title: Population and genomic lessons from genetic analysis of two Indian populations.
abstract: Indian demographic history includes special features such as founder effects, interpopulation segregation, complex social structure with a caste system and elevated frequency of consanguineous marriages. It also presents a higher frequency for some rare mendelian disorders and in the last two decades increased prevalence of some complex disorders. Despite the fact that India represents about one-sixth of the human population, deep genetic studies from this terrain have been scarce. In this study, we analyzed high-density genotyping and whole-exome sequencing data of a North and a South Indian population. Indian populations show higher differentiation levels than those reported between populations of other continents. In this work, we have analyzed its consequences, by specifically assessing the transferability of genetic markers from or to Indian populations. We show that there is limited genetic marker portability from available genetic resources such as HapMap or the 1,000 Genomes Project to Indian populations, which also present an excess of private rare variants. Conversely, tagSNPs show a high level of portability between the two Indian populations, in contrast to the common belief that North and South Indian populations are genetically very different. By estimating kinship from mates and consanguinity in our data from trios, we also describe different patterns of assortative mating and inbreeding in the two populations, in agreement with distinct mating preferences and social structures. In addition, this analysis has allowed us to describe genomic regions under recent adaptive selection, indicating differential adaptive histories for North and South Indian populations. Our findings highlight the importance of considering demography for design and analysis of genetic studies, as well as the need for extending human genetic variation catalogs to new populations and particularly to those with particular demographic histories.
authors: Department of Genetics, University of Delhi South Campus, New Delhi, 110 021, India.
authors: Garima
authors: G
authors: Juyal
authors: Mayukh
authors: M
authors: Mondal
authors: Pierre
authors: P
authors: Luisi
authors: Hafid
authors: H
authors: Laayouni
authors: Ajit
authors: A
authors: Sood
authors: Vandana
authors: V
authors: Midha
authors: Peter
authors: P
authors: Heutink
authors: Jaume
authors: J
authors: Bertranpetit
authors: B K
authors: BK
authors: Thelma
authors: Ferran
authors: F
authors: Casals
mesh_terms: D044466:Asian People / Q000235:genetics; D003241:Consanguinity; D059472:Exome; D018703:Founder Effect; D005828:Genetics, Population; D060005:Genotyping Techniques / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007194:India; D015810:Linkage Disequilibrium; D056186:Metagenomics; D009679:Nuclear Family; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D044465:White People / Q000235:genetics