A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodes
<p>Abstract</p> <p>Background</p> <p>An increasing number of studies show that genetic markers can aid in refining prognostic information and predicting the benefit from systemic therapy. Our goal was to develop a high throughput, cost-effective and simple methodology f...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-03-01
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| Series: | BMC Cancer |
| Online Access: | http://www.biomedcentral.com/1471-2407/10/101 |
| _version_ | 1818063846213943296 |
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| author | Paik Soonmyung Choi Hyun-Joo Kim Seung-Il Taniyama Yusuke Gavin Patrick G Fumagalli Debora Pogue-Geile Katherine L |
| author_facet | Paik Soonmyung Choi Hyun-Joo Kim Seung-Il Taniyama Yusuke Gavin Patrick G Fumagalli Debora Pogue-Geile Katherine L |
| author_sort | Paik Soonmyung |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>An increasing number of studies show that genetic markers can aid in refining prognostic information and predicting the benefit from systemic therapy. Our goal was to develop a high throughput, cost-effective and simple methodology for the detection of clinically relevant hot spot mutations in colon cancer.</p> <p>Methods</p> <p>The Maldi-Tof mass spectrometry platform and OncoCarta panel from Sequenom were used to profile 239 colon cancers and 39 metastatic lymph nodes from NSABP clinical trial C-07 utilizing routinely processed FFPET (formalin-fixed paraffin-embedded tissue).</p> <p>Results</p> <p>Among the 238 common hot-spot cancer mutations in 19 genes interrogated by the OncoCarta panel, mutations were detected in 7 different genes at 26 different nucleotide positions in our colon cancer samples. Twenty-four assays that detected mutations in more than 1% of the samples were reconfigured into a new multiplexed panel, termed here as ColoCarta. Mutation profiling was repeated on 32 mutant samples using ColoCarta and the results were identical to results with OncoCarta, demonstrating that this methodology was reproducible. Further evidence demonstrating the validity of the data was the fact that the mutation frequencies of the most common colon cancer mutations were similar to the COSMIC (Catalog of Somatic Mutations in Cancer) database. The frequencies were 43.5% for <it>KRAS</it>, 20.1% for <it>PIK3CA</it>, and 12.1% for <it>BRAF</it>. In addition, infrequent mutations in <it>NRAS</it>, <it>AKT1</it>, <it>ABL1</it>, and <it>MET </it>were detected. Mutation profiling of metastatic lymph nodes and their corresponding primary tumors showed that they were 89.7% concordant. All mutations found in the lymph nodes were also found in the corresponding primary tumors, but in 4 cases a mutation was present in the primary tumor only.</p> <p>Conclusions</p> <p>This study describes a high throughput technology that can be used to interrogate DNAs isolated from routinely processed FFPET and identifies the specific mutations that are common to colon cancer. The development of this technology and the ColoCarta panel may provide a mechanism for rapid screening of mutations in clinically relevant genes like <it>KRAS</it>, <it>PIK3CA</it>, and <it>BRAF</it>.</p> <p>Trial Registration</p> <p><b>ClinicalTrials.gov: </b>NSABP C-07: NCT00004931</p> |
| first_indexed | 2024-12-10T14:26:35Z |
| format | Article |
| id | doaj.art-cd462b553e52407281462446a012bfc9 |
| institution | Directory Open Access Journal |
| issn | 1471-2407 |
| language | English |
| last_indexed | 2024-12-10T14:26:35Z |
| publishDate | 2010-03-01 |
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| series | BMC Cancer |
| spelling | doaj.art-cd462b553e52407281462446a012bfc92022-12-22T01:45:04ZengBMCBMC Cancer1471-24072010-03-0110110110.1186/1471-2407-10-101A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodesPaik SoonmyungChoi Hyun-JooKim Seung-IlTaniyama YusukeGavin Patrick GFumagalli DeboraPogue-Geile Katherine L<p>Abstract</p> <p>Background</p> <p>An increasing number of studies show that genetic markers can aid in refining prognostic information and predicting the benefit from systemic therapy. Our goal was to develop a high throughput, cost-effective and simple methodology for the detection of clinically relevant hot spot mutations in colon cancer.</p> <p>Methods</p> <p>The Maldi-Tof mass spectrometry platform and OncoCarta panel from Sequenom were used to profile 239 colon cancers and 39 metastatic lymph nodes from NSABP clinical trial C-07 utilizing routinely processed FFPET (formalin-fixed paraffin-embedded tissue).</p> <p>Results</p> <p>Among the 238 common hot-spot cancer mutations in 19 genes interrogated by the OncoCarta panel, mutations were detected in 7 different genes at 26 different nucleotide positions in our colon cancer samples. Twenty-four assays that detected mutations in more than 1% of the samples were reconfigured into a new multiplexed panel, termed here as ColoCarta. Mutation profiling was repeated on 32 mutant samples using ColoCarta and the results were identical to results with OncoCarta, demonstrating that this methodology was reproducible. Further evidence demonstrating the validity of the data was the fact that the mutation frequencies of the most common colon cancer mutations were similar to the COSMIC (Catalog of Somatic Mutations in Cancer) database. The frequencies were 43.5% for <it>KRAS</it>, 20.1% for <it>PIK3CA</it>, and 12.1% for <it>BRAF</it>. In addition, infrequent mutations in <it>NRAS</it>, <it>AKT1</it>, <it>ABL1</it>, and <it>MET </it>were detected. Mutation profiling of metastatic lymph nodes and their corresponding primary tumors showed that they were 89.7% concordant. All mutations found in the lymph nodes were also found in the corresponding primary tumors, but in 4 cases a mutation was present in the primary tumor only.</p> <p>Conclusions</p> <p>This study describes a high throughput technology that can be used to interrogate DNAs isolated from routinely processed FFPET and identifies the specific mutations that are common to colon cancer. The development of this technology and the ColoCarta panel may provide a mechanism for rapid screening of mutations in clinically relevant genes like <it>KRAS</it>, <it>PIK3CA</it>, and <it>BRAF</it>.</p> <p>Trial Registration</p> <p><b>ClinicalTrials.gov: </b>NSABP C-07: NCT00004931</p>http://www.biomedcentral.com/1471-2407/10/101 |
| spellingShingle | Paik Soonmyung Choi Hyun-Joo Kim Seung-Il Taniyama Yusuke Gavin Patrick G Fumagalli Debora Pogue-Geile Katherine L A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodes BMC Cancer |
| title | A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodes |
| title_full | A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodes |
| title_fullStr | A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodes |
| title_full_unstemmed | A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodes |
| title_short | A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodes |
| title_sort | rapid sensitive reproducible and cost effective method for mutation profiling of colon cancer and metastatic lymph nodes |
| url | http://www.biomedcentral.com/1471-2407/10/101 |
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