Denilce R. Sumita

Genomic Engenharia Molecular Ltda, San Paulo, São Paulo, Brazil

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Publications (14)21.59 Total impact

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    ABSTRACT: In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend towards smaller genetic distances resulting from larger numbers of markers became apparent.
    Forensic Science International: Genetics 04/2014; 12:12-23. · 3.86 Impact Factor
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    [Show abstract] [Hide abstract]
    ABSTRACT: In a worldwide collaborative effort, 19,630 Y-chromosomes were sampled from 129 different populations in 51 countries. These chromosomes were typed for 23 short-tandem repeat (STR) loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385ab, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, DYS643) and using the PowerPlex Y23 System (PPY23, Promega Corporation, Madison, WI). Locus-specific allelic spectra of these markers were determined and a consistently high level of allelic diversity was observed. A considerable number of null, duplicate and off-ladder alleles were revealed. Standard single-locus and haplotype-based parameters were calculated and compared between subsets of Y-STR markers established for forensic casework. The PPY23 marker set provides substantially stronger discriminatory power than other available kits but at the same time reveals the same general patterns of population structure as other marker sets. A strong correlation was observed between the number of Y-STRs included in a marker set and some of the forensic parameters under study. Interestingly a weak but consistent trend towards smaller genetic distances resulting from larger numbers of markers became apparent.
    Forensic Science International: Genetics 01/2014; · 3.86 Impact Factor
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    ABSTRACT: Most laboratories presently carrying out forensic identification and parentage testing use capillary DNA sequencers to separate and visualize the alleles that are produced by multiplex PCR amplification, whether they be of STR, SNP or DIP loci. Because at least four, but usually five, different fluorophores are used simultaneously, each instrument must undergo its own spectral calibration in which a matrix is created and used to correct the overlapping of fluorescence emission spectra of the mixture of dyes. For this users must acquire matrix standards in addition to the multiplex PCR kits and it is not clear what these standards consist of. In our efforts to develop new multiplex STR and DIP amplification kits using different fluorophores from those commonly used, we were obliged to produce new matrix standards to calibrate our multicapillary sequencers, and we describe how this was done.
    Forensic Science International Genetics Supplement Series 12/2011;
  • Elaine C. Favaro, Denilce R. Sumita, Martin R. Whittle
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    ABSTRACT: At present forensic identification and parentage testing is invariably carried out using multiplex PCR amplification kits in which many loci, whether they be STRs, SNPs or DIPs are analyzed simultaneously using primers labelled with at least three, but usually four, different fluorophores. Should existing loci need to be substituted by newer, for instance, more polymorphic loci, new fluorescent primers need to be synthesized; indeed, the dye labels of several loci may need to be switched to allow a re-accommodation of the allele sizes in the single multiplex, and this can be costly. We sought to facilitate these substitutions and reduce costs by using four universal primers each labelled with a different fluorophore and employ these in a test multiplex PCR amplification of 20 DIP loci.
    Forensic Science International Genetics Supplement Series 12/2011;
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    ABSTRACT: Mitochondrial DNA (mtDNA) population data for forensic purposes are still scarce for some populations, which may limit the evaluation of forensic evidence especially when the rarity of a haplotype needs to be determined in a database search. In order to improve the collection of mtDNA lineages from the Iberian and South American subcontinents, we here report the results of a collaborative study involving nine laboratories from the Spanish and Portuguese Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG) and EMPOP. The individual laboratories contributed population data that were generated throughout the past 10 years, but in the majority of cases have not been made available to the scientific community. A total of 1019 haplotypes from Iberia (Basque Country, 2 general Spanish populations, 2 North and 1 Central Portugal populations), and Latin America (3 populations from São Paulo) were collected, reviewed and harmonized according to defined EMPOP criteria. The majority of data ambiguities that were found during the reviewing process (41 in total) were transcription errors confirming that the documentation process is still the most error-prone stage in reporting mtDNA population data, especially when performed manually. This GHEP-EMPOP collaboration has significantly improved the quality of the individual mtDNA datasets and adds mtDNA population data as valuable resource to the EMPOP database (www.empop.org).
