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Mutation profiling of tumor DNA from plasma and tumor tissue of colorectal cancer patients with a novel, high-sensitivity multiplexed mutation detection platform.

Kidess E, Heirich K, Wiggin M, Vysotskaia V, Visser BC, Marziali A, Wiedenmann B, Norton JA, Lee M, Jeffrey SS, Poultsides GA - Oncotarget (2015)

Bottom Line: In CRC patient samples (n=38), detected mutations were concordant in tissue and plasma for 93% of metastatic patients versus 54% of non-metastatic patients.In patients undergoing liver metastatectomy, ctDNA anticipated tumor recurrence earlier than carcinoembryonic antigen (CEA) value or imaging.The multiplexed SCODA mutation enrichment and detection method can be applied to mutation profiling and quantitation of ctDNA, and is likely to have particular utility in the metastatic setting, including patients undergoing metastatectomy.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.

ABSTRACT

Background: Circulating tumor DNA (ctDNA) holds promise as a non-invasive means for tumor monitoring in solid malignancies. Assays with high sensitivity and multiplexed analysis of mutations are needed to enable broad application.

Methods: We developed a new assay based on sequence-specific synchronous coefficient of drag alteration (SCODA) technology, which enriches for mutant DNA to achieve high sensitivity and specificity. This assay was applied to plasma and tumor tissue from non-metastatic and metastatic colorectal cancer (CRC) patients, including patients undergoing surgical resection for CRC liver metastases.

Results: Across multiple characterization experiments, the assay demonstrated a limit of detection of 0.001% (1 molecule in 100,000) for the majority of the 46 mutations in the panel. In CRC patient samples (n=38), detected mutations were concordant in tissue and plasma for 93% of metastatic patients versus 54% of non-metastatic patients. For three patients, ctDNA identified additional mutations not detected in tumor tissue. In patients undergoing liver metastatectomy, ctDNA anticipated tumor recurrence earlier than carcinoembryonic antigen (CEA) value or imaging.

Conclusions: The multiplexed SCODA mutation enrichment and detection method can be applied to mutation profiling and quantitation of ctDNA, and is likely to have particular utility in the metastatic setting, including patients undergoing metastatectomy.

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Related in: MedlinePlus

Mutations detected in tissue and plasma with the multiplexed SCODA mutation enrichment and detection assayIn highlighted cells, the detected mutation allele (or alleles) is specified, and for plasma, the number of detected copies (cp) of mutant DNA is also provided, normalized for a 5 mL input volume of plasma. ND, not detected.
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Figure 2: Mutations detected in tissue and plasma with the multiplexed SCODA mutation enrichment and detection assayIn highlighted cells, the detected mutation allele (or alleles) is specified, and for plasma, the number of detected copies (cp) of mutant DNA is also provided, normalized for a 5 mL input volume of plasma. ND, not detected.

Mentions: The multiplexed SCODA mutation detection assay was used to analyze extracted DNA from patient tumor tissue and pre-operative plasma samples for the presence of mutations in KRAS, PIK3CA, BRAF and EGFR as defined in our panel (Table 1). In tumor tissue, 68% of the cohort (26 of 38 patients) showed at least one detectable mutation from the panel, including 14 of 19 (74%) patients with metastatic disease and 12 of 19 (63%) patients with non-metastatic disease. The distribution of observed mutations was consistent with prior reports (Figure 2): 50% (19 of 38 patients) had a KRAS mutant tumor, 16% (6 of 38 patients) had a PIK3CA mutation, 8% (3 of 38 patients) showed a mutation in BRAF, and none showed an EGFR mutation. Of note, two patients harbored concurrent mutations in KRAS and PIK3CA. Importantly, the SCODA mutation detection platform demonstrated excellent concordance (18/19 cases tested, 95%) with a conventional quantitative PCR assay for KRAS performed on tumor tissue, a standard-of-care assessment for patients with metastatic CRC (Table 3). No discordances were observed when the conventional assay identified a KRAS mutation and the SCODA assay did not; the only discordance was a case where the SCODA assay found a very low KRAS mutant signal in tissue, at a level below the reported sensitivity for conventional KRAS PCR assays [32].


