of contributing scientific and objective data in legal processes. This study aims in estimating age of a person using DNA extracted from human saliva and to assess this methodology as a potential diagnostic measure in forensic odontology. Salivary samples were collected from 45 blinded participants aged 18 to 70 years with a DNA self-collection kit and stored at room temperature. DNA was extracted from the salivary samples using a separate kit and it was subjected to age estimation process by constructing an age predictive model. A constructed age predictive model of saliva has 6 selected CpG sites (5’—C---phosphate—G---3’) in genome-enabled age prediction with high accuracy. Univariate linear regression analysis was performed to test the association between age and gender.(p value<0.05). DNA methylation profiling of saliva was performed to identify age associated CpG markers. A model composed of 6 selected CpG sites enabled age prediction in saliva with high accuracy and this multiplex system can be integrated into the routine forensic laboratory workflow after further validation tests with various casework samples.
... The main protein responsible for pigmentation of skin, eyes and hair is melanin. This polymer is produced in a process that occurs in cutaneous melanocytes and can lead to the synthesis of two types of melanin: eumelanin, which is associated with brown and black pigment, and pheomelanin, related to red and yellow pigmentation [3,4]. ...
Article
Pigmentation is a variable and complex trait in humans and it is determined by the interaction of environmental factors, age, disease, hormones, exposure to ultraviolet radiation and genetic factors, including pigmentation genes. Many polymorphisms of these genes have been associated with phenotypic diversity of skin, eyes and hair color in homogeneous populations. Phenotype prediction from biological samples using genetic information has benefited forensic area in some countries, leading some criminal investigations. Herein, we evaluated the association between polymorphisms in the genes SLC24A5 (rs1426654) and ASIP (rs6058017) with skin, eyes and hair colors, in 483 healthy individuals from Brazilian population for attainable use in forensic practice. The volunteers answered a questionnaire where they self-reported their skin, eye and hair colors. The polymorphic homozygous genotype of rs1426654∗A and rs6058017∗A in SLC24A5 and ASIP respectively, showed strongest association with fairer skin (OR 47.8; CI 14.1-161.6 and OR 8.6; CI 2.5-29.8); SLC24A5 alone showed associations with blue eyes (OR 20.7; CI 1.2-346.3) and blond hair (OR 26.6; CI 1.5-460.9). Our data showed that polymorphic genotypes (AA), in both genes, are correlated with characteristics of light pigmentation, while the ancestral genotype (GG) is related to darker traits, corroborating with previous studies in European and African populations. These associations show that specific molecular information of an individual may be useful to access some phenotypic features in an attempt to help forensic investigations, not only on crime scene samples but also in cases of face reconstructions in unknown bodies. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
... For human hair colour, gene mapping studies also identified numerous highly associated SNPs (Box et al. 1997;Branicki et al. 2007Branicki et al. , 2008aFernandez et al. 2008;Flanagan et al. 2000;Graf et al. 2005;Grimes et al. 2001;Han et al. 2008;Harding et al. 2000, 2002, Kanetsky et al. 2004Mengel-From et al. 2009;Pastorino et al. 2004;Rana et al. 1999;Sulem et al. 2007Sulem et al. , 2008Valenzuela et al. 2010;Valverde et al. 1995;Voisey et al. 2006), 22 of which proved decidedly predictive for hair colour categories (Branicki et al. 2011). From this, and previous eye colour knowledge, the HIrisPlex system was developed and forensically validated for combined eye and hair colour prediction from DNA achieving AUCs of 0.92 for red, 0.85 for black, 0.81 for blond, and 0.75 for brown Walsh et al. 2013Walsh et al. , 2014. ...
Article
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Human skin colour is highly heritable and externally visible with relevance in medical, forensic, and anthropological genetics. Although eye and hair colour can already be predicted with high accuracies from small sets of carefully selected DNA markers, knowledge about the genetic predictability of skin colour is limited. Here, we investigate the skin colour predictive value of 77 single-nucleotide polymorphisms (SNPs) from 37 genetic loci previously associated with human pigmentation using 2025 individuals from 31 global populations. We identified a minimal set of 36 highly informative skin colour predictive SNPs and developed a statistical prediction model capable of skin colour prediction on a global scale. Average cross-validated prediction accuracies expressed as area under the receiver-operating characteristic curve (AUC) ± standard deviation were 0.97 ± 0.02 for Light, 0.83 ± 0.11 for Dark, and 0.96 ± 0.03 for Dark-Black. When using a 5-category, this resulted in 0.74 ± 0.05 for Very Pale, 0.72 ± 0.03 for Pale, 0.73 ± 0.03 for Intermediate, 0.87±0.1 for Dark, and 0.97 ± 0.03 for Dark-Black. A comparative analysis in 194 independent samples from 17 populations demonstrated that our model outperformed a previously proposed 10-SNP-classifier approach with AUCs rising from 0.79 to 0.82 for White, comparable at the intermediate level of 0.63 and 0.62, respectively, and a large increase from 0.64 to 0.92 for Black. Overall, this study demonstrates that the chosen DNA markers and prediction model, particularly the 5-category level; allow skin colour predictions within and between continental regions for the first time, which will serve as a valuable resource for future applications in forensic and anthropologic genetics. Electronic supplementary material The online version of this article (doi:10.1007/s00439-017-1808-5) contains supplementary material, which is available to authorized users.
... In a forensic era where intelligence information regarding an individual's physical appearance can be retrieved from DNA material [1][2][3], the accurate determination of chronological age from crime scene samples has the potential to significantly aid forensic investigations towards identifying and finding unknown individuals. In the majority of the forensic cases where intact skeletal remains are available, age determination can be conducted successfully by anthropological measurements and calculations as well as cross-referencing with medical records. ...
Poster
Forensic investigations can benefit substantially from intelligence information, and the accurate estimation of an individual’s age has the potential to serve as a great asset in numerous scenarios. Approaching ageing as a biological phenomenon that occurs in part through differentiation in gene expression, the search for age predictors has focused on epigenetic factors as these are known gene modulators. Amongst them, DNA methylation has been proven to correlate strongly with age, with recent projects yielding numerous methods for DNA methylation based age prediction. However, little research has so far been carried out on the computational/statistical approaches that can be employed when correlating methylation values with chronological age. This study investigates the advantages and disadvantages of various statistical modelling methods when used in DNA methylation based age prediction. From simple linear models, to support vector machines and the highly sophisticated modelling of artificial neural networks we have taken a closer look at the statistics in order to find out if there is, indeed, a statistical model that can make the most of every methylation dataset. These models have been tested on a DNA methylation based age prediction method developed in whole blood using 12 age-associated CpG sites.
... In a forensic era where intelligence information regarding an individual's physical appearance can be retrieved from DNA material [1][2][3], the accurate determination of chronological age from crime scene samples has the potential to significantly aid forensic investigations towards identifying and finding unknown individuals. In the majority of the forensic cases where intact skeletal remains are available, age determination can be conducted successfully by anthropological measurements and calculations as well as cross-referencing with medical records. ...
