Genomic Proximity Mapping (GPM): Evaluation of a Next Generation Cytogenomic Assay for Improved Risk Stratification in Acute Myeloid Leukemia
Authors: Malig Maika , Sala-Torra Olga , Wood Mary , Langford Kyle , Beppu Lan W. , Madarang Ellen Cvejanovich , Woolston David , Nong Tiffany , Wu Yu , Fang He , Liu Yajuan , Watts Justin M. , Taylor Justin , Liachko Ivan , Megan Othus , Muratov Alexander , Fang Min , Yeung Cecilia C.S. , Radich Jerald , Eacker Stephen 
Published: December 2024

Cytogenetics encompasses a suite of diagnostics assays that provides critical diagnostic and prognostic information that can help guide care for acute myeloid leukemias (AML) patients. Routine cytogenetic workup for AML includes karyotyping and fluorescence in situ hybridization (FISH) for known recurrent variants. The workup can be extended to include chromosome genome array testing (CGAT) but because all 3 of these tests have a non-overlapping set of limitations that can necessitate multiple, often iterative, rounds of testing in complex cases and may miss information in cases with cryptic fusions or small copy number alterations. Therefore, there is an unmet need for an accurate, fast and reliable test that can provide a solution to these limitations. In this study, we evaluate Genomic Proximity Mapping (GPM), a novel method that captures much of the same information as karyotyping, FISH, and CGAT in a single assay.
GPM uses proximity ligation sequencing to capture ultra-long range contiguity information from conventional short-read sequencing. In brief, 200,000-500,000 cells from bone marrow, peripheral blood, or aphersis samples are crosslinked with formalin prior to library preparation. Because sequences that are closer on a chromosome are more likely to physically interact and be crosslinked, GPM can use the frequency pairwise of crosslinked sequence interactions to determine the structure of chromosomes.
In order to evaluate its performance, we benchmarked GPM against standard-of-care cytogenetics conducted on newly diagnosed 166 AML cases in a multicenter, retrospective study utilizing real-world patient samples. There was a strong concordance between GPM and cytogenetic findings, with 100% of European LeukemiaNet (ELN) specified cytogenetic risk variants identified by cytogenetic being identified by GPM. However, GPM also identified additional variants of known clinical significance not observed by standard-of-care cytogenetics. To determine if GPM findings had clinical benefits for risk stratification, we compared overall survival (OS) of patients, risk-stratified using ELN 2022 criteria, using either cytogenetics or GPM to determine the cytogenetic abnormalities. Separation of favorable, intermediate, and adverse risk categories were statistically significant when variants identified either by cytogenetics or GPM were used for risk categorization (GPM, P = 0.0006; cytogenetics P = 0.0009 for GPM and cytogenetics, Mantel-Cox log rank test). However, Kaplan-Meier analysis demonstrated that GPM greater separation in intermediate (median OS 2.1 years for GPM and 2.4 years for cyto), and adverse (median OS 1.1 yrs for GPM and 0.9 years for cytogenetics) categories. The ELN-directed risk based on karyotype and FISH presentation was revised for 14 (8.4%) out of 166 cases with available data based on GPM assay results.
These findings argue that GPM can be used as a single assay to accurately stratify AML patient risk and may provide additional benefits over cytogenetics, yielding more accurate risk stratification.
Support: NIH/NCI U10CA180888, U10CA180819, U24CA196175, R44CA278140