The optimized method for identifying copy number variation (CNV) at the STRC locus

Mutational changes in the STRC gene cause an autosomal recessive form of hearing loss (HL) type 16 (DFNB16, OMIM 603720), which in most cases is characterized by non-progressive, mild or moderate HL. One of the troubles of the testing STRC gene variants is the presence of the STRCP1 pseudogene (99.6% identity). In this regard, to detect and confirm various types of STRC mutations, a combined approach is used, since no single method detects all types of mutations. In this work, on a sample of 124 GJB2-negative patients with HL in Yakutia, we used optimized method for identifying copy number variations (CNVs) in the STRC locus, which allows us to detect homozygous cases of extended deletions using standard PCR, followed by direct detection of amplified fragments in 8% polyacrylamide gel. Using this method, homozygous cases of large deletions were detected in three patients, accounting for 2.41% (3/124). The identified CNV cases were verified using allele-specific PCR with an assessment of the approximate boundaries of the deleted fragments, to determine which we developed a primer system covering the analyzed chromosomal region. As a result, it was established that in one patient the large deletion covered only a copy of the STRC gene, in another – a copy of two genes STRC and CATSPER2, and in the third patient copies of the CKMT1A gene and the STRCP1 pseudogene were deleted. Taking into account affected individuals carrying causative homozygous deletions in the STRC gene region, the contribution of DFNB16 among GJB2-negative patients in Yakutia is at least 1.6% (2/124). Thus, the optimized method for searching for homozygous large deletions using standard PCR and the developed primer system for assessing the boundaries of the identified CNVs can be used as primary or alternative first-line tests for screening/ verification of large deletions in the STRC locus.

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