Smart approach for cost-effective genotyping of single nucleotide polymorphisms

Single Nucleotide Polymorphisms (SNPs) are in the prime focus of genomic studies for their probable roles in diagnostics and prognosis of diseases and forensic science. SNaPshot/minisequencing reaction-based genotyping of targeted SNPs is a method of choice due to its fast and reliable detection assay. Here we described smart modifications in minisequencing reaction to make it cost-effective to detect 15 SNPs in a single assay. The target SNPs were amplified in a multiplex PCR from genomic DNA, and these multiplex PCR amplicons were utilized as a template in modified SNaPshot reaction for SNPs identification. The modified protocol was assessed for reproducibility on more than 50 human DNA samples, and it was observed that this modified method is at least five times more productive than the original protocol recommended by the manufacturer. The current smart modifications in SNaPshot reaction were successfully optimized for susceptible asthma SNPs. However, these can be applied for cost-effective genotyping of any type of genomic Single Nucleotide Polymorphisms.

Biallelic Expression of Mucin-1 in Autosomal Dominant Tubulointerstitial Kidney Disease: Implications for Nongenetic Disease Recognition

BackgroundProviding the correct diagnosis for patients with tubulointerstitial kidney disease and secondary degenerative disorders, such as hypertension, remains a challenge. The autosomal dominant tubulointerstitial kidney disease (ADTKD) subtype caused by MUC1 mutations (ADTKD-MUC1) is particularly difficult to diagnose, because the mutational hotspot is a complex repeat domain, inaccessible with routine sequencing techniques. Here, we further evaluated SNaPshot minisequencing as a technique for diagnosing ADTKD-MUC1 and assessed immunodetection of the disease-associated mucin 1 frameshift protein (MUC1-fs) as a nongenetic technique.MethodsWe re-evaluated detection of MUC1 mutations by targeted repeat enrichment and SNaPshot minisequencing by haplotype reconstruction via microsatellite analysis in three independent ADTKD-MUC1 families. Additionally, we generated rabbit polyclonal antibodies against MUC1-fs and evaluated immunodetection of wild-type and mutated allele products in human kidney biopsy specimens.ResultsThe detection of MUC1 mutations by SNaPshot minisequencing was robust. Immunostaining with our MUC1-fs antibodies and an MUC1 antibody showed that both proteins are readily detectable in human ADTKD-MUC1 kidneys, with mucin 1 localized to the apical membrane and MUC1-fs abundantly distributed throughout the cytoplasm. Notably, immunohistochemical analysis of MUC1-fs expression in clinical kidney samples facilitated reliable prediction of the disease status of individual patients.ConclusionsDiagnosing ADTKD-MUC1 by molecular genetics is possible, but it is technically demanding and labor intensive. However, immunohistochemistry on kidney biopsy specimens is feasible for nongenetic diagnosis of ADTKD-MUC1 and therefore, a valid method to select families for further diagnostics. Our data are compatible with the hypothesis that specific molecular effects of MUC1-fs underlie the pathogenesis of this disease.