9 research outputs found
Low Levels of Genetic Divergence across Geographically and Linguistically Diverse Populations from India
Ongoing modernization in India has elevated the prevalence of many complex genetic diseases associated with a western lifestyle and diet to near-epidemic proportions. However, although India comprises more than one sixth of the world's human population, it has largely been omitted from genomic surveys that provide the backdrop for association studies of genetic disease. Here, by genotyping India-born individuals sampled in the United States, we carry out an extensive study of Indian genetic variation. We analyze 1,200 genome-wide polymorphisms in 432 individuals from 15 Indian populations. We find that populations from India, and populations from South Asia more generally, constitute one of the major human subgroups with increased similarity of genetic ancestry. However, only a relatively small amount of genetic differentiation exists among the Indian populations. Although caution is warranted due to the fact that United States–sampled Indian populations do not represent a random sample from India, these results suggest that the frequencies of many genetic variants are distinctive in India compared to other parts of the world and that the effects of population heterogeneity on the production of false positives in association studies may be smaller in Indians (and particularly in Indian-Americans) than might be expected for such a geographically and linguistically diverse subset of the human population
Is the Novel Sckl3 at 14Q23 the Predominant Seckel Locus?
Seckel syndrome (SCKL) is a rare disease with wide phenotypic heterogeneity. A locus (SCKL1) has been identified at 3q and another (SCKL2) at 18p, both in single kindreds afflicted with the syndrome. We report here a novel locus (SCKL3) at 14q by linkage analysis in 13 Turkish families. In total, 18 affected and 10 unaffected sibs were included in the study. Of the 10 informative families, nine with parental consanguinity and one reportedly nonconsanguineous but with two affected sibs, five were indicative of linkage to the novel locus. One of those families also linked to the SCKL1 locus. A consanguineous family with one affected sib was indicative of linkage to SCKL2. The novel gene locus SCKL3 is 1.18 cM and harbors menage a trois 1, a gene with a role in DNA repair.Wo
Correlation Coefficient of Allele Frequencies in India with Linear Combinations of the Allele Frequencies in Europe and East Asia, as a Function of the Fraction of the Linear Combination Drawn from Europe
<p>Graphs with “all populations” compare the frequencies in the pooled Indian sample with linear combinations of the pooled European/Middle Eastern sample and the pooled East Asian sample; graphs with “larger populations” exclude the Parsi group from the Indian sample and utilize only the pooled French, Italian, and Russian genotypes in Europe and the pooled Han Chinese and Japanese genotypes in East Asia. The maxima of the four graphs, from top to bottom, occur at (0.685, 0.967), (0.656, 0.957), (0.679, 0.918), and (0.654, 0.898), respectively. The analysis considers all alleles found worldwide at the 715 microsatellites and 207 indels.</p
Mean <i>F<sub>st</sub></i> Values for Each Indian Group across Comparisons with 18 Populations from East Asia, 12 Populations from Europe and the Middle East, and the Other 14 Groups from India
<div><p>(A) 715 microsatellites.</p><p>(B) 207 indels.</p><p>Error bars denote standard deviations across comparisons.</p></div
Sample Sizes and Geographic Origins of Samples
<p>The latitudes and longitudes used for the various groups are given in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020215#pgen-0020215-st002" target="_blank">Table S2</a>.</p
Comparison of Allele Frequencies in India to Allele Frequencies in East Asia and Europe/Middle East
<div><p>(A) East Asia, 8,618 alleles at 715 microsatellites.</p><p>(B) East Asia, 414 alleles at 207 indels.</p><p>(C) Europe/Middle East, 8,618 alleles at 715 microsatellites.</p><p>(D) Europe/Middle East, 414 alleles at 207 indels.</p></div
Cumulative Distribution Function for the Absolute Allele Frequency Difference between Various Populations and (Non-Gujarati) Indians
<div><p>(A) All alleles at 715 microsatellites.</p><p>(B) All alleles at 207 indels.</p><p>(C) Common alleles at 715 microsatellites (alleles whose frequencies average more than 0.05 in the two groups).</p><p>(D) Common alleles at 207 indels (alleles whose frequencies have a mean above 0.05 and below 0.95 in the two groups).</p></div
Relationship of <i>F<sub>st</sub></i> and Geographic Distance for Pairs of Groups from India
<div><p>(A) 715 microsatellites (correlation coefficient of −0.10 [<i>p</i> = 0.32], or 0.09 [<i>p</i> = 0.41] if comparisons involving the Parsi group are excluded).</p><p>(B) 207 indels (correlation coefficient of −0.02 [<i>p</i> = 0.84], or 0.28 [<i>p</i> = 0.007] when excluding comparisons involving the Parsi group). </p><p>A complete list of pairwise values of <i>F<sub>st</sub></i> is contained in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020215#pgen-0020215-st003" target="_blank">Table S3</a>.</p></div