Abstract 1362: Genome-wide sequencing of cell-free DNA enables detection of copy number alterations in cancer patients where tissue biopsy is not feasible
Authors: Jensen Taylor J. , Goodman Aaron M. , Kato Shumei , Ellison Christopher K. , Kelly Kimberly , Kim Lisa , Daniels Gregory A. , Fitzgerald Kerry , McCarthy Erin , Nakashe Prachi , Mazloom Amin R. , McLennan Graham , Almasri Eyad , Grosu Daniel S. , Eisenberg Marcia , Kurzrock Razelle 
Published: August 2019

Abstract
In instances where tissue biopsy is not medically prudent or tumor tissue material is insufficient for molecular testing, alternative methods are needed. Since cell-free DNA (cfDNA) has been shown to provide a representative surrogate for tumor tissue, we sought to evaluate its utility in this scenario. Here we present data from 91 patients with known neoplasms whose tumors were not able to be tested using conventional tissue biopsy. The cfDNA from each patient was assayed with low-coverage (~0.3X) genome-wide sequencing and copy number alteration (CNA) events were identified and characterized using analytical methods originally developed for noninvasive prenatal testing (NIPT). To quantify the level of CNAs present in the plasma of cancer patients, we utilized the genomic instability number (GIN). First, the technical variability of the GIN was evaluated in a large sample cohort. We therefore processed genome-wide sequencing results from 27,742 pregnant women who consented to have their samples used for research and whose NIPT results yielded no detected CNAs. Utilizing these data, we established a threshold whereby we could differentiate technical noise from biological signal when CNAs were present down to a 1% ctDNA fraction with 99.7% specificity. Applied broadly, CNAs were detected in 32 of the 91 patients with difficult-to-biopsy cancers evaluated (35%) with detection frequencies tightly linked to cancer type. Importantly, there was a significant reduction in progression-free survival for the first treatment after liquid biopsy for patients with an elevated GIN relative to those without, suggesting a prognostic link between GIN and patient outcome across a wide variety of tumor types. In addition, samples with an elevated GIN also showed a significant concomitant reduction in cfDNA fragment length, consistent with previous reports suggesting that cfDNA derived from tumors is shorter in length than cfDNA from healthy tissue. Finally, we characterized the genomic location of the detected CNAs to potentially enable the utility and interpretation of these results clinically. Collectively, the detected CNAs covered more than 95% of all autosomes, highlighting a benefit of using genome-wide sequencing. Taken together, these data demonstrate a proof-of-concept for using low-coverage, genome-wide sequencing of cfDNA in patients where tissue biopsy is not feasible or medically recommended.
Citation Format: Taylor J. Jensen, Aaron M. Goodman, Shumei Kato, Christopher K. Ellison, Kimberly Kelly, Lisa Kim, Gregory A. Daniels, Kerry Fitzgerald, Erin McCarthy, Prachi Nakashe, Amin R. Mazloom, Graham McLennan, Eyad Almasri, Daniel S. Grosu, Marcia Eisenberg, Razelle Kurzrock. Genome-wide sequencing of cell-free DNA enables detection of copy number alterations in cancer patients where tissue biopsy is not feasible [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1362.