Article
Full-text available
The field of DNA intelligence focuses on retrieving information from DNA evidence that can help narrow down large groups of suspects or define target groups of interest. With recent breakthroughs on the estimation of geographical ancestry and physical appearance, the estimation of chronological age comes to complete this circle of information. Recent studies have identified methylation sites in the human genome that correlate strongly with age and can be used for the development of age-estimation algorithms. In this study, 110 whole blood samples from individuals aged 11-93 years were analysed using a DNA methylation quantification assay based on bisulphite conversion and massively parallel sequencing (Illumina MiSeq) of 12 CpG sites. Using this data, 17 different statistical modelling approaches were compared based on root mean square error (RMSE) and a Support Vector Machine with polynomial function (SVMp) model was selected for further testing. For the selected model (RMSE = 4.9 years) the mean average error (MAE) of the blind test (n = 33) was calculated at 4.1 years, with 52% of the samples predicting with less than 4 years of error and 86% with less than 7 years. Furthermore, the sensitivity of the method was assessed both in terms of methylation quantification accuracy and prediction accuracy in the first validation of this kind. The described method retained its accuracy down to 10 ng of initial DNA input or ~2 ng bisulphite PCR input. Finally, 34 saliva samples were analysed and following basic normalisation, the chronological age of the donors was predicted with less than 4 years of error for 50% of the samples and with less than 7 years of error for 70%.
... In a forensic era where intelligence information regarding an individual's physical appearance can be retrieved from DNA material [1][2][3], the accurate determination of chronological age from crime scene samples has the potential to significantly aid forensic investigations towards identifying and finding unknown individuals. In the majority of the forensic cases where intact skeletal remains are available, age determination can be conducted successfully by anthropological measurements and calculations as well as cross-referencing with medical records. ...
Presentation
Retrieving information from crime scene stains, that can help point forensic investigators in the right direction when it comes to identifying unknown individuals, has been the major focus of recent forensic research. With information on date of birth being officially registered and available to the police, the ability to accurately determine an individual’s age from a DNA sample is the top priority in cases without identified suspects. The most promising method for the estimation of age from DNA is the quantification of DNA methylation, a reversible chemical modification of cytosine residues that can affect gene expression and has been proven to correlate strongly with age at certain loci. With multiple reports demonstrating the potential of DNA methylation-based prediction for application in forensic casework, this study takes the next step by assessing a previously developed method on statistical modelling, sensitivity and multi-tissue applicability simultaneously for the first time. Using a set of 12 previously described age-correlated DNA methylation markers, 110 whole blood samples were analysed, and the data collected was used to train a series of 17 different machine-learning prediction algorithms. The best performing algorithm was able to predict 52% of samples in an external blind set with an absolute error smaller than 4 years and 86% with an error smaller than 7 years. At the same time, a sensitivity assessment conducted on both methylation standards and real samples showed that the accuracy was retained down to ~2ng of DNA, which is by far the lowest limit ever reported in a study of this kind. Finally, sets of saliva and sperm samples were also tested and, like blood, for 50% of saliva samples the absolute prediction error was less than 4 years and for 70% less than 7 years. However, the selected markers showed no correlation with the donor’s age in sperm.
... The binding of α-MSH to MC1R causes a cAMP signal cascade resulting in an increased production of eumelanin. Non-synonymous SNPs, including rs1805007, used in this study, have been associated with red hair and fair skin [4,6]. Functional and bioinformatics studies have demonstrated that SNP rs1805007 alters the function of MC1R [7][8][9], and hence, melanin production. ...
Article
In a past study, we developed multiple linear regression (MLR) models that employed three single nucleotide polymorphisms (SNPs) that predicted a significant proportion of variation in pigmentation phenotypes from a large population cohort (n=789, training sample). Multiple linear regression models were developed for skin reflectance, eye color, and two aspects of hair color (log of the ratio of eumelanin-to-pheomelanin and total melanin). In this report , using an independent cohort (n=242 , test sample), we 1) externally cross-validated the prediction models, and 2) tested and refined the algorithm presented in the study by Valenzuela and colleagues, (2010). Relative shrinkage was moderate for skin reflectance (23.4%), eye color (19.4%), and the log of the ratio of eumelanin-to-pheomelanin in hair (37.3%), and largest for total melanin (67%) in hair. Independent construction of predictive models using our algorithm for the test sample set yielded the same or similar models as the training sample set. Two of the three SNPs composing the models were the same, with some variability in the third SNP of the model.
... In this context, it is expected that the genotyping of such genetic markers in crime scene evidence, or in an unidentified body, can contribute significantly to increase the accurate information on the physical characteristics of those involved. 5,6 Although some following inferences may not present definitive value as forensic evidence, they may be an important factor leading police investigation and reducing the number of suspects to a small set. 5 ...
... Research on the genetics of common characteristics may allow prediction of aspects of appearance from a trace forensic DNA sample-red hair and fair skin, for example (Branicki et al. 2007). DNAPrint Genomics, Inc. (Sarasota, FL), offer a product permitting the inference of ancestry from a DNA profile (Frudakis et al. 2004). ...
Article
Pigmentation of the skin, hair, and eyes is a complex trait controlled by multiple genetic loci. Recently a non-synonymous mutation in the pigmentation candidate gene TYRP1 was shown to be significantly associated with a blond-hair phenotype in populations from the Solomon Islands. The distribution of this mutation in the islands of Northern Island Melanesia, where the blondism phenotype is also prevalent, was unknown. Here, we present data describing the distribution of this allele in 550 individuals sampled from across this region, and test for associations between genotype at this locus and quantitatively measured skin and hair pigmentation phenotype. We report that the frequency of the 93C allele is notably lower than observed in the Solomons (0.12 vs. 0.26). The allele exhibits significant geographic heterogeneity across the islands sampled (χ(2) = 108.4, P < 0.0001). It is observed at its highest frequencies on the islands of New Ireland and New Hanover, while being almost completely absent from the large island of New Britain. Using linear regression with age, sex, and island as covariates we report that, as in the Solomons, the 93C allele is significantly associated with a decrease in hair pigmentation but not skin pigmentation. We discuss the distribution of the 93C allele across the Southwest Pacific in light of its possible place of origin and dispersal. Am J Phys Anthropol, 2014. © 2014 Wiley Periodicals, Inc.
Article
Prediction of visible traits from genetic data in certain forensic cases may provide important information that can speed up the process of investigation. Research that has been conducted on the genetics of pigmentation has revealed polymorphisms that explain a significant proportion of the variation observed in human iris color. Here, on the basis of genetic data for the six most relevant eye color predictors, two alternative Bayesian network model variants were developed and evaluated for their accuracy in prediction of eye color. The first model assumed eye color to be categorized into blue, brown, green, and hazel, while the second variant assumed a simplified classification with two states: light and dark. It was found that particularly high accuracy was obtained for the second model, and this proved that reliable differentiation between light and dark irises is possible based on analysis of six single nucleotide polymorphisms and a Bayesian procedure of evidence interpretation.
