Genomic structural variation (SV) means the variation of chromosome structures. SV contains many types of variations including deletion, duplication, copy number variations (CNV), insertions, translocation etc. It normally affects a sequence of 1 kb to 3 Mb in length.
SV is larger than SNP and more difficult to detect than SNPs. Some diseased are suspected to be associated with SV, but the relation between phenotype and SV is not very certain.
CNV including insertions, deletions and duplications, is a type of SV. Many of the CNVs are not located in coding regions.
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ENCODE, CNV track, https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=wgEncodeHudsonalphaCnv
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CNV are normally called from whole genome sequencing (WGS) data or whole exome sequencing (WES) data.
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Comparing to short-read sequencing and bulk tissue sequencing, long read genome sequencing and single cell sequencing is not widely used at present. So we look at short-read sequencing for now.
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There are some pipelines (tutorial) for CNV calling from DNA sequencing data:
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Pipeline from Broad Instititue (bash): http://software.broadinstitute.org/software/genomestrip/node_CNVPipelineOverview.html
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CNVkit (python): https://cnvkit.readthedocs.io/en/stable/pipeline.html
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DNA-seq analysis pipeline from NIH: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
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'Copy-number variants in clinical genome sequencing: deployment and interpretation for rare and undiagnosed disease' https://www.nature.com/articles/s41436-018-0295-y
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'A highly sensitive and specific workflow for detecting rare copy-number variants from exome sequencing data' https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-020-0712-0
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'Validation of an ultra-fast CNV calling tool for Next Generation Sequencing data using MLPA-verified copy number alterations' https://www.biorxiv.org/content/10.1101/340505v1