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The aim of the present study was to determine the mutant genes and mutation sites in a family with maturity‑onset diabetes of the young (MODY), in order to provide evidence for the diagnosis and treatment of clinical MODY. Based on the clinical characteristics of MODY, one family was selected from the Department of Endocrinology of Shanxi Provincial People's Hospital (Shanxi, China). The family comprised seven individuals, four of which were healthy (without MODY), and the whole exome of the individual with MODY, her father and her mother were sequenced. A suspected case (patient's uncle) and a healthy individual (patient's aunt) were sequenced for verification. The Q30 ratio was >90% in the family of three and the sequencing quality was good. The alignment rate was >95%, while the repeat sequence was <10%, with a mean sequencing depth of >120x, which is sufficient to identify mutations. According to Mutation Taster and LRT, it was predicted that the p.leu73Pro mutation of the pancreatic and duodenal homeobox 1 (PDX1) gene was deleterious. The mutation was verified by next‑generation sequencing as the pathogenic site in this family. In conclusion, a novel mutation site of MODY type 4 in the PDX1 gene was identified in a family with MODY, which may provide a basis for its clinical treatment. Whole‑exome sequencing appears to be of assistance in accurately diagnosing MODY.
Pubmed ID: 31322178
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A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)
View all literature mentionsOriginal SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsDatabase as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.
View all literature mentionsA tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications.
View all literature mentionsArchive of aggregated information about sequence variation and its relationship to human health. Provides reports of relationships among human variations and phenotypes along with supporting evidence. Submissions from clinical testing labs, research labs, locus-specific databases, expert panels and professional societies are welcome. Collects reports of variants found in patient samples, assertions made regarding their clinical significance, information about submitter, and other supporting data. Alleles described in submissions are mapped to reference sequences, and reported according to HGVS standard.
View all literature mentionsA Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment.
View all literature mentionsQuality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.
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