Article
“Familial searching” in law enforcement DNA databases has been pilloried as a step “towards eugenics and corruption of blood” and “lifelong genetic surveillance” that is “inconsistent with a basic pillar of American political thought.” Courts have yet to address the issue fully, but several commentators contend that the practice is unwise, unjust, or unconstitutional. This Article examines the more significant constitutional claims. It concludes that although kinship matching should not be implemented simply because it is technologically seductive, neither should it be removed from the realm of permissible law enforcement information gathering on constitutional grounds. In reaching this conclusion, the Article describes the logic of kinship analysis; clarifies the nature of partial-match searching; shows how an advanced system of DNA databases could yield additional, accurate leads in the investigation of both routine and high profile crimes; and why this system, if properly implemented, is compatible with constitutionally protected interests of both convicted offenders and their close relatives.
Article
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For complex diseases like cancer, pooled-analysis of individual data represents a powerful tool to investigate the joint contribution of genetic, phenotypic and environmental factors to the development of a disease. Pooled-analysis of epidemiological studies has many advantages over meta-analysis, and preliminary results may be obtained faster and with lower costs than with prospective consortia. Design and methods Based on our experience with the study design of the Melanocortin-1 receptor (MC1R) gene, SKin cancer and Phenotypic characteristics (M-SKIP) project, we describe the most important steps in planning and conducting a pooled-analysis of genetic epidemiological studies. We then present the statistical analysis plan that we are going to apply, giving particular attention to methods of analysis recently proposed to account for between-study heterogeneity and to explore the joint contribution of genetic, phenotypic and environmental factors in the development of a disease. Within the M-SKIP project, data on 10,959 skin cancer cases and 14,785 controls from 31 international investigators were checked for quality and recoded for standardization. We first proposed to fit the aggregated data with random-effects logistic regression models. However, for the M-SKIP project, a two-stage analysis will be preferred to overcome the problem regarding the availability of different study covariates. The joint contribution of MC1R variants and phenotypic characteristics to skin cancer development will be studied via logic regression modeling. Methodological guidelines to correctly design and conduct pooled-analyses are needed to facilitate application of such methods, thus providing a better summary of the actual findings on specific fields.
Article
The melanocortin 1 receptor, a Gs protein-coupled receptor expressed in epidermal melanocytes, is a major determinant of skin pigmentation and phototype and an important contributor to melanoma risk. MC1R activation stimulates synthesis of black, strongly photoprotective eumelanin pigments. Several MC1R alleles are associated with red hair, fair skin, increased sensitivity to ultraviolet radiation, and increased skin cancer risk. The MC1R gene is highly polymorphic, but only a few naturally occurring alleles have been functionally characterized, which complicates the establishment of accurate correlations between the signaling properties of mutant alleles and defined cutaneous phenotypes. We report the functional characterization of six MC1R alleles found in Spanish melanoma patients. Two variants (c.152T>C, p.Val51Ala and c.865T>C, p.Cys289Arg) have never been described, and the others (c.112G>A, p.Val38Met; c.122C>T, p.Ser41Phe; c.383T>C, p.Met128Thr; and c.842A>G, p.Asn281Ser) have not been analyzed for function. p.Asn281Ser corresponds to a functionally silent polymorphism. The other mutations are associated with varying degrees of loss of function (LOF), from moderate decreases in coupling to the cAMP pathway (p.Val38Met and p.Val51Ala) to nearly complete absence of functional coupling (p.Ser41Phe, p.Met128Thr, and p.Cys289Arg). The LOF p.Met128Thr and p.Cys289Arg mutants are trafficked to the cell surface, but are unable to bind agonists efficiently. Conversely, LOF of p.Val38Met, p.Ser41Phe, and p.Val51Ala is due to reduced cell surface expression as a consequence of retention in the endoplasmic reticulum (ER). Therefore, LOF of MC1R alleles is frequently associated with aberrant forward trafficking and accumulation within the ER or with inability to bind properly the activatory ligand. Hum Mutat 30:1–12, 2009. © 2009 Wiley-Liss, Inc.
Article
Introduction Forensic DNA Phenotyping (FDP) has provided better understanding of various phenotypic features (e.g., height, skin colour, eye colour, structure and shape of scalp hair, baldness, facial features etc.) and associated genetic variations. The current study was designed to investigate the genetic variants and their potential contribution towards accurate phenotype prediction systems. Short Tandem Repeat (STR) based DNA typing method can be uninformative or with little potential to solve a crime in absence of suspect DNA profile in the database. Forensic DNA Phenotyping (FDP), prediction of externally visible characteristics (EVCs) from the crime scene DNA would certainly provide a new dimension to personal identification. The aim of this review paper is to highlight the significance and future prospects of FDP. Results A comprehensive literature review was conducted using PubMed and similar e-databases with keywords from two main components-phenotype and the associated genetic variants. To ensure a thorough literature review, searches were extended using the snowballing technique from reference lists. Key data extracted were type of study, sample characteristics (sample size, age, geographical location and ancestry), details of SNPs studied and prediction accuracies. Conclusion Phenotyping tools based on genotyping and statistical analysis for the prediction of human pigmentation are propitious in solving cold cases. This indicates the inevitability of future studies for the identification of new genetic markers for accurate prediction of phenotype or EVCs via genome-wide association study (GWAS) in diverse global populations.
Article
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Background: The MC1R gene implicated in melanogenesis and skin pigmentation is highly polymorphic. Several alleles are associated with red hair and fair skin phenotypes and contribute to melanoma risk. Objective: This work aims to assess the effect of different classes of MC1R variants, notably rare variants, on melanoma risk. Methods. MC1R coding region was sequenced in 1131 melanoma patients and 869 healthy controls. MC1R variants were classified as RHC (R) and non-RHC (r). Rare variants (frequency < 1%) were subdivided into two subgroups, predicted to be damaging (D) or not (nD). Results: Both R and r alleles were associated with melanoma (OR = 2.66 [2.20-3.23] and 1.51 [1.32-1.73]) and had similar population attributable risks (15.8% and 16.6%). We also identified 69 rare variants, of which 25 were novel. D variants were strongly associated with melanoma (OR = 2.38 [1.38-4.15]) and clustered in the same MC1R domains as R alleles (intracellular 2, transmembrane 2 and 7). Conclusion: This work confirms the role of R and r alleles in melanoma risk in the French population and proposes a novel class of rare D variants as important melanoma risk factors. These findings may improve the definition of high-risk subjects that could be targeted for melanoma prevention and screening.
