Genomic profiling of cell-free circulating tumor DNA in patients with colorectal cancer and its fidelity to the genomics of the tumor biopsy

Gerald Li, Dean Pavlick, Jon H. Chung, Todd Bauer, Bradford A. Tan, Julio Peguero, Patrick Ward, Andre Kallab, Jose Bufill, Anthony Hoffman, Ahad Sadiq, Jeff Edenfield, Jie He, Matthew Cooke, Jason Hughes, Brady Forcier, Michelle Nahas, Phil Stephens, Siraj M. Ali, Alexa B. SchrockJeffrey S. Ross, Vincent A. Miller, Jeffrey P. Gregg

Research output: Contribution to journalArticle

Abstract

Background: Liquid biopsy offers the ability to non-invasively analyze the genome of a tumor through circulating tumor DNA (ctDNA) to identify targetable and prognostic genomic alterations. Few studies have rigorously analyzed ctDNA results and determined the fidelity with which they recapitulate the genomics of a sequenced tissue sample obtained from the same tumor. The clinical utility study (CUS) for the FoundationACT™ ctDNA assay (Foundation Medicine, Cambridge, MA, USA; NCT02620527) is a multi-center prospective clinical study for multiple solid tumor types to compare genomic profiling of paired tissue and blood samples from the same patient. In this subset of the study, paired specimens from 96 patients with colorectal cancer (CRC) were analyzed with comprehensive genomic profiling (CGP) of the tumor tissue sample (FoundationOne®) and blood sample (FoundationACT™). Methods: Both samples underwent CGP using the hybrid capture-based Illumina Hi-Seq technology. Maximum somatic allele frequency (MSAF) was used to estimate the fraction of ctDNA in the sample. The set of genes and targeted regions common to both tumor and liquid were compared for each subject. Results: Among these patients, 61% were male; 74% had clinical stage IV disease, 19% had clinical stage III disease, and 7% had clinical stage II disease. Time between the tissue biopsy and liquid biopsy (range, 0-709 days) had a significant impact on the positive percent agreement (PPA) between the two assays. Eighty percent of cases had evidence of ctDNA in the blood (MSAF >0). For all cases with MSAF >0, 171 base substitutions and insertions/deletions (indels) were identified in the tumor, and 79% (PPA) of these identical alterations were also identified in matched ctDNA samples; PPA increased to 87% for cases <270 days between the tissue and liquid biopsy, 95% for <90 days, and 100% PPA for <30 days. All known and likely short variants in KRAS, NRAS, and BRAF were analyzed independently as testing of these genes is recommended by the National Comprehensive Cancer Network (NCCN) for patients with CRC and have therapeutic implications. For NCCN genes, PPA was 80% for all time points for short variants; PPA increased to 90% for cases <270 days between the tissue and liquid biopsy. There was high concordance for KRAS G12X between tissue and liquid: Overall percent agreement (97%), PPA (93%), negative percent agreement (NPA) (100%), positive predictive value (PPV) (100%), and negative predictive value (NPV) (96%) for the <270 day cohort. Conclusions: In cases where tumor tissue profiling is not possible, these results provide compelling evidence that genomic profiling of ctDNA in late stage CRC shows a high concordance with tumor tissue sequencing results and can be used to identify most clinically relevant alterations capable of guiding therapy for these patients.

Original languageEnglish (US)
Pages (from-to)831-840
Number of pages10
JournalJournal of Gastrointestinal Oncology
Volume10
Issue number5
DOIs
StatePublished - Oct 1 2019

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Circulating Neoplastic Cells
Genomics
Colorectal Neoplasms
Biopsy
DNA
Neoplasms
Gene Frequency
Neoplasm Genes

Keywords

  • Circulating tumor DNA (ctDNA)
  • Colorectal
  • Genomics
  • Liquid biopsy

ASJC Scopus subject areas

  • Oncology
  • Gastroenterology

Cite this

Genomic profiling of cell-free circulating tumor DNA in patients with colorectal cancer and its fidelity to the genomics of the tumor biopsy. / Li, Gerald; Pavlick, Dean; Chung, Jon H.; Bauer, Todd; Tan, Bradford A.; Peguero, Julio; Ward, Patrick; Kallab, Andre; Bufill, Jose; Hoffman, Anthony; Sadiq, Ahad; Edenfield, Jeff; He, Jie; Cooke, Matthew; Hughes, Jason; Forcier, Brady; Nahas, Michelle; Stephens, Phil; Ali, Siraj M.; Schrock, Alexa B.; Ross, Jeffrey S.; Miller, Vincent A.; Gregg, Jeffrey P.

In: Journal of Gastrointestinal Oncology, Vol. 10, No. 5, 01.10.2019, p. 831-840.

