To minimize bias and spurious associations that may occur with using combined data from different studies and conducting a large number of statistical tests, GENEVA has built upon previous efforts [Chanock et al., 2007; Miyagawa et al., 2008] and provides an extensive guide for QC and quality assurance (QA) for users [Laurie et al., 2009; submitted]. The consortium has developed new approaches to (1) distinguish gender misidentification from sex chromosome aberrations, (2) detect autosomal chromosome aberrations that may affect genotype calling accuracy, (3) measure DNA quality, (4) infer relatedness through identity-by-descent estimates and (5) use duplicate concordance to filter SNP quality. Genotypic data are distributed to the entire project team for quality assessment, which occurs as a collaborative process led by the CC and involving the appropriate SI team, GCs, NHGRI, NCBI, and any interested GENEVA investigators or NIH staff who wish to listen in.