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The estimation of age is an important issue in forensic science, and the forensic community has attempted many times to establish methods for solving this issue. Aging leads to alterations in tissues and organs at the molecular level. These alterations at the molecular level may aid forensic scientists to estimate the age of a living person or a dead body. Initially, the focus was on the genetic components of aging, but recently, epigenetic mechanisms have emerged as the key contributors to the alterations in genome structure and function that accompany aging. In particular, DNA methylation is one of the best-understood mechanisms, and it has been suggested as a promising biomarker for age estimation in many studies. In this review, we summarize the recent studies on age-associated DNA methylation changes in different tissues and discuss its possible and practical applications in forensics.
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Forensic DNA Phenotyping refers to the prediction of appearance traits of unknown sample donors, or unknown deceased (missing) persons, directly from biological materials found at the scene. "Biological witness" outcomes of Forensic DNA Phenotyping can provide investigative leads to trace unknown persons, who are unidentifiable with current comparative DNA profiling. This intelligence application of DNA marks a substantially different forensic use of genetic material rather than that of current DNA profiling presented in the courtroom. Currently, group-specific pigmentation traits are already predictable from DNA with reasonably high accuracies, while several other externally visible characteristics are under genetic investigation. Until individual-specific appearance becomes accurately predictable from DNA, conventional DNA profiling needs to be performed subsequent to appearance DNA prediction. Notably, and where Forensic DNA Phenotyping shows great promise, this is on a (much) smaller group of potential suspects, who match the appearance characteristics DNA-predicted from the crime scene stain or from the deceased person's remains. Provided sufficient funding being made available, future research to better understand the genetic basis of human appearance will expectedly lead to a substantially more detailed description of an unknown person's appearance from DNA, delivering increased value for police investigations in criminal and missing person cases involving unknowns. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
Article
Single nucleotide polymorphism (SNP) refers to the single base sequence variation in specific location of the human genome. Phenotype informative SNP has gradually become one of the research hot spots in forensic science. In this paper, the forensic research situation and application prospect of phenotype informative SNP in the characteristics of hair, eye and skin color, height, and facial feature are reviewed.
Article
Single nucleotide polymorphism is a single base pair position in genomic DNA at which different sequence alternatives exist in normal individuals in some populations. Phenotype informative SNPs are those SNPs which can provide a high probability that individual has particular phenotypes. This review offers to the reader the definition, research methods and development of PISNPs in forensic genetics and provides several suggestions to enhance the application of PISNPs.
Chapter
This chapter focuses on efforts with single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) biallelic polymorphisms and their applications including ancestry estimation and phenotype prediction. A single-base sequence variation between individuals at a particular point in the genome is referred to as a single nucleotide polymorphism, or SNP (pronounced “snip”). SNPs are abundant in the human genome and, as such, are being used for linkage studies to track genetic diseases. Millions of SNPs exist per individual and thus the abundance of SNPs means that they could be used to help differentiate individuals from one another. A number of technologies have been developed to minaturize and automate the procedure for SNP analysis. SNPs are considered as potential genetic markers by the forensic DNA community for several reasons. The polymerase chain reaction (PCR) products from SNPs is less than 100 bp in size, which means that these markers are able to recover information from degraded DNA samples better than short tandem repeats (STRs) that have amplicons as large as 300 bp to 400 bp. A number of SNP typing methods are available, each with its own strengths and weaknesses.
Chapter
This chapter examines other DNA markers that are being used or being developed for forensic DNA typing purposes or other applications. Additional autosomal or Y-chromosomal short tandem repeat (STR) loci can be beneficial or even necessary to address a variety of other human identity/relationship testing questions. Some desirable characteristics in potential supplemental STR loci as compared to the core loci that are now widely used are given in the chapter. A single-base sequence variation among individuals at a particular point in the genome is often referred to as a “single nucleotide polymorphism” (SNP). The chapter presents pros and cons of SNPs. A number of SNP typing methods are available, each with its own strengths and weaknesses. A few SNP analysis techniques are summarized in the chapter. SNP markers may be classified into four general uses: human identification SNPs, ancestry informative SNPs, lineage informative SNPs, and phenotype informative SNPs. The chapter discusses the value of non human DNA testing in forensic casework. Domestic animals, such as cats and dogs, live in human habitats and deposit hair that may be used to place a suspect at the crime scene. A botanical specimen came from a particular plant can aid the linkage of a crime to a suspect or help demonstrate that the body of a deceased victim may have been moved from the murder site. DNA testing can now be used to link sources of marijuana. A large area of future application for forensic DNA typing involves identification of bioterrorism materials such as anthrax. The chapter also presents the challenges with presenting non human DNA in court.
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The focus in this chapter is on hair form or fiber diameter and curvature and on hair color or pigmentation. These important hair characteristics are controlled by single nucleotide polymorphisms which are single nucleotide changes in genes. The three primary hair forms today (African, Asian and Caucasian) and their hair pigmentations arose from genetic mutations that are consistent with geographic migrations of Asians and Caucasians. Therefore, these hair forms and pigmentations are probably remnants of prior adaptations to temperature, sun exposure and other environmental influences. Other hair traits related to genetics including different alopecia and several genetically involved hair abnormalities are described along with a brief summary of current directions in forensic science which has expanded into DNA analysis and is moving into the analysis of SNPs.
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Driven by recent evolutionary history, pigmentation traits significantly contribute to the most obvious parts of the overall human phenotypic diversity with skin colour varying between worldwide individuals, while eye and hair colour differences only exist in individuals of European (and neighbouring region) descent. Genetic association studies have discovered various DNA variants that together explain large proportion of phenotypic variance in eye, hair and skin colouration. Besides providing leads in the molecular understanding of human pigmentation, multiple associated DNA variants have also been used for prediction modelling of pigmentation traits. The success of DNA-based pigmentation prediction laid the foundation for a new subfield of forensic genetics known as Forensic DNA Phenotyping, which aims to help finding unknown perpetrators. Pigmentation DNA prediction is further relevant in anthropological research from old and ancient human remains for reconstructing colour phenotypes of deceased persons including those of historical importance.
Article
With recent advances in DNA sequencing technologies it has become feasible and cost effective to genotype larger marker sets for forensic purposes. Two technologies that make use of the larger marker sets have come into focus in forensic research and applications; inference of biogeographic ancestry (BGA) and forensic DNA phenotyping (FDP). These methods hold the promise to reveal information about a yet unknown perpetrator from a DNA sample. In contrast, DNA-profiling, that is a standard practice in case work, relies on matching DNA-profiles between crime scene material and suspects on a database of DNA-profiles. Markers for DNA-profiling were developed under the premise to reveal as little additional information about the human source of the profile as possible, the rationale being that personal privacy rights have to be balanced against the public interest in solving a crime. The same argument holds for markers used in BGA and FDP; these markers might also reveal information on off-target phenotypes (OTPs), that go beyond BGA and the phenotypes targeted in FDP. In particular, health related OTPs might shift the balance between privacy protection and public interest. However, to our knowledge, there is currently no convenient resource available to incorporate knowledge on OTPs in BGA and FDP assay design and application. In order to provide such a resource, we performed a systematic search for OTPs associated with a comprehensive set of markers (1766 SNPs) used or suggested to be used for BGA inference and FDP. In this set, we identified a relatively small number of 27 SNPs (1.53%) that convey information on diverse health related OTPs such as cancer risk, induced asthma, or risk of alcoholism. Some of these SNPs are commonly used for FDP and BGA across different marker sets. We conclude that the effects of SNP markers used in FDP and BGA on OTPs are currently limited, with few exceptions that should be considered in a balanced decision on assay design and application.
