Computational protocol: Somatic mosaicism for copy-neutral loss of heterozygosity and DNA copy number variations in the human genome

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Protocol publication

[…] We studied both CNVs and cn-LOHs that display somatic mosaicism in various tissues from four unrelated subjects using HumanOmniExpress-12 BeadChip (Illumina, Inc, San Diego, CA, USA) arrays. These arrays contain 733,202 markers that cover the entire human genome with a median spacing of 2.1 kb and provide an average effective resolution of ~20 kb (i.e. 10 consecutive markers). We processed 200 ng of total DNA per sample and performed each assay according to the protocol supplied by the manufacturer.The resulting array data was first analysed using Illumina GenomeStudio Software (Illumina, Inc) using a call rate of >99 % as the validity cutoff for each sample. With this criterion, three samples (SJ600-1; SJ600-2; SJ600-11) were excluded from further CNV analysis (Additional file : Table S2). In addition, relatedness analysis was performed using the PLINK software package (, []) to exclude the unlikely event of sample mix-ups between individuals.We employed two independent algorithms, PennCNV and QuantiSNP, to detect DNA copy number changes using their default settings as previously described [, ]. For this, normalized signal intensities (log R ratios) and B-allele frequencies (BAF) for each marker were exported from GenomeStudio. Only CNVs detected by both programs and with a Log Bayes Factor >10 were included in further analysis. QuantiSNP was then used to identify cn-LOH regions for each tissue sample that passed the above criteria. The minimum threshold for each cn-LOH region was set at 5 Mb. All results were visually evaluated using the Illumina GenomeStudio software Genome Viewer tool (Illumina, Inc).Next, we manually selected tissue-specific CNVs and cn-LOH regions that appeared only in a portion of tissues from the same individual. These CNVs were further compared with those recurrently present in both the DGV and in the Estonian general population (n = 6489, genotyped with HumanOmniExpress-12 BeadChips). The genomic context of each observed region was studied using Ensembl database ( version 54 (based on NCBI36) and later re-evaluated using version 78 (based on GRCh38). […]

Pipeline specifications

Software tools GenomeStudio, PLINK, PennCNV, QuantiSNP
Applications GWAS, Genome data visualization
Organisms Homo sapiens, Cucumber necrosis virus