Similar protocols

Pipeline publication

[…] b'eviously described . Platelet phenotyping was undertaken for each participant in parallel with a healthy volunteer, and results were compared with the control reference ranges for platelet aggregation and secretion previously established by our group , ., Genomic DNA was isolated from peripheral blood using the Puregene DNA extraction kit (Qiagen, Manchester, UK) and, after enrichment of coding regions and intron/exon boundaries (10\xc2\xa0bp flanking the exons) using the Agilent SureSelect All Exon 50\xc2\xa0Mb kit (Agilent Technologies, Wokingham, UK), DNA sequencing was undertaken on the HiSeq 2000 from Illumina (Little Chesterford, UK). Sequence reads were aligned to the reference genome (hg19) using Novoalign (Novocraft Technologies, Sdn Bhd, Malaysia). Duplicate reads and reads that mapped to multiple locations in the exome were excluded from further analysis. Depth of sequence coverage was calculated using custom scripts and the BedTools package , and those with a sequence coverage below four were excluded. Single nucleotide variations (SNVs) and small insertions/deletions (indels) were identified and filtered for quality using the SAM tools package and in\xe2\x80\x90house software tools. Variants were annotated with respect to genes and transcripts using the ANNOVAR tool . Further analysis was targeted at variants within a panel of 329 candidate PFD genes, which represents an extension of a previously published list of candidate genes (Data S1). The original list consisted of 216 genes previously associated with PFDs in humans, orthologs of genes linked to platelet dysfunction in selected animal models, and genes that encoded recognized mediators of platelet activation that had not been previously associated with PFDs . For this study, the panel was extended to include genes that have been more recently identified as encoding proteins with a role in platelet function, as well as genes encoding proteins involved in the regulation of platelet for' […]

Pipeline specifications

Software tools NovoAlign, BEDTools, ANNOVAR