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Article: Homozygosity mapping on a single patient-identification of homozygous regions of recent common ancestry by using population data

TitleHomozygosity mapping on a single patient-identification of homozygous regions of recent common ancestry by using population data
Authors
KeywordsFounder mutation
Homozygosity mapping
Population-based linkage
Rare variants
Recessive mutation
Issue Date2011
PublisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www3.interscience.wiley.com/cgi-bin/jhome/38515
Citation
Human Mutation, 2011, v. 32 n. 3, p. 345-353 How to Cite?
AbstractHomozygosity mapping has played an important role in detecting recessive mutations using families of consanguineous marriages. However, detection of regions identical and homozygosity by descent (HBD) when family data are not available, or when relationships are unknown, is still a challenge. Making use of population data from high-density SNP genotyping may allow detection of regions HBD from recent common founders in singleton patients without genealogy information. We report a novel algorithm that detects such regions by estimating the population haplotype frequencies (HF) for an entire homozygous region. We also developed a simulation method to evaluate the probability of HBD and linkage to disease for a homozygous region by examining the best regions in unaffected controls from the host population. The method can be applied to diseases of Mendelian inheritance but can also be extended to complex diseases to detect rare founder mutations that affect a very small number of patients using either multiplex families or sporadic cases. Testing of the method on both real cases (singleton affected) and simulated data demonstrated its superb sensitivity and robustness under genetic heterogeneity. © 2011 Wiley-Liss, Inc.
Persistent Identifierhttp://hdl.handle.net/10722/135440
ISSN
2015 Impact Factor: 5.089
2015 SCImago Journal Rankings: 3.670
ISI Accession Number ID
Funding AgencyGrant Number
Strategic Research Theme on Genomics of the University of Hong Kong
Funding Information:

Contract grant sponsor: Strategic Research Theme on Genomics of the University of Hong Kong.

References

 

DC FieldValueLanguage
dc.contributor.authorZhang, Len_HK
dc.contributor.authorYang, Wen_HK
dc.contributor.authorYing, Den_HK
dc.contributor.authorCherny, SSen_HK
dc.contributor.authorHildebrandt, Fen_HK
dc.contributor.authorSham, PCen_HK
dc.contributor.authorLau, YLen_HK
dc.date.accessioned2011-07-27T01:35:10Z-
dc.date.available2011-07-27T01:35:10Z-
dc.date.issued2011en_HK
dc.identifier.citationHuman Mutation, 2011, v. 32 n. 3, p. 345-353en_HK
dc.identifier.issn1059-7794en_HK
dc.identifier.urihttp://hdl.handle.net/10722/135440-
dc.description.abstractHomozygosity mapping has played an important role in detecting recessive mutations using families of consanguineous marriages. However, detection of regions identical and homozygosity by descent (HBD) when family data are not available, or when relationships are unknown, is still a challenge. Making use of population data from high-density SNP genotyping may allow detection of regions HBD from recent common founders in singleton patients without genealogy information. We report a novel algorithm that detects such regions by estimating the population haplotype frequencies (HF) for an entire homozygous region. We also developed a simulation method to evaluate the probability of HBD and linkage to disease for a homozygous region by examining the best regions in unaffected controls from the host population. The method can be applied to diseases of Mendelian inheritance but can also be extended to complex diseases to detect rare founder mutations that affect a very small number of patients using either multiplex families or sporadic cases. Testing of the method on both real cases (singleton affected) and simulated data demonstrated its superb sensitivity and robustness under genetic heterogeneity. © 2011 Wiley-Liss, Inc.en_HK
dc.languageengen_US
dc.publisherJohn Wiley & Sons, Inc. The Journal's web site is located at http://www3.interscience.wiley.com/cgi-bin/jhome/38515en_HK
dc.relation.ispartofHuman Mutationen_HK
dc.rightsHuman Mutation. Copyright © John Wiley & Sons, Inc.-
dc.subjectFounder mutationen_HK
dc.subjectHomozygosity mappingen_HK
dc.subjectPopulation-based linkageen_HK
dc.subjectRare variantsen_HK
dc.subjectRecessive mutationen_HK
dc.titleHomozygosity mapping on a single patient-identification of homozygous regions of recent common ancestry by using population dataen_HK
dc.typeArticleen_HK
dc.identifier.openurlhttp://library.hku.hk:4550/resserv?sid=HKU:IR&issn=1059-7794&volume=32&issue=3&spage=345&epage=353&date=2011&atitle=Homozygosity+mapping+on+a+single+patient-identification+of+homozygous+regions+of+recent+common+ancestry+by+using+population+data-
dc.identifier.emailYang, W: yangwl@hkucc.hku.hken_HK
dc.identifier.emailCherny, SS: cherny@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.authorityCherny, SS=rp00232en_HK
dc.identifier.authoritySham, PC=rp00459en_HK
dc.identifier.authorityLau, YL=rp00361en_HK
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1002/humu.21432en_HK
dc.identifier.pmid21309031en_HK
dc.identifier.scopuseid_2-s2.0-79951795825en_HK
dc.identifier.hkuros188316en_US
dc.identifier.hkuros185567en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-79951795825&selection=ref&src=s&origin=recordpageen_HK
dc.identifier.volume32en_HK
dc.identifier.issue3en_HK
dc.identifier.spage345en_HK
dc.identifier.epage353en_HK
dc.identifier.eissn1098-1004-
dc.identifier.isiWOS:000288034100012-
dc.publisher.placeUnited Statesen_HK
dc.identifier.scopusauthoridZhang, L=39763382300en_HK
dc.identifier.scopusauthoridYang, W=23101349500en_HK
dc.identifier.scopusauthoridYing, D=35197469900en_HK
dc.identifier.scopusauthoridCherny, SS=7004670001en_HK
dc.identifier.scopusauthoridHildebrandt, F=7006208592en_HK
dc.identifier.scopusauthoridSham, PC=34573429300en_HK
dc.identifier.scopusauthoridLau, YL=7201403380en_HK

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