Research output: Contribution to journalArticle

Li, G, Pavlick, D, Chung, JH, Bauer, T, Tan, BA, Peguero, J, Ward, P, Kallab, A, Bufill, J, Hoffman, A, Sadiq, A, Edenfield, J, He, J, Cooke, M, Hughes, J, Forcier, B, Nahas, M, Stephens, P, Ali, SM, Schrock, AB, Ross, JS, Miller, VA & Gregg, JP 2019, 'Genomic profiling of cell-free circulating tumor DNA in patients with colorectal cancer and its fidelity to the genomics of the tumor biopsy', Journal of Gastrointestinal Oncology, vol. 10, no. 5, pp. 831-840. https://doi.org/10.21037/jgo.2019.05.05
Li, Gerald ; Pavlick, Dean ; Chung, Jon H. ; Bauer, Todd ; Tan, Bradford A. ; Peguero, Julio ; Ward, Patrick ; Kallab, Andre ; Bufill, Jose ; Hoffman, Anthony ; Sadiq, Ahad ; Edenfield, Jeff ; He, Jie ; Cooke, Matthew ; Hughes, Jason ; Forcier, Brady ; Nahas, Michelle ; Stephens, Phil ; Ali, Siraj M. ; Schrock, Alexa B. ; Ross, Jeffrey S. ; Miller, Vincent A. ; Gregg, Jeffrey P. / Genomic profiling of cell-free circulating tumor DNA in patients with colorectal cancer and its fidelity to the genomics of the tumor biopsy. In: Journal of Gastrointestinal Oncology. 2019 ; Vol. 10, No. 5. pp. 831-840.
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abstract = "Background: Liquid biopsy offers the ability to non-invasively analyze the genome of a tumor through circulating tumor DNA (ctDNA) to identify targetable and prognostic genomic alterations. Few studies have rigorously analyzed ctDNA results and determined the fidelity with which they recapitulate the genomics of a sequenced tissue sample obtained from the same tumor. The clinical utility study (CUS) for the FoundationACT™ ctDNA assay (Foundation Medicine, Cambridge, MA, USA; NCT02620527) is a multi-center prospective clinical study for multiple solid tumor types to compare genomic profiling of paired tissue and blood samples from the same patient. In this subset of the study, paired specimens from 96 patients with colorectal cancer (CRC) were analyzed with comprehensive genomic profiling (CGP) of the tumor tissue sample (FoundationOne{\circledR}) and blood sample (FoundationACT™). Methods: Both samples underwent CGP using the hybrid capture-based Illumina Hi-Seq technology. Maximum somatic allele frequency (MSAF) was used to estimate the fraction of ctDNA in the sample. The set of genes and targeted regions common to both tumor and liquid were compared for each subject. Results: Among these patients, 61{\%} were male; 74{\%} had clinical stage IV disease, 19{\%} had clinical stage III disease, and 7{\%} had clinical stage II disease. Time between the tissue biopsy and liquid biopsy (range, 0-709 days) had a significant impact on the positive percent agreement (PPA) between the two assays. Eighty percent of cases had evidence of ctDNA in the blood (MSAF >0). For all cases with MSAF >0, 171 base substitutions and insertions/deletions (indels) were identified in the tumor, and 79{\%} (PPA) of these identical alterations were also identified in matched ctDNA samples; PPA increased to 87{\%} for cases <270 days between the tissue and liquid biopsy, 95{\%} for <90 days, and 100{\%} PPA for <30 days. All known and likely short variants in KRAS, NRAS, and BRAF were analyzed independently as testing of these genes is recommended by the National Comprehensive Cancer Network (NCCN) for patients with CRC and have therapeutic implications. For NCCN genes, PPA was 80{\%} for all time points for short variants; PPA increased to 90{\%} for cases <270 days between the tissue and liquid biopsy. There was high concordance for KRAS G12X between tissue and liquid: Overall percent agreement (97{\%}), PPA (93{\%}), negative percent agreement (NPA) (100{\%}), positive predictive value (PPV) (100{\%}), and negative predictive value (NPV) (96{\%}) for the <270 day cohort. Conclusions: In cases where tumor tissue profiling is not possible, these results provide compelling evidence that genomic profiling of ctDNA in late stage CRC shows a high concordance with tumor tissue sequencing results and can be used to identify most clinically relevant alterations capable of guiding therapy for these patients.",
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TY - JOUR

T1 - Genomic profiling of cell-free circulating tumor DNA in patients with colorectal cancer and its fidelity to the genomics of the tumor biopsy

AU - Li, Gerald

AU - Pavlick, Dean

AU - Chung, Jon H.

AU - Bauer, Todd

AU - Tan, Bradford A.

AU - Peguero, Julio

AU - Ward, Patrick

AU - Kallab, Andre

AU - Bufill, Jose

AU - Hoffman, Anthony

AU - Sadiq, Ahad

AU - Edenfield, Jeff

AU - He, Jie

AU - Cooke, Matthew

AU - Hughes, Jason

AU - Forcier, Brady

AU - Nahas, Michelle

AU - Stephens, Phil

AU - Ali, Siraj M.

AU - Schrock, Alexa B.

AU - Ross, Jeffrey S.

AU - Miller, Vincent A.

AU - Gregg, Jeffrey P.