Chapter
Forensic DNA Phenotyping (FDP) is evolving as a new technology in forensic science which can make predictions on the externally visible characteristics (EVCs) of an individual based on the information derived from DNA left at a crime scene. FDP as a forensic tool is gaining tremendous importance for successfully predicting the phenotype from biological samples such as blood stains, hair strands or body parts especially in the cases where no witnesses or suspects are accessible. The technique is rapidly progressing from science fiction to science fact and is already been able to predict a number of EVCs e.g. gender, height, male baldness pattern, colour of iris, hair and skin and facial features. Although, many countries are making use of FDP in solving real life criminal cases but certain legal and ethical burdens are still attached to it. These dilemmas are substantial but not invincible and can be overcome with suitable regulatory protocols. There is an urgent need to take into account several ethical and legal issues along with extensive work which is to be done on scientific research and technological advancement to make the technique readily available for forensic investigations and judicial authorities.
Article
The melanocortin 1 receptor (MC1R) gene plays a key role in the control of melanin formation. Polymorphism in the MC1R gene have been associated with Cutaneous melanoma risk and therefore molecular investigation is essential to prevent the pathology and to reduce melanoma mortality. In the current study, we investigated single nucleotide polymorphism for the MC1R target gene using a miniaturized silicon-based microarray-chip. The microarray substrates were properly designed with a multilayer component (Si/Al/SiO2) to enhance the hybridization optical signal by Al layer acting as a mirror while the SiO2 thickness was optimized for light constructive interference. The microarray probe density was found to be 1.900 ± 200 molecules μm⁻². The genotyping experiments performed at different wild type and mutated target amount have shown good sensitivity with discrimination factor >4 for all investigated variants namely rs1805005 V60 L (252 C→T), rs1805006 D84E (425 G→A) and rs885479 R163Q (451 C→T). The obtained Discrimination Factor (DF) values highlights that the assay would allow detection of SNP in an unknown genotype with a >99 % confidence level. Results pave the way for future development of genetic assay in portable format for molecular detection of MC1R gene.
Article
In this study, the suitability of the Investigator DIPplex insertion/deletion polymorphism (indel) kit for forensic casework was assessed through the genotyping of 151 Finns and 175 Somalis. Allele frequency and heterozygosity (H) of this 30-indel marker set were determined, and forensic efficacy was evaluated through estimation of discrimination power (DP), match probability (MP), typical paternity index (TPI), power of paternity exclusion (PE), and polymorphic information content (PIC). A high level of discrimination power was observed for the marker set in both sample groups (CDP>0.9999). East-west population substructure found previously in uniparental markers within Finland was not evident for this autosomal set (E-W F(ST)=0.003). High exclusion probability and low subdivision together demonstrate that these markers are well-suited for identification of individuals in Finland. However, values for typical paternity index and power of paternity exclusion were low (TPI range Finns=0.750-1.190, PE=0.996; TPI Somalis=0.680-1.090, PE=0.986) in comparison to standard STR sets, and thus indels are not recommended for use in paternity or kinship investigations, except as a supplement to other more powerful tools.
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The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers approximately 99% of the euchromatic genome and is accurate to an error rate of approximately 1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human genome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.
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The association between MSHR coding region variation and hair colour in humans has been examined by genotyping 25 red haired and 62 non-red Caucasians, all of whom were 12 years of age and members of a twin pair study. Twelve amino acid substitutions were seen at 11 different sites, nine of these being newly described MSHR variants. The previously reported Val92Met allele shows no association with hair colour, but the three alleles Arg151Cys, Arg160Trp and Asp294His were associated with red hair and one Val60Leu variant was most frequent in fair/blonde and light brown hair colours. Variant MSHR genotypes are associated with lighter skin types and red hair (P < 0.001). However, comparison of the MSHR genotypes in dizygotic twin pairs discordant for red hair colour indicates that the MSHR gene cannot be solely responsible for the red hair phenotype, since five of 13 pairs tested had both haplotypes identical by state (with three of the five having both identical by descent). Rather, it is likely that additional modifier genes exist, making variance in the MSHR gene necessary but not always sufficient, for red hair production.
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Sequential cleavage of the precursor protein pre-pro-opiomelanocortin (POMC) generates the melanocortin peptides adrenocorticotrophin (ACTH), melanocyte-stimulating hormones (MSH) alpha, beta and gamma as well as the opioid-receptor ligand beta-endorphin. While a few cases of isolated ACTH deficiency have been reported (OMIM 201400), an inherited POMC defect has not been described so far. Recent studies in animal models elucidated a central role of alpha-MSH in the regulation of food intake by activation of the brain melanocortin-4-receptor (MC4-R; refs 3-5) and the linkage of human obesity to chromosome 2 in close proximity to the POMC locus, led to the proposal of an association of POMC with human obesity. The dual role of alpha-MSH in regulating food intake and influencing hair pigmentation predicts that the phenotype associated with a defect in POMC function would include obesity, alteration in pigmentation and ACTH deficiency. The observation of these symptoms in two probands prompted us to search for mutations within their POMC genes. Patient 1 was found to be a compound heterozygote for two mutations in exon 3 (G7013T, C7133delta) which interfere with appropriate synthesis of ACTH and alpha-MSH. Patient 2 was homozygous for a mutation in exon 2 (C3804A) which abolishes POMC translation. These findings represent the first examples of a genetic defect within the POMC gene and define a new monogenic endocrine disorder resulting in early-onset obesity, adrenal insufficiency and red hair pigmentation.
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Variants of the melanocortin 1 receptor (MC1R) gene are common in individuals with red hair and fair skin, but the relative contribution to these pigmentary traits in heterozygotes, homozygotes and compound heterozygotes for variants at this locus from the multiple alleles present in Caucasian populations is unclear. We have investigated 174 individuals from 11 large kindreds with a preponderance of red hair and an additional 99 unrelated redheads, for MC1R variants and have confirmed that red hair is usually inherited as a recessive characteristic with the R151C, R160W, D294H, R142H, 86insA and 537insC alleles at this locus. The V60L variant, which is common in the population may act as a partially penetrant recessive allele. These individuals plus 167 randomly ascertained Caucasians demonstrate that heterozygotes for two alleles, R151C and 537insC, have a significantly elevated risk of red hair. The shade of red hair frequently differs in heterozygotes from that in homozygotes/compound heterozygotes and there is also evidence for a heterozygote effect on beard hair colour, skin type and freckling. The data provide evidence for a dosage effect of MC1R variants on hair as well as skin colour.
