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Liquid biopsy concordance based on clonality and timing of testing in patients with metastatic colorectal cancer
abstracts
Annals of Oncology
Liquid biopsy concordance based on clonality and timing of testing in patients with metastatic colorectal cancer
P.M. Kasi1, S. Kamatham2, F. Shahjehan2, Z. Li3, P.W. Johnson3, A. Merchea4, D.T. Colibaseanu4 1 Hematology/Oncology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA, 2Hematology/Oncology, Mayo Clinic, Jacksonville, FL, USA, 3 Biostatistics, Mayo Clinic, Jacksonville, FL, USA, 4Colorectal Surgery, Mayo Clinic, Jacksonville, FL, USA Background: The most recent consensus statement on the use of liquid biopsies (circulating tumor DNA – ctDNA testing) has been that it is not yet ready for prime time. However, in patients with metastatic colorectal cancer (mCRC), there is significantly more ‘shedding’ of DNA detectable in blood allowing this test to be of value. We aimed at reporting the concordance of liquid biopsies based on clonality and timing of testing in patients with mCRC. Methods: A total of 92 mCRC patients were identified who had both a commercially available liquid and tissue next generation sequencing assay done from December 2016 to February 2019. Arbitrarily, mutations were classified as clonal or subclonal based on the 50% cutoff of the highest variant allele frequency (VAF) reported. Concordance rates, including clonal (BRAF-V600E/ RAS), subclonal and amplification concordance were calculated separately for patients for whom the liquid biopsy testing was done before initiation of treatment (n ¼ 27) and after initiation of treatment (n ¼ 65). Results: Clonal concordance rates were 96.3% for patients when the liquid biopsy was done before initiation of treatment versus 64.6% for patients when the test was obtained after they were already on some systemic therapy (p value: 0.001). Similarly, subclonal and amplification concordance rates for patients in the test before treatment and test after treatment groups are summarized in the table. Moreover, the median of highest VAF% was noted to be 3.1% and 1.1% in test before treatment and test after treatment groups respectively (p value: 0.092). Conclusions: Liquid biopsies show a very high concordance rate in patients with metastatic colorectal cancer. It is important to take the timing of the assay into consideration alongside relevant clonal mutations while assessing the concordance of liquid biopsies, not just for mCRC but for other malignancies. Legal entity responsible for the study: The authors. Funding: Has not received any funding. Disclosure: All authors have declared no conflicts of interest.
Table: 622P Summary of concordance rates by timing of liquid biopsy test
*Clonal Concordance BRAF RAS Subclonal Concordance BRAF RAS Amplification Concordance Highest Variant Allele Frequency (VAF)%
Test before treatment (N ¼ 27)
Test after treatment (N ¼ 65)
Total (N ¼ 92)
P value
26: 96.3 (81.0, 99.9) 27: 100.0 (87.2, 100.0) 26: 96.3 (81.0, 99.9) 21: 77.8 (57.7, 91.4) 27: 100.0 (87.2, 100.0) 27: 100.0 (87.2, 100.0) 22: 81.5 (61.9, 93.7) 3.1 (0.0, 84.6)
42: 64.6 (51.8, 76.1) 64: 98.5 (91.7, 100.0) 52: 80.0 (68.2, 88.9) 44: 67.7 (54.9, 78.8) 65: 100.0 (94.5, 100.0) 62: 95.4 (87.1, 99.0) 41: 63.1 (50.2, 74.7) 1.1 (0.0, 90.1)
68: 73.9 (63.7, 82.5) 91: 98.9 (94.1, 100.0) 78: 84.8 (75.8, 91.4) 65: 70.7 (60.2, 79.7) 92: 100.0 (96.1, 100.0) 89: 96.7 (90.8, 99.3) 63: 68.5 (58.0, 77.8) 1.5 (0.0, 90.1)
0.001 1.000 0.058 0.452 1.000 0.553 0.092 0.092
Concordance rates are summarized by count: percent (95% binomial confidence interval). P values arise from Fisher’s exact tests; *Arbitrarily, 50% of the highest variant allele frequency (VAF)% value in the liquid biopsy results has been used to differentiate clonal from subclonal mutations. Highest VAF% is summarized by median (range). P values arise from Wilcoxon rank sum test
Volume 30 | Supplement 5 | October 2019
doi:10.1093/annonc/mdz246 | v235
