A new method to reconstruct recombination events at a genomic scale.

Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence o...

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Autores principales:	Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit, Genographic Consortium Members
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2010
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/c64d578fbe1c415fa48bbb4f5b5c3da3
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spelling	oai:doaj.org-article:c64d578fbe1c415fa48bbb4f5b5c3da32021-11-18T05:51:53ZA new method to reconstruct recombination events at a genomic scale.1553-734X1553-735810.1371/journal.pcbi.1001010https://doaj.org/article/c64d578fbe1c415fa48bbb4f5b5c3da32010-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21124860/pdf/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have fine-tuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 X-chromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation.Marta MeléAsif JavedMarc PybusFrancesc CalafellLaxmi ParidaJaume BertranpetitGenographic Consortium MembersPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 6, Iss 11, p e1001010 (2010)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Marta Melé Asif Javed Marc Pybus Francesc Calafell Laxmi Parida Jaume Bertranpetit Genographic Consortium Members A new method to reconstruct recombination events at a genomic scale.
description	Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have fine-tuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 X-chromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation.
format	article
author	Marta Melé Asif Javed Marc Pybus Francesc Calafell Laxmi Parida Jaume Bertranpetit Genographic Consortium Members
author_facet	Marta Melé Asif Javed Marc Pybus Francesc Calafell Laxmi Parida Jaume Bertranpetit Genographic Consortium Members
author_sort	Marta Melé
title	A new method to reconstruct recombination events at a genomic scale.
title_short	A new method to reconstruct recombination events at a genomic scale.
title_full	A new method to reconstruct recombination events at a genomic scale.
title_fullStr	A new method to reconstruct recombination events at a genomic scale.
title_full_unstemmed	A new method to reconstruct recombination events at a genomic scale.
title_sort	new method to reconstruct recombination events at a genomic scale.
publisher	Public Library of Science (PLoS)
publishDate	2010
url	https://doaj.org/article/c64d578fbe1c415fa48bbb4f5b5c3da3
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A new method to reconstruct recombination events at a genomic scale.

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