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The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
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Ancestry informative markers (AIMs) are genetic loci showing alleles with large frequency differences between populations. AIMs can be used to estimate biogeographical ancestry at the level of the population, subgroup (e.g. cases and controls) and individual. Ancestry estimates at both the subgroup and individual level can be directly instructive regarding the genetics of the phenotypes that differ qualitatively or in frequency between populations. These estimates can provide a compelling foundation for the use of admixture mapping (AM) methods to identify the genes underlying these traits. We present details of a panel of 34 AIMs and demonstrate how such studies can proceed, by using skin pigmentation as a model phenotype. We have genotyped these markers in two population samples with primarily African ancestry, viz. African Americans from Washington D.C. and an African Caribbean sample from Britain, and in a sample of European Americans from Pennsylvania. In the two African population samples, we observed significant correlations between estimates of individual ancestry and skin pigmentation as measured by reflectometry (R(2)=0.21, P<0.0001 for the African-American sample and R(2)=0.16, P<0.0001 for the British African-Caribbean sample). These correlations confirm the validity of the ancestry estimates and also indicate the high level of population structure related to admixture, a level that characterizes these populations and that is detectable by using other tests to identify genetic structure. We have also applied two methods of admixture mapping to test for the effects of three candidate genes (TYR, OCA2, MC1R) on pigmentation. We show that TYR and OCA2 have measurable effects on skin pigmentation differences between the west African and west European parental populations. This work indicates that it is possible to estimate the individual ancestry of a person based on DNA analysis with a reasonable number of well-defined genetic markers. The implications and applications of ancestry estimates in biomedical research are discussed.
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There is a large range of human skin color, yet we know very little about the underlying genetic architecture. Is the number of skin color genes close to five, 50, or 500?
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Differences in skin and hair color are principally genetically determined and are due to variation in the amount, type, and packaging of melanin polymers produced by melanocytes secreted into keratinocytes. Pigmentary phenotype is genetically complex and at a physiological level complicated. Genes determining a number of rare Mendelian disorders of pigmentation such as albinism have been identified, but only one gene, the melanocortin 1 receptor (MCR1), has so far been identified to explain variation in the normal population such as that leading to red hair, freckling, and sun-sensitivity. Genotype-phenotype relations of the MC1R are reviewed, as well as methods to improve the phenotypic assessment of human pigmentary status. It is argued that given advances in model systems, increases in technical facility, and the lower cost of genotype assessment, the lack of standardized phenotype assessment is now a major limit on advance.
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Knowledge of inherited genetic variation has a fundamental impact on understanding human disease. Unfortunately, our understanding of the functional significance of many inherited genetic variants is limited. New approaches to assessing functional significance of inherited genetic variation, which combine molecular genetics, epidemiology and bioinformatics, promise to enhance reproducibility and plausibility of associations between genotypes and disease.
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The human melanocortin-1 receptor gene (MC1R) encodes a G-protein coupled receptor that is primarily expressed on melanocytes, where it plays a key role in pigmentation regulation. Variant alleles are associated with red hair colour and fair skin, known as the RHC phenotype, as well as skin cancer risk. The R151C, R160W and D294H alleles, designated 'R', are strongly associated with the RHC phenotype and have been proposed to result in loss of function receptors due to impaired G-protein coupling. We recently provided evidence that the R151C and R160W variants can efficiently couple to G-proteins in response to alpha-melanocyte stimulating hormone. The possibility that altered cellular localization of the R151C and R160W variant receptors could underlie their association with RHC was therefore considered. Using immunofluorescence and ligand binding studies, we found that melanocytic cells exogenously or endogenously expressing MC1R show strong surface localization of the wild-type and D294H alleles but markedly reduced cell surface expression of the R151C and R160W receptors. In additional exogenous expression studies, the R variant D84E and the rare I155T variant, also demonstrated a significant reduction in plasma membrane receptor numbers. The V60L, V92M and R163Q weakly associated RHC alleles, designated 'r', were expressed with normal or intermediate cell surface receptor levels. These results indicate that reduced receptor coupling activity may not be the only contributing factor to the genetic association between the MC1R variants and the RHC phenotype, with MC1R polymorphisms now linked to a change in receptor localization.
Article
Variants of the melanocortin 1 receptor (MC1R) gene are common in individuals with red hair and fair skin, but the relative contribution to these pigmentary traits in heterozygotes, homozygotes and compound heterozygotes for variants at this locus from the multiple alleles present in Caucasian populations is unclear. We have investigated 174 individuals from 11 large kindreds with a preponderance of red hair and an additional 99 unrelated redheads, for MC1R variants and have confirmed that red hair is usually inherited as a recessive characteristic with the R151C, R160W, D294H, R142H, 86insA and 537insC alleles at this locus. The V60L variant, which is common in the population may act as a partially penetrant recessive allele. These individuals plus 167 randomly ascertained Caucasians demonstrate that heterozygotes for two alleles, R151C and 537insC, have a significantly elevated risk of red hair. The shade of red hair frequently differs in heterozygotes from that in homozygotes/compound heterozygotes and there is also evidence for a heterozygote effect on beard hair colour, skin type and freckling. The data provide evidence for a dosage effect of MC1R variants on hair as well as skin colour.
Article
The extension locus has been identified in many mammalian species as a gene that determines the relative amounts of eumelanin and phaeomelanin pigments in hair and skin. In at least three species, this locus has been demonstrated to encode the melanocyte-stimulating hormone receptor (MC1-R), and functionally variant alleles have been demonstrated to cause a broad range of pigmentation phenotypes. To test for MC1-R allelic variation in man, genomic DNA was extracted from skin samples collected from patients with different skin types (I-VI), and eye and hair color. A PCR-based approach was used to amplify the full-length coding sequence of the MC1-R and the resulting products were sequenced. Two polymorphic alleles were identified with single point mutations in the coding sequence: a valine-to-methionine substitution at position 92 (V92M), and an aspartic acid-to-glutamic acid substitution at position 84 (D84E). RFLP analysis demonstrated the presence of the V92M allele in 4 out of 60 (6.6%) of individuals examined, predominantly those with blue eyes and blond hair. This polymorphism was found in both heterozygous and homozygous states in individuals with type I skin. The D84E allele was found in one individual with skin type I; this person also has the V92 M allele and thus is a compound heterozygote.
Article
It is widely assumed that genes that influence variation in skin and hair pigmentation are under selection. To date, the melanocortin 1 receptor (MC1R) is the only gene identified that explains substantial phenotypic variance in human pigmentation. Here we investigate MC1R polymorphism in several populations, for evidence of selection. We conclude that MC1R is under strong functional constraint in Africa, where any diversion from eumelanin production (black pigmentation) appears to be evolutionarily deleterious. Although many of the MC1R amino acid variants observed in non-African populations do affect MC1R function and contribute to high levels of MC1R diversity in Europeans, we found no evidence, in either the magnitude or the patterns of diversity, for its enhancement by selection; rather, our analyses show that levels of MC1R polymorphism simply reflect neutral expectations under relaxation of strong functional constraint outside Africa.
