SCIP: software for efficient clinical interpretation of copy number variants detected by whole-genome sequencing
| العنوان: | SCIP: software for efficient clinical interpretation of copy number variants detected by whole-genome sequencing |
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| المؤلفون: | Qiliang Ding, Cherith Somerville, Roozbeh Manshaei, Brett Trost, Miriam S. Reuter, Kelsey Kalbfleisch, Kaitlin Stanley, John B. A. Okello, S. Mohsen Hosseini, Eriskay Liston, Meredith Curtis, Mehdi Zarrei, Edward J. Higginbotham, Ada J. S. Chan, Worrawat Engchuan, Bhooma Thiruvahindrapuram, Stephen W. Scherer, Raymond H. Kim, Rebekah K. Jobling |
| المصدر: | Human Genetics. 142:201-216 |
| بيانات النشر: | Springer Science and Business Media LLC, 2022. |
| سنة النشر: | 2022 |
| مصطلحات موضوعية: | Genetics, Genetics (clinical) |
| الوصف: | Copy number variants (CNVs) represent major etiologic factors in rare genetic diseases. Current clinical CNV interpretation workflows require extensive back-and-forth with multiple tools and databases. This increases complexity and time burden, potentially resulting in missed genetic diagnoses. We present the Suite for CNV Interpretation and Prioritization (SCIP), a software package for the clinical interpretation of CNVs detected by whole-genome sequencing (WGS). The SCIP Visualization Module near-instantaneously displays all information necessary for CNV interpretation (variant quality, population frequency, inheritance pattern, and clinical relevance) on a single page—supported by modules providing variant filtration and prioritization. SCIP was comprehensively evaluated using WGS data from 1027 families with congenital cardiac disease and/or autism spectrum disorder, containing 187 pathogenic or likely pathogenic (P/LP) CNVs identified in previous curations. SCIP was efficient in filtration and prioritization: a median of just two CNVs per case were selected for review, yet it captured all P/LP findings (92.5% of which ranked 1st). SCIP was also able to identify one pathogenic CNV previously missed. SCIP was benchmarked against AnnotSV and a spreadsheet-based manual workflow and performed superiorly than both. In conclusion, SCIP is a novel software package for efficient clinical CNV interpretation, substantially faster and more accurate than previous tools (available at https://github.com/qd29/SCIP, a video tutorial series is available at https://bit.ly/SCIPVideos). |
| تدمد: | 1432-1203 0340-6717 |
| DOI: | 10.1007/s00439-022-02494-1 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_________::c3d8cdae1fbc7797f1130d8f79784994 https://doi.org/10.1007/s00439-022-02494-1 |
| Rights: | OPEN |
| رقم الانضمام: | edsair.doi...........c3d8cdae1fbc7797f1130d8f79784994 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14321203 03406717 |
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| DOI: | 10.1007/s00439-022-02494-1 |