This is usually accomplished by direct sequencing of GJB2 and exclusion of other loci using homozygosity mapping with STR markers. Fluorescently labeled microsatellite markers have various applications such as DNA fingerprinting, paternal analyses, genetic mapping or genetic structure analyses.īefore proceeding to identify new loci for hearing loss, it is important to exclude known genes which cause deafness. As a consequence of their elevated mutation rates, STRs are typically highly polymorphic: different individuals exhibit variations manifested as repeat number differences. They consist of motifs of two to six nucleotides tandemly repeated several times that have a characteristic mutational behavior ( Kelkar et al., 2010). Microsatellites, also known as simple sequence repeats (SSRs) or short tandem repeats (STRs), remain a popular marker type in population genetic studies. Many of these loci were first mapped in Pakistani families. About 66 loci and 38 genes are known which cause autosomal recessive non-syndromic hearing loss ( last updated 8 September, 2011). Recessive deafness is more prevalent in endogamous and isolated populations ( Friedman and Griffith, 2003) and Pakistan represents a treasure for molecular dissection of hearing disorder because 60% of marriages are consanguineous in which approximately 80% are between first cousins ( Hussain and Bittles, 1998). Non-syndromic forms of deafness transmitted as a recessive trait are the most common cause of hereditary hearing loss ( Cohen and Gorlin, 1995). Phenotypically, hearing impairment is classified as syndromic and non-syndromic. Furthermore, primers for some known microsatellites were redesigned for multiplexing and finally a protocol of genotyping with fluorescently labeled universal M13 primers was incorporated in the strategy.Īlarge number of genes are anticipated to be responsible for controlling the anatomic and physiological function of the ear ( Friedman and Griffith, 2003). It involves selecting microsatellite markers close to the known deafness genes thereby decreasing the number of markers required to screen for each locus and multiplexing the PCR reactions. Here we describe a protocol to reduce the time and costs of microsatellite based screening. This makes screening a large number of loci very laborious and expensive. Microsatellite based homozygosity mapping is an excellent option but throughput is low as it yields genotype information at only one locus per reaction. Due to extreme genetic heterogeneity of ARNSHL, many known loci have to be screened to find linkage to deafness genes or before proceeding to a genome wide analysis to identify a new locus for the disorder. Autosomal-recessive nonsyndromic hearing loss (ARNSHL) is the most frequent form among inherited forms of deafness and accounts for greater than 70% of the cases. Hearing loss is one of the most common sensorineural defects in humans.
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