Browsing by Author "King, M. C."

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Open Access
Causal mutation discovery using next generation sequencing data: development and application of a pipeline to reduce false positive calls and to map regions of shared homozygosity and IBD
(American Society of Human Genetics, 2012-11) Gülsüner, Süleyman; Walsh, T.; Watts, A. C.; Lee, M. K.; Özçelik, Tayfun; King, M. C.
Next generation sequencing technologies have brought enormous successes for disease gene discovery but also challenges for data analysis, particularly in genomic regions with low or low quality sequence coverage. Errors in variant calling may lead to missing true variants or to calling many false positives. The false discovery rate can be reduced by optimizing variant calling thresholds such as quality of base pair identification, mapping, and alignment. However, such optimization strategies are often associated with the loss of true variants. We present and apply a pipeline for variant identification and verification using aligned sequences of related individuals. It is comprised of three modules: (1) an identification pipeline for de novo variants where data of parents and siblings are aligned in order to rule out false positive calls in children, false negative calls in parents, and indel artifacts; (2) a homozygosity mapping and IBD analysis module; and (3) a variant read depth module that reveals variants that may have been missed due to sequence coverage and quality issues. We applied module (1) to a large trio-based gene discovery project and reduced the number of variant calling errors by 74%, thereby significantly streamlining the experimental validation protocol for potential de novo variants. We also applied the pipeline to the discovery of the gene responsible for mega corpus callosum and microcephaly with developmental delay, and epilepsy in a brother and sister whose unaffected parents were first cousins. Our error correction pipeline significantly improved homozygosity mapping and IBD analysis and facilitated the rapid identification of the causal allele in this family.
Open Access
Mitochondrial serine protease HTRA2 p.G3999S in a kindred with essential tremor and Parkinson disease
(National Academy of Sciences, 2014) Gülümser, Hilal Ünal; Gulsuner, S.; Mercan, F. N.; Onat, Onur Emre; Walsh, T.; Shahin, H.; Lee, M. K.; Dogu, O.; Kansu, T.; Topaloglu, H.; Elibol, B.; Akbostanci, C.; King, M. C.; Özçelik, Tayfun; Tekinay, Ayşe B.
Essential tremor is one of the most frequent movement disorders of humans and can be associated with substantial disability. Some but not all persons with essential tremor develop signs of Parkinson disease, and the relationship between the conditions has not been clear. In a six-generation consanguineous Turkish kindred with both essential tremor and Parkinson disease, we carried out whole exome sequencing and pedigree analysis, identifying HTRA2 p.G399S as the allele likely responsible for both conditions. Essential tremor was present in persons either heterozygous or homozygous for this allele. Homozygosity was associated with earlier age at onset of tremor (P < 0.0001), more severe postural tremor (P < 0.0001), and more severe kinetic tremor (P = 0.0019). Homozygotes, but not heterozygotes, developed Parkinson signs in the middle age. Among population controls from the same Anatolian region as the family, frequency of HTRA2 p.G399S was 0.0027, slightly lower than other populations. HTRA2 encodes a mitochondrial serine protease. Loss of function of HtrA2 was previously shown to lead to parkinsonian features in motor neuron degeneration (mnd2) mice. HTRA2 p.G399S was previously shown to lead to mitochondrial dysfunction, altered mitochondrial morphology, and decreased protease activity, but epidemiologic studies of an association between HTRA2 and Parkinson disease yielded conflicting results. Our results suggest that in some families, HTRA2 p.G399S is responsible for hereditary essential tremor and that homozygotes for this allele develop Parkinson disease. This hypothesis has implications for understanding the pathogenesis of essential tremor and its relationship to Parkinson disease.