PT - JOURNAL ARTICLE
AU - Piepho, Hans-Peter
TI - A Quick Method for Computing Approximate Thresholds for Quantitative Trait Loci Detection
DP - 2001 Jan 01
TA - Genetics
PG - 425--432
VI - 157
IP - 1
4099 - http://www.genetics.org/content/157/1/425.short
4100 - http://www.genetics.org/content/157/1/425.full
SO - Genetics2001 Jan 01; 157
AB - This article proposes a quick method for computing approximate threshold levels that control the genome-wise type I error rate of tests for quantitative trait locus (QTL) detection in interval mapping (IM) and composite interval mapping (CIM). The procedure is completely general, allowing any population structure to be handled, e.g., BC1, advanced backcross, F2, and advanced intercross lines. Its main advantage is applicability in complex situations where no closed form approximate thresholds are available. Extensive simulations demonstrate that the method works well over a range of situations. Moreover, the method is computationally inexpensive and may thus be used as an alternative to permutation procedures. For given values of the likelihood-ratio (LR)-profile, computations involve just a few seconds on a Pentium PC. Computations are simple to perform, requiring only the values of the LR statistics (or LOD scores) of a QTL scan across the genome as input. For CIM, the window size and the position of cofactors are also needed. For the approximation to work well, it is suggested that scans be performed with a relatively small step size between 1 and 2 cM.