ArticleBMC genetics2009
An experimental assessment of in silico haplotype association mapping in laboratory mice.
Article in BMC genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- The Potential ofGenes · 2023Article
- In silico mapping of quantitative trait loci (QTL) regulating the milk ionome in mice identifies a milk iron locus on chromosome 1.Mammalian genome : official journal of the International Mammalian Genome Society · 2018Article
- In-silico QTL mapping of postpubertal mammary ductal development in the mouse uncovers potential human breast cancer risk loci.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Article
- Genetic analysis of tissue glutathione concentrations and redox balance.Free radical biology & medicine · 2014Article
- Deconstructing Mus gemischus: advances in understanding ancestry, structure, and variation in the genome of the laboratory mouse.Mammalian genome : official journal of the International Mammalian Genome Society · 2013Review
- Natural genetic variation of integrin alpha L (Itgal) modulates ischemic brain injury in stroke.PLoS genetics · 2013Article
- Integrative assessment of chlorine-induced acute lung injury in mice.American journal of respiratory cell and molecular biology · 2012Article
- Haplotype Association Mapping Identifies a Candidate Gene Region in Mice Infected With Staphylococcus aureus.G3 (Bethesda, Md.) · 2012Article
- The genome architecture of the Collaborative Cross mouse genetic reference population.Genetics · 2012Article
- Forward genetic approaches to understanding complex behaviors.Current topics in behavioral neurosciences · 2012Review
- Haplotype association mapping of acute lung injury in mice implicates activin a receptor, type 1.American journal of respiratory and critical care medicine · 2011Article
- Glucuronic acid epimerase is associated with plasma triglyceride and high-density lipoprotein cholesterol levels in Turks.Annals of human genetics · 2011Article
- In silico QTL mapping of basal liver iron levels in inbred mouse strains.Physiological genomics · 2011Article
- Article
- Genome-wide association studies and genetic risk assessment of liver diseases.Nature reviews. Gastroenterology & hepatology · 2010Review
- Strain screen and haplotype association mapping of wheel running in inbred mouse strains.Journal of applied physiology (Bethesda, Md. : 1985) · 2010Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundTo assess the utility of haplotype association mapping (HAM) as a quantitative trait locus (QTL) discovery tool, we conducted HAM analyses for red blood cell count (RBC) and high density lipoprotein cholesterol (HDL) in mice. We then experimentally tested each HAM QTL using published crosses or new F2 intercrosses guided by the haplotype at the HAM peaks.
resultsThe HAM for RBC, using 33 classic inbred lines, revealed 8 QTLs; 2 of these were true positives as shown by published crosses. A HAM-guided (C57BL/6J x CBA/J)F2 intercross we carried out verified 2 more as true positives and 4 as false positives. The HAM for HDL, using 81 strains including recombinant inbred lines and chromosome substitution strains, detected 46 QTLs. Of these, 36 were true positives as shown by published crosses. A HAM-guided (C57BL/6J x A/J)F2 intercross that we carried out verified 2 more as true positives and 8 as false positives. By testing each HAM QTL for RBC and HDL, we demonstrated that 78% of the 54 HAM peaks were true positives and 22% were false positives. Interestingly, all false positives were in significant allelic association with one or more real QTL.
conclusionBecause type I errors (false positives) can be detected experimentally, we conclude that HAM is useful for QTL detection and narrowing. We advocate the powerful and economical combined approach demonstrated here: the use of HAM for QTL discovery, followed by mitigation of the false positive problem by testing the HAM-predicted QTLs with small HAM-guided experimental crosses.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.