Article
We describe a minisequencing protocol for screening DNA samples for the presence of 12 mutations in the human melanocortin 1 receptor gene (MC1R), eight of which are associated with the red hair phenotype. A minisequencing profile which shows homozygosity for one of these mutations or the presence of two different mutations would strongly indicate that the sample donor is red haired. The absence of any red hair causing mutations would indicate that the sample donor does not have red hair. We report the frequencies of MC1R variants in the British red haired population.
Article
In mice and humans, binding of alpha-melanocyte--stimulating hormone to the melanocyte-stimulating--hormone receptor (MSHR), the protein product of melanocortin-1 receptor (MC1R) gene, leads to the synthesis of eumelanin. In the mouse, ligation of MSHR by agouti signaling protein (ASP) results in the production of pheomelanin. The role of ASP in humans is unclear. We sought to characterize the agouti signaling protein gene (ASIP) in a group of white subjects, to assess whether ASIP was a determinant of human pigmentation and whether this gene may be associated with increased melanoma risk. We found no evidence of coding-region sequence variation in ASIP, but detected a g.8818A-->G polymorphism in the 3' untranslated region. We genotyped 746 participants in a study of melanoma susceptibility for g.8818A-->G, by means of polymerase chain reaction and restriction fragment--length polymorphism analysis. Among the 147 healthy controls, the frequency of the G allele was.12. Carriage of the G allele was significantly associated with dark hair (odds ratio 1.8; 95% confidence interval [CI] 1.2--2.8) and brown eyes (odds ratio 1.9; 95% CI 1.3--2.8) after adjusting for age, gender, and disease status. ASIP g.8818A-->G was not associated independently with disease status. This is the first report of an association of ASIP with specific human pigmentation characteristics. It remains to be investigated whether the interaction of MC1R and ASIP can enhance prediction of human pigmentation and melanoma risk.
Article
We have surveyed and summarized several aspects of DNA variability among humans. The variation described is the result of mutation followed by a combination of drift, migration and selection bringing the frequencies high enough to be observed. This paper describes what we have learned about how DNA variability differs among genes and populations. We sequenced functional regions of a set of 3950 genes. DNA was sampled from 82 unrelated humans: 20 African-Americans, 20 East Asians, 21 Caucasians, 18 Hispanic-Latinos and 3 Native Americans. Different aspects of variability showed a great deal of concordance. In particular, we studied patterns of single nucleotide polymorphism (SNP) allele and haplotype sharing among the four, large sample populations. We also examined how linkage disequilibrium (LD) between SNPs relates to physical distance in the different populations. It is clear from our findings that while many variants are common to all populations, many others have a more restricted distribution. Research that attempts to find genetic variants that explain phenotypic variants must be careful in their choice of study population.
Article
We have examined MC1R variant allele frequencies in the general population of South East Queensland and in a collection of adolescent dizygotic and monozygotic twins and family members to define statistical associations with hair and skin color, freckling, and mole count. Results of these studies are consistent with a linear recessive allelic model with multiplicative penetrance in the inheritance of red hair. Four alleles, D84E, R151C, R160W, and D294H, are strongly associated with red hair and fair skin with multinomial regression analysis showing odds ratios of 63, 118, 50, and 94, respectively. An additional three low-penetrance alleles V60L, V92M, and R163Q have odds ratios 6, 5, and 2 relative to the wild-type allele. To address the cellular effects of MC1R variant alleles in signal transduction, we expressed these receptors in permanently transfected HEK293 cells. Measurement of receptor activity via induction of a cAMP-responsive luciferase reporter gene found that the R151C and R160W receptors were active in the presence of NDP-MSH ligand, but at much reduced levels compared with that seen with the wild-type receptor. The ability to stimulate phosphorylation of the cAMP response element binding protein (CREB) transcription factor was also apparent in all stimulated MC1R variant allele-expressing HEK293 cell extracts as assessed by immunoblotting. In contrast, human melanoma cell lines showed wide variation in the their ability to undergo cAMP-mediated CREB phosphorylation. Culture of human melanocytes of known MC1R genotype may provide the best experimental approach to examine the functional consequences for each MC1R variant allele. With this objective, we have established more than 300 melanocyte cell strains of defined MC1R genotype.
Article
Ancestral inference from DNA could serve as an important adjunct for both standard and future human identity testing procedures. However, current STR methods for the inference of ancestral affiliation have inherent statistical and technical limitations. In an effort to identify bi-allelic markers that can be used to infer ancestral affiliation from DNA, we screened 211 SNPs in the human pigmentation and xenobiotic metabolism genes. Allele frequencies of 56 SNPs (most from pigmentation genes) were dramatically different between groups of unrelated individuals of Asian, African, and European descent, and both observed and simulated log likelihood ratios revealed that the markers were of exceptional value for ancestral inference. Log likelihood ratios of the multilocus estimates of biological ancestry (EAE/EBA) ranged from 7 to 10, which are on par with the best of the STR batteries yet described. A linear classification method was developed for incorporating these SNPs into a classifier model that was 99, 98, and 100% accurate for identifying individuals of European, African, and Asian descent, respectively. The methods and markers we describe are therefore an important first step for the development of a practical multiplex test for the inference of ancestry in a forensics setting.
Article
We have developed a robust single nucleotide polymorphism (SNPs) typing assay with co-amplification of 25 DNA-fragments and the detection of 35 human Y chromosome SNPs. The sizes of the PCR products ranged from 79 to 186 base pairs. PCR primers were designed to have a theoretical Tm of 60 +/- 5 degrees C at a salt concentration of 180 mM. The sizes of the primers ranged from 19 to 34 nucleotides. The concentration of amplification primers was adjusted to obtain balanced amounts of PCR products in 8mM MgCl2. For routine purposes, 1 ng of genomic DNA was amplified and the lower limit was approximately 100 pg DNA. The minisequencing reactions were performed simultaneously for all 35 SNPs with fluorescently labelled dideoxynucleotides. The size of the minisequencing primers ranged from 19 to 106 nucleotides. The minisequencing reactions were analysed by capillary electrophoresis and multicolour fluorescence detection. Female DNA did not influence the results of Y chromosome SNP typing when added in concentrations more than 300 times the concentrations of male DNA. The frequencies of the 35 SNPs were determined in 194 male Danes. The gene diversity of the SNPs ranged from 0.01 to 0.5.
