About: Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing

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An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	MHC is linked to individual fitness and is important in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high polymorphism in the MHC region, making genotyping of MHC a challenging task. We compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: CE-SSCP analysis and 454 GS FLX Titanium pyrosequencing. According to our findings, the number of MHC alleles detected by CE-SSCP is significantly lower than detected by 454. To resolve discrepancies between the two methods, we cloned and Sanger sequenced a MHC class I amplicon for an individual with high number of alleles. We found perfect congruence between cloning/Sanger sequencing and 454. Thus, in case of multi-locus amplification, CE-SSCP considerably underestimates individual MHC diversity. Numbers of alleles detected by both methods are significantly correlated, although the correlation is weak (r=0.32). MHC is linked to individual fitness and is important in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high polymorphism in the MHC region, making genotyping of MHC a challenging task. We compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: CE-SSCP analysis and 454 GS FLX Titanium pyrosequencing. According to our findings, the number of MHC alleles detected by CE-SSCP is significantly lower than detected by 454. To resolve discrepancies between the two methods, we cloned and Sanger sequenced a MHC class I amplicon for an individual with high number of alleles. We found perfect congruence between cloning/Sanger sequencing and 454. Thus, in case of multi-locus amplification, CE-SSCP considerably underestimates individual MHC diversity. Numbers of alleles detected by both methods are significantly correlated, although the correlation is weak (r=0.32). (en)
Title	Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing (en)
skos:prefLabel	Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing (en)
skos:notation	RIV/00216208:11310/12:10100936!RIV13-GA0-11310___
http://linked.open...avai/riv/aktivita	I P Z
http://linked.open...avai/riv/aktivity	I, P(GA206/06/0851), P(GAP505/10/1871), P(IAA600930608), Z(AV0Z60930519)
http://linked.open...iv/cisloPeriodika	2
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Albrecht, Tomáš
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Univerzita Karlova v Praze / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	135230
http://linked.open...ai/riv/idVysledku	RIV/00216208:11310/12:10100936
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	scarlet rosefinch; next-generation sequencing; major histocompatibility complex; Carpodacus erythrinus; avian (en)
http://linked.open.../riv/klicoveSlovo	next-generation sequencing major histocompatibility complex Carpodacus erythrinus scarlet rosefinch avian
http://linked.open...odStatuVydavatele	GB - Spojené království Velké Británie a Severního Irska
http://linked.open...ontrolniKodProRIV	[0219AF92C0C0]
http://linked.open...i/riv/nazevZdroje	Molecular Ecology Resources
http://linked.open...in/vavai/riv/obor	EG
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	6 (xsd:int)
http://linked.open...vavai/riv/projekt	The role of MHC in sexual selection - observational and experimental study in three model vertebrate species Toll-like receptors in passerine birds: description, characterization of polymorphism and evolutionary consequences of allelic variation Extra-pair fertilizations and the strength of sexual selection in socially monogamous passerine
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	12
http://linked.open...iv/tvurceVysledku	Albrecht, Tomáš Bryja, Josef Promerová, Marta Babik, Wieslav Radwan, Jacek Stuglik, Michal
http://linked.open...ain/vavai/riv/wos	000299930300011
http://linked.open...n/vavai/riv/zamer	Biodiverzita a ekologie obratlovců: Strategie ochrany a využívání přírodních populací
issn	1755-098X
number of pages	8 (xsd:int)
http://bibframe.org/vocab/doi	10.1111/j.1755-0998.2011.03082.x
http://localhost/t...ganizacniJednotka	11310

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