Challenges and solutions for gene identification in the presence of familial locus heterogeneity.

Next-generation sequencing (NGS) of exomes and genomes has accelerated the identification of genes involved in Mendelian phenotypes. However, many NGS studies fall short of identifying causal variants, with estimates for success rates as low as 25% for uncovering the pathological variant underlying disease etiology. An important reason for such failures is familial locus heterogeneity, where within a single pedigree causal variants in two or more genes underlie Mendelian trait etiology. As examples of intra- and inter-sibship familial locus heterogeneity, we present 10 consanguineous Pakistani families segregating hearing impairment due to homozygous variants in two different hearing impairment genes and a European-American pedigree in which hearing impairment is caused by four variants in three different genes. We have identified 41 additional pedigrees with syndromic and nonsyndromic hearing impairment for which a single previously reported hearing impairment gene has been identified but only segregates with the phenotype in a subset of affected pedigree members. We estimate that locus heterogeneity occurs in 15.3% (95% confidence interval: 11.9%, 19.9%) of the families in our collection. We demonstrate novel approaches to apply linkage analysis and homozygosity mapping (for autosomal recessive consanguineous pedigrees), which can be used to detect locus heterogeneity using either NGS or SNP array data. Results from linkage analysis and homozygosity mapping can also be used to group sibships or individuals most likely to be segregating the same causal variants and thereby increase the success rate of gene identification.

DFNB3, spectrum of MYO15A recessive mutant alleles and an emerging genotype-phenotype correlation.

We have now identified seven MYO15A mutations that cause congenital profound neurosensory hearing loss and a possible hypomorphic allele of MYO15A associated with moderately-severe hearing loss in 1 of 8 SMS patients. Because myosin XVA is encoded by 66 exons, screening for mutations in hearing-impaired individuals is expensive and labor-intensive in comparison to a screen for mutations in GJB2 (Cx26), for example, which has only a single protein coding exon. Among consanguineous families segregating profound, congenital hearing loss from Pakistan, approximately 10% are consistent with linkage to DFNB3 (11 of 112 DFNB families). In one-half of these DFNB3 families, we found a homozygous mutation in 1 of the 66 exons of MYO15A [25]. This suggests that mutations of MYO15A are responsible for at least 5% of recessively inherited, profound hearing loss in Pakistan. However, without the benefit of a pre-screen for linkage to DFNB3, it will be a challenge to determine the extent to which mutations of MYO15A contribute to hereditary hearing loss among isolated cases and small families in other populations.