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Oncotarget. 2016 Oct 4;7(40):65364-65373. doi: 10.18632/oncotarget.11692.

Concordance between genomic alterations assessed by next-generation sequencing in tumor tissue or circulating cell-free DNA.

Chae YK1,2,3, Davis AA2, Carneiro BA1,2,3, Chandra S1,2,3, Mohindra N2,3, Kalyan A1,2,3, Kaplan J1,2,3, Matsangou M1,2,3, Pai S1,3, Costa R1,3, Jovanovic B2,3, Cristofanilli M1,2,3, Platanias LC1,2,3,4, Giles FJ1,2,3.

Author information

1
Developmental Therapeutics Program of Division of Hematology Oncology, Northwestern University, Chicago, IL, USA.
2
Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
3
Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
4
Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA.

Abstract

Genomic analysis of tumor tissue is the standard technique for identifying DNA alterations in malignancies. Genomic analysis of circulating tumor cell-free DNA (cfDNA) represents a relatively non-invasive method of assessing genomic alterations using peripheral blood. We compared the concordance of genomic alterations between cfDNA and tissue biopsies in this retrospective study. Twenty-eight patients with advanced solid tumors with paired next-generation sequencing tissue and cfDNA biopsies were identified. Sixty-five genes were common to both assays. Concordance was defined as the presence or absence of the identical genomic alteration(s) in a single gene on both molecular platforms. Including all aberrations, the average number of alterations per patient for tissue and cfDNA analysis was 4.82 and 2.96, respectively. When eliminating alterations not detectable in the cfDNA assay, mean number of alterations for tissue and cfDNA was 3.21 and 2.96, respectively. Overall, concordance was 91.9-93.9%. However, the concordance rate decreased to 11.8-17.1% when considering only genes with reported genomic alterations in either assay. Over 50% of mutations detected in either technique were not detected using the other biopsy technique, indicating a potential complementary role of each assay. Across 5 genes (TP53, EGFR, KRAS, APC, CDKN2A), sensitivity and specificity were 59.1% and 94.8%, respectively. Potential explanations for the lack of concordance include differences in assay platform, spatial and temporal factors, tumor heterogeneity, interval treatment, subclones, and potential germline DNA contamination. These results highlight the importance of prospective studies to evaluate concordance of genomic findings between distinct platforms that ultimately may inform treatment decisions.

KEYWORDS:

cell-free DNA; genomic alterations; lung cancer; metastatic disease; next-generation sequencing

PMID:
27588476
PMCID:
PMC5323161
DOI:
10.18632/oncotarget.11692
[Indexed for MEDLINE]
Free PMC Article

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