Article
The increasing availability of polymorphism data has allowed more gene association studies to be carried out and the number of published genetic association studies is growing rapidly. Studies done secondarily to successful linkage studies over the last decade have also fueled the increase in published association studies. Although there are single-nucleotide polymorphism and human variation databases1, 2, there is currently no public repository for genetic association data. It is difficult to query association data in a systematic manner or to integrate association data with other molecular databases. OMIM3, the main repository of genetic information for mendelian disorders, is largely text based and is of a historical narrative design, making it difficult to compare large sets of molecular data. Moreover, OMIM archives mature, high-quality data of high significance, the standard in rare mendelian disorders. Although this data is useful, OMIM does not routinely collect findings of lower significance or negative findings. The study of nonmendelian, common complex disorders is often a struggle to find disease relevance with lower significance values, and often conflicting evidence. Negative data are often not reported or are marginalized into obscure and less accessible scientific journals, resulting in a publication bias favoring positive genetic associations4. Here, we describe the development of a genetic association database (GAD; http://geneticassociationdb.nih.gov) that aims to collect, standardize and archive genetic association study data and to make it easily accessible to the scientific community.
Article
The melanocortin-1 receptor gene (MC1R) encodes a membrane-bound receptor protein that is central to melanin synthesis. The coding region of MC1R is highly polymorphic and associations of variants with pigmentation phenotypes and risk for cutaneous neoplasms have been reported. We sought to determine the distribution and frequency of MC1R variants and their relationship to pigmentation characteristics in 179 Caucasian controls from the United States. One hundred thirty-five (75.4%) subjects carried one or more variants, and we determined that carriage of the previously designated "red hair color" (RHC) alleles, R151C, R160W, and D294H was strongly associated with fair pigmentation phenotypes including light hair and eye color, tendency to burn, decreased tendency to tan, and freckling. We used SIFT software to define MC1R protein positions that were predicted intolerant to amino acid substitutions; detected variants that corresponded to intolerant substitutions were D84E, R142H, R151C, I155T, R160W, and D294H. Carriage of one or more of these putative functionally important variants or the frameshift variant ins86A was significantly associated with fair pigmentation phenotypes. Analyses limited to carriage of ins86A and the three non-RHC alleles identified by SIFT were attenuated and no longer reached statistical significance. This is the first study to describe MC1R variants among control subjects from the U.S. Our results indicate that the frequency of variants is similar to that previously observed among non-U.S. Caucasians. Risk variants defined by either the published literature or by evolutionary criteria are strongly and significantly associated with all fair pigmentation phenotypes that were measured.
Article
Several variant forms of the melanocortin-1 receptor gene (MC1R) have been associated with red hair, fair skin and an increased risk for melanoma. Their involvement in melanoma susceptibility is apparently linked both to skin sensitivity and to non-pigmentary pathways. We investigated the frequency of the MC1R variants in the Italian region of Liguria, where the occurrence and penetrance of melanoma are low and primary susceptibility is characterized by prevalence of the CDKN2A c.301G>T [p.G101W] founder mutation. Additionally, we attempted to establish the frequency of the red hair/fair skin phenotype in our region. As predicted by anecdotal evidence, the frequency of red hair/phototype I was very low (0.7%). Screening of 17 red-haired individuals and their red-haired relatives, 207 controls and 214 melanoma patients unselected for hair color but all of Ligurian descent, led to the detection of 8 novel substitutions (c.133T>C [p.F45L], c.248C>T [p.S83L], c.332C>T [p. A111V], c.479G>A [p.R160Q], c.637C>T [p.R213W], c.793G>A [p. V265I], c.923C>T [p. T308M], c.943T>C [p.C315R]), 1 novel deletion (c.520_523delGTC [p.V174del]) and 3 novel synonymous variants (c.366G>C [p. V122V], c.684G>A [p. Q228Q], c.726C>T [p.T241T]). Preliminary genotype/phenotype correlation seems to indicate that other genes involved in the regulation of human pigmentation may mask the recessive action of high-penetrance MC1R alleles, thus determining the low frequency of at-risk phototypes and of incidence and/or penetrance of melanoma in Liguria.
Article
Humans vary >100-fold in their sensitivity to the harmful effects of ultraviolet radiation. The main determinants of sensitivity are melanin pigmentation and less-well-characterized differences in skin inflammation and repair processes. Pigmentation has a high heritability, but susceptibility to cancers of the skin, a key marker of sun sensitivity, is less heritable. Despite a large number of murine coat-color mutations, only one gene in humans, the melanocortin 1 receptor (MC1R), is known to account for substantial variation in skin and hair color and in skin cancer incidence. MC1R encodes a 317-amino acid G-coupled receptor that controls the relative amounts of the two major melanin classes, eumelanin and pheomelanin. Most persons with red hair are homozygous for alleles of the MC1R gene that show varying degrees of diminished function. More than 65 human MC1R alleles with nonsynonymous changes have been identified, and current evidence suggests that many of them vary in their physiological activity, such that a graded series of responses can be achieved on the basis of (i) dosage effects (of one or two alleles) and (ii) individual differences in the pharmacological profile in response to ligand. Thus, a single locus, identified within a Mendelian framework, can contribute significantly to human pigmentary variation.
Article
The constitutive color of our skin plays a dramatic role in our photoprotection from solar ultraviolet radiation (UVR) that reaches the Earth and in minimizing DNA damage that gives rise to skin cancer. More than 120 genes have been identified and shown to regulate pigmentation, one of the key genes being melanocortin 1 receptor (MC1R) that encodes the melanocortin 1 receptor (MC1R), a seven-transmembrane G protein-coupled receptor expressed on the surface of melanocytes. Modulation of MC1R function regulates melanin synthesis by melanocytes qualitatively and quantitatively. The MC1R is regulated by the physiological agonists alpha-melanocyte-stimulating hormone (alphaMSH) and adrenocorticotropic hormone (ACTH), and antagonist agouti signaling protein (ASP). Activation of the MC1R by binding of an agonist stimulates the synthesis of eumelanin primarily via activation of adenylate cyclase. The significance of cutaneous pigmentation lies in the photoprotective effect of melanin, particularly eumelanin, against sun-induced carcinogenesis. Epidermal melanocytes and keratinocytes respond to UVR by increasing their expression of alphaMSH and ACTH, which up-regulate the expression of MC1R, and consequently enhance the response of melanocytes to melanocortins. Constitutive skin pigmentation dramatically affects the incidence of skin cancer. The pigmentary phenotype characterized by red hair, fair complexion, inability to tan and tendency to freckle is an independent risk factor for all skin cancers, including melanoma. The MC1R gene is highly polymorphic in human populations, and allelic variation at this locus accounts, to a large extent, for the variation in pigmentary phenotypes and skin phototypes (SPT) in humans. Several allelic variants of the MC1R gene are associated with the red hair and fair skin (RHC) phenotype, and carrying one of these variants is thought to diminish the ability of the epidermis to respond to DNA damage elicited by UVR. The MC1R gene is considered a melanoma susceptibility gene, and its significance in determining the risk for skin cancer is of tremendous interest.