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Pipeline publication

[…] -wide profiling of bisulfite-converted DNA was determined using the Infinium HumanMethylation450 BeadChip array (Illumina, Paris, France), according to the manufacturer’s instructions. Probe annotation information including sequence and chromosome location for the Infinium HumanMethylation450 BeadChip array was retrieved from the HumanMethylation450 v1.2 manifest file., WGS was performed using our standard protocols at the McGill University and Génome Québec Innovation Center. All samples were sequenced using the HiSeq X Ten Illumina System sequencer with paired-end 150-bp read length and the mean average of 35–37X. Bioinformatics analysis was performed as previously described. Briefly, the Burrows-Wheeler Aligner (BWA-MEM, version 0.7.7) was used to map all reads to UCSC hg19. PCR duplicates were removed from alignments using Picard version 1.96 (http://picard.sourceforge.net). Indels were realigned using the Genome Analysis Toolkit (GATK). SNVs and short indels were called using GATK haplotype caller (version 3.4–46). All variants were annotated with ANNOVAR and in-house scripts, and most likely protein damage variants (nonsense, splice site, frameshift indel, and missense) were considered for further analysis. The variants were also annotated for the allele frequency in public databases such as ExAC (http://exac.broadinstitute.org/), the National Heart, Lung, and Blood Institute (NHLBI) exomes (V.0.0.14, http://evs.gs.washington.edy/EVS/), the 1000 Genomes Project database, and our in-house database of >2000 exomes. In order to remove common variants and sequencing artifacts, variants with MAF >0.001 in any of the aforementioned databases were removed from further analysis., ChIP-Seq was performed in patient’s fibroblasts and cont […]

Pipeline specifications

Software tools BWA, Picard, GATK, ANNOVAR
Organisms Homo sapiens
Chemicals Ribonucleosides, Pyrimidine Nucleosides, Azacitidine, Pyrimidines