Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis

Abstract

BackgroundSolid tumors present a panoply of genomic alterations, from single base changes to the gain or loss of entire chromosomes. Although aberrations at the two extremes of this spectrum are readily defined, comprehensive discernment of the complex and disperse mutational spectrum of cancer genomes remains a significant challenge for current genome analysis platforms. In this context, high throughput, single molecule platforms like Optical Mapping offer a unique perspective.ResultsUsing measurements from large ensembles of individual DNA molecules, we have discovered genomic structural alterations in the solid tumor oligodendroglioma. Over a thousand structural variants were identified in each tumor sample, without any prior hypotheses, and often in genomic regions deemed intractable by other technologies. These findings were then validated by comprehensive comparisons to variants reported in external and internal databases, and by selected experimental corroborations. Alterations range in size from under 5 kb to hundreds of kilobases, and comprise insertions, deletions, inversions and compound events. Candidate mutations were scored at sub-genic resolution and unambiguously reveal structural details at aberrant loci.ConclusionsThe Optical Mapping system provides a rich description of the complex genomes of solid tumors, including sequence level aberrations, structural alterations and copy number variants that power generation of functional hypotheses for oligodendroglioma genetics.

Single-molecule analysis reveals widespread structural variation in multiple myeloma

“…In any region of the genome, the total number of aligned Rmaps (depth of coverage) serves as an indicator of copy number. For somatic copy number analysis using optical mapping data, we compared the depth of coverage of both tumor samples (MM-S and MM-R) to a reference dataset (normal) using a hidden Markov model-based coverage analysis algorithm (18,19). As a result, the tumor genomes were partitioned into low, normal, and high copy number states.…”

“…To address these issues, we have used optical mapping (7,(13)(14)(15)(16)(17)(18)(19) and DNA sequencing to comprehensively characterize structural variation in a primary MM genome at two stages of tumor progression and drug response. The two stages represent a sensitive relapse (MM-S; patient responded to subsequent treatments) and a subsequent refractory relapse (MM-R; no response to any treatments) (SI Materials and Methods and Fig.…”

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

“…Due to the much longer length of optical maps (up to 1Mbp) compared to sequencing reads, OM has been found very powerful in SV discovery (Cao et al, 2014;Dong et al, 2013;Lam et al, 2012;Ray et al, 2013;Teague et al, 2009). Current high-throughput OM methods can produce optical maps for a hundred thousand molecules within a few hours, at an average size of several hundred kbps per molecule.…”

“…Finally, labels of close restriction sites may merge into a single label in the observed data due to limitations in imaging resolution. As a result of all these error types, specialized methods have been proposed for various computational tasks related to the analysis of optical maps, including error modeling (Tong et al, 2007;Tong, 2010), molecule alignment (Leung et al, 2017b;Nagarajan et al, 2008;Shelton et al, 2015;Teague et al, 2009;Valouev et al, 2006), de novo and reference-assisted assembly (Kim et al, 2013;Lin et al, 2012;Valouev et al, 2006), and detection of SVs (Hastie et al, 2013;Lam et al, 2012;Ray et al, 2013;Teague et al, 2009).…”

Estudo de variações genômicas para a identificação de biomarcadores personalizados e novos alvos terapêuticos em tumores colorretais

“…Interestingly, when we compared the set of ICR candidates in each tumor genome we found a significant number of recurrent events (Table S1). Since solid tumors are well known for their lack of recurrent tumor-specific rearrangements (3) we assumed that these recurrent events (Table S1) might correspond to artifacts that could be removed by comparison with the matched normal samples (21)(22)(23). The presence of recurrent structural variation breakpoints was recently observed in a study of complex genomic rearrangements (24) and as a validation strategy only breakpoints present in a single tumor were considered somatic.…”