Medical Biology - Research Publications

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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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    Genomic characterisation of E mu-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene
    Lefebure, M ; Tothill, RW ; Kruse, E ; Hawkins, ED ; Shortt, J ; Matthews, GM ; Gregory, GP ; Martin, BP ; Kelly, MJ ; Todorovski, I ; Doyle, MA ; Lupat, R ; Li, J ; Schroeder, J ; Wall, M ; Craig, S ; Poortinga, G ; Cameron, D ; Bywater, M ; Kats, L ; Gearhart, MD ; Bardwell, VJ ; Dickins, RA ; Hannan, RD ; Papenfuss, AT ; Johnstone, RW (NATURE PUBLISHING GROUP, 2017-03-06)
    The Eμ-Myc mouse is an extensively used model of MYC driven malignancy; however to date there has only been partial characterization of MYC co-operative mutations leading to spontaneous lymphomagenesis. Here we sequence spontaneously arising Eμ-Myc lymphomas to define transgene architecture, somatic mutations, and structural alterations. We identify frequent disruptive mutations in the PRC1-like component and BCL6-corepressor gene Bcor. Moreover, we find unexpected concomitant multigenic lesions involving Cdkn2a loss and other cancer genes including Nras, Kras and Bcor. These findings challenge the assumed two-hit model of Eμ-Myc lymphoma and demonstrate a functional in vivo role for Bcor in suppressing tumorigenesis.
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    HYSYS: have you swapped your samples?
    Schroder, J ; Corbin, V ; Papenfuss, AT (OXFORD UNIV PRESS, 2017-02-15)
    MOTIVATION: The application of a genomics assay to samples from a cohort is a frequently applied experimental design in cancer genomics studies. The collection and analysis of cancer sequencing data in the clinical setting is an elaborate process that may involve consenting patients, obtaining possibly-multiple DNA samples, sequencing and analysis. Many of these steps are manual. At any stage mistakes can occur that cause a DNA sample to be labelled incorrectly. However, there is a paucity of methods in the literature to identify such swaps specifically in cancer studies. RESULTS: Here, we introduce a simple method, HYSYS, to estimate the relatedness of samples and test for sample swaps and contamination. The test uses the concordance of homozygous SNPs between samples. The method is motivated by the observation that homozygous germline population variants rarely change in the disease and are not affected by loss of heterozygosity. Our tools include visualization and a testing framework to flag possible sample swaps. We demonstrate the utility of this approach on a small cohort. AVAILABILITY AND IMPLEMENTATION: http://github.com/PapenfussLab/HaveYouSwappedYourSamples. CONTACT: papenfuss@wehi.edu.au. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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    CLOVE: classification of genomic fusions into structural variation events
    Schroder, J ; Wirawan, A ; Schmidt, B ; Papenfuss, AT (BIOMED CENTRAL LTD, 2017-07-20)
    BACKGROUND: A precise understanding of structural variants (SVs) in DNA is important in the study of cancer and population diversity. Many methods have been designed to identify SVs from DNA sequencing data. However, the problem remains challenging because existing approaches suffer from low sensitivity, precision, and positional accuracy. Furthermore, many existing tools only identify breakpoints, and so not collect related breakpoints and classify them as a particular type of SV. Due to the rapidly increasing usage of high throughput sequencing technologies in this area, there is an urgent need for algorithms that can accurately classify complex genomic rearrangements (involving more than one breakpoint or fusion). RESULTS: We present CLOVE, an algorithm for integrating the results of multiple breakpoint or SV callers and classifying the results as a particular SV. CLOVE is based on a graph data structure that is created from the breakpoint information. The algorithm looks for patterns in the graph that are characteristic of more complex rearrangement types. CLOVE is able to integrate the results of multiple callers, producing a consensus call. CONCLUSIONS: We demonstrate using simulated and real data that re-classified SV calls produced by CLOVE improve on the raw call set of existing SV algorithms, particularly in terms of accuracy. CLOVE is freely available from http://www.github.com/PapenfussLab .
