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Albert Johannes Buitenhuis

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisKonferenceartikelForskningpeer review

Dokumenter

DOI

  • Vincent Jouffe, Laboratoire PsyNuGen, INRA, Frankrig
  • Suzanne Rowe, The Roslin Institute and R(D)SVS, University of Edinburgh, Storbritannien
  • Laurence Liaubet, Laboratoire de Génétique Cellulaire, INRA, Frankrig
  • Bart Buitenhuis
  • Henrik Hornshøj, Danmark
  • Magali SanCristobal, Laboratoire de Génétique Cellulaire, INRA, Frankrig
  • Pierre Mormède, Laboratoire PsyNuGen, INRA, Frankrig
  • DJ de Koning, The Roslin Institute and R(D)SVS, University of Edinburgh, Storbritannien
  • Biostatistik
  • Molekylær Genetik og Systembiologi
  • Institut for Genetik og Bioteknologi

Background: Microarray studies can supplement QTL studies by suggesting potential candidate. Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH)

Microarray studies can supplement QTL studies by suggesting potential candidate genes in the QTL regions, which by themselves are too large to provide a limited selection of candidate genes. Here we provide a case study where we explore ways to integrate QTL data and microarray data for the pig, which has only a partial genome sequence. We outline various procedures to localize differentially expressed genes on the pig genome and link this with information on published QTL. The starting point is a set of 237 differentially expressed cDNA clones in adrenal tissue from two pig breeds, before and after treatment with adrenocorticotropic hormone (ACTH)

Results: Different approaches to localize the differentially expressed (DE) genes to the pig genome. Different approaches to localize the differentially expressed (DE) genes to the pig genome showed different levels of success and a clear lack of concordance for some genes between the various approaches. For a focused analysis on 12 genes, overlapping QTL from the public domain were presented. Also, differentially expressed genes underlying QTL for ACTH response were described. Using the latest version of the draft sequence, the differentially expressed genes were mapped to the pig genome. This enabled co-location of DE genes and previously studied QTL regions, but the draft genome sequence is still incomplete and will contain many errors. A further step to explore links between DE genes and QTL at the pathway level was largely unsuccessful due to the lack of annotation of the pig genome. This could be improved by further comparative mapping analyses but this would be time consuming

OriginalsprogEngelsk
TidsskriftBMC Proceedings
Nummer4:S14
Sider (fra-til)1-10
Antal sider11
ISSN1753-6561
DOI
StatusUdgivet - 2009
BegivenhedEADGENE and SABRE Post-analyses Workshop - Lelystad, Holland
Varighed: 12 nov. 200814 nov. 2008

Konference

KonferenceEADGENE and SABRE Post-analyses Workshop
LandHolland
ByLelystad
Periode12/11/200814/11/2008

Bibliografisk note

Udgivelsesdato: 16. July
Volumne: 3

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