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Pipeline publication

[…] committee of Xiangya Hospital affiliated to Central South University. The methods in this study were performed in accordance with the approved guidelines. Written informed consent was obtained from all subjects., We conducted WES of a proband-parent trio to identify the causal gene. The SureSelect Human All ExonV5 Kit (Agilent) was used for exome capture. The IlluminaHiseq 2500 platform (San Diego, CA) was utilized for genomic DNA sequencing of the proband and her parents in Novogene (Beijing, China)., Raw image analyses and base calling were performed using Illumina‚Äôs Pipeline (version 1.3.4) with default parameters. Sequence data were aligned to the reference human genome (hg19) using the Burrows-Wheeler Aligner (BWA), and duplicate reads were removed using Picard tools. We used the Genome Analysis ToolKit (GATK) to perform the re-alignment and variation (SNP and Indel) detection. Annovar was utilized to catalogue the detected variations. Then, we filtered variations with a homopolymer length >6 (and synonymous substitutions) or that were common (>0.5%) in dbSNP ( http://www.ncbi.nlm.nih.gov/projects/SNP/), HapMap, and the 1000 Genomes Project ( http://www.1000 genomes.org). Variants that were not present in any of the above databases were considered novel., Given to the characteristics of the pedigree, homozygous, compound heterozygous or de novo variations were considered to be candidate causal variations., We confirmed the candidate causal variations identified via WES and conducted co-segregation analyses among the family. The primers of the candidate variat […]

Pipeline specifications

Software tools BWA, Picard, GATK, ANNOVAR
Organisms Homo sapiens
Diseases Atrophy, Movement Disorders, Nervous System Diseases, Neuromuscular Manifestations, Muscle Weakness, Neurologic Manifestations, Genetic Diseases, Inborn