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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.
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    The Scalloped and Nerfin-1 Transcription Factors Cooperate to Maintain Neuronal Cell Fate
    Vissers, JHA ; Froldi, F ; Schroder, J ; Papenfuss, AT ; Cheng, LY ; Harvey, KF (CELL PRESS, 2018-11-06)
    The ability of cells to stably maintain their fate is governed by specific transcription regulators. Here, we show that the Scalloped (Sd) and Nervous fingers-1 (Nerfin-1) transcription factors physically and functionally interact to maintain medulla neuron fate in the Drosophila melanogaster CNS. Using Targeted DamID, we find that Sd and Nerfin-1 occupy a highly overlapping set of target genes, including regulators of neural stem cell and neuron fate, and signaling pathways that regulate CNS development such as Notch and Hippo. Modulation of either Sd or Nerfin-1 activity causes medulla neurons to dedifferentiate to a stem cell-like state, and this is mediated at least in part by Notch pathway deregulation. Intriguingly, orthologs of Sd and Nerfin-1 have also been implicated in control of neuronal cell fate decisions in both worms and mammals. Our data indicate that this transcription factor pair exhibits remarkable biochemical and functional conservation across metazoans.
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    Embryonic Lethality in Homozygous Human Her-2 Transgenic Mice Due to Disruption of the Pds5b Gene
    Yong, CSM ; Sharkey, J ; Duscio, B ; Venville, B ; Wei, W-Z ; Jones, RF ; Slaney, CY ; Arnau, GM ; Papenfuss, AT ; Schroeder, J ; Darcy, PK ; Kershaw, MH ; Lydon, JP (PUBLIC LIBRARY SCIENCE, 2015-09-03)
    The development of antigen-targeted therapeutics is dependent on the preferential expression of tumor-associated antigens (TAA) at targetable levels on the tumor. Tumor-associated antigens can be generated de novo or can arise from altered expression of normal basal proteins, such as the up-regulation of human epidermal growth factor receptor 2 (Her2/ErbB2). To properly assess the development of Her2 therapeutics in an immune tolerant model, we previously generated a transgenic mouse model in which expression of the human Her2 protein was present in both the brain and mammary tissue. This mouse model has facilitated the development of Her2 targeted therapies in a clinically relevant and suitable model. While heterozygous Her2+/- mice appear to develop in a similar manner to wild type mice (Her2-/-), it has proven difficult to generate homozygous Her2+/+ mice, potentially due to embryonic lethality. In this study, we performed whole genome sequencing to determine if the integration site of the Her2 transgene was responsible for this lethality. Indeed, we report that the Her2 transgene had integrated into the Pds5b (precocious dissociation of sisters) gene on chromosome 5, as a 162 copy concatemer. Furthermore, our findings demonstrate that Her2+/+ mice, similar to Pds5b-/- mice, are embryonic lethal and confirm the necessity for Pds5b in embryonic development. This study confirms the value of whole genome sequencing in determining the integration site of transgenes to gain insight into associated phenotypes.
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    Improving the Power of Structural Variation Detection by Augmenting the Reference
    Schroeder, J ; Girirajan, S ; Papenfuss, AT ; Medvedev, P ; Boden, M (PUBLIC LIBRARY SCIENCE, 2015-08-31)
    The uses of the Genome Reference Consortium's human reference sequence can be roughly categorized into three related but distinct categories: as a representative species genome, as a coordinate system for identifying variants, and as an alignment reference for variation detection algorithms. However, the use of this reference sequence as simultaneously a representative species genome and as an alignment reference leads to unnecessary artifacts for structural variation detection algorithms and limits their accuracy. We show how decoupling these two references and developing a separate alignment reference can significantly improve the accuracy of structural variation detection, lead to improved genotyping of disease related genes, and decrease the cost of studying polymorphism in a population.