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    MINTIE: identifying novel structural and splice variants in transcriptomes using RNA-seq data
    Cmero, M ; Schmidt, B ; Majewski, IJ ; Ekert, PG ; Oshlack, A ; Davidson, NM (BMC, 2021-10-22)
    Calling fusion genes from RNA-seq data is well established, but other transcriptional variants are difficult to detect using existing approaches. To identify all types of variants in transcriptomes we developed MINTIE, an integrated pipeline for RNA-seq data. We take a reference-free approach, combining de novo assembly of transcripts with differential expression analysis to identify up-regulated novel variants in a case sample. We compare MINTIE with eight other approaches, detecting > 85% of variants while no other method is able to achieve this. We posit that MINTIE will be able to identify new disease variants across a range of disease types.
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    Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
    Schroeder, J ; Hsu, A ; Boyle, SE ; Macintyre, G ; Cmero, M ; Tothill, RW ; Johnstone, RW ; Shackleton, M ; Papenfuss, AT (OXFORD UNIV PRESS, 2014-04-15)
    MOTIVATION: Methods for detecting somatic genome rearrangements in tumours using next-generation sequencing are vital in cancer genomics. Available algorithms use one or more sources of evidence, such as read depth, paired-end reads or split reads to predict structural variants. However, the problem remains challenging due to the significant computational burden and high false-positive or false-negative rates. RESULTS: In this article, we present Socrates (SOft Clip re-alignment To idEntify Structural variants), a highly efficient and effective method for detecting genomic rearrangements in tumours that uses only split-read data. Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. We demonstrate using simulated and real data that Socrates performs well compared with a number of existing structural variant detection tools. AVAILABILITY AND IMPLEMENTATION: Socrates is released as open source and available from http://bioinf.wehi.edu.au/socrates CONTACT: papenfuss@wehi.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
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    Prostate cancer cell-intrinsic interferon signaling regulates dormancy and metastatic outgrowth in bone
    Owen, KL ; Gearing, LJ ; Zanker, DJ ; Brockwell, NK ; Khoo, WH ; Roden, DL ; Cmero, M ; Mangiola, S ; Hong, MK ; Spurling, AJ ; McDonald, M ; Chan, C-L ; Pasam, A ; Lyons, RJ ; Duivenvoorden, HM ; Ryan, A ; Butler, LM ; Mariadason, JM ; Phan, TG ; Hayes, VM ; Sandhu, S ; Swarbrick, A ; Corcoran, NM ; Hertzog, PJ ; Croucher, P ; Hovens, C ; Parker, BS (WILEY, 2020-06-04)
    The latency associated with bone metastasis emergence in castrate-resistant prostate cancer is attributed to dormancy, a state in which cancer cells persist prior to overt lesion formation. Using single-cell transcriptomics and ex vivo profiling, we have uncovered the critical role of tumor-intrinsic immune signaling in the retention of cancer cell dormancy. We demonstrate that loss of tumor-intrinsic type I IFN occurs in proliferating prostate cancer cells in bone. This loss suppresses tumor immunogenicity and therapeutic response and promotes bone cell activation to drive cancer progression. Restoration of tumor-intrinsic IFN signaling by HDAC inhibition increased tumor cell visibility, promoted long-term antitumor immunity, and blocked cancer growth in bone. Key findings were validated in patients, including loss of tumor-intrinsic IFN signaling and immunogenicity in bone metastases compared to primary tumors. Data herein provide a rationale as to why current immunotherapeutics fail in bone-metastatic prostate cancer, and provide a new therapeutic strategy to overcome the inefficacy of immune-based therapies in solid cancers.
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    Inferring structural variant cancer cell fraction
    Cmero, M ; Yuan, K ; Ong, CS ; Schröder, J ; PCAWG Evolution and Heterogeneity Working Group, ; Corcoran, NM ; Papenfuss, T ; Hovens, CM ; Markowetz, F ; Macintyre, G ; PCAWG Consortium, (Nature Research (part of Springer Nature), 2020-02-05)
    We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV breakends, then simultaneously estimates the cancer cell fraction and SV copy number. We assess performance using in silico mixtures of real samples, at known proportions, created from two clonal metastases from the same patient. We find that SVclone's performance is comparable to single-nucleotide variant-based methods, despite having an order of magnitude fewer data points. As part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) consortium, which aggregated whole-genome sequencing data from 2658 cancers across 38 tumour types, we use SVclone to reveal a subset of liver, ovarian and pancreatic cancers with subclonally enriched copy-number neutral rearrangements that show decreased overall survival. SVclone enables improved characterisation of SV intra-tumour heterogeneity.