Variance component linkage analyses were applied to the quantitative subphenotypes SOC and BEH using Merlin (v1.0.1) (44). Multipoint nonparametric linkage analyses (NPL) from Merlin were applied to the ASD families that had two or more affected individuals defined by the four binary subphenotypes—DelayedWord, DelayedPhrase, Verbal, and IQ ≥ 70 (45). The NPL results were presented as logarithm of odds (LOD) scores under the exponential allele-sharing model (46). Since all the affected individuals defined by the four binary subphenotypes had ASD, the linkage analyses were for both the subphenotypes and ASD using a subset of families that met the criteria. To compare the linkage results of the subsets with the results of the whole data, a linkage analysis on the diagnosis of ASD from the whole data was also performed. LOD scores as well as asymptotic p values were reported for these linkage analyses. For the most significant linkage results from the subset analyses, the FLexible Ordered SubSet (FLOSS v1.4.1, http://www.stat.auckland.ac.nz/∼browning/floss/floss.htm#osa) software was used to generate empirical p values (47). More details are provided in the Supplement 1.
