We will use a combination of second and third generation deep sequencing of selected candidate regions, whole exomes and mRNAs to identify both common and uncommon variants that predispose to PBC susceptibility. The sequencing of selected chromosome regions in 150 cases and 150 controls will target identification of variants that underlie the association of IL12A, SPIB, and a chromosome 17 locus (IKZF3/ORMDL3) that are identified in our PBC GWAS. The paired sequencing of these regions will provide the opportunity to ascertain coding and non-coding variation including copy number variants. The exome sequencing of 400 cases and 400 controls will screen for uncommon genetic variants that are not amenable to GWAS detection and provide the opportunity to test an alternate paradigm that does not depend on the common variant hypothesis. Importantly, mRNA sequencing of two cell populations implicated in PBC pathogenesis (CD8+ and CD4+ T cells) will complement both the chromosome region and exome results. For this aspect, mRNA will be sequenced in 75 cases and 75 controls. This mRNA sequencing together with the targeted chromosomal region sequencing and exome sequencing will provide the ability to correlate sequence variation with 1) gene expression, 2) eQTN data, 3) alternative exon usage, 4) RNA editing and 5) preferential allelic expression. A variety of informatics approaches using the combined data will establish a prioritization of SNPs for validation and testing in large numbers 1100 PBC cases and 2200 controls (not including discovery subject set) using a Golden Gate 1536 SNPlex. Both the sequencing and replication studies will be performed using a homogeneous Italian population. Together this design should maximize our ability to identify uncommon as well as more common variants that are important in the etiopathogenesis of this autoimmune disease.