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Fine-Scale Mapping and Sequencing of Structural Variation from Eight Human Genomes


ABSTRACT: 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.

ORGANISM(S): Homo sapiens

SUBMITTER: Lin Chen 

PROVIDER: E-GEOD-10008 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Mapping and sequencing of structural variation from eight human genomes.

Kidd Jeffrey M JM   Cooper Gregory M GM   Donahue William F WF   Hayden Hillary S HS   Sampas Nick N   Graves Tina T   Hansen Nancy N   Teague Brian B   Alkan Can C   Antonacci Francesca F   Haugen Eric E   Zerr Troy T   Yamada N Alice NA   Tsang Peter P   Newman Tera L TL   Tüzün Eray E   Cheng Ze Z   Ebling Heather M HM   Tusneem Nadeem N   David Robert R   Gillett Will W   Phelps Karen A KA   Weaver Molly M   Saranga David D   Brand Adrianne A   Tao Wei W   Gustafson Erik E   McKernan Kevin K   Chen Lin L   Malig Maika M   Smith Joshua D JD   Korn Joshua M JM   McCarroll Steven A SA   Altshuler David A DA   Peiffer Daniel A DA   Dorschner Michael M   Stamatoyannopoulos John J   Schwartz David D   Nickerson Deborah A DA   Mullikin James C JC   Wilson Richard K RK   Bruhn Laurakay L   Olson Maynard V MV   Kaul Rajinder R   Smith Douglas R DR   Eichler Evan E EE  

Nature 20080501 7191


Genetic variation among individual humans occurs on many different scales, ranging from gross alterations in the human karyotype to single nucleotide changes. Here 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 ov  ...[more]

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