Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform

Abstract

Background: Hereditary hearing loss (HL) can originate from mutations in one of many genes involved in the complex process of hearing. Identification of the genetic defects in patients is currently labor intensive and expensive. While screening with Sanger sequencing for GJB2 mutations is common, this is not the case for the other known deafness genes (> 60). Next generation sequencing technology (NGS) has the potential to be much more cost efficient. Published methods mainly use hybridization based target enrichment procedures that are time saving and efficient, but lead to loss in sensitivity. In this study we used a semi-automated PCR amplification and NGS in order to combine high sensitivity, speed and cost efficiency.

Results: In this proof of concept study, we screened 15 autosomal recessive deafness genes in 5 patients with congenital genetic deafness. 646 specific primer pairs for all exons and most of the UTR of the 15 selected genes were designed using primerXL. Using patient specific identifiers, all amplicons were pooled and analyzed using the Roche 454 NGS technology. Three of these patients are members of families in which a region of interest has previously been characterized by linkage studies. In these, we were able to identify two new mutations in CDH23 and OTOF. For another patient, the etiology of deafness was unclear, and no causal mutation was found. In a fifth patient, included as a positive control, we could confirm a known mutation in TMC1.

Conclusions: We have developed an assay that holds great promise as a tool for screening patients with familial autosomal recessive nonsyndromal hearing loss (ARNSHL). For the first time, an efficient, reliable and cost effective genetic test, based on PCR enrichment, for newborns with undiagnosed deafness is available.

Figure 1

Cq values for OTOF and CDH23 . The Cq value is displayed in function of the corresponding amplicon for the OTOF and CDH23 gene. The plot shows a drop-out of two amplicons (red).

Figure 2

Cq values for the 15 genes. The Cq values for the amplicons covering all of the 15 genes are displayed. One amplicon of the TRIOBP gene failed during this PCR (red).

Figure 3

Workflow for the PCR enrichment approach. Amplicons are equimolar pooled per patient, continuously the A and B (454) adapters with MID are ligated to each pool of amplicons. All the patients, each tagged with a unique MID, can be pooled before proceeding to emulsion PCR.