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Pipeline publication

[…] DNA samples were extracted from their ethylenediaminetetraacetic acid anticoagulated peripheral blood using a TIANamp Blood DNA Kit (TIANGEN)., For the proband's DNA sample, whole genome library was prepared using KAPA Library Preparation Kits for Illumina sequencing platforms, and all the coding sequences together with exon flanking sequences of 439 known pathogenic genes involving inborn errors of metabolism (IEM) were captured using an Agilent SureSelect Target Enrichment System. Then paired-end sequencing for the proband's target sequence was performed using an Illumina HiSeq2500 next-generation sequencer., Clean reads were mapped to the reference human genome hg19/GRCh37 using software Burrows-Wheeler Aligner. Genome Analysis ToolKit was used to identify single-nucleotide variations and insertions/deletions. All of the identified variants were annotated using software ANNOVAR, and significant variants were obtained using the single-nucleotide polymorphism database (NCBI dbSNP),[] Exome Aggregation Consortium (ExAC), 1000 Genomes Project, and Exome Sequencing Project (ESP6500)., For all subjects’ DNA samples, exons 11 and 12 of ATP7B including target variants were amplified by polymerase chain reaction (PCR) according to previously published primers.[] Sanger sequencing was then performed in the 2 WD sibs’ DNA samples to verify the target variants, and in the other 3 subjects’ DNA samples to determine target variants status., The pathogenicity assessment of the target variants was performed strictly according to the guidelines published by the American Col […]

Pipeline specifications

Software tools BWA, GATK, ANNOVAR
Organisms Homo sapiens
Diseases Heredodegenerative Disorders, Nervous System, Brain Diseases, Metabolic, Metabolism, Inborn Errors, Movement Disorders, Hepatolenticular Degeneration, Brain Diseases, Movement Disorders, Osteoarthritis, Arthritis