Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients
Аутори
Prosenc-Zmrzljak, UrsulaKosir, Rok
Krivokapić, Zoran
Radojković, Dragica
Nikolić, Aleksandra
Чланак у часопису (Објављена верзија)
Метаподаци
Приказ свих података о документуАпстракт
Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups-patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/mu L, 5.17 ng/mu L, and 0.29 ng/mu L for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations wa...s 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management.
Кључне речи:
somatic mutations / liquid biopsy / KRAS / hemorrhoids / ddPCR / colorectal cancer / cell-free DNA / BRAFИзвор:
Genes, 2021, 12, 2Издавач:
- MDPI, Basel
Финансирање / пројекти:
- ddPCR Grant challenge initiative from Labena Ltd., Verovskova, Ljubljana, Slovenia
- COST Action [CA17118 TransColonCan]
- Улога преоперативног одређивања стадијума болести, прогностичких, терапијских маркера, објективизирање функционалних резултата у одлуци о стратегији лечења карцинома ректума, а у циљу унапређења онколошких резултата и квалитета живота (RS-MESTD-Integrated and Interdisciplinary Research (IIR or III)-41033)
- Комплексне болести као модел систем за проучавање модулације фенотипа-структурна и функционална анализа молекуларних биомаркера (RS-MESTD-Basic Research (BR or ON)-173008)
DOI: 10.3390/genes12020289
ISSN: 2073-4425
PubMed: 33669856
WoS: 000622592300001
Scopus: 2-s2.0-85101875555
Колекције
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - JOUR AU - Prosenc-Zmrzljak, Ursula AU - Kosir, Rok AU - Krivokapić, Zoran AU - Radojković, Dragica AU - Nikolić, Aleksandra PY - 2021 UR - https://imagine.imgge.bg.ac.rs/handle/123456789/1494 AB - Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups-patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/mu L, 5.17 ng/mu L, and 0.29 ng/mu L for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations was 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management. PB - MDPI, Basel T2 - Genes T1 - Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients IS - 2 VL - 12 DO - 10.3390/genes12020289 ER -
@article{ author = "Prosenc-Zmrzljak, Ursula and Kosir, Rok and Krivokapić, Zoran and Radojković, Dragica and Nikolić, Aleksandra", year = "2021", abstract = "Liquid biopsy and cell-free DNA (cfDNA) show great promise in cancer diagnostics. In this study, we designed a custom droplet digital PCR (ddPCR) assay for the quantification and quality control of cfDNA isolated from serum. The assay was validated on a group of locally advanced colorectal cancer (CRC) patients and two control groups-patients with hemorrhoids and healthy individuals. The assay shows a high correlation with Qubit measurement (r = 0.976) but offers a higher dynamic range. Mean concentrations of cfDNA were 12.36 ng/mu L, 5.17 ng/mu L, and 0.29 ng/mu L for CRC, hemorrhoid patients, and healthy controls, respectively. The quality of cfDNA was assessed with the measurement of B-cell DNA contamination. On a subset of CRC patients, we compared the mutation status on KRAS (G12A, G12D, G12V, G13D) and BRAF (V600E) genes in the primary tumor and cfDNA isolated from the serum. A total of 70.6% of primary tumor samples were mutated, and the mean fractional abundance of mutations was 9.50%. The matching serum samples were mutated in 38% cases with an average fractional abundance of 0.23%. We conclude that any decisions based solely on the amount of cfDNA present in patient serum must be interpreted carefully and in the context of co-morbidities. This study explores the potential of ddPCR somatic mutations detection from liquid biopsy as a supplement to tissue biopsy in targeted personalized CRC patient management.", publisher = "MDPI, Basel", journal = "Genes", title = "Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients", number = "2", volume = "12", doi = "10.3390/genes12020289" }
Prosenc-Zmrzljak, U., Kosir, R., Krivokapić, Z., Radojković, D.,& Nikolić, A.. (2021). Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients. in Genes MDPI, Basel., 12(2). https://doi.org/10.3390/genes12020289
Prosenc-Zmrzljak U, Kosir R, Krivokapić Z, Radojković D, Nikolić A. Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients. in Genes. 2021;12(2). doi:10.3390/genes12020289 .
Prosenc-Zmrzljak, Ursula, Kosir, Rok, Krivokapić, Zoran, Radojković, Dragica, Nikolić, Aleksandra, "Detection of Somatic Mutations with ddPCR from Liquid Biopsy of Colorectal Cancer Patients" in Genes, 12, no. 2 (2021), https://doi.org/10.3390/genes12020289 . .