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Genotype-matched therapeutics have become widely adopted in the management of human cancers and can be guided by testing tumor tissue or cell-free DNA from plasma. OncoKB (Oncology Knowledge Base) is the first FDA-recognized database that contains information about these targetable somatic variants and corresponding therapeutic agents, including levels of evidence. Many of the human OncoKB variants have orthologs in the canine genome. This study was conducted to determine the feasibility of detecting these orthologs in dogs using liquid biopsy. This study involved two cohorts: The first was a cohort of 619 client-owned dogs with a variety of cancer diagnoses across all disease stages enrolled in a clinical validation study for a liquid biopsy test (herein the “research cohort”). All dogs had pre-treatment plasma samples collected at enrollment, and a subset of dogs also had matched tumor tissue collected. The second cohort comprised 457 client-owned dogs that had testing as part of the clinical deployment of the above-mentioned liquid biopsy test (herein the “clinical cohort”); 31% of these dogs had samples submitted as an aid in diagnosis (for dogs in which cancer was suspected clinically), and 69% had samples submitted for screening (in dogs with no a priori suspicion of cancer). Blood samples (and tumor samples, when available) were subjected to DNA extraction, proprietary library preparation, and next-generation sequencing. Sequencing data were analyzed using an internally developed bioinformatics pipeline to detect genomic alterations associated with the presence of cancer. Only canine orthologs of variants in the OncoKB database were evaluated in this study. Variants were called if they were observed in plasma at an allele frequency of at least 0.5%, with at least 6 unique supporting reads. Variants identified from plasma were subsequently genotyped in tissue without additional variant-level filtering. Analysis of plasma identified canine orthologs of OncoKB variants in ~8% of dogs in the research cohort, and ~4% of dogs in the clinical cohort. The higher percentage observed in the research cohort is likely due to the higher percentage of patients with confirmed cancer diagnosis. In the patients with an OncoKB ortholog in the research cohort, the dog had a cancer type that matched the human indication for the detected variant in 15% of cases. Of dogs in which an ortholog was identified in plasma, 44% had matched tumor tissue; and the variant observed in plasma was confirmed in tissue in >50% of these subjects. This study demonstrates the feasibility of detecting canine orthologs of targetable human cancer somatic variants in the blood of dogs using next-generation sequencing. Although it is currently unclear how human databases can be used to inform targeted treatment decisions in dogs, these findings may have relevance for comparative oncology studies and future precision therapeutics development for both species. Citation Format: Daniel S. Grosu, Ilya Chorny, Kristina M. Kruglyak, John A. Tynan, Susan C. Hicks, Todd A. Cohen, Allison L. O'Kell, Jill M. Rafalko, Jason Chibuk, Angela L. McCleary-Wheeler, Andi Flory, Dana W. Tsui. Liquid biopsy analysis reveals orthologs of actionable human cancer variants in dogs [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3377.

The concept of age-related somatic alterations in the blood or bone marrow of humans, commonly referred to as clonal hematopoiesis of indeterminate potential (CHIP) or age-related clonal hematopoiesis (ARCH), has been well characterized. In humans, these abnormalities tend to be associated with advanced age, often exhibit consistent signal over time, and typically involve recurrent locations in the genome. Though these somatic alterations may be associated with an increased risk of cancer, they do not originate from the tumor when cancer is concurrently present in the body. This study describes early findings that suggest similar age-related somatic alterations may also be present in dogs. Recently, next-generation sequencing-based liquid biopsy testing was developed for cancer detection in dogs. The clinical validation of this test involved 1,100 cancer-diagnosed and presumably cancer-free client-owned dogs. The test has also been performed commercially in thousands of additional dogs since 2021. This recent ability to test large numbers of dogs using liquid biopsy affords an unprecedented opportunity to study the genomic profiles of a broad population of canine subjects. Blood samples from over three thousand dogs ranging in age from 1 to >15 years were used in this analysis. Cell-free DNA (cfDNA) was extracted from the plasma, and genomic DNA (gDNA) was extracted from the white blood cells present in the buffy coat. Both cfDNA and gDNA were analyzed using next-generation sequencing to identify somatic genomic alterations. In a subset of patients, tumor tissue was also available for evaluation. Recurrent variants (e.g., involving CFA6 and CFA25, among others) were identified in the gDNA of a small fraction of patients. These findings occurred more commonly in older dogs and were typically persistent in gDNA across subsequent timepoints (when available) with no significant change in signal over time. When a clinical cancer evaluation was pursued, the majority of dogs with these findings had no evidence of cancer. For those in which cancer was identified, and tumor tissue was available for testing, the genomic profiles of the tumor tissue and gDNA were uncorrelated in almost all cases, suggesting the concomitant presence of age-related somatic alterations was incidental to the patient’s cancer. Additionally, regardless of whether cancer was present in the patient, the variants detected in gDNA were typically not encountered in cfDNA. These findings may be early evidence for the existence of age-related somatic alterations in dogs that potentially resemble the phenomenon of CHIP/ARCH previously observed in humans. Additional studies are ongoing to determine if these incidental findings may represent a risk factor for cancer development in dogs. Citation Format: Dana W.Y. Tsui, Allison L. O'Kell, Todd A. Cohen, Katherine M. Lytle, Kristina M. Kruglyak, Maggie A. Marshall, Carlos A. Ruiz-Perez, John A. Tynan, Susan C. Hicks, Jill M. Rafalko, Daniel S. Grosu, Jason Chibuk, Ilya Chorny, Angela L. McCleary-Wheeler, Andi Flory. Incidental detection of age-related somatic genomic alterations in blood samples from dogs with and without cancer [abstract]. In: Proceedings of the AACR Special Conference: Aging and Cancer; 2022 Nov 17-20; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2022;83(2 Suppl_1):Abstract nr A028.