Abstract 6570: HLA genotyping and HLA-based clinical trial matching using MSK-IMPACT, a targeted next-generation sequencing assay
Authors: Chen Monica F. , Gormally Michael V. , Noronha Anne Marie , Panageas Kristalla , Reynolds Maggie , Kohlasch Kaelyn , Novak Bryan , Kee-Velez Tatiana , Clarke Nikeysha , Kyi Chrisann , Friedman Claire , D'Angelo Sandra , Kris Mark G. , Klebanoff Christopher A. , Shah Ronak , Berger Michael , Bandlamudi Chaitanya , Drilon Alexander , Donoghue Mark T. 
Published: March 2024

Purpose: Performing tumor next-generation sequencing (NGS) and human leukocyte antigen (HLA) typing in a single test can maximize the likelihood of matching patients with cancer to clinical trials. We investigated the utility of a clinical-grade NGS assay for this purpose.

Methods: HLA class I genotypes were determined on an investigational basis by MSK-IMPACT (FDA-authorized hybrid-capture, tumor and matched normal DNA-based NGS) using POLYSOLVER for patients with cancers of any histology between March 2014 and September 2023. Patient HLA genotype matches for phase I clinical trials were identified; for a subset of patients, concordance between HLA genotyping was compared to a CLIA-certified laboratory test.

Results: 60,565 patients successfully underwent complete class I HLA genotyping (two alleles each of HLA-A, HLA-B, and HLA-C). The median age at diagnosis was 64 years old and most patients were female (55%) and white (76%). The most common genotypes were HLA-A*02:01 (42%, n=25,457), HLA-C*04:01 (28%, n=17,274), HLA-A*01:01 (25%, n=14,867), HLA-C*07:01 (24%, n=14,538), HLA-A*03:01 (21%, n=12,668), HLA-C*07:02 (21%, n=12,493), and HLA-B*07:02 (16%, n=9,787). Most patients (96%, n=58,287) were HLA genotype eligible [HLA-A*02:01 (n=28), HLA-A*11:01 (n=3), HLA-A*01:01 (n=1), and HLA-C*07:02 (n=1)] for ≥1 of 33 active early phase adoptive T cell therapy or T cell receptor bispecific trials on Clinicialtrials.gov. 280 patients with HLA class I matches were screened for phase I trial candidacy by the MSK phase I group. 117 were candidates for confirmatory HLA and neoantigen testing, of whom 43 patients were enrolled on a trial after additional screening. 72 patients had HLA genotyping both by MSK-IMPACT and an outside CLIA-certified laboratory; 100% (72/72) of these subjects had concordant genotypes.

Conclusions: MSK-IMPACT successfully determined class I HLA genotypes in a large, multi-ethnic population of patients. A substantial proportion of patients were identified as potential candidates for HLA-matched trials, supporting local trial enrollment.

Citation Format: Monica F. Chen, Michael V. Gormally, Anne Marie Noronha, Kristalla Panageas, Maggie Reynolds, Kaelyn Kohlasch, Bryan Novak, Tatiana Kee-Velez, Nikeysha Clarke, Chrisann Kyi, Claire Friedman, Sandra D'Angelo, Mark G. Kris, Christopher A. Klebanoff, Ronak Shah, Michael Berger, Chaitanya Bandlamudi, Alexander Drilon, Mark T. Donoghue. HLA genotyping and HLA-based clinical trial matching using MSK-IMPACT, a targeted next-generation sequencing assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6570.