Kosoy, R., Nassir, R., Tian, C., White, P. A., Butler, L. M., Silva, G. et al. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum. Mutat. 30, 69-78

Rowe Program in Human Genetics, Department of Biochemistry, University of California Davis, Davis, California 95616, USA.
Human Mutation (Impact Factor: 5.14). 01/2009; 30(1):69-78. DOI: 10.1002/humu.20822
Source: PubMed


To provide a resource for assessing continental ancestry in a wide variety of genetic studies, we identified, validated, and characterized a set of 128 ancestry informative markers (AIMs). The markers were chosen for informativeness, genome-wide distribution, and genotype reproducibility on two platforms (TaqMan assays and Illumina arrays). We analyzed genotyping data from 825 subjects with diverse ancestry, including European, East Asian, Amerindian, African, South Asian, Mexican, and Puerto Rican. A comprehensive set of 128 AIMs and subsets as small as 24 AIMs are shown to be useful tools for ascertaining the origin of subjects from particular continents, and to correct for population stratification in admixed population sample sets. Our findings provide general guidelines for the application of specific AIM subsets as a resource for wide application. We conclude that investigators can use TaqMan assays for the selected AIMs as a simple and cost efficient tool to control for differences in continental ancestry when conducting association studies in ethnically diverse populations.

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    • "c o m / l o c a t e / f s i g have shown the suitability of SNP markers for use with degraded samples7891011. Also during this time period, publications in both the forensic and clinical realms have characterized SNPs suitable for human identification [12] and ancestry determination [13,14]. In early 2014, a commercial multiplex SNP assay for human identity (HID) applications became available for the Ion Torrent Personal Genome Machine (Ion PGM) (Thermo Fisher Scientific, Waltham, MA, USA) and the HID-Ion AmpliSeq Identity Community Panel (Thermo Fisher Scientific), which allows simultaneous genotyping of 90 autosomal and 30 Y-SNP markers chosen for forensic identification purposes. "
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    ABSTRACT: Forensic DNA casework samples are often of insufficient quantity or quality to generate full profiles by conventional DNA typing methods. Polymerase chain reaction (PCR) amplification of short tandem repeat (STR) loci is inherently limited in samples containing degraded DNA, as the cumulative size of repeat regions, primer binding regions, and flanking sequence is necessarily larger than the PCR template. Additionally, traditional capillary electrophoresis (CE) assay design further inherently limits shortening amplicons because the markers must be separated by size. Non-traditional markers, such as single nucleotide polymorphisms (SNPs) and insertion deletion polymorphisms (InDels), may yield more information from challenging samples due to their smaller amplicon size. In this study, the performance of a next generation sequencing (NGS) SNP assay and CE-based STR, mini-STR, and InDel assays was evaluated with a series of fragmented, size-selected samples. Information obtained from the NGS SNP assay exhibited higher overall inverse random match probability (1/RMP) values compared to the CE-based typing assays, with particular benefit for fragment sizes ≤150 base pairs (bp). The InDel, mini-STR, and NGS SNP assays all had similar percentages of loci with reportable alleles at this level of degradation; however, the relatively fewer number of loci in the InDel and mini-STR assays results in the NGS SNP assay having at least nine orders of magnitude higher 1/RMP values. In addition, the NGS SNP assay and three CE-based assays (two STR and one InDel assay) were tested using a dilution series consisting of 0.5ng, 0.1ng, and 0.05ng non-degraded DNA. All tested assays showed similar percentages of loci with reportable alleles at these levels of input DNA; however, due to the larger number of loci, the NGS SNP assay and the larger of the two tested CE-based STR assays both resulted in considerably higher 1/RMP values than the other assays. These results indicate the potential advantage of NGS SNP assays for forensic analysis of degraded DNA samples. Published by Elsevier Ireland Ltd.
    Full-text · Article · May 2015 · Forensic Science International: Genetics
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    • "We evaluated the genomic ancestries of the patients and controls following the methodology of Kosoy et al. (2009), with an in-house modification consisting of the genotyping of 12 genetic ancestry markers (Coelho et al. 2014, unpublished observations). The cases and controls presented the following similar distributions of genomic contribution: approximately 60% contribution from European , 23% from African and 17% from Amerindian ancestral populations. "
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    ABSTRACT: The human beta defensin 1 (hBD-1) antimicrobial peptide is a member of the innate immune system known to act in the first line of defence against microorganisms, including viruses such as human papillomavirus (HPV). In this study, five functional polymorphisms (namely g-52G>A, g-44C>G and g-20G>A in the 5’UTR and c.*5G>A and c.*87A>G in the 3’UTR) in the DEFB1 gene encoding for hBD-1 were analysed to investigate the possible involvement of these genetic variants in susceptibility to HPV infection and in the development of HPV-associated lesions in a population of Brazilian women. The DEFB1 g-52G>A and c.*5G>A single-nucleotide polymorphisms (SNPs) and the GCAAA haplotype showed associations with HPV-negative status; in particular, the c.*5G>A SNP was significantly associated after multiple test corrections. These findings suggest a possible role for the constitutively expressed beta defensin-1 peptide as a natural defence against HPV in the genital tract mucosa.
    Full-text · Article · Nov 2014 · Memórias do Instituto Oswaldo Cruz
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    • "The inclusion of ancestry informative markers could help reduce this threat ( Kosoy et al . , 2009 ) . Future directions that manipulate the dopaminergic system through phar - macology or dietary depletion may provide supporting evidence for these findings ( e . g . , use of a medication with D4 properties such as olanzapine to lend credence to initial association findings ; Hutchison et al . , 2003 ) . Similarly , more comprehensive"
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    ABSTRACT: Humans with seven or more repeats in exon III of the DRD4 gene (long DRD4 carriers) sometimes demonstrate impaired attention, as seen in attention-deficit hyperactivity disorder, and at other times demonstrate heightened attention, as seen in addictive behavior. Although the clinical effects of DRD4 are the focus of much work, this gene may not necessarily serve as a "risk" gene for attentional deficits, but as a plasticity gene where attention is heightened for priority items in the environment and impaired for minor items. Here we examine the role of DRD4 in two tasks that benefit from selective attention to high-priority information. We examine a category learning task where performance is supported by focusing on features and updating verbal rules. Here, selective attention to the most salient features is associated with good performance. In addition, we examine the Operation Span (OSPAN) task, a working memory capacity task that relies on selective attention to update and maintain items in memory while also performing a secondary task. Long DRD4 carriers show superior performance relative to short DRD4 homozygotes (six or less tandem repeats) in both the category learning and OSPAN tasks. These results suggest that DRD4 may serve as a "plasticity" gene where individuals with the long allele show heightened selective attention to high-priority items in the environment, which can be beneficial in the appropriate context.
    Full-text · Article · Sep 2014 · Journal of Cognitive Neuroscience
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