Nikhil S Sahajpal, Ashis K Mondal, Alex Hastie, Alka Chaubey, Ravindra Kolhe
Cell lines have revolutionized scientific research as they are employed as primary tools in both basic and clinical research. Cell lines are extensively used to understand disease mechanisms, drug responses, drug metabolism, drug cytotoxicity, antibody production, vaccine development, gene function, generation of artificial tissues, synthesis of biological compounds, and develop transgenic preclinical models. However, the cells acquire additional genetic aberrations from the time the cell lines are established that might significantly impact the research for which the cell line is being used. The current methods to assess structural variants and copy number variants are limited in resolution (Karyotype), targeted (FISH), cannot detect balanced SVs (CMA), and cannot detect SVs in repetitive regions of the genome (NGS). Optical genome mapping (OGM) is an emerging next-generation cytogenenomics technology that can detect SVs including CNVs and complex rearrangements, using Saphyr platform that images ultra-long DNA molecules labelled at unique 6 base-pair motifs that span the entire genome, enabling genome-wide coverage and the ability to detect large SVs throughout the genome. In this study, we analyzed eight different cell lines that included seven cell lines of syndromes such as Fragile X (n=2), FSHD (n=2), DMD1 (n=1), Prader Willi (n=1), deafness (n=1), and one cell line for a transgenic mouse model. We have additionally analyzed 104 lymphoblast cell lines from the 1000 genomes project which do not have known clinical features. Briefly, ultra-high molecular weight DNA (150kb to >1Mb) was isolated from cultured cells using ~1.5 million cells as per manufacturer’s protocol, uniformly labeled at a specific 6-base sequence motif, and loaded into a cartridge, where the molecules were electrophoretically linearized and imaged multiple times using the Bionano Genomics Saphyr® platform. Using the captured images, a de novo genome map indicating the positions of the labels was constructed and compared to a reference genome to detect structural differences in the 2 maps. Chromosomal aberrations were detected by comparing optical maps to a reference and control dataset, and a coverage-based CNV calling was performed. In the present study, all eight cell lines were characterized with the concordance of reported genetic aberration in the syndromic cell lines. However, in the transgenic mouse cell line, several additional clinically pathogenic variants were detected in addition to the know variation. The study demonstrates the strength of OGM technology for detecting SVs and CNVs and its utility in the chromosomal characterization of cell lines that might significantly contribute towards accurate and reproducible research in a particular phenotype.