    Forensic Science International: Genetics 11/2010; 5(2):146-51. · 3.86 Impact Factor
  • M. R. Whittle, E. C. Favaro, D. R. Sumita
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    ABSTRACT: With both the SNPforID and the Kidd panels of autosomal SNPs available, we selected the 40 most informative and population-independent SNPs from both these sets for evaluation in paternity testing and as a prelude for forensic human identification.We used the published primer sequences and constructed PCR multiplexes for genotyping using the SNaPshot assay. Fifty trios and 50 duos previously analysed using conventional autosomal STR markers were re-analysed using the 40 SNPs. We report our findings regarding the practical use of these markers including unexpected mutations which impacted significantly on the use of this panel.
    Forensic Science International Genetics Supplement Series 01/2009; 2(1):149-150.
  • D. R. Sumita, M. R. Whittle
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    ABSTRACT: DXS10135 and DXS10078 are two highly polymorphic STR loci situated in two different linkage groups on the short arm of the human X chromosome. Both loci comprise complex tetrameric repeat units which may partially explain their high degree of polymorphism. DXS10135 is relatively well characterized and is included in a commercially available kit, while DXS10078 has not been well described. We sequenced a large number of alleles of both loci to try and understand the allelic variation and as a prelude to construct allelic ladders from cloned alleles. Our data show interesting features and should encourage other workers to use these loci in forensic genetic investigations.
    Forensic Science International Genetics Supplement Series 01/2009; 2(1):51-52.
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    ABSTRACT: A collaborative work was carried out by the Spanish and Portuguese International Society for Forensic Genetics Working Group in order to extend the existing data on Y-short tandem repeat (STR) mutations at the 17 Y chromosome STR loci included in the AmpFlSTR YFiler kit (Applied Biosystems): DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and GATA H4.1. In a sample of 701 father/son pairs, 26 mutations were observed among 11,917 allele transfers across the 17 loci. After summing previously reported mutation data with our sample, mutation rates varied between 4.25 x 10(-4) (95% CI 0.05 x 10(-3)-1.53 x 10(-3)) at DYS438 and 6.36 x 10(-3) (95% CI 2.75 x 10(-3)-12.49 x 10(-3)) at DYS458. All mutations were single step, and mutations in the same father/son pair were found twice.
    Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin 11/2008; 122(6):529-33. · 2.69 Impact Factor
  • Denilce R. Sumita, Martin R. Whittle
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    ABSTRACT: Six commercially available DNA polymerases together with their respective buffers were compared as to their ability to generate profiles of commonly used short tandem repeat loci. Extracted FTA paper discs were used in two fluorescent multiplex PCRs containing the same number of units of DNA polymerase to amplify 21 STR loci and the resultant alleles were visualized after electrophoresis on a capillary sequencer. Significant differences were observed upon comparing the profiles: one polymerase failed to amplify larger alleles and presence of additional peaks varied according to the enzyme used. The use of hot-start polymerases did not affect the quality of the resultant profiles in this comparison.
    Forensic Science International Genetics Supplement Series 01/2008; 1(1):128-129.
  • Martin R. Whittle, Denilce R. Sumita
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    ABSTRACT: Forensic DNA quantitation is an important initial step preceding PCR amplification of the STR loci even though information concerning the quality of the DNA is not revealed. A quadruplex real-time PCR (qPCR) assay was developed to quantify four DNA targets: (1) the human RB1 gene in nuclear DNA, (2) the DAZ gene present on the human Y chromosome, (3) the ATPase8 gene present in human mitochondrial DNA and (4) an artificial internal positive control to reveal possible PCR inhibition. Primers labeled with four different fluorophores are used together with a single quencher using the antiprimer quenching-based qPCR method in one reaction, in which the resultant amplicons are less than 127bp in size. Sensitivity was shown to be less than ten copies for all four targets in the absence of amplification inhibition. The amplification remained sensitive in the presence of an excess of non-human DNA.
