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Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
Published on: June 23, 2012
Haplotype variation and linkage disequilibrium in 313 human genes
J C Stephens1, J A Schneider, D A Tanguay
1Genaissance Pharmaceuticals, Inc., Five Science Park, New Haven, CT 06511, USA. c.stephens@genaissance.com
Summary
Genetic variation, including single nucleotide polymorphisms (SNPs) and haplotypes, was analyzed across human genes. This genetic diversity data supports recent human population expansion.
Area of Science:
- Genetics and Genomics
- Human Population Genetics
Background:
- Genetic variation within genes influences biological traits.
- Understanding gene and haplotype diversity is crucial for population studies.
Purpose of the Study:
- To identify and characterize single nucleotide polymorphisms (SNPs) and haplotypes within a diverse set of human genes.
- To analyze patterns of genetic variation and linkage disequilibrium across different populations.
- To investigate whether observed variation supports models of recent human population expansion.
Main Methods:
- Identification of 3899 single nucleotide polymorphisms (SNPs) within 313 genes from 82 diverse individuals.
- Organization of identified SNPs into 4304 distinct haplotypes.
- Analysis of linkage disequilibrium between SNP pairs based on location, distance, and population frequency.
Main Results:
- Variable SNPs and haplotypes were found within all analyzed genes, with some being population-specific.
- Haplotypes generally exhibited higher heterozygosity (information content) than individual SNPs.
- Linkage disequilibrium patterns varied based on multiple genetic and population factors.
Conclusions:
- The identified patterns of genetic variation and haplotype diversity provide strong evidence for a recent human population expansion.
- Gene and haplotype variability differ across populations, highlighting the complexity of human genetic diversity.
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