GENE IDENTIFICATION IN MENDELIAN DISORDERS USING STR MAPPING, SNP GENOTYPING AND WHOLE-EXOME SEQUENCING

Abstract

Recent data from 1000 Genomes Project suggest that human genome has large number of variations. While some of the variations in human genome are tolerated others result in pathogenic consequences. Consanguinity increases the probability of inheriting the variants in homozygous state in children that result in abnormal phenotype. Familial disorders are relatively prevalent in Pakistani population where consanguineous marriages are common practice. In this study, 12 inbred families belonging to various regions of Pakistan and inheriting different genetic disorders were sampled for molecular genetics analysis. Three different mutant gene identification strategies namely STR mapping, SNP array and whole-exome sequencing were used, either separately or complementary to each other. Linkage analysis of candidate genes/loci was done by STR markers and SNP genotyping. Families linked to the candidate genes were Sanger sequenced to identify causal mutations. Families excluded to reported loci were subjected to whole exome sequencing and if required to CytoScan® HD array for copy number variation detection. A series of filtering steps were followed to narrow the spectrum of variations down to a single functional variant among the several thousand variations. This study reports on three novel and six reported mutations responsible for causing familial diseases. A novel mutation, each in a family with hyponychia, Cenani-Lenz syndrome and spastic paraplegia 3A was found. Additionally, evidence were found for polymorphic initiation codon (p:M1I) in RSPO4 gene and for autosomal recessive inheritance in spastic paraplegia 3A. Whole-exome sequencing technology was successfully applied for gene identification in autosomal recessive and autosomal dominant disorders. Specific diagnosis of; spastic paraplegia 3A, pseudoachondroplasia, generalized lipodystrophy using variants derived by exome sequencing suggest that it has a dual role of mutation identification in heterogeneous disorders as well as a diagnostic tool in clinically overlapping phenotypes. The findings of current investigations will set the basis for establishing carrier screening and prenatal diagnosis to control the disease as well as for the better understanding of disease pathways.