Abstract 1913: Quality control workflows developed for the NCI Patient-Derived Models Repository using low pass whole genome sequencing and whole exome sequencing
Authors: Chang Ting-Chia , Chen Li , Das Biswajit , Evrard Yvonne A. , Karlovich Chris A. , Vilimas Tomas , Chapman Alyssa , Nair Nikitha , Romero Luis , Fong Anna J. Lee , Peach Amanda , Fullmer Brandie , Dutko Lindsay , Benauer Kelly , Rivera Gloryvee , Cantu Erin , Jiwani Shahanawaz , Neishaboori Nastaran , Forbes Tomas , Camalier Corinne , Stockwin Luke , Mullendore Michael , Eugeni Michelle A. , Newton Dianne , Hollingshead Melinda G. , Williams Mickey P. , Doroshow James H. 
Published: June 2022

Background: The National Cancer Institute's Patient-Derived Models Repository (NCI PDMR; pdmr.cancer.gov) is developing a variety of patient-derived xenograft (PDX) models for pre-clinical drug studies. All NCI PDMR models undergo quality control (QC) processes. Two unique QC challenges are: a) to assess genomic stability across PDX model passages; and b) to confirm the suitability of PDX-derived cancer associated fibroblasts (CAFs) as germline surrogates when blood is not available. Multiple bioinformatics QC assessments have been developed to measure the genomic fidelity in these PDX models using low-pass whole genome sequencing (LP-WGS) and in CAFs using whole exome sequencing (WES).

Methods: LP-WGS was performed on 502 PDX samples from 38 models of rare cancer across passages 2 through 9 and WES was performed on 92 CAFs from 32 different histologies. In the QC workflow for estimating the genomic stability of passages within models, BBSplit was used for the assessment of human/mouse DNA content. CNVkit was utilized for copy number (CN) detection. The fraction of genome changed was calculated by comparing the copy numbers of each passage sample to the original patient sample. To evaluate purity of CAFs, three QC steps were constructed: a) plot of SNP variant allele frequency (ideogram); b) variant annotation using OncoKB (www.oncokb.org); c) percentage of genomic loss of heterozygosity (LOH), based on a set of ~800,000 heterozygous SNPs from a population-level genomic database (gnomAD) based on WES data.

Results: PDX models showed genomic stability in CN profile when measured by LP-WGS. Human tumor DNA content remains stable ranging from 75-85% across different tiers of PDX passages from Donor +1 to Donor +6 and more. No models showed statistically significant evolution in CN profile, given the average 5 samples per model in each tier of passages. The QC workflow for CAFs generated five categories based on SNP ideograms, the presence/absence of oncogenic variants and LOH. Following observations were made: a) 72.5% CAFs were confirmed as matched diploid CAFs (category 1); b) 6.6% of CAFs were diploid and had &gt;= 1 germline oncogenic variant - classified as category 2. CAFs in category 1&2 were suitable as germline surrogates; c) 12% of CAFs (category 3) showed putative polyploidy on SNP ideograms with no oncogenic variants and suitable for somatic variant calling; d) 8.8% of CAFs (category 4) had polyploidy and oncogenic variants present; e) LOH high CAF (category 5) - we identified a CAF with 42% LOH, later confirmed to be a tumor cell line by immunohistochemistry (IHC). Other CAFs (n=91) showed little variance, ranging from 0.6%-1.7% LOH.

Conclusions: We developed standard QC workflows to evaluate genomic stability of PDX models during passaging and qualify CAFs as germline surrogates for pre-clinical study.

Citation Format: Ting-Chia Chang, Li Chen, Biswajit Das, Yvonne A. Evrard, Chris A. Karlovich, Tomas Vilimas, Alyssa Chapman, Nikitha Nair, Luis Romero, Anna J. Lee Fong, Amanda Peach, Brandie Fullmer, Lindsay Dutko, Kelly Benauer, Gloryvee Rivera, Erin Cantu, Shahanawaz Jiwani, Nastaran Neishaboori, Tomas Forbes, Corinne Camalier, Luke Stockwin, Michael Mullendore, Michelle A. Eugeni, Dianne Newton, Melinda G. Hollingshead, Mickey P. Williams, James H. Doroshow. Quality control workflows developed for the NCI Patient-Derived Models Repository using low pass whole genome sequencing and whole exome sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1913.