PY - 2019/10/1

Y1 - 2019/10/1

N2 - Background: Liquid biopsy offers the ability to non-invasively analyze the genome of a tumor through circulating tumor DNA (ctDNA) to identify targetable and prognostic genomic alterations. Few studies have rigorously analyzed ctDNA results and determined the fidelity with which they recapitulate the genomics of a sequenced tissue sample obtained from the same tumor. The clinical utility study (CUS) for the FoundationACT™ ctDNA assay (Foundation Medicine, Cambridge, MA, USA; NCT02620527) is a multi-center prospective clinical study for multiple solid tumor types to compare genomic profiling of paired tissue and blood samples from the same patient. In this subset of the study, paired specimens from 96 patients with colorectal cancer (CRC) were analyzed with comprehensive genomic profiling (CGP) of the tumor tissue sample (FoundationOne®) and blood sample (FoundationACT™). Methods: Both samples underwent CGP using the hybrid capture-based Illumina Hi-Seq technology. Maximum somatic allele frequency (MSAF) was used to estimate the fraction of ctDNA in the sample. The set of genes and targeted regions common to both tumor and liquid were compared for each subject. Results: Among these patients, 61% were male; 74% had clinical stage IV disease, 19% had clinical stage III disease, and 7% had clinical stage II disease. Time between the tissue biopsy and liquid biopsy (range, 0-709 days) had a significant impact on the positive percent agreement (PPA) between the two assays. Eighty percent of cases had evidence of ctDNA in the blood (MSAF >0). For all cases with MSAF >0, 171 base substitutions and insertions/deletions (indels) were identified in the tumor, and 79% (PPA) of these identical alterations were also identified in matched ctDNA samples; PPA increased to 87% for cases <270 days between the tissue and liquid biopsy, 95% for <90 days, and 100% PPA for <30 days. All known and likely short variants in KRAS, NRAS, and BRAF were analyzed independently as testing of these genes is recommended by the National Comprehensive Cancer Network (NCCN) for patients with CRC and have therapeutic implications. For NCCN genes, PPA was 80% for all time points for short variants; PPA increased to 90% for cases <270 days between the tissue and liquid biopsy. There was high concordance for KRAS G12X between tissue and liquid: Overall percent agreement (97%), PPA (93%), negative percent agreement (NPA) (100%), positive predictive value (PPV) (100%), and negative predictive value (NPV) (96%) for the <270 day cohort. Conclusions: In cases where tumor tissue profiling is not possible, these results provide compelling evidence that genomic profiling of ctDNA in late stage CRC shows a high concordance with tumor tissue sequencing results and can be used to identify most clinically relevant alterations capable of guiding therapy for these patients.

AB - Background: Liquid biopsy offers the ability to non-invasively analyze the genome of a tumor through circulating tumor DNA (ctDNA) to identify targetable and prognostic genomic alterations. Few studies have rigorously analyzed ctDNA results and determined the fidelity with which they recapitulate the genomics of a sequenced tissue sample obtained from the same tumor. The clinical utility study (CUS) for the FoundationACT™ ctDNA assay (Foundation Medicine, Cambridge, MA, USA; NCT02620527) is a multi-center prospective clinical study for multiple solid tumor types to compare genomic profiling of paired tissue and blood samples from the same patient. In this subset of the study, paired specimens from 96 patients with colorectal cancer (CRC) were analyzed with comprehensive genomic profiling (CGP) of the tumor tissue sample (FoundationOne®) and blood sample (FoundationACT™). Methods: Both samples underwent CGP using the hybrid capture-based Illumina Hi-Seq technology. Maximum somatic allele frequency (MSAF) was used to estimate the fraction of ctDNA in the sample. The set of genes and targeted regions common to both tumor and liquid were compared for each subject. Results: Among these patients, 61% were male; 74% had clinical stage IV disease, 19% had clinical stage III disease, and 7% had clinical stage II disease. Time between the tissue biopsy and liquid biopsy (range, 0-709 days) had a significant impact on the positive percent agreement (PPA) between the two assays. Eighty percent of cases had evidence of ctDNA in the blood (MSAF >0). For all cases with MSAF >0, 171 base substitutions and insertions/deletions (indels) were identified in the tumor, and 79% (PPA) of these identical alterations were also identified in matched ctDNA samples; PPA increased to 87% for cases <270 days between the tissue and liquid biopsy, 95% for <90 days, and 100% PPA for <30 days. All known and likely short variants in KRAS, NRAS, and BRAF were analyzed independently as testing of these genes is recommended by the National Comprehensive Cancer Network (NCCN) for patients with CRC and have therapeutic implications. For NCCN genes, PPA was 80% for all time points for short variants; PPA increased to 90% for cases <270 days between the tissue and liquid biopsy. There was high concordance for KRAS G12X between tissue and liquid: Overall percent agreement (97%), PPA (93%), negative percent agreement (NPA) (100%), positive predictive value (PPV) (100%), and negative predictive value (NPV) (96%) for the <270 day cohort. Conclusions: In cases where tumor tissue profiling is not possible, these results provide compelling evidence that genomic profiling of ctDNA in late stage CRC shows a high concordance with tumor tissue sequencing results and can be used to identify most clinically relevant alterations capable of guiding therapy for these patients.

KW - Circulating tumor DNA (ctDNA)

KW - Colorectal

KW - Genomics

KW - Liquid biopsy

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