A missense SNP rs2476601 in the protein tyrosine phosphatase non-receptor type 22 gene on chromosome 1 (PTPN22) was shown to be associated with the autoimmune disease rheumatoid arthritis (Begovich et al., 2004; Lee et al., 2005). The rheumatoid arthritis samples were collected by the North American Rheumatoid Arthritis Consortium (NARAC) for genetic linkage analysis (Jawaheer et al., 2001, 2003), and all pedigrees contain two or more affected siblings. In the original report (Begovich et al., 2004), one sib per affected sibpair is randomly selected from 377 affected sibpairs for the association analysis (plus 86 singletons). This procedure cuts the number of case samples almost by half. An association analysis of all affected sibs with a correction of the correlation between sibs was not carried out. We reproduce this dataset in Table 4 (corresponds to the “replication study” in Table 1 of (Begovich et al., 2004)).
