Detection of somatic mutations in tumors using unaligned clonal sequencing data
Most cancers arise and evolve as a consequence of somatic mutations. These mutations influence tumor behavior and clinical outcome. Consequently, there is considerable interest in identifying somatic variants within specific genes (such as BRAF , KRAS and EGFR ) so that chemotherapy can be tailored...
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| Published in | Laboratory investigation Vol. 94; no. 10; pp. 1173 - 1183 |
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| Main Authors | , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.10.2014
Nature Publishing Group |
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| Abstract | Most cancers arise and evolve as a consequence of somatic mutations. These mutations influence tumor behavior and clinical outcome. Consequently, there is considerable interest in identifying somatic variants within specific genes (such as
BRAF
,
KRAS
and
EGFR
) so that chemotherapy can be tailored to the patient’s tumor genotype rather than using a generic treatment based on histological diagnosis alone. Owing to the heterogeneous nature of tumors, a somatic mutation may be present in only a subset of cells, necessitating the use of quantitative techniques to detect rare variants. The highly quantitative nature of next-generation sequencing (NGS), together with the ability to multiplex numerous samples, makes NGS an attractive choice with which to screen for somatic variants. However, the large volumes of sequence data present significant difficulties when applying NGS for the detection of somatic mutations. To alleviate this, we have developed methodologies including a set of data analysis programs, which allow the rapid screening of multiple formalin-fixed, paraffin-embedded samples for the presence of specified somatic variants using unaligned Illumina NGS data. |
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| AbstractList | Most cancers arise and evolve as a consequence of somatic mutations. These mutations influence tumor behavior and clinical outcome. Consequently, there is considerable interest in identifying somatic variants within specific genes (such as BRAF, KRAS and EGFR) so that chemotherapy can be tailored to the patient's tumor genotype rather than using a generic treatment based on histological diagnosis alone. Owing to the heterogeneous nature of tumors, a somatic mutation may be present in only a subset of cells, necessitating the use of quantitative techniques to detect rare variants. The highly quantitative nature of next-generation sequencing (NGS), together with the ability to multiplex numerous samples, makes NGS an attractive choice with which to screen for somatic variants. However, the large volumes of sequence data present significant difficulties when applying NGS for the detection of somatic mutations. To alleviate this, we have developed methodologies including a set of data analysis programs, which allow the rapid screening of multiple formalin-fixed, paraffin-embedded samples for the presence of specified somatic variants using unaligned Illumina NGS data. Most cancers arise and evolve as a consequence of somatic mutations. These mutations influence tumor behavior and clinical outcome. Consequently, there is considerable interest in identifying somatic variants within specific genes (such as BRAF , KRAS and EGFR ) so that chemotherapy can be tailored to the patient’s tumor genotype rather than using a generic treatment based on histological diagnosis alone. Owing to the heterogeneous nature of tumors, a somatic mutation may be present in only a subset of cells, necessitating the use of quantitative techniques to detect rare variants. The highly quantitative nature of next-generation sequencing (NGS), together with the ability to multiplex numerous samples, makes NGS an attractive choice with which to screen for somatic variants. However, the large volumes of sequence data present significant difficulties when applying NGS for the detection of somatic mutations. To alleviate this, we have developed methodologies including a set of data analysis programs, which allow the rapid screening of multiple formalin-fixed, paraffin-embedded samples for the presence of specified somatic variants using unaligned Illumina NGS data. |
| Author | Quirke, Philip Sutton, Kate M Watson, Christopher M Wallace, David Crinnion, Laura A Roberts, Paul Markham, Alexander F Carr, Ian M Harrison, Sally Bonthron, David T |
| Author_xml | – sequence: 1 givenname: Kate M surname: Sutton fullname: Sutton, Kate M organization: Section of Pathology and Tumour Biology, Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital – sequence: 2 givenname: Laura A surname: Crinnion fullname: Crinnion, Laura A organization: Yorkshire Regional Genetics Service, St James’s University Hospital – sequence: 3 givenname: David surname: Wallace fullname: Wallace, David organization: Yorkshire Regional Genetics Service, St James’s University Hospital – sequence: 4 givenname: Sally surname: Harrison fullname: Harrison, Sally organization: Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James’s University Hospital – sequence: 5 givenname: Paul surname: Roberts fullname: Roberts, Paul organization: Yorkshire Regional Genetics Service, St James’s University Hospital – sequence: 6 givenname: Christopher M orcidid: 0000-0003-2371-1844 surname: Watson fullname: Watson, Christopher M organization: Yorkshire Regional Genetics Service, St James’s University Hospital – sequence: 7 givenname: Alexander F surname: Markham fullname: Markham, Alexander F organization: Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James’s University Hospital – sequence: 8 givenname: David T surname: Bonthron fullname: Bonthron, David T organization: Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James’s University Hospital – sequence: 9 givenname: Philip surname: Quirke fullname: Quirke, Philip organization: Section of Pathology and Tumour Biology, Institute of Cancer and Pathology, University of Leeds, St James’s University Hospital – sequence: 10 givenname: Ian M surname: Carr fullname: Carr, Ian M email: I.M.Carr@leeds.ac.uk organization: Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James’s University Hospital |
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| Cites_doi | 10.1016/S0002-9440(10)65461-2 10.1093/bioinformatics/btq214 10.1038/nature00766 10.1002/humu.22439 10.1186/1476-4598-8-82 10.1186/1471-2164-14-S8-S4 10.1093/nar/gkr861 10.1038/nmeth.1419 10.1038/bjc.2011.250 10.1101/gr.129684.111 10.1038/nrd3360 10.1101/gr.109157.110 10.1186/1472-6890-4-1 10.1038/nbt1486 10.1186/1471-2164-15-63 10.1002/humu.22207 10.1136/jmg.2010.082081 10.1101/gad.190678.112 10.1093/bioinformatics/btr295 10.1186/1471-2164-14-530 10.1093/bioinformatics/btp324 10.1038/459146b 10.1016/S0002-9440(10)64472-0 10.1093/bioinformatics/btp352 10.1093/nar/gkr599 10.1016/S0065-3101(24)00153-1 |
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| Copyright | United States & Canadian Academy of Pathology 2014 Copyright Nature Publishing Group Oct 2014 |
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| Title | Detection of somatic mutations in tumors using unaligned clonal sequencing data |
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