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| Content Provider | Springer Nature : BioMed Central |
|---|---|
| Author | Kozareva, Velina Stroff, Clayton Silver, Maxwell Freidin, Jonathan F. Delaney, Nigel F. |
| Abstract | Background Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe amplification (MLPA). However, since many genetic carrier screens depend instead on next-generation sequencing (NGS) for wider discovery of small variants, they often do not include CNV analysis. Moreover, most computational techniques developed to detect CNVs from exome sequencing data are not suitable for carrier screening, as they require matched normals, very large cohorts, or extensive gene panels. Methods We present a computational software package, geneCNV ( http://github.com/vkozareva/geneCNV ), which can identify exon-level CNVs using exome sequencing data from only a few genes. The tool relies on a hierarchical parametric model trained on a small cohort of reference samples. Results Using geneCNV, we accurately inferred heterozygous CNVs in the DMD gene across a cohort of 15 test subjects. These results were validated against MLPA, the current standard for clinical CNV analysis in DMD. We also benchmarked the tool’s performance against other computational techniques and found comparable or improved CNV detection in DMD using data from panels ranging from 4,000 genes to as few as 8 genes. Conclusions geneCNV allows for the creation of cost-effective screening panels by allowing NGS sequencing approaches to generate results equivalent to bespoke genotyping assays like MLPA. By using a parametric model to detect CNVs, it also fulfills regulatory requirements to define a reference range for a genetic test. It is freely available and can be incorporated into any Illumina sequencing pipeline to create clinical assays for detection of exon duplications and deletions. |
| Related Links | https://bmcmedgenomics.biomedcentral.com/counter/pdf/10.1186/s12920-018-0404-4.pdf |
| Ending Page | 12 |
| Page Count | 12 |
| Starting Page | 1 |
| File Format | HTM / HTML |
| ISSN | 17558794 |
| DOI | 10.1186/s12920-018-0404-4 |
| Journal | BMC Medical Genomics |
| Issue Number | 1 |
| Volume Number | 11 |
| Language | English |
| Publisher | BioMed Central |
| Publisher Date | 2018-10-20 |
| Access Restriction | Open |
| Subject Keyword | Human Genetics Microarrays Gene Expression DMD Copy number variation (CNV) Carrier screening Exome sequencing Muscular dystrophy Logit-normal distribution Logistic normal distribution |
| Content Type | Text |
| Resource Type | Article |
| Subject | Genetics (clinical) Genetics |
| Journal Impact Factor | 2.1/2023 |
| 5-Year Journal Impact Factor | 2.5/2023 |
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