On April 12, 2022 Personalis, Inc. (Nasdaq: PSNL), a leader in advanced genomics for precision oncology, reported the publication of its study titled, "A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity," in Nature Communications (Press release, Personalis, APR 12, 2022, View Source [SID1234612091]).
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Human leukocyte antigen loss of heterozygosity (HLA LOH) allows cancer cells to escape immune recognition by deleting HLA alleles, causing the suppressed presentation of tumor neoantigens. Despite its importance in immunotherapy response, few methods exist to detect HLA LOH, and their accuracy is not well understood. Further, detecting HLA LOH accurately from sequencing data is of interest given the growing ubiquity of tumor molecular profiling.
The Personalis study details the development of DASH (Deletion of Allele-Specific HLAs), a novel machine learning-based algorithm to detect HLA LOH from paired tumor-normal sequencing data. Through validation with cell line mixtures and patient-specific digital PCR, the study demonstrates increased sensitivity of HLA LOH detection by DASH compared to previously published tools and paves the way for clinical utility. Using DASH for 610 patients across 15 tumor types, the study found that a large percentage of patients are impacted by HLA LOH, including patients with non-small cell lung cancer adenocarcinoma (NSCLC-A) (24 percent), cervical cancer (38 percent), and head and neck squamous cell carcinomas (HNSCC) (40 percent). Additionally, the study showed inflated HLA LOH rates compared to genome-wide LOH, and correlations between CD274 (PD-L1) expression and microsatellite instability status, suggesting that HLA LOH is a key immune resistance strategy.
"Accurate detection of HLA LOH is critical for its use as a biomarker for cancer immunotherapy. This study demonstrates DASH’s ability to sensitively detect subclonal events in samples with low tumor purity, enabling comprehensive profiling of widespread HLA LOH across tumor types," said Richard Chen, MD, chief medical officer and SVP of R&D for Personalis. "Integrated with Personalis’ NeXT Platform, these DASH-identified HLA LOH events are a key input to our composite, multi-omic biomarker, NEOPS, to better predict immunotherapy response."