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Article: Predicting the number and sizes of IBD regions among family members and evaluating the family size requirement for linkage studies

TitlePredicting the number and sizes of IBD regions among family members and evaluating the family size requirement for linkage studies
Authors
Issue Date2008
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ejhg
Citation
European Journal Of Human Genetics, 2008, v. 16 n. 12, p. 1535-1543 How to Cite?
AbstractWith genotyping of high-density single nucleotide polymorphisms (SNPs) replacing that of microsatellite markers in linkage studies, it becomes possible to accurately determine the genomic regions shared identity by descent (IBD) by family members. In addition to evaluating the likelihood of linkage for a region with the underlining disease (the LOD score approach), an appropriate question to ask is what would be the expected number and sizes of IBD regions among the affecteds, as there could be more than one region reaching the maximum achievable LOD score for a given family. Here, we introduce a computer program to allow the prediction of the total number of IBD regions among family members and their sizes. Reversely, it can be used to predict the portion of the genome that can be excluded from consideration according to the family size and user-defined inheritance mode and penetrance. Such information has implications on the feasibility of conducting linkage analysis on a given family of certain size and structure or on a few small families when interfamily homogeneity can be assumed. It can also help determine the most relevant members to be genotyped for such a study. Simulation results showed that the IBD regions containing true mutations are usually larger than regions IBD due to random chance. We have made use of this feature in our program to allow evaluation of the identified IBD regions based on Bayesian probability calculation and simulation results.
Persistent Identifierhttp://hdl.handle.net/10722/59528
ISSN
2015 Impact Factor: 4.58
2015 SCImago Journal Rankings: 2.077
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorYang, Wen_HK
dc.contributor.authorWang, Zen_HK
dc.contributor.authorWang, Len_HK
dc.contributor.authorSham, PCen_HK
dc.contributor.authorHuang, Pen_HK
dc.contributor.authorLau, YLen_HK
dc.date.accessioned2010-05-31T03:52:02Z-
dc.date.available2010-05-31T03:52:02Z-
dc.date.issued2008en_HK
dc.identifier.citationEuropean Journal Of Human Genetics, 2008, v. 16 n. 12, p. 1535-1543en_HK
dc.identifier.issn1018-4813en_HK
dc.identifier.urihttp://hdl.handle.net/10722/59528-
dc.description.abstractWith genotyping of high-density single nucleotide polymorphisms (SNPs) replacing that of microsatellite markers in linkage studies, it becomes possible to accurately determine the genomic regions shared identity by descent (IBD) by family members. In addition to evaluating the likelihood of linkage for a region with the underlining disease (the LOD score approach), an appropriate question to ask is what would be the expected number and sizes of IBD regions among the affecteds, as there could be more than one region reaching the maximum achievable LOD score for a given family. Here, we introduce a computer program to allow the prediction of the total number of IBD regions among family members and their sizes. Reversely, it can be used to predict the portion of the genome that can be excluded from consideration according to the family size and user-defined inheritance mode and penetrance. Such information has implications on the feasibility of conducting linkage analysis on a given family of certain size and structure or on a few small families when interfamily homogeneity can be assumed. It can also help determine the most relevant members to be genotyped for such a study. Simulation results showed that the IBD regions containing true mutations are usually larger than regions IBD due to random chance. We have made use of this feature in our program to allow evaluation of the identified IBD regions based on Bayesian probability calculation and simulation results.en_HK
dc.languageengen_HK
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ejhgen_HK
dc.relation.ispartofEuropean Journal of Human Geneticsen_HK
dc.titlePredicting the number and sizes of IBD regions among family members and evaluating the family size requirement for linkage studiesen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1018-4813&volume=16 &issue=12&spage=1535&epage=1543&date=2008&atitle=Predicting+the+number+and+sizes+of+IBD+regions+among+family+members+and+evaluating+the+family+size+requirement+for+linkage+studiesen_HK
dc.identifier.emailYang, W: yangwl@hkucc.hku.hken_HK
dc.identifier.emailSham, PC: pcsham@hku.hken_HK
dc.identifier.emailLau, YL: lauylung@hku.hken_HK
dc.identifier.authorityYang, W=rp00524en_HK
dc.identifier.authoritySham, PC=rp00459en_HK
dc.identifier.authorityLau, YL=rp00361en_HK
dc.description.naturelink_to_OA_fulltext-
dc.identifier.doi10.1038/ejhg.2008.116en_HK
dc.identifier.pmid18575462-
dc.identifier.scopuseid_2-s2.0-56749146148en_HK
dc.identifier.hkuros158076en_HK
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-56749146148&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume16en_HK
dc.identifier.issue12en_HK
dc.identifier.spage1535en_HK
dc.identifier.epage1543en_HK
dc.identifier.isiWOS:000261108600015-
dc.publisher.placeUnited Kingdomen_HK
dc.identifier.scopusauthoridYang, W=23101349500en_HK
dc.identifier.scopusauthoridWang, Z=8211361600en_HK
dc.identifier.scopusauthoridWang, L=7409188146en_HK
dc.identifier.scopusauthoridSham, PC=34573429300en_HK
dc.identifier.scopusauthoridHuang, P=25724369400en_HK
dc.identifier.scopusauthoridLau, YL=7201403380en_HK
dc.identifier.citeulike2926352-

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