Audio: Genome-wide Studies of Copy Number Variation and Exome Sequencing Identify Rare Variants in BAG3 as a Cause of Dilated Cardiomyopathy

Summary: Dilated cardiomyopathy (DCM), a common primary myocardial disease, causes systolic dysfunction and heart failure, a major public health problem. Its mode of transmission is mostly autosomal dominant but the disease is extremely heterogeneous with point mutations identified in over 30 genes. However, only ~35% of DCM genetic cause can be explained by point mutations in the known DCM genes, leaving most genetic cause unknown. In a multigenerational family with autosomal dominant transmission, we employed whole-exome sequencing in a proband and three of his affected family members, and genome-wide copy number variation in the proband and his affected father and unaffected mother. Exome sequencing identified 428 single point variants resulting in missense, nonsense, or splice site changes and 51 small insertion deletions; however, all were excluded based upon their presence in dbSNP, in-house population controls or their lack of segregation with those affected with DCM. Genome-wide copy number analysis using NimbleGen 2.1 M arrays identified 440 copy number variants > 1 kb, (median size ~13 kb). We then validated putative novel variants (not present in the database of genomic variants) with NimbleGen 135K custom arrays. Of these, a 8733 bp deletion, encompassing exon 4 of the heat shock protein cochaperone BCL2-associated athanogene 3 (BAG3), was found in seven affected family members and was absent in 355 controls. To establish the relevance of BAG3 rare variants in genetic DCM, we sequenced the coding exons in 311 other unrelated DCM probands and identified one frameshift, two nonsense, and four missense variants that were absent in over 967 exomes sequenced at Seattle Seq, four of which were familial and segregated with disease. Knockdown of bag3 in a zebrafish model recapitulated DCM and heart failure. We conclude that new comprehensive genomic approaches have identified rare variants in BAG3 as causative of DCM.