/sv-cnv-studies

:books: Relevant papers for CNV and SV approaches

Awesome papers and projects about CNV and SV using NGS data 📚

Relevant studies with Structual Variants and Copy Number Variants in NGS (Genome, Exome and Amplicon Sequencing) pipelines.

Background CNV and SV

An example using ExomeDepth

An example of manual calculation of CNV ratio "The NGS data were analyzed for detection of CNV by comparing the number of sequence reads between patient and control samples. First, the number of each exon sequence reads from patient and control was counted. For the purposes of this comparison, we used sequencing data from 20 control samples, including both males and females, without POMGNT1 deletions (genomic sequencing was performed in these patients for diagnosis of other diseases). Data were obtained from samples using the same sequencing chip, sequenced on the same Illumina platform, and trimmed to the same read length as each patient sample. Next, the patient/control ratios were calculated by dividing the number of each exon sequence reads from patient by the average number of each exon sequence reads from the 20 control samples. Patient/control ratio lower than 0.65 indicates heterozygous deletions and ratios higher than 1.3 indicates duplications. Statistical analyses and graphs were obtained using GraphPad Prism7 (GraphPad Software, La Jolla, CA, USA)."

Long read

WGS

... an ASCN tool and open-source software with a broad application to whole genome, whole-exome, as well as targeted panel sequencing platforms.

WES

KaryoScan: abnormal karyotype detection from whole-exome sequence - github

AS

Our findings suggest that the best methods for CNV detection in tg-NGS panels are DECoN, ExomeDepth, and ExomeCNV.

RNAseq

Annotation

Visualization

Orchestrators

Others