The 1000 Genomes Project is an initiative to sequence the complete genomes of over 1000 individuals and create a reference set of common and uncommon genetic variation among various ethnic populations. This project aims to more comprehensively identify all types of genetic variation, including Single nucleotide polymorphisms (SNPs) and Structural genome variants (SVs) which include regions that have been duplicated, deleted, inverted, or translocated through the course of human evolution. Some of these structural variants have been correlated with many different disease phenotypes and thus play a major role in human health. In the course of the pilot phase of this project, numerous diverse, yet complementary, analytical methods have been developed to detect these types of variation on multiple sequencing platforms. Our research team includes members of the structural genomic variation analysis group for the 1000 genome project who have been conducting analysis from the 1000 genome project over the past year. We now propose to conduct a coordinated analysis of the complete SV dataset from the 1000 genome production project. Our common goal is to enhance the value of the thousand genomes project data by carrying out more detailed characterization of variants in terms (1) structure at the nucleotide sequence-level (2) functional impact on genes and proteins and (3) their distribution in human populations. Our work will take over where the data processing ends, and aim to make the complete 1000 genomes SV call set maximally useful to the biological community.
| Yang, Lixing; Luquette, Lovelace J; Gehlenborg, Nils et al. (2013) Diverse mechanisms of somatic structural variations in human cancer genomes. Cell 153:919-29 |
| 1000 Genomes Project Consortium; Abecasis, Goncalo R; Auton, Adam et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491:56-65 |
| Malhotra, Dheeraj; Sebat, Jonathan (2012) CNVs: harbingers of a rare variant revolution in psychiatric genetics. Cell 148:1223-41 |
| Michaelson, Jacob J; Shi, Yujian; Gujral, Madhusudan et al. (2012) Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 151:1431-42 |
| Michaelson, Jacob J; Sebat, Jonathan (2012) forestSV: structural variant discovery through statistical learning. Nat Methods 9:819-21 |
| Lee, Eunjung; Iskow, Rebecca; Yang, Lixing et al. (2012) Landscape of somatic retrotransposition in human cancers. Science 337:967-71 |
| Lee, Charles (2010) The future of prenatal cytogenetic diagnostics: a personal perspective. Prenat Diagn 30:706-9 |
