Tens of millions of base pairs of euchromatic human genome sequence, including many protein-coding genes, have no known location in the human genome. We describe an approach for localizing the human genome's missing pieces using the patterns of genome sequence variation created by population admixture. We mapped the locations of 70 scaffolds spanning 4 million base pairs of the human genome's unplaced euchromatic sequence, including more than a dozen protein-coding genes, and identified 8 new large interchromosomal segmental duplications. We find that most of these sequences are hidden in the genome's heterochromatin, particularly its pericentromeric regions. Many cryptic, pericentromeric genes are expressed at the RNA level and have been maintained intact for millions of years while their expression patterns diverged from those of paralogous genes elsewhere in the genome. We describe how knowledge of the locations of these sequences can inform disease association and genome biology studies.
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This study was supported by grants RC1 GM091332-01 (S.A.M. and J.G.W.), R01 HG006855 (S.A.M.) and R01DK54931 (G.G. and M.R.P.) from the US National Institutes of Health and by a Smith Family Foundation Award for Excellence in Biomedical Research (S.A.M.).
The Jackson Heart Study is supported and conducted in collaboration with Jackson State University (N01-HC-95170), University of Mississippi Medical Center (N01-HC-95171) and Touglaoo College (N01-HC-95172) contracts from the National Heart, Lung, and Blood Institute (NHLBI) and the National Institute for Minority Health and Health Disparities (NIMHD), with additional support from the National Institute on Biomedical Imaging and Bioengineering (NIBIB).
The Atherosclerosis Risk in Communities Study is carried out as a collaborative study supported by NHLBI contracts (HHSN268201100005C, HHSN268201100006C, HHSN268201100007C, HHSN268201100008C, HHSN268201100009C, HHSN268201100010C, HHSN268201100011C and HHSN268201100012C).
The Coronary Artery Risk Development in Young Adults Study (CARDIA) is conducted and supported by the NHLBI in collaboration with the University of Alabama at Birmingham (N01-HC95095 and N01-HC48047), the University of Minnesota (N01-HC48048), Northwestern University (N01-HC48049) and the Kaiser Foundation Research Institute (N01-HC48050).
MESA, MESA Family and the MESA SHARe project are conducted and supported by the NHLBI in collaboration with the MESA investigators. Support for MESA is provided by contracts N01-HC-95159, through N01-HC-95169, and RR-024156. Funding for MESA Family is provided by grants R01-HL-071051, R01-HL-071205, R01-HL-071250, R01-HL-071251, R01-HL-071252, R01-HL-071258 and R01-HL-071259. MESA Air is funded by the US Environmental Protection Agency (EPA)–Science to Achieve Results (STAR) Program Grant RD831697. Funding for genotyping was provided by NHLBI contracts N02-HL-6-4278 and N01-HC-65226.
This manuscript does not necessarily reflect the opinions or views of ARIC, CARDIA, JHS, MESA or the NHLBI.
The authors declare no competing financial interests.
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Genovese, G., Handsaker, R., Li, H. et al. Using population admixture to help complete maps of the human genome. Nat Genet 45, 406–414 (2013). https://doi.org/10.1038/ng.2565
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