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Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture

ABSTRACT: To understand the full range of expression variation, alternative splicing, and the genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of 45 individuals in the Human Genome Diversity Panel (HGDP) from seven worldwide populations that span the geographic breadth of human migration history. We find few genes that are systematically differentially expressed among populations. Further, allelic expression analysis indicates that previously mapped common regulatory variants identified in eight HapMap3 populations have similar effects across HGDP populations, suggesting that the cellular effects of common variants are shared even across very diverse populations. In contrast, comparisons of alternative splicing across pairwise populations reveal highly significant differences, with ~20% of alternatively spliced exons varying significantly by population. Greater genomic differences are associated with significantly more splicing variability overall. Together, these results provide a resource and an estimate for the degree of sharing of gene expression, alternative splicing, and regulatory genetics across populations.

ORGANISM(S): Homo sapiens

PROVIDER: GSE54308 | GEO | 2014/08/25

SECONDARY ACCESSION(S): PRJNA236130

REPOSITORIES: GEO

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Project description:Genetic variation amongst individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single-nucleotide changes. In this manuscript we explore variation on an intermediate scale-particularly insertions, deletions, and inversions affecting from a few thousand to a few million base pairs. We employed a clone-based method to interrogate this intermediate structural variation in eight individuals of diverse geographic ancestry. Our analysis provides a comprehensive overview of the normal pattern of structural variation present in these genomes, refining the location of 1695 structural variants. We find that 50% were seen in more than one individual and that nearly half lay outside regions of the genome previously described as structurally variant. We discover 525 new insertion sequences that are not present in the human reference genome and show that many of these are variable in copy number among individuals. Sequencing of a subset of structural variants reveals considerable locus complexity and provides insights into the different mutational processes that have shaped the human genome. These data provide the first high-resolution sequence-map of human structural variation-an important standard for genotyping platforms and a prelude to future individual genome sequencing projects. Keywords: comparative genomic hybridization The DNA samples are a panel of 8 Hapmap samples, described by E. Eichler et al. (2007, Nature 447, 161-165). This set of 7 female, and one male samples are from from the Coriell Cell Repository, and is comprised of samples from four populations: four Yoruban, two CEPH, one Chinese, and one Japanese. The reference sample, NA15510, is female and also from the Corriel Cell Repository. This sample has been extensively characterized, (for example in Tuzan et al. 2005, Nature Genetics 10, p1038) and has been recommended for use in CNV detection programs to allow meaningful comparison of data between studies (discussed in Scherer, et al. 2007, Nature Genetics Supplement 39: S7-S15). Each of these samples was hybridized in pairs with the reversed labeling polarities. Additionally, 3 self-self control hybridizations were carried out for the reference sample, NA15510, one on each hybridization date.

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Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture

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