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SCIP: software for efficient clinical interpretation of copy number variants detected by whole-genome sequencing.
Ding, Qiliang; Somerville, Cherith; Manshaei, Roozbeh; Trost, Brett; Reuter, Miriam S; Kalbfleisch, Kelsey; Stanley, Kaitlin; Okello, John B A; Hosseini, S Mohsen; Liston, Eriskay; Curtis, Meredith; Zarrei, Mehdi; Higginbotham, Edward J; Chan, Ada J S; Engchuan, Worrawat; Thiruvahindrapuram, Bhooma; Scherer, Stephen W; Kim, Raymond H; Jobling, Rebekah K.
Affiliation
  • Ding Q; Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
  • Somerville C; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Manshaei R; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Trost B; Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
  • Reuter MS; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Kalbfleisch K; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Stanley K; Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
  • Okello JBA; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Hosseini SM; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Liston E; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
  • Curtis M; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Zarrei M; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada.
  • Higginbotham EJ; CGEn, The Hospital for Sick Children, Toronto, ON, Canada.
  • Chan AJS; Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
  • Engchuan W; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Thiruvahindrapuram B; Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
  • Scherer SW; Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
  • Kim RH; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
  • Jobling RK; The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Hum Genet ; 142(2): 201-216, 2023 Feb.
Article in En | MEDLINE | ID: mdl-36376761
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 ).
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: DNA Copy Number Variations / Autism Spectrum Disorder Type of study: Guideline / Prognostic_studies Limits: Humans Language: En Journal: Hum Genet Year: 2023 Document type: Article Affiliation country: Canada Country of publication: Germany
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: DNA Copy Number Variations / Autism Spectrum Disorder Type of study: Guideline / Prognostic_studies Limits: Humans Language: En Journal: Hum Genet Year: 2023 Document type: Article Affiliation country: Canada Country of publication: Germany