The primary aim of the current study was to conduct a genome-wide linkage scan of nicotine dependence in the UCSF Family Alcoholism Study sample to support and extend the findings of previous studies. A linkage peak was observed on chromosome 2 at 184 cM that achieved genome-wide significance when a variance components approach was used based on criteria described by Lander and Kruglyak (1995). This region continued to yield strong evidence for linkage when the Kong and Cox (1997) statistic was used to test for linkage, but failed to reach genome-wide significance. This divergence in the results limits claims of genome-wide significance, though the consistency in LOD scores across analytic methods provides strong evidence of linkage to this region. Additional peaks of interest were found on a second region of chromosome 2 at 123 cM, chromosome 4 at 27 cM, chromosome 11 at 135 cM, and chromosome 12 at 50 cM, though these should be interpreted tentatively given the weaker evidence for linkage.
