Targeted Droplet‐Digital PCR as a Tool for Novel Deletion Discovery at the DFNB1 Locus

Pathogenic variants at the DFNB1 locus encompassing the GJB2 and GJB6 genes account for 50% of autosomal‐recessive, congenital nonsyndromic hearing loss in the United States. Most cases are caused by sequence variants within the GJB2 gene, but a significant number of DFNB1 patients carry a large deletion (GJB6‐D13S1830) in trans with a GJB2 variant. This deletion lies upstream of GJB2 and was shown to reduce GJB2 expression by disrupting unidentified regulatory elements. First‐tier genetic testing for hearing loss includes GJB2 sequence and GJB6‐D13S1830 deletion analysis; however, several other deletions in this locus, each with distinct breakpoints, have been reported in DFNB1 patients and are missed by current panels. Here, we report the development of a targeted droplet digital polymerase chain reaction‐based assay for comprehensive copy‐number analysis at the DFNB1 locus that detects all deletions reported to date. This assay increased detection rates in a multiethnic cohort of 87 hearing loss patients with only one identified pathogenic GJB2 variant. We identify two deletions, one of which is novel, in two patients (2/87 or 2.3%), suggesting that other pathogenic deletions at the DFNB1 locus may be missed. Mapping the assayed DFNB1 deletions also revealed a ～95 kb critical region, which may harbor the GJB2 regulatory element(s).     

No Evidence for Association of β‐Defensin Genomic Copy Number with HIV Susceptibility,HIV Load during Clinical Latency,or Progression to AIDS

Common single‐nucleotide variation in the host accounts for 25% of the variability in the plasma levels of HIV during the clinical latency stage (viral load set point). However, the role of rare variants and copy number variants remains relatively unexplored. Previous work has suggested copy number variation of a cluster of β‐defensin genes affects HIV load in treatment‐naïve sub‐Saharan Africans and rate of response to antiretroviral treatment. Here we analyse a total of 1827 individuals from two cohorts of HIV‐infected individuals from Europe and sub‐Saharan Africa to investigate the role of β‐defensin copy number variation on HIV load at set point. We find no evidence for association of copy number with viral load. We also compare distribution of β‐defensin copy number between European cases and controls and find no differences, arguing against a role of β‐defensin copy number in HIV acquisition. Taken together, our data argue against an effect of copy number variation of the β‐defensin region in the spontaneous control of HIV infection.