Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCR
Next Generation Sequencing (NGS) has become powerful tool in molecular oncology. It allows multiparallel targeted sequencing that enables comprehensive assessment of tumor heterogeneity. Detection of mutations in colorectal cancer (CRC) and non-small cell lung cancer (NSCLC) defines patients diagnos...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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University of Sarajevo, Institute for Genetic Engineering and Biotechnology
2019-06-01
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| Series: | Genetics & Applications |
| Online Access: | http://www.genapp.ba/index.php/genapp/article/view/90 |
| _version_ | 1818141132643631104 |
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| author | Lana Salihefendić Dino Pećar Rijad Konjhodžić |
| author_facet | Lana Salihefendić Dino Pećar Rijad Konjhodžić |
| author_sort | Lana Salihefendić |
| collection | DOAJ |
| description | Next Generation Sequencing (NGS) has become powerful tool in molecular oncology. It allows multiparallel targeted sequencing that enables comprehensive assessment of tumor heterogeneity. Detection of mutations in colorectal cancer (CRC) and non-small cell lung cancer (NSCLC) defines patients diagnosis, therapy and prognosis. Multiple genes, their somatic mutations to be precise, carry different degrees of importance for any of these stages. Ion AmpliSeq™ Colon and Lung Cancer Research Panel v2, which was used in this study, allows detection of hotspot mutations on 22 genes in a single reaction. Droplet digital PCR (ddPCR) has a unique advantage in low frequency mutation detection and it has been used as a validation method for mutations that were detected with NGS. It has high sensitivity and enables accurate detection of mutant allele in a background of abundant wild type alleles. For this study 35 samples of CRC and NSCLC were sequenced and same samples were analysed on ddPCR for KRAS, NRAS, EGFR and BRAF genes. All processed samples were successfully sequenced and had average base coverage >500X. NGS sequencing proved itself to be cost effective, has shorter turnaround time and is highly sensitive. Out of 35 samples, 25 had genetic alterations, while 10 samples are reported as wild type but were still tested on ddPCR as controls. In three samples low frequency somatic mutations were detected by NGS and verified using ddPCR, which leads us to conclusion that ddPCR is a good tool for verification of somatic mutations in CRC and NSCLC. |
| first_indexed | 2024-12-11T10:55:01Z |
| format | Article |
| id | doaj.art-8db1289fa7a44036ba263ba4440206ff |
| institution | Directory Open Access Journal |
| issn | 2566-2937 2566-431X |
| language | English |
| last_indexed | 2024-12-11T10:55:01Z |
| publishDate | 2019-06-01 |
| publisher | University of Sarajevo, Institute for Genetic Engineering and Biotechnology |
| record_format | Article |
| series | Genetics & Applications |
| spelling | doaj.art-8db1289fa7a44036ba263ba4440206ff2022-12-22T01:10:07ZengUniversity of Sarajevo, Institute for Genetic Engineering and BiotechnologyGenetics & Applications2566-29372566-431X2019-06-0131717610.31383/ga.vol3iss1pp71-7690Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCRLana Salihefendić0Dino Pećar1Rijad Konjhodžić2ALEA Genetic Center, Sarajevo, Bosnia and HerzegovinaALEA Genetic Center, Sarajevo, Bosnia and HerzegovinaALEA Genetic Center, Sarajevo, Bosnia and HerzegovinaNext Generation Sequencing (NGS) has become powerful tool in molecular oncology. It allows multiparallel targeted sequencing that enables comprehensive assessment of tumor heterogeneity. Detection of mutations in colorectal cancer (CRC) and non-small cell lung cancer (NSCLC) defines patients diagnosis, therapy and prognosis. Multiple genes, their somatic mutations to be precise, carry different degrees of importance for any of these stages. Ion AmpliSeq™ Colon and Lung Cancer Research Panel v2, which was used in this study, allows detection of hotspot mutations on 22 genes in a single reaction. Droplet digital PCR (ddPCR) has a unique advantage in low frequency mutation detection and it has been used as a validation method for mutations that were detected with NGS. It has high sensitivity and enables accurate detection of mutant allele in a background of abundant wild type alleles. For this study 35 samples of CRC and NSCLC were sequenced and same samples were analysed on ddPCR for KRAS, NRAS, EGFR and BRAF genes. All processed samples were successfully sequenced and had average base coverage >500X. NGS sequencing proved itself to be cost effective, has shorter turnaround time and is highly sensitive. Out of 35 samples, 25 had genetic alterations, while 10 samples are reported as wild type but were still tested on ddPCR as controls. In three samples low frequency somatic mutations were detected by NGS and verified using ddPCR, which leads us to conclusion that ddPCR is a good tool for verification of somatic mutations in CRC and NSCLC.http://www.genapp.ba/index.php/genapp/article/view/90 |
| spellingShingle | Lana Salihefendić Dino Pećar Rijad Konjhodžić Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCR Genetics & Applications |
| title | Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCR |
| title_full | Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCR |
| title_fullStr | Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCR |
| title_full_unstemmed | Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCR |
| title_short | Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCR |
| title_sort | validation of crc and nsclc somatic mutations detected by ngs using ddpcr |
| url | http://www.genapp.ba/index.php/genapp/article/view/90 |
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