An Integrated Framework for Genome Analysis Reveals Numerous Previously Unrecognizable Structural Variants in Leukemia Patients’ Samples

Abstract

While genomic analysis of tumors has stimulated major advances in cancer diagnosis, prognosis and treatment, current methods fail to identify a large fraction of somatic structural variants in tumors. We have applied a combination of whole genome sequencing and optical genome mapping to a number of adult and pediatric leukemia samples, which revealed in each of these samples a large number of structural variants not recognizable by current tools of genomic analyses. We developed computational methods to determine which of those variants likely arose as somatic mutations. The method identified 97% of the structural variants previously reported by karyotype analysis of these samples and revealed an additional fivefold more such somatic rearrangements. The method identified on average tens of previously unrecognizable inversions and duplications and hundreds of previously unrecognizable insertions and deletions. These structural variants recurrently affected a number of leukemia associated genes as well as cancer driver genes not previously associated with leukemia and genes not previously associated with cancer. A number of variants only affected intergenic regions but caused cis-acting alterations in expression of neighboring genes. Analysis of TCGA data indicates that the status of several of the recurrently mutated genes identified in this study significantly affect survival of AML patients. Our results suggest that current genomic analysis methods fail to identify a majority of structural variants in leukemia samples and this lacunae may hamper diagnostic and prognostic efforts.

Identification of Somatic Structural Variants in Solid Tumors by Optical Genome Mapping

“…For instance, recurrent translocations, such as the Philadelphia chromosome, can activate oncogenes but at the same time reveal avenues for implementing or developing effective targeted drug therapies [ 1 , 2 , 3 , 4 ]. Likewise, SV identification plays an increasingly important role in cancer diagnosis and prognosis [ 5 , 6 ], and SVs have been shown to play a crucial role in intra-tumoral genetic heterogeneity [ 7 ]. Therefore, SV identification and analysis are important to understanding oncogenesis and tumor behavior.…”

“…OGM preparation and analysis workflow has been successfully applied to liquid-phase tumor and cell culture SV analyses. For instance, investigators have analyzed primary leukemic cells with OGM to identify previously unrecognized SVs implicated in oncogenesis and patients’ survival and have combined OGM with chromosome conformation capture to demonstrate enhancer highjacking resulting from SVs [ 5 , 29 , 30 ]. Similarly, investigators used OGM to visualize complex gene fusions and novel somatic SVs in liposarcoma, melanoma and other well-studied cancer cell lines [ 31 , 32 ].…”

Identification of Somatic Structural Variants in Solid Tumors By Optical Genome Mapping

“…For instance, recurrent translocations, such as the Philadelphia chromosome, can activate oncogenes but at the same time reveal avenues for implementing or developing effective targeted drug therapies [1][2][3][4]. Likewise, SV identification plays an increasingly important role in cancer diagnosis and prognosis [5,6], and SVs have been shown to play a crucial role in intratumoral genetic heterogeneity [7]. Therefore, SV identification and analysis is important to understanding oncogenesis and tumor behavior.…”

“…For instance, Neveling et al successfully analyzed SV and CNV calls and identified novel potential drivers of leukemia using bone marrow and blood samples [29]. Xu et al utilized OGM to detect previously unrecognized SVs in leukemia patients implicated in oncogenesis and patients’ survival [5]. Chan et al used OGM to visualize complex gene fusion maps in previously studied liposarcoma cell line [30].…”

Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing

“…The present study is limited by the fact that we have not compared the linked-reads to other next generation approaches such as standard paired-end WGS, Hi-C, third-generation single-molecule sequencing, or optical mapping technologies, which when used in a multiplatform approach have been demonstrated to be a powerful method for resolving complex structural rearrangements [33][34][35] . Future studies will be required for more formal benchmarking of linked-read WGS and other next generation technologies for digital karyotyping specifically in ALL and for other cancer types.…”