Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel
Biomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. Discovery of novel variants in local population provides confident targets for developing biomarkers for personalized medicine. We identified the need to genera...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-06-01
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| Series: | Journal of Personalized Medicine |
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| Online Access: | https://www.mdpi.com/2075-4426/11/6/535 |
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| author | Bader Almuzzaini Jahad Alghamdi Alhanouf Alomani Saleh AlGhamdi Abdullah A. Alsharm Saeed Alshieban Ahood Sayed Abdulmohsen G. Alhejaily Feda S. Aljaser Manal Abudawood Faisal Almajed Abdulhadi Samman Mohammed A. Al Balwi Mohammad Azhar Aziz |
| author_facet | Bader Almuzzaini Jahad Alghamdi Alhanouf Alomani Saleh AlGhamdi Abdullah A. Alsharm Saeed Alshieban Ahood Sayed Abdulmohsen G. Alhejaily Feda S. Aljaser Manal Abudawood Faisal Almajed Abdulhadi Samman Mohammed A. Al Balwi Mohammad Azhar Aziz |
| author_sort | Bader Almuzzaini |
| collection | DOAJ |
| description | Biomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. Discovery of novel variants in local population provides confident targets for developing biomarkers for personalized medicine. We identified the need to generate high-quality sequencing data from local colorectal cancer patients and understand the pattern of occurrence of variants. In this report, we used archived samples from Saudi Arabia and used the AmpliSeq comprehensive cancer panel to identify novel somatic variants. We report a comprehensive analysis of next-generation sequencing results with a coverage of >300X. We identified 466 novel variants which were previously unreported in COSMIC and ICGC databases. We analyzed the genes associated with these variants in terms of their frequency of occurrence, probable pathogenicity, and clinicopathological features. Among pathogenic somatic variants, 174 were identified for the first time in the large intestine. APC, RET, and EGFR genes were most frequently mutated. A higher number of variants were identified in the left colon. Occurrence of variants in ERBB2 was significantly correlated with those of EGFR and ATR genes. Network analyses of the identified genes provide functional perspective of the identified genes and suggest affected pathways and probable biomarker candidates. This report lays the ground work for biomarker discovery and identification of driver gene mutations in local population. |
| first_indexed | 2024-03-10T10:33:12Z |
| format | Article |
| id | doaj.art-663f56499c8f4eb993eb78f3c36409ac |
| institution | Directory Open Access Journal |
| issn | 2075-4426 |
| language | English |
| last_indexed | 2024-03-10T10:33:12Z |
| publishDate | 2021-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Journal of Personalized Medicine |
| spelling | doaj.art-663f56499c8f4eb993eb78f3c36409ac2023-11-21T23:27:25ZengMDPI AGJournal of Personalized Medicine2075-44262021-06-0111653510.3390/jpm11060535Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer PanelBader Almuzzaini0Jahad Alghamdi1Alhanouf Alomani2Saleh AlGhamdi3Abdullah A. Alsharm4Saeed Alshieban5Ahood Sayed6Abdulmohsen G. Alhejaily7Feda S. Aljaser8Manal Abudawood9Faisal Almajed10Abdulhadi Samman11Mohammed A. Al Balwi12Mohammad Azhar Aziz13King Abdullah International Medical Research Center, Medical Genomics Research Department, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi ArabiaKing Abdullah International Medical Research Center, Saudi Biobank, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi ArabiaDepartment of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 13318, Saudi ArabiaClinical Research Department, Research Center, King Fahad Medical City, Riyadh 11564, Saudi ArabiaComprehensive Cancer Center, King Fahad Medical City, Riyadh 11564, Saudi ArabiaKing Abdul Aziz Medical City-National Guard Health Affairs (NGHA), King Abdullah International Medical Research Center, King Saud Bin Abdul Aziz University for Health Sciences (KSAU-HS), Riyadh 14611, Saudi ArabiaKing Abdullah International Medical Research Center, Saudi Biobank, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi ArabiaFaculty of Medicine, King Fahad Medical City, Riyadh 11564, Saudi ArabiaDepartment of Clinical Laboratory Sciences, Chair of Medical and Molecular Genetics Research, College of Applied Medical Sciences, King Saud University Riyadh, Riyadh 11564, Saudi ArabiaDepartment of Clinical Laboratory Sciences, Chair of Medical and Molecular Genetics Research, College of Applied Medical Sciences, King Saud University Riyadh, Riyadh 11564, Saudi ArabiaDepartment of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11481, Saudi ArabiaDepartment of Pathology, Faculty of Medicine, University of Jeddah, Jeddah 23218, Saudi ArabiaKing Abdullah International Medical Research Center, Medical Genomics Research Department, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi ArabiaKing Abdullah International Medical Research Center, Colorectal Cancer Research Program, Department of Cellular Therapy and Cancer Research, Ministry of National Guard Health Affairs, King Saud Bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi ArabiaBiomarker discovery would be an important tool in advancing and utilizing the concept of precision and personalized medicine in the clinic. Discovery of novel variants in local population provides confident targets for developing biomarkers for personalized medicine. We identified the need to generate high-quality sequencing data from local colorectal cancer patients and understand the pattern of occurrence of variants. In this report, we used archived samples from Saudi Arabia and used the AmpliSeq comprehensive cancer panel to identify novel somatic variants. We report a comprehensive analysis of next-generation sequencing results with a coverage of >300X. We identified 466 novel variants which were previously unreported in COSMIC and ICGC databases. We analyzed the genes associated with these variants in terms of their frequency of occurrence, probable pathogenicity, and clinicopathological features. Among pathogenic somatic variants, 174 were identified for the first time in the large intestine. APC, RET, and EGFR genes were most frequently mutated. A higher number of variants were identified in the left colon. Occurrence of variants in ERBB2 was significantly correlated with those of EGFR and ATR genes. Network analyses of the identified genes provide functional perspective of the identified genes and suggest affected pathways and probable biomarker candidates. This report lays the ground work for biomarker discovery and identification of driver gene mutations in local population.https://www.mdpi.com/2075-4426/11/6/535colorectal cancerpersonalized medicinebiomarkerAmpliSeq |
| spellingShingle | Bader Almuzzaini Jahad Alghamdi Alhanouf Alomani Saleh AlGhamdi Abdullah A. Alsharm Saeed Alshieban Ahood Sayed Abdulmohsen G. Alhejaily Feda S. Aljaser Manal Abudawood Faisal Almajed Abdulhadi Samman Mohammed A. Al Balwi Mohammad Azhar Aziz Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel Journal of Personalized Medicine colorectal cancer personalized medicine biomarker AmpliSeq |
| title | Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel |
| title_full | Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel |
| title_fullStr | Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel |
| title_full_unstemmed | Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel |
| title_short | Identification of Novel Mutations in Colorectal Cancer Patients Using AmpliSeq Comprehensive Cancer Panel |
| title_sort | identification of novel mutations in colorectal cancer patients using ampliseq comprehensive cancer panel |
| topic | colorectal cancer personalized medicine biomarker AmpliSeq |
| url | https://www.mdpi.com/2075-4426/11/6/535 |
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