title: Genetic variation and haplotype structures of innate immunity genes in eastern India.
abstract: This study reports results of an extensive and comprehensive study of genetic diversity in 12 genes of the innate immune system in a population of eastern India. Genomic variation was assayed in 171 individuals by resequencing approximately 75kb of DNA comprising these genes in each individual. Almost half of the 548 DNA variants discovered was novel. DNA sequence comparisons with human and chimpanzee reference sequences revealed evolutionary features indicative of natural selection operating among individuals, who are residents of an area with a high load of microbial and other pathogens. Significant differences in allele and haplotype frequencies of the study population were observed with the HapMap populations. Gene and haplotype diversities were observed to be high. The genetic positioning of the study population among the HapMap populations based on data of the innate immunity genes substantially differed from what has been observed for Indian populations based on data of other genes. The reported range of variation in SNP density in the human genome is one SNP per 1.19kb (chromosome 22) to one SNP per 2.18kb (chromosome 19). The SNP density in innate immunity genes observed in this study (>3SNPskb(-1)) exceeds the highest density observed for any autosomal chromosome in the human genome. The extensive genomic variation and the distinct haplotype structure of innate immunity genes observed among individuals have possibly resulted from the impact of natural selection.
authors.affiliation: TCG-ISI Centre for Population Genomics, Kolkata, India.
authors.forename: Bijan B
authors.initials: BB
authors.lastname: Bairagya
authors.forename: Paramita
authors.initials: P
authors.lastname: Bhattacharya
authors.forename: Sujit K
authors.initials: SK
authors.lastname: Bhattacharya
authors.forename: Biplab
authors.initials: B
authors.lastname: Dey
authors.forename: Uposoma
authors.initials: U
authors.lastname: Dey
authors.forename: Trina
authors.initials: T
authors.lastname: Ghosh
authors.forename: Sujit
authors.initials: S
authors.lastname: Maiti
authors.forename: Partha P
authors.initials: PP
authors.lastname: Majumder
authors.forename: Kankadeb
authors.initials: K
authors.lastname: Mishra
authors.forename: Sinchita
authors.initials: S
authors.lastname: Mukherjee
authors.forename: Souvik
authors.initials: S
authors.lastname: Mukherjee
authors.forename: K
authors.initials: K
authors.lastname: Narayanasamy
authors.forename: Sonia
authors.initials: S
authors.lastname: Poddar
authors.forename: Neeta Sarkar
authors.initials: NS
authors.lastname: Roy
authors.forename: Priya
authors.initials: P
authors.lastname: Sengupta
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Sharma
authors.forename: Dipika
authors.initials: D
authors.lastname: Sur
authors.forename: Debabrata
authors.initials: D
authors.lastname: Sutradhar
authors.forename: Diane K
authors.initials: DK
authors.lastname: Wagener
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002648:Child; D005006:Ethnicity / Q000235:genetics; D005260:Female; D005787:Gene Frequency; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D007113:Immunity, Innate / Q000235:genetics*; D007194:India; D008297:Male; D008875:Middle Aged; D010802:Phylogeny