LAUSR

Despite significant advances in genetic technology, variant detection is still not as successful as it might be, even for cases and conditions that are clearly Mendelian. One way to increase the detection rate is by learning from successful discoveries. However, a successful story may include lengthy troubleshooting and failed attempts that are rarely described in scientific papers. Often, information provided in most genetic publications is only the tip of the iceberg, lacking behind-the-scenes stories about the bumpy road that led to the final results. While most troubleshooting steps may be routine and do not present new lessons, sharing those that do with the research community could be beneficial, particularly those related to false-negative variant discoveries or failed attempts caused by the complexity of the genome and exacerbated by technical limitations and human errors. In a collaborative paper, we reported on the identification of a splice-site variant in the COL11A1 gene resulting in exon 5 skipping as a causative variant in DFNA37, a type of autosomal dominant nonsyndromic hearing loss (ADNSHL). As noted in the paper, the DFNA37 gene discovery odyssey started almost 20 years ago with the initial mapping of the DFNA37 locus, a process in which I was involved. Lessons learned from the long journey toward identification of the COL11A1 pathogenic variant encouraged me to reconnect pieces of a puzzle, to figure out why this variant was missed earlier by routine molecular techniques. Twenty years ago, as a graduate student, I was working on mapping the deafness genes in multiple ADNSHL families. Hearing loss in one of the examined families was mapped to a novel locus on chromosome 1p21, which was designated DFNA37. The linked region was large, containing a great number of genes. A paper published around that time on COL11A1 variants in Marshall syndrome made it our top candidate gene for DFNA37. So why was the COL11A1 variant not identified at that time? Screening of individual exons from genomic DNA (gDNA) using Sanger sequencing was a standard approach two decades ago. In addition to isolating DNA from all the DFNA37 family members, a small amount of RNA was isolated from the proband and one unaffected family member, and complementary DNA (cDNA) primers were used in an attempt to quickly scan the COL11A1 transcript for the causative variant. In the proband’s RNA sample, but not the unaffected family member, sequencing of a cDNA fragment covering the 5’ end of the gene produced a messy electropherogram pattern (data not shown). This pattern started at the junction between exons 4 and 5, indicative of a heterozygous transcript (i.e., with and without exon 5). Absence of this heterozygous sequencing product in the unaffected subject prompted us to further sequence the intron/exon junction in gDNA from these two individuals. Surprisingly, sequencing the genomic area spanning exon 5 with a forward primer inside intron 4 resulted in an out-ofphase electropherogram starting upstream of the intron 4/ exon 5 junction, in both the proband and the unaffected subject. This unexpected finding in gDNA diminished our enthusiasm for pursuing the potential exon 5 skipping of COL11A1 transcript in the proband’s cDNA. The findings in cDNA and gDNA could not have been fully explained at that time. So, considering that the region harbors a rather highly polymorphic and complex sequence, we assumed that the findings were due to polymerase chain reaction (PCR) artifacts! After this false-negative exclusion of the COL11A1 gene, we turned our attention to other potential candidate genes. We screened more than a dozen genes, particularly those enriched in the cochlea, throughout the years, but did not detect any variant. After this exhaustive, lengthy, and unsuccessful candidate gene screening, as with other variant detection odysseys, DFNA37 needed a fresh perspective and a new approach. Next-generation sequencing (NGS) provided that opportunity. The unresolved ADNSHL case later found its way into two laboratories, at the University of Nebraska Medical Center and the University of Iowa. Coincidentally, both labs independently restarted the investigation of the diseasecausing gene in this family using exome sequencing. During an exchange of information, they both discovered that they had solved the mystery of DFNA37. A novel splice-site variant (c.652-2 A>C) resulting in COL11A1 exon 5 skipping was confirmed by both teams. This finding provided a