Detection of copy-number variations from NGS data using read depth information: a diagnostic performance evaluation.
Journal
European journal of human genetics : EJHG
ISSN: 1476-5438
Titre abrégé: Eur J Hum Genet
Pays: England
ID NLM: 9302235
Informations de publication
Date de publication:
01 2021
01 2021
Historique:
received:
22
11
2019
accepted:
09
06
2020
revised:
20
05
2020
pubmed:
28
6
2020
medline:
17
8
2021
entrez:
28
6
2020
Statut:
ppublish
Résumé
The detection of copy-number variations (CNVs) from NGS data is underexploited as chip-based or targeted techniques are still commonly used. We assessed the performances of a workflow centered on CANOES, a bioinformatics tool based on read depth information. We applied our workflow to gene panel (GP) and whole-exome sequencing (WES) data, and compared CNV calls to quantitative multiplex PCR of short fluorescent fragments (QMSPF) or array comparative genomic hybridization (aCGH) results. From GP data of 3776 samples, we reached an overall positive predictive value (PPV) of 87.8%. This dataset included a complete comprehensive QMPSF comparison of four genes (60 exons) on which we obtained 100% sensitivity and specificity. From WES data, we first compared 137 samples with aCGH and filtered comparable events (exonic CNVs encompassing enough aCGH probes) and obtained an 87.25% sensitivity. The overall PPV was 86.4% following the targeted confirmation of candidate CNVs from 1056 additional WES. In addition, our CANOES-centered workflow on WES data allowed the detection of CNVs with a resolution of single exons, allowing the detection of CNVs that were missed by aCGH. Overall, switching to an NGS-only approach should be cost-effective as it allows a reduction in overall costs together with likely stable diagnostic yields. Our bioinformatics pipeline is available at: https://gitlab.bioinfo-diag.fr/nc4gpm/canoes-centered-workflow .
Identifiants
pubmed: 32591635
doi: 10.1038/s41431-020-0672-2
pii: 10.1038/s41431-020-0672-2
pmc: PMC7852510
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
99-109Investigateurs
Emmanuelle Génin
(E)
Dominique Campion
(D)
Jean-François Dartigues
(JF)
Jean-François Deleuze
(JF)
Jean-Charles Lambert
(JC)
Richard Redon
(R)
Thomas Ludwig
(T)
Benjamin Grenier-Boley
(B)
Sébastien Letort
(S)
Pierre Lindenbaum
(P)
Vincent Meyer
(V)
Olivier Quenez
(O)
Christian Dina
(C)
Céline Bellenguez
(C)
Camille Charbonnier
(C)
Joanna Giemza
(J)
Stéphanie Chatel
(S)
Claude Férec
(C)
Hervé Le Marec
(H)
Luc Letenneur
(L)
Gaël Nicolas
(G)
Karen Rouault
(K)
Delphine Bacq
(D)
Anne Boland
(A)
Doris Lechner
(D)
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