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 diagno...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
University of Sarajevo, Institute for Genetic Engineering and Biotechnology
2019-06-01
|
| Series: | Genetics & Applications |
| Subjects: | |
| Online Access: | https://genapp.ba/editions/index.php/journal/article/view/59 |
| _version_ | 1811299056898539520 |
|---|---|
| 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 each of these
aspects. Ion AmpliSeq™ Colon and Lung Cancer Research Panel v2, which was
used in this study, allows detection of hotspot mutations in 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 tool for mutations that
were detected with NGS. It has high sensitivity and enables accurate detection of
a mutant allele against a background of abundant wild type alleles. For this study
35 samples of CRC and NSCLC were sequenced and selected samples were
analysed with ddPCR for KRAS, NRAS, EGFR and BRAF genes. All the
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 were reported as wild type but were still tested with
ddPCR as controls. In three samples low frequency somatic mutations were
detected with NGS and mutation frequencies were verified using ddPCR.
|
| first_indexed | 2024-04-13T06:29:32Z |
| format | Article |
| id | doaj.art-e6fa04fc3eae45acb98c9530299b131e |
| institution | Directory Open Access Journal |
| issn | 2566-2937 2566-431X |
| language | English |
| last_indexed | 2024-04-13T06:29:32Z |
| publishDate | 2019-06-01 |
| publisher | University of Sarajevo, Institute for Genetic Engineering and Biotechnology |
| record_format | Article |
| series | Genetics & Applications |
| spelling | doaj.art-e6fa04fc3eae45acb98c9530299b131e2022-12-22T02:58:14ZengUniversity of Sarajevo, Institute for Genetic Engineering and BiotechnologyGenetics & Applications2566-29372566-431X2019-06-0131Validation 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 Herzegovina 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 each of these aspects. Ion AmpliSeq™ Colon and Lung Cancer Research Panel v2, which was used in this study, allows detection of hotspot mutations in 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 tool for mutations that were detected with NGS. It has high sensitivity and enables accurate detection of a mutant allele against a background of abundant wild type alleles. For this study 35 samples of CRC and NSCLC were sequenced and selected samples were analysed with ddPCR for KRAS, NRAS, EGFR and BRAF genes. All the 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 were reported as wild type but were still tested with ddPCR as controls. In three samples low frequency somatic mutations were detected with NGS and mutation frequencies were verified using ddPCR. https://genapp.ba/editions/index.php/journal/article/view/59NGSddPCRcolorectal cancernonsmall cell lung cancermolecular oncology |
| spellingShingle | Lana Salihefendić Dino Pećar Rijad Konjhodžić Validation of CRC and NSCLC somatic mutations detected by NGS using ddPCR Genetics & Applications NGS ddPCR colorectal cancer nonsmall cell lung cancer molecular oncology |
| 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 |
| topic | NGS ddPCR colorectal cancer nonsmall cell lung cancer molecular oncology |
| url | https://genapp.ba/editions/index.php/journal/article/view/59 |
| work_keys_str_mv | AT lanasalihefendic validationofcrcandnsclcsomaticmutationsdetectedbyngsusingddpcr AT dinopecar validationofcrcandnsclcsomaticmutationsdetectedbyngsusingddpcr AT rijadkonjhodzic validationofcrcandnsclcsomaticmutationsdetectedbyngsusingddpcr |