Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits.

Genome Research
Carlos Ruiz-ArenasJuan R Gonzalez

Abstract

Recombination is a main source of genetic variability. However, the potential role of the variation generated by recombination in phenotypic traits, including diseases, remains unexplored because there is currently no method to infer chromosomal subpopulations based on recombination pattern differences. We developed recombClust, a method that uses SNP-phased data to detect differences in historic recombination in a chromosome population. We validated our method by performing simulations and by using real data to accurately predict the alleles of well-known recombination modifiers, including common inversions in Drosophila melanogaster and human, and the chromosomes under selective pressure at the lactase locus in humans. We then applied recombClust to the complex human 1q21.1 region, where nonallelic homologous recombination produces deleterious phenotypes. We discovered and validated the presence of two different recombination histories in these regions that significantly associated with the differential expression of ANKRD35 in whole blood and that were in high linkage with variants previously associated with hypertension. By detecting differences in historic recombination, our method opens a way to assess the influence of re...Continue Reading

References

Jan 1, 1996·Annual Review of Genetics·M W FeldmanF B Christiansen
Nov 25, 2003·Nature Reviews. Genetics·Michael P H Stumpf, Gilean A T McVean
Apr 24, 2004·Science·Gilean A T McVeanPeter Donnelly
Jan 18, 2005·Nature Genetics·Hreinn StefanssonKari Stefansson
Feb 12, 2005·Science·Wendy WincklerDavid Altshuler
Oct 6, 2005·Genetics·Mark Kirkpatrick, Nick Barton
Dec 6, 2006·Nature Reviews. Genetics·Graham Coop, Molly Przeworski
Feb 3, 2007·Bioinformatics·Juan R GonzálezVíctor Moreno
Sep 12, 2008·The New England Journal of Medicine·Heather C MeffordEvan E Eichler
Apr 8, 2009·Nature Genetics·Alec J Jeffreys, Rita Neumann
Jan 29, 2010·Bioinformatics·Paul F O'ReillyClive J Hoggart
Feb 19, 2010·Nature Reviews. Molecular Cell Biology·Mariko SasakiScott Keeney
Apr 10, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Suzanne S Sindi, Benjamin J Raphael
Jun 16, 2011·Heredity·C S Smukowski, M A F Noor
Feb 10, 2012·European Journal of Human Genetics : EJHG·Jill A RosenfeldUNKNOWN 1q21.1 Study Group
Feb 10, 2012·Nature·Trudy F C MackayRichard A Gibbs
Mar 9, 2012·Methods in Molecular Biology·Adam Auton, Gil McVean
Jul 4, 2012·Nature Genetics·Karyn Meltz SteinbergEvan E Eichler
Dec 12, 2012·Genome Research·Julie HussinPhilip Awadalla
May 30, 2013·Nature Genetics·UNKNOWN GTEx Consortium
Nov 21, 2013·Nucleic Acids Research·Alexander Martínez-FundichelyMario Cáceres
Dec 3, 2013·Nature Chemical Biology·Luc G Berthiaume
Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth
Apr 1, 2014·Genome Biology and Evolution·Joao M AlvesAlexandra M Lopes
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Feb 13, 2015·Nucleic Acids Research·Alejandro Cáceres, Juan R González
May 23, 2015·Briefings in Functional Genomics·Marta PuigMario Cáceres
Oct 4, 2015·Nature·Peter H SudmantJan O Korbel
Feb 14, 2017·American Journal of Human Genetics·Brent S Pedersen, Aaron R Quinlan
Apr 12, 2017·Nature Biotechnology·Leonardo Collado-TorresJeffrey T Leek
Nov 8, 2017·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Isabel AlvesPhilip Awadalla
Sep 19, 2018·Nature Genetics·Evangelos EvangelouUNKNOWN Million Veteran Program
Oct 20, 2018·Nucleic Acids Research·Jesús Murga-MorenoSònia Casillas

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Citations

Nov 7, 2021·Mammalian Genome : Official Journal of the International Mammalian Genome Society·M L KaldunskiA E Kwitek

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