The International Complex Trait Consortium

QTX and WebQTL: software for analysis of complex traits

Kenneth Manly1, Jane M. Meer1, Jintao Wang1, Robert W. Williams2

1Roswell Park Cancer Institute, Department of Molecular and Cellular Biology, Buffalo, NY 14263-0001, USA
2University of Tennessee Health Science Center, Center of Genomics and Bioinformatics, Memphis, TN 38163 USA

QTX software (Map Manager QTX) is cross-platform desktop software that analyzes the results of experimental genetic crosses to map Mendelian and quantitative trait loci (QTLs). QTX is distinguished by a rich graphic user interface and is available in versions for both Microsoft Windows and Mac OS operating systems. QTX functions for mapping Mendelian markers include rapid automatic methods for separating newly typed loci into linkage groups and for distributing newly typed loci among previously defined linkage groups. It uses regression to detect and map QTLs by four methods: association with single marker loci, simple interval mapping, composite interval mapping, and a search for pairs of interacting QTLs. It will search exhaustively for interacting QTLs by marker regression over a single chromosome or a range of chromosome, detecting even interactions of QTLs that do not have detectable individual effects. QTX uses a Markov-chain algorithm to estimate the genotypes of missing marker data during QTL mapping. QTX supports advanced backcross, advanced intercross, and recombinant inbred intercross (RIX) designs, and it offers weighted regression for designs in which an estimate of the trait variance is available for each line.
WebQTL, also known as the Neurogenetics Tool Box, is Web-based software to identify and map QTLs. It consists of Python CGI scripts, custom C library functions, and supporting genotype data files. The data files are taken from release 1 of the BXN data, a curated set of genotypes for over 100 recombinant inbred strains at about 1500 markers. The recombinant inbred strains include those of the AXB, BXA, CXB, BXD, and BXH sets. WebQTL now supports QTL mapping in these recombinant inbred strains by either single marker regression or simple interval mapping. Permutation tests to establish significance limits are provided for both methods, and bootstrap tests to estimate confidence intervals are provided for interval mapping. Results are returned as Web pages or optional email messages.


BXN data:

[The development and distribution of QTX is supported by grant HG01656 from the National Human Genome Research Institute.
WebQTL is supported by the Informatics Center for Mouse Neurogenetics, a Human Brain Project/Neuroinformatics program funded jointly by the National Institute of Mental Health, National Institute on Drug Abuse, and the National Science Foundation (P20-MH 62009)]