Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads
| Main Author: | |
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| Publication Date: | 2024 |
| Other Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Article |
| Language: | eng |
| Source: | Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) |
| Download full: | http://hdl.handle.net/10362/166083 |
Summary: | Publisher Copyright: © 2024 The Author(s) |
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Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing readsGeneticsGenetics(clinical)SDG 3 - Good Health and Well-beingPublisher Copyright: © 2024 The Author(s)Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of “off-target” DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM)RUNQuinodoz, MathieuKaminska, KarolinaCancellieri, FrancescaHan, Ji HoonPeter, Virginie G.Celik, ElifnazJaneschitz-Kriegl, LucasSchärer, NilsHauenstein, DanielaGyörgy, BenceCalzetti, GiacomoHahaut, VincentCustódio, SóniaSousa, Ana CristinaWada, YukoMurakami, YusukeFernández, Almudena AvilaHernández, Cristina RodillaMinguez, PabloAyuso, CarmenNishiguchi, Koji M.Santos, CristinaSantos, Luisa CoutinhoTran, Viet H.Vaclavik, VeronikaScholl, Hendrik P.N.Rivolta, Carlo2024-04-11T00:36:27Z2024-04-042024-04-04T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article13application/pdfhttp://hdl.handle.net/10362/166083eng0002-9297PURE: 87219251https://doi.org/10.1016/j.ajhg.2024.03.001info:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2024-05-22T18:20:23Zoai:run.unl.pt:10362/166083Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-28T17:51:04.965698Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse |
| dc.title.none.fl_str_mv |
Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads |
| title |
Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads |
| spellingShingle |
Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads Quinodoz, Mathieu Genetics Genetics(clinical) SDG 3 - Good Health and Well-being |
| title_short |
Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads |
| title_full |
Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads |
| title_fullStr |
Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads |
| title_full_unstemmed |
Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads |
| title_sort |
Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads |
| author |
Quinodoz, Mathieu |
| author_facet |
Quinodoz, Mathieu Kaminska, Karolina Cancellieri, Francesca Han, Ji Hoon Peter, Virginie G. Celik, Elifnaz Janeschitz-Kriegl, Lucas Schärer, Nils Hauenstein, Daniela György, Bence Calzetti, Giacomo Hahaut, Vincent Custódio, Sónia Sousa, Ana Cristina Wada, Yuko Murakami, Yusuke Fernández, Almudena Avila Hernández, Cristina Rodilla Minguez, Pablo Ayuso, Carmen Nishiguchi, Koji M. Santos, Cristina Santos, Luisa Coutinho Tran, Viet H. Vaclavik, Veronika Scholl, Hendrik P.N. Rivolta, Carlo |
| author_role |
author |
| author2 |
Kaminska, Karolina Cancellieri, Francesca Han, Ji Hoon Peter, Virginie G. Celik, Elifnaz Janeschitz-Kriegl, Lucas Schärer, Nils Hauenstein, Daniela György, Bence Calzetti, Giacomo Hahaut, Vincent Custódio, Sónia Sousa, Ana Cristina Wada, Yuko Murakami, Yusuke Fernández, Almudena Avila Hernández, Cristina Rodilla Minguez, Pablo Ayuso, Carmen Nishiguchi, Koji M. Santos, Cristina Santos, Luisa Coutinho Tran, Viet H. Vaclavik, Veronika Scholl, Hendrik P.N. Rivolta, Carlo |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM) RUN |
| dc.contributor.author.fl_str_mv |
Quinodoz, Mathieu Kaminska, Karolina Cancellieri, Francesca Han, Ji Hoon Peter, Virginie G. Celik, Elifnaz Janeschitz-Kriegl, Lucas Schärer, Nils Hauenstein, Daniela György, Bence Calzetti, Giacomo Hahaut, Vincent Custódio, Sónia Sousa, Ana Cristina Wada, Yuko Murakami, Yusuke Fernández, Almudena Avila Hernández, Cristina Rodilla Minguez, Pablo Ayuso, Carmen Nishiguchi, Koji M. Santos, Cristina Santos, Luisa Coutinho Tran, Viet H. Vaclavik, Veronika Scholl, Hendrik P.N. Rivolta, Carlo |
| dc.subject.por.fl_str_mv |
Genetics Genetics(clinical) SDG 3 - Good Health and Well-being |
| topic |
Genetics Genetics(clinical) SDG 3 - Good Health and Well-being |
| description |
Publisher Copyright: © 2024 The Author(s) |
| publishDate |
2024 |
| dc.date.none.fl_str_mv |
2024-04-11T00:36:27Z 2024-04-04 2024-04-04T00:00:00Z |
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info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
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article |
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publishedVersion |
| dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10362/166083 |
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http://hdl.handle.net/10362/166083 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
0002-9297 PURE: 87219251 https://doi.org/10.1016/j.ajhg.2024.03.001 |
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info:eu-repo/semantics/openAccess |
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openAccess |
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13 application/pdf |
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