Showing papers by "Ranjan Deka published in 2010"

Analysis of human CYP1A1 and CYP1A2 genes and their shared bidirectional promoter in eight world populations.

Abstract: The human CYP1A1_CYP1A2 locus comprises the CYP1A1 (5,988 bp) and CYP1A2 (7,759 bp) transcribed regions, oriented head-to-head, sharing a bidirectional promoter of 23,306 bp The older CYP1A1 gene appears more conserved and responsible for critical life function(s), whereas the younger CYP1A2 gene might have evolved more rapidly due to environmental (dietary) pressures A population genetics study might confirm this premise We combined 60 CYP1A1_CYP1A2 SNPs found in the present study (eight New Guinea Highlanders, eight Samoans, four Dogrib, four Teribe, four Pehuenche, and one Caucasian) with those found in a previous study (six West Africans, four Han Chinese, six Germans, four Samoans, and four Dogrib), yielding a total of 106 SNPs in 106 chromosomes Resequencing of Oceanians plus Amerindians in the present study yielded 21 New World SNPs (∼20%), of which 17 are not previously reported in any SNP database Various tests revealed selective pressures for both genes and both haploblocks; unfortunately, differences in rates of evolution between the two genes were undetectable Fay & Wu's H test revealed a “hitchhiking event” centered around four SNPs in the CYP1A1 3′-UTR; a study in silico identified different microRNA-binding patterns in the hitchhiked region, when the mutations were present compared with the mutations absent Hum Mutat 30:1–14, 2009 © 2009 Wiley-Liss, Inc

The Relationship Between Smoking and Replicated Sequence Variants on Chromosomes 8 and 9 With Familial Intracranial Aneurysm

Abstract: Background and Purpose— The purpose of this study was to replicate the previous association of single nucleotide polymorphisms (SNPs) with risk of intracranial aneurysm (IA) and to examine the rela...

Association of FTO Gene Variants With Adiposity in African-American Adolescents

Abstract: The prevalence of obesity continues to increase significantly, with the largest rise in the African-American adolescents. Genetic contributions to obesity are being identified with the advent of genome-wide association studies (GWAS). Specifically, variants of the fat mass and obesity associated (FTO) gene have been associated with obesity in populations of European descent. The studies in African Americans have been inconclusive. To further evaluate the association of the FTO gene and adiposity in African Americans, we genotyped 47 single-nucleotide polymorphisms (SNPs), including seven SNPs previously reported to be significant in the literature in a cohort consisting of 561 non-Hispanic white and 497 African-American individuals. Analysis of our data showed 17 SNPs to be associated with BMI Z-score (BMI-Z) in our study population. The strongest association was found in the African Americans. The most significant SNP was rs8057044, which was associated with BMI-Z in the African Americans (P = 0.00054). SNP rs9939609 was found to be significant in the non-Hispanic white population (P = 0.028). Our data confirm the association between FTO and adiposity suggesting that FTO is a childhood obesity susceptibility gene. Our data also identify a novel SNP of the FTO gene (rs8057044) that is associated with measures of adiposity in the African-American population.

Common SNPs in FTO Gene Are Associated with Obesity Related Anthropometric Traits in an Island Population from the Eastern Adriatic Coast of Croatia

Abstract: Background Multiple studies have provided compelling evidence that the FTO gene variants are associated with obesity measures. The objective of the study was to investigate whether FTO variants are associated with a broad range of obesity related anthropometric traits in an island population. Methodology/Principal Findings We examined genetic association between 29 FTO SNPs and a comprehensive set of anthropometric traits in 843 unrelated individuals from an island population in the eastern Adriatic coast of Croatia. The traits include 11 anthropometrics (height, weight, waist circumference, hip circumference, bicondilar upper arm width, upper arm circumference, and biceps, triceps, subscapular, suprailiac and abdominal skin-fold thicknesses) and two derived measures (BMI and WHR). Using single locus score tests, 15 common SNPs were found to be significantly associated with “body fatness” measures such as weight, BMI, hip and waist circumferences with P-values ranging from 0.0004 to 0.01. Similar but less significant associations were also observed between these markers and bicondilar upper arm width and upper arm circumference. Most of these significant findings could be explained by a mediating effect of “body fatness”. However, one unique association signal between upper arm width and rs16952517 (P-value = 0.00156) could not be explained by this mediating effect. In addition, using a principle component analysis and conditional association tests adjusted for “body fatness”, two novel association signals were identified between upper arm circumference and rs11075986 (P-value = 0.00211) and rs16945088 (P-value = 0.00203). Conclusions/Significance The current study confirmed the association of common variants of FTO gene with “body fatness” measures in an isolated island population. We also observed evidence of pleiotropic effects of FTO gene on fat-free mass, such as frame size and muscle mass assessed by bicondilar upper arm width and upper arm circumference respectively and these pleiotropic effects might be influenced by variants that are different from the ones associated with “body fatness”.

Genetic structure of native circumpolar populations based on autosomal, mitochondrial, and Y chromosome DNA markers

Abstract: This study investigates the genetic structure of the present-day inhabitants of Beringia in order to answer questions concerning their origins and evolution. According to recent studies, the ancestors of Native Americans paused for a time in Beringia, during which they differentiated genetically from other Asians before peopling the New World. Furthermore, the Koryaks of Kamchatka share a "ubiquitous" allele (D9S1120) with Native Americans, indicating they may have descended from the same ancestral Beringian population that gave rise to the New World founders. Our results show that a genetic barrier exists between Kamchatkans (Koryaks and Even) and Bering Island inhabitants (Aleuts, mixed Aleuts, and Russians), based on Analysis of Molecular Variance (AMOVA) and structure analysis of nine autosomal short tandem repeats (STRs). This is supported by mitochondrial DNA evidence, but not by analysis of Y chromosome markers, as recent non-native male admixture into the region appears to have partially obscured ancient population relationships. Our study indicates that while Aleuts are descended from the original New World founders, the Koryaks are unlikely to represent a Beringian remnant of the ancestral population that gave rise to Native Americans. They are instead, like the Even, more recent arrivals to Kamchatka from interior Siberia, and the "ubiquitous" allele in Koryaks may result from recent gene flow from Chukotka. Genbank accession numbers for mtDNA sequences: GQ922935-GQ922973.

Genetic architecture of a small, recently aggregated aleut population: Bering Island, Russia

Abstract: The fishing community of Bering Island, located in the Russian Commander Islands off the Kamchatka Peninsula, was originally founded by a small number of Russian soldiers and merchants, along with Aleuts forcibly relocated from the western region of the Aleutian archipelago. The purpose of this study is to characterize the genetic variation of Bering Island inhabitants for autosomal, mitochondrial, and Y-chromosome DNA and classic genetic markers and to investigate the genetic impact of the 19th-century founding and subsequent demographic events on this heterogeneous community. Our results show a loss of diversity among maternal lineages in the Bering Aleut population, with fixation of mtDNA haplogroup D, as revealed by median-joining network analysis and mismatch differences. Conversely, paternal haplotypes exhibit an increase in diversity and the presence of a substantial number of non-Native lineages. Admixture results, based on autosomal STR data, indicate that parental contributions to the mixed Aleut population of Bering are approximately 60% Aleut and 40% Russian. Classic genetic markers show affinities between the Bering Island Aleuts and the other historically founded Aleut communities of St. Paul and St. George in the Pribilof Islands, Alaska. This study demonstrates that the opposing evolutionary forces of genetic drift and gene flow acted on the maternal and paternal lineages, respectively, to shape the genetic structure of the present-day inhabitants of Bering Island.