PMC:5069600 / 8011-9810 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5069600","sourcedb":"PMC","sourceid":"5069600","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5069600","text":"Development of the Exome‐Based Shared Variants Detection System\nTo extract candidate genes or variants from the WES data, Maze Inc. (Tokyo, Japan) developed user‐friendly analysis software, called the exome‐based shared variants detection (ESVD) system, under our supervision. This system consists of two parts: a “variant‐filtering system” and a “shared variants/genes pickup system.” The variant‐filtering system provides users with many options for filtering the raw variant data. The conditions for filtering variants include mutation type, genotype, quality, read depth, minor allele frequency (MAF), and presence in public databases; dbSNP137, 1000 Genomes project database (http://browser.1000genomes.org), and The Human Genetic Variation Database (HGVD) comprised of exome sequencing of 1,208 Japanese individuals (http://www.genome.med.kyoto‐u.ac.jp/SnpDB/). Moreover, the shared variants/genes pickup system allowed us to detect the variants and genes shared among cases with similar phenotypes, and the number can be custom defined. In this study, using the ESVD system, we automatically performed variant filtering under the following conditions: (1) mutation type (single‐nucleotide variation [SNV]; not including insertion and deletion); (2) mutation classification (nonsynonymous, nonsense, and splicing site variants); (3) genotype (homozygous); (4) Phred‐scaled quality score/mapping quality (both \u003e20); (5) read depth (\u003e 10); and (6) existence in the public database (none or MAF \u003c1%). Subsequently, we manually selected the variants on an autosome. Eventually, after filtering, the variants that were shared by three or more cases were extracted (Fig 1). We also manually extracted presumed compound heterozygous variants of the MME gene from the WES data set of the 163 patients.","divisions":[{"label":"Title","span":{"begin":0,"end":63}}],"tracks":[]}