Evidence map›Paper›PMID 36376761›Full record

ArticleHuman genetics2023

SCIP: software for efficient clinical interpretation of copy number variants detected by whole-genome sequencing.

Qiliang Ding, Cherith Somerville, Roozbeh Manshaei, Brett Trost, Miriam S Reuter, Kelsey Kalbfleisch, Kaitlin Stanley, John B A Okello, S Mohsen Hosseini, Eriskay Liston and 9 more

Open access · hybridAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Human genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed, 1 pooled it
0.7field-weighted citation impact, top 24% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 1 synthesis or guideline pooled it, 5 citations in OpenAlex.

  1. Pooled it
  2. Article
  3. Article
  4. Article
  5. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors at 3 institutions in 2 countries.

Qiliang DingTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.ORCID http://orcid.org/0000-0003-1771-2891
Cherith SomervilleTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Roozbeh ManshaeiTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Brett TrostThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Miriam S ReuterThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Kelsey KalbfleischTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Kaitlin StanleyTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
John B A OkelloTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
S Mohsen HosseiniTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Eriskay ListonTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Meredith CurtisTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
Mehdi ZarreiThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Edward J HigginbothamThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Ada J S ChanThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Worrawat EngchuanThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Bhooma ThiruvahindrapuramThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Stephen W SchererThe Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.
Raymond H KimTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada. raymond.kim@sickkids.ca.
Rebekah K JoblingTed Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada. rebekah.jobling@sickkids.ca.
Hospital for Sick Children · CAUniversity of Toronto · CAThe University of Texas MD Anderson Cancer Center · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

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 ).

Indexed as

Autism Spectrum DisorderDNA Copy Number VariationsHumansRare DiseasesSoftwareWhole Genome Sequencing

Identifiers

PMID36376761
PMCPMC9918589
OpenAlexW4308989302

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.