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Pipeline publication

[…] prioritization. In Geneva, genomic DNA of 59 affected individuals (belonging to 47 families) was fragmented by sonication to 200 bp fragments then liquid phase captured against whole human exome probes to select all coding sequences (SureselectXT Target Enrichment System Version 1.2, Agilent). Sequencing was performed on an Illumina HiSeq 2000 instrument (paired ends, 2 × 95 bp). Each exome library was indexed, separated into two equal halves and sequenced in two different lanes, up to five half-libraries were sequenced in each HiSeq lane. The raw results were analysed using a local bioinformatics pipeline, which as previously described combines published algorithms in a sequential manner (BWA for map reads, SAMtool for detection of variants, Pindel for the detection of indels, ANNOVAR for annotation of sequence changes). The entire coding sequence corresponding to RefSeq (http://www.ncbi.nlm.nih.gov/refseq/) coding genes was used as the reference for the calculation of coverage and reads on target., In both centres, for subsequent filtering of variants, only exonic and splicing variants (±10 bp of the intron–exon boundary) were retained for further analysis. These were filtered to exclude synonymous variants, variants with a minimum allele frequency ≥0.01 in dbSNP version 137, 1000Genomes (http://1000genomes.org/), local databases and variants found within segmental duplications of the genome. Minor allele frequency was then checked on Exome Variant Server (http:/ […]

Pipeline specifications

Software tools BWA, VarScan, VEP
Diseases Neurotoxicity Syndromes, Movement Disorders, Dyskinesias, Dyskinesia, Drug-Induced, Neurologic Manifestations, Genetic Diseases, Inborn