Browsing by Subject "next generation sequencing"

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    Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair
    (2014) Dal, Gülşah Merve
    Characterizing the patterns and rate of de novo mutations is crucial for our perception of evolution and genetic basis of human disease. Direct observation of de novo single nucleotide variation (SNV) rate in healthy individuals revealed a rate in a range of 0.82 – 1.70 ×10-8 base pair per generation. However, the developmental timing of the de novo mutations is unknown and thus, contribution of the early post-zygotic mutations to the human de novo SNV rate remained unknown. In an attempt to estimate the rate of de novo mutations regarding the developmental timing of mutagenesis, we sequenced the whole genomes of a healthy monozygotic twin pair and their parents with a total of 170 fold coverage. We identified the de novo SNVs through examination of the genotypes of each individual for each of the variants in a synchronous manner. Subsequent to the Sanger sequencing based validation, we conservatively characterized a total of 32 de novo SNVs. Of these 23 were shared by the twin pair, 8 were specific to twin I, and 1 was specific to twin II. We estimated the overall de novo SNV rate of 1.31 × 10-8 for twin I and 1.01 × 10-8 for twin II. The rate of the early post-zygotic de novo SNVs was calculated to be 0.34 × 10-8 and 0.04 × 10-8 for twin I and twin II, respectively. These data indicate the growing importance of genome mosaicism which might be resulted from de novo mutations of early post-zygotic origin in disease pathogenesis.
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    Quadrupedal gait in humans : identification and partial characterization of a novel gene WD repeat domain 81 (WDR81)
    (2011) Gülsüner, Süleyman İsmail
    Identi cation of disease genes responsible for cerebellar phenotypes provides mechanistic insights into the development of cerebellum. Neural pathways involved in bipedal gait in humans is not completely understood. Cerebellar ataxia, mental retardation, and disequilibrium syndrome (CAMRQ) is a rare neurodevelopmental disorder accompanied by quadrupedal gait, dysarthric speech and cerebellar hypoplasia. A large consanguineous family exhibiting this rare disorder was investigated in this study. Disease locus was mapped to a 7.1 Mb region on chromosome 17p by genetic analysis. Targeted capture and massively parallel DNA sequencing using the DNA of three a ected and two carrier individuals enabled the identi cation of a novel variant, p.P856L, in a predicted transcript of WD repeat domain 81 gene (WDR81). Several exclusion lters including segregation analysis, identi cation of rare polymorphisms, extended pedigree screen and bioinformatics evaluation was performed. Expression analysis revealed highest levels of transcripts in cerebellum and corpus callosum. In mouse brain Wdr81 RNA was observed in cerebellum, especially in Purkinje cell layer. The major structural abnormalities of the patients were atrophy of superior, middle and inferior cerebellar peduncles and corpus callosum. These ndings are compatible with the expression pattern of the gene. Analysis of the developing mouse brain revealed that, the expression pattern of the gene was correlated with those involved in neuronal di erentiation. This study was one of the rst examples of the utility of next generation sequencing in discovery of genes associated with Mendelian phenotypes.