Atlas of Cryptic Genetic Relatedness Among 1000 Human Genomes

Genome Biology and Evolution
Larisa FedorovaAlexei Fedorov

Abstract

A novel computational method for detecting identical-by-descent (IBD) chromosomal segments between sequenced genomes is presented. It utilizes the distribution patterns of very rare genetic variants (vrGVs), which have minor allele frequencies <0.2%. Contrary to the existing probabilistic approaches our method is rather deterministic, because it considers a group of very rare events which cannot happen together only by chance. This method has been applied for exhaustive computational search of shared IBD segments among 1,092 sequenced individuals from 14 populations. It demonstrated that clusters of vrGVs are unique and powerful markers of genetic relatedness, that uncover IBD chromosomal segments between and within populations, irrespective of whether divergence was recent or occurred hundreds-to-thousands of years ago. We found that several IBD segments are shared by practically any possible pair of individuals belonging to the same population. Moreover, shared short IBD segments (median size 183 kb) were found in 10% of inter-continental human pairs, each comprising of a person from sub-Saharan Africa and a person from Southern Europe. The shortest shared IBD segments (median size 54 kb) were found in 0.42% of inter-continen...Continue Reading

References

Oct 18, 2000·American Journal of Human Genetics·M RichardsH J Bandelt
Mar 10, 2001·Nature·E S LanderUNKNOWN International Human Genome Sequencing Consortium
Mar 26, 2002·Human Molecular Genetics·Alexey S Kondrashov, Svetlana A Shabalina
May 29, 2003·American Journal of Human Genetics·Norman ArnheimMagnus Nordborg
Dec 20, 2003·Nature·UNKNOWN International HapMap Consortium
Oct 1, 2004·Nature·Douglas L T RohdeJoseph T Chang
May 5, 2005·Proceedings. Biological Sciences·Mathias Currat, Laurent Excoffier
Apr 29, 2006·Gene·Tuuli LappalainenPäivi Lahermo
Dec 7, 2006·European Journal of Human Genetics : EJHG·Siiri RootsiRichard Villems
Oct 19, 2007·Nature·UNKNOWN International HapMap ConsortiumJohn Stewart
Oct 31, 2008·Genome Research·Alexander GusevItsik Pe'er
Jan 24, 2009·Nature Genetics·Augustine KongKari Stefansson
May 8, 2009·Molecular Biology and Evolution·Jeffrey D WallVincent Plagnol
May 8, 2010·Science·Richard E GreenSvante Pääbo
Sep 30, 2010·Nature Reviews. Genetics·Joseph E PowellMichael E Goddard
Feb 18, 2011·Genome Research·Chad D HuffLynn B Jorde
Feb 18, 2011·Molecular Biology and Evolution·Eric Y DurandMontgomery Slatkin
May 3, 2011·PLoS Genetics·Priya MoorjaniDavid Reich
Jun 15, 2011·Nature Genetics·Donald F ConradUNKNOWN 1000 Genomes Project
Jul 19, 2011·American Journal of Human Genetics·Sharon R Browning, Brian L Browning
Mar 29, 2012·Genome Research·María CerezoAntonio Salas
Jun 8, 2012·BMC Bioinformatics·Shu-Yi SuEric Jorgenson
Sep 1, 2012·Science·Matthias MeyerSvante Pääbo
Sep 11, 2012·Genetics·Nick PattersonDavid Reich
Sep 22, 2012·Annual Review of Genetics·Sharon R Browning, Brian L Browning
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Jun 5, 2013·Proceedings of the National Academy of Sciences of the United States of America·Laura R BotiguéCarlos D Bustamante
Nov 12, 2013·American Journal of Human Genetics·Brian L Browning, Sharon R Browning
Jan 5, 2014·Cold Spring Harbor Perspectives in Biology·Kenneth M Weiss, Brian W Lambert
Jan 31, 2014·Science·Benjamin Vernot, Joshua M Akey
Jan 31, 2014·Nature·Sriram SankararamanDavid Reich
Feb 6, 2014·PLoS Genetics·Hong LiChad D Huff
Apr 12, 2014·Genome Biology and Evolution·Shuhao QiuAlexei Fedorov
Apr 23, 2014·Proceedings of the National Academy of Sciences of the United States of America·Sergi CastellanoSvante Pääbo
May 3, 2014·Molecular Biology and Evolution·Eric Y DurandCory Y McLean
Jul 6, 2014·Cold Spring Harbor Perspectives in Biology·Felicia GomezSarah A Tishkoff
Aug 26, 2014·Theoretical Population Biology·Shai CarmiItsik Pe'er
Nov 8, 2014·Science·Andaine Seguin-OrlandoEske Willerslev
Jan 13, 2015·Genome Biology and Evolution·Ahmed Al-KhudhairAlexei Fedorov

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Citations

Mar 24, 2017·Bioinformatics·Daniel SchlauchChristoph Lange

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Software Mentioned

Variant Call Format
pl
STRUCTURE
Linux
. pl
PLINK
R package R Development Core Team
IBDsimulator
Perl
GERMLINE

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