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2015-12-09

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cc-by (c) Alioto, Tyler et al., 2015
Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/120214

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

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https://doi.org/10.1038/ncomms10001

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As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.

Matèries

Genètica humana, Mutació (Biologia), Càncer, Genètica mèdica

Matèries (anglès)

Human genetics, Mutation (Biology), Cancer, Medical genetics

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Articles publicats en revistes (Fonaments Clínics)
Articles publicats en revistes (IDIBAPS: Institut d'investigacions Biomèdiques August Pi i Sunyer)

Citació

ALIOTO, Tyler s., BUCHHALTER, Ivo, DERDAK, Sophia, HUTTER, Barbara, ELDRIDGE, Matthew d., HOVIG, Eivind, HEISLER, Lawrence e., BECK, Timothy a., SIMPSON, Jared t., TONON, Laurie, SERTIER, Anne-sophie, PATCH, Ann-marie, JÄGER, Natalie, GINSBACH, Philip, DREWS, Ruben, PARAMASIVAM, Nagarajan, KABBE, Rolf, CHOTEWUTMONTRI, Sasithorn, DIESSL, Nicolle, PREVITI, Christopher, SCHMIDT, Sabine, BRORS, Benedikt, FEUERBACH, Lars, HEINOLD, Michael, GRÖBNER, Susanne, KORSHUNOV, Andrey, TARPEY, Patrick, BUTLER, Adam p., HINTON, Jonathan, JONES, David t.w., MENZIES, Andrew, RAINE, Keiran, SHEPHERD, Rebecca, STEBBINGS, Lucy, TEAGUE, John w., RIBECA, Paolo, CASTRO GINER, Francesc, BELTRAN I AGULLÓ, Sergi, RAINERI, Emanuele, DABAD, Marc, HEATH, Simon c., GUT, Marta, DENROCHE, Robert e., HARDING, Nicholas j., YAMAGUCHI, Takafumi n., NAKAGAWA, Hidewaki, QUESADA, Victor, VALDÉS MAS, Rafael, NAKKEN, Sigve, VODÁK, Daniel, BOWER, Lawrence, LYNCH, Andrew g., ANDERSON, Charlotte l., WADDELL, Nicola, PEARSON, John v., GRIMMOND, Sean m., PETO, Myron, SPELLMAN, Paul, HE, Minghui, KANDOTH, Cyriac, LEE, Semin, ZHANG, John, LÉTOURNEAU, Louis, MA, Singer, SETH, Sahil, TORRENTS ARENALES, David, XI, Liu, WHEELER, David a., LÓPEZ-OTIN, Carlos, CAMPO GÜERRI, Elias, CAMPBELL, Peter j., BOUTROS, Paul c., PUENTE, Xose s., GERHARD, Daniela s., PFISTER, Stefan m., MCPHERSON, John d., HUDSON, Thomas j., SCHLESNER, Matthias, LICHTER, Peter, EILS, Roland, JONES, David t.w., GUT, Ivo g.. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.. _Nature Communications_. 2015. Vol. 6, núm. 10001. [consulta: 24 de gener de 2026]. ISSN: 2041-1723. [Disponible a: https://hdl.handle.net/2445/120214]

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