    Forensic Science International Genetics Supplement Series 01/2008; 1(1):86-88.
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    ABSTRACT: The mitochondrial DNA (mtDNA) working group of the GEP-ISFG (Spanish and Portuguese Group of the International Society for Forensic Genetics) carried out an inter-laboratory exercise consisting of the analysis of mtDNA sequencing patterns in mixed stains (saliva/semen and blood/semen). Mixtures were prepared with saliva or blood from a female donor and three different semen dilutions (pure, 1:10 and 1:20) in order to simulate forensic casework. All labs extracted the DNA by preferential lysis and amplified and sequenced the first mtDNA hypervariable region (HVS-I). Autosomal and Y-STR markers were also analysed in order to compare nuclear and mitochondrial results from the same DNA extracts. A mixed stain prepared using semen from a vasectomized individual was also analysed. The results were reasonably consistent among labs for the first fractions but not for the second ones, for which some laboratories reported contamination problems. In the first fractions, both the female and male haplotypes were generally detected in those samples prepared with undiluted semen. In contrast, most of the mixtures prepared with diluted semen only yielded the female haplotype, suggesting that the mtDNA copy number per cell is smaller in semen than in saliva or blood. Although the detection level of the male component decreased in accordance with the degree of semen dilution, it was found that the loss of signal was not consistently uniform throughout each electropherogram. Moreover, differences between mixtures prepared from different donors and different body fluids were also observed. We conclude that the particular characteristics of each mixed stain can deeply influence the interpretation of the mtDNA evidence in forensic mixtures (leading in some cases to false exclusions). In this sense, the implementation of preliminary tests with the aim of identifying the fluids involved in the mixture is an essential tool. In addition, in order to prevent incorrect conclusions in the interpretation of electropherograms we strongly recommend: (i) the use of additional sequencing primers to confirm the sequencing results and (ii) interpreting the results to the light of the phylogenetic perspective.
    Forensic science international 06/2007; 168(1):42-56. · 2.10 Impact Factor
  • M. R. Whittle, D. R. Sumita
    Forensic Science International-genetics - FORENSIC SCI INT-GENET. 01/2007;
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    ABSTRACT: A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) to estimate Y-STR mutation rates. Seventeen Y chromosome STR loci (DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635 [GATA C4], GATA H4, and GATA A10) were analyzed in a sample of 3,026 father/son pairs. Among 27,029 allele transfers, 54 mutations were observed, with an overall mutation rate across the 17 loci of 1.998 x 10(-3) (95% CI, 1.501 x 10(-3) to 2.606 x 10(-3)). With just one exception, all of the mutations were single-step, and they were observed only once per gametogenesis. Repeat gains were more frequent than losses, longer alleles were found to be more mutable, and the mutation rate seemed to increase with the father's age. Hum Mutat 26(6), 520-528, 2005. (c) 2005 Wiley-Liss, Inc.
    Human Mutation 01/2006; 26(6):520-8. · 5.21 Impact Factor
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    ABSTRACT: The mitochondrial DNA (mtDNA) working group of the GEP-ISFG carried out an inter-laboratory exercise consisting of the study of mixture stains (saliva/semen and blood/semen) in order to investigate the behaviour of these common forensic samples when analysing their mtDNA using standard sequencing methodology. All labs extracted the DNA by preferential lysis and amplified and sequenced the first hypervariable region I (HVS-I). The results showed high consensus between labs for the first fraction of the lysis but not for the second one. We also observed differences between mixtures prepared from different donors and different body fluids. The present study has important consequences for the analysis and interpretation of mtDNA mixtures.
    International Congress Series 01/2006; 1288:130–132.