RT Journal Article
SR Electronic
T1 A Quick Method for Computing Approximate Thresholds for Quantitative Trait Loci Detection
JF Genetics
JO Genetics
FD Genetics Society of America
SP 425
OP 432
VO 157
IS 1
A1 Piepho, Hans-Peter
YR 2001
UL http://www.genetics.org/content/157/1/425.abstract
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.