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Using population admixture to help complete maps of the human genome

Nature Genetics volume 45, pages 406–414 (2013)Cite this article

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Abstract

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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Figure 1: Admixture mapping of the human genome's missing pieces.
Figure 2: Approximate locations of previously unplaced genome sequence scaffolds that were mapped by our approach.
Figure 3: Cryptic paralogs of the PRIM2 gene.
Figure 4: FISH analysis confirmed the presence of cryptic segmental duplications.
Figure 5: Expression of cryptic gene paralogs from pericentromeric regions of the human genome.

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Acknowledgements

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.

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Authors and Affiliations

  1. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA

    Giulio Genovese, Robert E Handsaker, Heng Li, Kimberly Chambert, Alkes L Price, Cynthia C Morton, Martin R Pollak & Steven A McCarroll

  2. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA

    Giulio Genovese, Robert E Handsaker, Heng Li, Nicolas Altemose, David Reich & Steven A McCarroll

  3. Division of Nephrology, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA

    Giulio Genovese & Martin R Pollak

  4. Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA

    Giulio Genovese, Robert E Handsaker, Kimberly Chambert & Steven A McCarroll

  5. Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts, USA

    Amelia M Lindgren & Cynthia C Morton

  6. Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, USA

    Bogdan Pasaniuc & Alkes L Price

  7. Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA

    Cynthia C Morton

  8. Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, USA

    James G Wilson

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  1. Giulio Genovese
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Contributions

G.G. and S.A.M. conceived the project, designed the analyses and wrote the manuscript. G.G. performed the analysis of the CARe, ICDB, JHS and BodyMap 2.0 data sets. R.E.H. performed the sequence read depth analysis of selected regions. H.L. performed the alignments of HuRef scaffolds and GenBank clones. N.A. contributed the analysis of the HuRef unplaced scaffolds. A.M.L. performed the FISH experiments. K.C. organized and contributed to the design of the Sequenom experiment. B.P., A.L.P. and D.R. provided advice for the local ancestry inference. C.C.M. participated in the interpretation of the FISH experiments. M.R.P. participated in planning discussions for the linkage analysis. J.G.W. participated in planning discussions, coordinated interactions with JHS and edited the manuscript.

Corresponding authors

Correspondence to Giulio Genovese or Steven A McCarroll.

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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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