Abstract 1329: Identifying low allele frequency somatic variants using the Saphyr System
Authors: Lee Joyce , PANG Andy Wing Chun , Groß Caspar , Admard Jakob , Buena-Atienza Elena , Ossowski Stephan , Anantharaman Thomas , Oldakowski Mark , Bocklandt Sven , Hastie Alex 
Published: September 2020

Abstract
Cancer is known to be a dynamic disease with subclones evolving throughout the stages. These progresses create a sample of high heterogeneity, in which high throughput and high sensitivity structural variant calling sensitivity are essential to detect the low frequency events in order to have a thorough understanding of the cancer. Using the Bionano Saphyr® System, a genome imaging platform with a throughput of up to 1.3 Tbp per flowcell, sensitive detection of these low allele frequency structural rearrangements is facilitated by the Bionano data analysis tools, the Rare Variant Pipeline and Variant Annotation Pipeline.
Here we compared three tumor-normal pairs of cell lines: the HCC2218, HCC1395 and HCC1954. We first collected about 1.3 Tbp for each of the six tumor and normal cell lines. Each dataset has molecule N50s above 270 kbp. These datasets were input into the Rare Variant Pipeline, where molecules deviating from the reference were locally assembled and structural variants were detected with the local assemblies. Running the Variant Annotation Pipeline then compared the structural variants between the tumor and the control samples and identified variants that are somatic in each pair. With the somatic calls found, we identified various numbers of low allele frequency events in each pair. For example, we observed a low frequency translocation t(2,12) that is unique to the HCC1954 tumor sample. This translocation involves the protein kinase ZAK, a gene known to take part in cell cycle checkpoint regulation (Tosti et al., 2004). In the HCC2218 tumor sample, we found a 381 kbp deletion at AUTS2 (autism susceptibility candidate 2), a gene which has also been associated with acute lymphoblastic leukemia (Denk et al., 2012) and other cancers (Stadler et al., 2012). These events are of low allele frequency and are found to be somatic.
In conclusion, cancer samples are heterogeneous and thus, high throughput and sensitive structural variant calling methods are required for a complete examination of the structural mutations that may be present in tumor samples. Bionano has provided an efficient and streamlined data collection platform as well as a smooth and intuitive bioinformatics workflow for expeditious detection of low allele frequency events such as those herein illustrated.
References
Denk, Dagmar, et al. "PAX5-AUTS2: a recurrent fusion gene in childhood B-cell precursor acute lymphoblastic leukemia." Leukemia research 36.8 (2012): e178-e181.
Stadler, Zsofia K., et al. "Rare de novo germline copy-number variation in testicular cancer." The American Journal of Human Genetics 91.2 (2012): 379-383.
Tosti, Elena, et al. "The stress kinase MRK contributes to regulation of DNA damage checkpoints through a p38γ-independent pathway." Journal of Biological Chemistry 279.46 (2004): 47652-47660.
Citation Format: Joyce Lee, Andy Wing Chun PANG, Caspar Groß, Jakob Admard, Elena Buena-Atienza, Stephan Ossowski, Thomas Anantharaman, Mark Oldakowski, Sven Bocklandt, Alex Hastie. Identifying low allele frequency somatic variants using the Saphyr System [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1329.