Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases.

Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Research Abstract Details 

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Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Abstract Text:

Richard A Radcliffe,Michael J Lee,Robert W Williams,

Cis-QTLs are important candidates for any other trait that maps to the same locus. In this article we have used publicly available databases and a small microarray data set to "map" cis-QTLs in the ILS and ISS inbred mouse strains without the need to generate microarray data from an ILSXISS segregating population. Expression data were obtained from brains of C57BL/6, DBA/2, ILS, and ISS. Cis-QTLs were mapped for the 760 transcripts found to be differentially expressed between the C57BL/6 and DBA/2 using expression data previously obtained from the BXD RIs. The 469 detected cis-QTLs were then examined for SNP haplotypes and expression patterns that could relate the ILS and ISS to the C57BL/6 and DBA/2. Of the 338 cis-QTL transcripts that had informative haplotypes, 189 were significantly different between the ILS and ISS with 184 showing segregation of haplotype with expression. These were considered to be probable cis-QTLs in the ILS and ISS. There were almost certainly additional ILS/ISS cis-QTLs among the other transcripts with informative haplotypes, but in the absence of an ILS/ISS expression difference, the level of confidence was reduced. Several of the putative ILS/ISS cis-QTLs are considered important candidate genes because they are linked to ILS/ISS behavioral QTLs. A potential ascertainment bias related to strain-dependent target sequences was observed suggesting that as much as 35% of the cis-QTLs were hybridization artifacts. Nonetheless, the results suggest that this approach is an economical and widely applicable method for mapping cis-QTLs in a strain pair of interest.

Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Publishing Authors By Initials

RA Radcliffe,MJ Lee,RW Williams,

For similar genetic structures: genome: genome components: genes: quantitative trait loci research abstracts see: genetic structures: genome: genome components: genes: quantitative trait loci research

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Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Mammalian genome : official journal of the Interna

VOLUME: 17

Page Numbers: 629-42

Journal Abbreviation: Mamm. Genome

ISSN: 0938-8990

DAY: 12

MONTH: 06

YEAR: 2006

Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Information

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LANGUAGE: eng

NlmUniqueID: 9100916

Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Keywords Mesh Terms:

KEYWORDS: Quantitative Trait Loci

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Chemical & Substance for Abstract: Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases. Information

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Grant and Affiliation Information for Prediction of cis-QTLs in a pair of inbred mouse strains with the use of expression and haplotype data from public databases.

AFFILIATION: Department of Pharmaceutical Sciences, University of Colorado at Denver and Health Sciences Center, 4200 E. Ninth Avenue, Denver, CO 80262, USA. Richard.Radcliffe@UCHSC.edu

Country: United States

AGENCY: United States NIAAA

GRANT: U01 AA 13499

ACRONYM: AA

MEDLINETA: Mamm Genome

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