Mutation profiling of tumor DNA from plasma and tumor tissue of colorectal cancer patients with a novel, high-sensitivity multiplexed mutation detection platform.

Kidess E, Heirich K, Wiggin M, Vysotskaia V, Visser BC, Marziali A, Wiedenmann B, Norton JA, Lee M, Jeffrey SS, Poultsides GA - Oncotarget (2015)

Mutations detected in tissue and plasma with the multiplexed SCODA mutation enrichment and detection assayIn highlighted cells, the detected mutation allele (or alleles) is specified, and for plasma, the number of detected copies (cp) of mutant DNA is also provided, normalized for a 5 mL input volume of plasma. ND, not detected.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4385870&req=5

Figure 2: Mutations detected in tissue and plasma with the multiplexed SCODA mutation enrichment and detection assayIn highlighted cells, the detected mutation allele (or alleles) is specified, and for plasma, the number of detected copies (cp) of mutant DNA is also provided, normalized for a 5 mL input volume of plasma. ND, not detected.
Mentions: The multiplexed SCODA mutation detection assay was used to analyze extracted DNA from patient tumor tissue and pre-operative plasma samples for the presence of mutations in KRAS, PIK3CA, BRAF and EGFR as defined in our panel (Table 1). In tumor tissue, 68% of the cohort (26 of 38 patients) showed at least one detectable mutation from the panel, including 14 of 19 (74%) patients with metastatic disease and 12 of 19 (63%) patients with non-metastatic disease. The distribution of observed mutations was consistent with prior reports (Figure 2): 50% (19 of 38 patients) had a KRAS mutant tumor, 16% (6 of 38 patients) had a PIK3CA mutation, 8% (3 of 38 patients) showed a mutation in BRAF, and none showed an EGFR mutation. Of note, two patients harbored concurrent mutations in KRAS and PIK3CA. Importantly, the SCODA mutation detection platform demonstrated excellent concordance (18/19 cases tested, 95%) with a conventional quantitative PCR assay for KRAS performed on tumor tissue, a standard-of-care assessment for patients with metastatic CRC (Table 3). No discordances were observed when the conventional assay identified a KRAS mutation and the SCODA assay did not; the only discordance was a case where the SCODA assay found a very low KRAS mutant signal in tissue, at a level below the reported sensitivity for conventional KRAS PCR assays [32].

Bottom Line: In CRC patient samples (n=38), detected mutations were concordant in tissue and plasma for 93% of metastatic patients versus 54% of non-metastatic patients.In patients undergoing liver metastatectomy, ctDNA anticipated tumor recurrence earlier than carcinoembryonic antigen (CEA) value or imaging.The multiplexed SCODA mutation enrichment and detection method can be applied to mutation profiling and quantitation of ctDNA, and is likely to have particular utility in the metastatic setting, including patients undergoing metastatectomy.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA.

ABSTRACT

Background: Circulating tumor DNA (ctDNA) holds promise as a non-invasive means for tumor monitoring in solid malignancies. Assays with high sensitivity and multiplexed analysis of mutations are needed to enable broad application.

Methods: We developed a new assay based on sequence-specific synchronous coefficient of drag alteration (SCODA) technology, which enriches for mutant DNA to achieve high sensitivity and specificity. This assay was applied to plasma and tumor tissue from non-metastatic and metastatic colorectal cancer (CRC) patients, including patients undergoing surgical resection for CRC liver metastases.

Results: Across multiple characterization experiments, the assay demonstrated a limit of detection of 0.001% (1 molecule in 100,000) for the majority of the 46 mutations in the panel. In CRC patient samples (n=38), detected mutations were concordant in tissue and plasma for 93% of metastatic patients versus 54% of non-metastatic patients. For three patients, ctDNA identified additional mutations not detected in tumor tissue. In patients undergoing liver metastatectomy, ctDNA anticipated tumor recurrence earlier than carcinoembryonic antigen (CEA) value or imaging.

Conclusions: The multiplexed SCODA mutation enrichment and detection method can be applied to mutation profiling and quantitation of ctDNA, and is likely to have particular utility in the metastatic setting, including patients undergoing metastatectomy.

Show MeSH
Related in: MedlinePlus