Downloaded from https://academic.oup.com/annonc/article-abstract/30/Supplement_5/mdz246.099/5577833 by guest on 24 October 2019
622P
Annals of Oncology
Liquid biopsy concordance based on clonality and timing of testing in patients with metastatic colorectal cancer
P.M. Kasi1, S. Kamatham2, F. Shahjehan2, Z. Li3, P.W. Johnson3, A. Merchea4, D.T. Colibaseanu4 1 Hematology/Oncology, Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA, USA, 2Hematology/Oncology, Mayo Clinic, Jacksonville, FL, USA, 3 Biostatistics, Mayo Clinic, Jacksonville, FL, USA, 4Colorectal Surgery, Mayo Clinic, Jacksonville, FL, USA Background: The most recent consensus statement on the use of liquid biopsies (circulating tumor DNA – ctDNA testing) has been that it is not yet ready for prime time. However, in patients with metastatic colorectal cancer (mCRC), there is significantly more ‘shedding’ of DNA detectable in blood allowing this test to be of value. We aimed at reporting the concordance of liquid biopsies based on clonality and timing of testing in patients with mCRC. Methods: A total of 92 mCRC patients were identified who had both a commercially available liquid and tissue next generation sequencing assay done from December 2016 to February 2019. Arbitrarily, mutations were classified as clonal or subclonal based on the 50% cutoff of the highest variant allele frequency (VAF) reported. Concordance rates, including clonal (BRAF-V600E/ RAS), subclonal and amplification concordance were calculated separately for patients for whom the liquid biopsy testing was done before initiation of treatment (n ¼ 27) and after initiation of treatment (n ¼ 65). Results: Clonal concordance rates were 96.3% for patients when the liquid biopsy was done before initiation of treatment versus 64.6% for patients when the test was obtained after they were already on some systemic therapy (p value: 0.001). Similarly, subclonal and amplification concordance rates for patients in the test before treatment and test after treatment groups are summarized in the table. Moreover, the median of highest VAF% was noted to be 3.1% and 1.1% in test before treatment and test after treatment groups respectively (p value: 0.092). Conclusions: Liquid biopsies show a very high concordance rate in patients with metastatic colorectal cancer. It is important to take the timing of the assay into consideration alongside relevant clonal mutations while assessing the concordance of liquid biopsies, not just for mCRC but for other malignancies. Legal entity responsible for the study: The authors. Funding: Has not received any funding. Disclosure: All authors have declared no conflicts of interest.
Table: 622P Summary of concordance rates by timing of liquid biopsy test
*Clonal Concordance BRAF RAS Subclonal Concordance BRAF RAS Amplification Concordance Highest Variant Allele Frequency (VAF)%
Test before treatment (N ¼ 27)
Test after treatment (N ¼ 65)
Total (N ¼ 92)
P value
26: 96.3 (81.0, 99.9) 27: 100.0 (87.2, 100.0) 26: 96.3 (81.0, 99.9) 21: 77.8 (57.7, 91.4) 27: 100.0 (87.2, 100.0) 27: 100.0 (87.2, 100.0) 22: 81.5 (61.9, 93.7) 3.1 (0.0, 84.6)
42: 64.6 (51.8, 76.1) 64: 98.5 (91.7, 100.0) 52: 80.0 (68.2, 88.9) 44: 67.7 (54.9, 78.8) 65: 100.0 (94.5, 100.0) 62: 95.4 (87.1, 99.0) 41: 63.1 (50.2, 74.7) 1.1 (0.0, 90.1)
68: 73.9 (63.7, 82.5) 91: 98.9 (94.1, 100.0) 78: 84.8 (75.8, 91.4) 65: 70.7 (60.2, 79.7) 92: 100.0 (96.1, 100.0) 89: 96.7 (90.8, 99.3) 63: 68.5 (58.0, 77.8) 1.5 (0.0, 90.1)
0.001 1.000 0.058 0.452 1.000 0.553 0.092 0.092
Concordance rates are summarized by count: percent (95% binomial confidence interval). P values arise from Fisher’s exact tests; *Arbitrarily, 50% of the highest variant allele frequency (VAF)% value in the liquid biopsy results has been used to differentiate clonal from subclonal mutations. Highest VAF% is summarized by median (range). P values arise from Wilcoxon rank sum test
Volume 30 | Supplement 5 | October 2019
doi:10.1093/annonc/mdz246 | v235
Downloaded from https://academic.oup.com/annonc/article-abstract/30/Supplement_5/mdz246.099/5577833 by guest on 24 October 2019
622P