Using population admixture to help complete maps of the human genome.

Nat Genet
Authors
Keywords
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.

Year of Publication
2013
Journal
Nat Genet
Volume
45
Issue
4
Pages
406-14, 414e1-2
Date Published
2013 Apr
ISSN
1546-1718
URL
DOI
10.1038/ng.2565
PubMed ID
23435088
PubMed Central ID
PMC3683849
Links
Grant list
HHSN268201100012C / HL / NHLBI NIH HHS / United States
R01DK54931 / DK / NIDDK NIH HHS / United States
N02-HL-6-4278 / HL / NHLBI NIH HHS / United States
HHSN268201100009I / HL / NHLBI NIH HHS / United States
N01-HC48049 / HC / NHLBI NIH HHS / United States
R01 DK054931 / DK / NIDDK NIH HHS / United States
R01-HL-071252 / HL / NHLBI NIH HHS / United States
R01 HL071251 / HL / NHLBI NIH HHS / United States
N01-HC48050 / HC / NHLBI NIH HHS / United States
R01-HL-071258 / HL / NHLBI NIH HHS / United States
HHSN268201100010C / HL / NHLBI NIH HHS / United States
R01 HL071259 / HL / NHLBI NIH HHS / United States
R01 GM100233 / GM / NIGMS NIH HHS / United States
HHSN268201100008C / HL / NHLBI NIH HHS / United States
HHSN268201100005G / HL / NHLBI NIH HHS / United States
R01 HL071252 / HL / NHLBI NIH HHS / United States
N01HC48049 / HL / NHLBI NIH HHS / United States
RC1 GM091332 / GM / NIGMS NIH HHS / United States
HHSN268201100008I / HL / NHLBI NIH HHS / United States
HHSN268201100005C / PHS HHS / United States
HHSN268201100007C / HL / NHLBI NIH HHS / United States
N01-HC48048 / HC / NHLBI NIH HHS / United States
RR-024156 / RR / NCRR NIH HHS / United States
R01-HL-071250 / HL / NHLBI NIH HHS / United States
N01HC95169 / HL / NHLBI NIH HHS / United States
HHSN268201100009C / PHS HHS / United States
HHSN268201100011I / HL / NHLBI NIH HHS / United States
R01 HL071250 / HL / NHLBI NIH HHS / United States
HHSN268201100011C / HL / NHLBI NIH HHS / United States
R01 HG006399 / HG / NHGRI NIH HHS / United States
UL1 RR024156 / RR / NCRR NIH HHS / United States
N01-HC-95159 / HC / NHLBI NIH HHS / United States
R01-HL-071251 / HL / NHLBI NIH HHS / United States
HHSN268201100010C / PHS HHS / United States
R01 HL071051 / HL / NHLBI NIH HHS / United States
N01HC95170 / HL / NHLBI NIH HHS / United States
HHSN268201100006C / HL / NHLBI NIH HHS / United States
R01 MD007092 / MD / NIMHD NIH HHS / United States
HHSN268201100008C / PHS HHS / United States
HHSN268201100012C / PHS HHS / United States
R01-HL-071259 / HL / NHLBI NIH HHS / United States
N01HC95095 / HL / NHLBI NIH HHS / United States
N01-HC48047 / HC / NHLBI NIH HHS / United States
N01-HC-95169 / HC / NHLBI NIH HHS / United States
HHSN268201100005I / HL / NHLBI NIH HHS / United States
N01HC95159 / HL / NHLBI NIH HHS / United States
R01-HL-071205 / HL / NHLBI NIH HHS / United States
R01 HG006855 / HG / NHGRI NIH HHS / United States
N01HC65226 / HL / NHLBI NIH HHS / United States
HHSN268201100007C / PHS HHS / United States
N01-HC-95171 / HC / NHLBI NIH HHS / United States
N01HC48050 / HL / NHLBI NIH HHS / United States
N01-HC-95172 / HC / NHLBI NIH HHS / United States
HHSN268201100009C / HL / NHLBI NIH HHS / United States
N01HC48047 / HL / NHLBI NIH HHS / United States
HHSN268201100011C / PHS HHS / United States
HHSN268201100005C / HL / NHLBI NIH HHS / United States
N01HC95171 / HL / NHLBI NIH HHS / United States
R01 HL071205 / HL / NHLBI NIH HHS / United States
HHSN268201100007I / HL / NHLBI NIH HHS / United States
R01-HL-071051 / HL / NHLBI NIH HHS / United States
HHSN268201100006C / PHS HHS / United States
RC1 GM091332-01 / GM / NIGMS NIH HHS / United States
N01-HC-95170 / HC / NHLBI NIH HHS / United States
R01 HL071258 / HL / NHLBI NIH HHS / United States
N01HC48048 / HL / NHLBI NIH HHS / United States
N01-HC95095 / HC / NHLBI NIH HHS / United States
N01-HC-65226 / HC / NHLBI NIH HHS / United States
N01HC95172 / HL / NHLBI NIH HHS / United States