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Pipeline publication

[…] Illumina’s Nextera prep, library preparation generally entailed: (i) A-tailing of the 3′ ends to facilitate ligation to sequencing adapters, (ii) ligation of indexed adapters, and (iii) ten PCR cycles to enrich for products with adapters ligated to both ends. Subsequent amplicon sequencing using Illumina miseq PE300 mode was carried out by the Zhejiang Dian diagnostics Co. Ltd., From the sequencing reactions, 0.04 Mb of read data per sample was obtained, and were assessed using stringent bioinformatic filters. The resultant 560× average target coverage meant that 100% of the amplicons had at least 30× coverage. Sequence reads were aligned to the reference human genome (UCSC hg19) using the BWA software (bio-bwa.sourceforge.net). Sequence variation annotation was performed using the GATK pipeline (https://software.broadinstitute.org/gatk) and annotated using ANNOVA (annovar.openbioinformatics.org), which comprises gene annotations from multiple sources (including RefSeq, dbSNP 138, Clinvar, and 1000genome)., Mutation hotspots in SLC12A3 were detected using next generation sequencing (NGS) and subsequently confirmed using Sanger sequencing., Primary laboratory results of the proband are summarized in Table . Laboratory test showed severe hypokalemia, hypomagnesemia, hypocalciuria, and metabolic alkalosis, along with elevated renin activity. The electrocardiogram suggested sinus tachycardia (107 beats per minute), high voltage of the left ventricle, and ST-segment change of the anterolateral wall. An echocardiogram showed thickening of the left ventricula […]

Pipeline specifications

Software tools BWA, GATK, ANNOVAR
Organisms Homo sapiens
Diseases Acid-Base Imbalance, Water-Electrolyte Imbalance, Metabolic Diseases, Neuromuscular Manifestations, Neurologic Manifestations, Calcium Metabolism Disorders, Genetic Diseases, Inborn, Urologic Diseases, Kidney Diseases, Metabolism, Inborn Errors
Chemicals Metals, Alkali, Metals, Light