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Other Cancers

Research & Diagnostics

Any genes or gene panels for which complete sequencing is relevant to detect both small mutations and structural variants, can be targeted with TLA.

 

Examples of analyses that can benefit from TLA:

  • Detection of gene fusions with recurrent and novel fusion partners
  • Complete sequencing of tumor suppressor genes such as BRCA1/2, TP53 to detect all mutations, including intronic and promoter events and structural variation
  • Detection of viral integrations in the human (cancer) genome
  • Analyses of complex rearrangements, genomic events underlying CNVs and novel resistance mechanisms

 

Examples of genes for which we provide TLA are BRCA1,2, MLL, ETV6, RUNX1, NTRK1, NRG1, MYC, BCL2, BCL6. Please note that TLA can be tailored to any (combination of) gene(s) of interest.

  • Application notes
  • Publications
  • Webinars
  • Application notes
  • Robust detection of structural variants and single nucleotide variants in FFPE
    Robust detection of structural variants and single nucleotide variants in FFPE
  • Publications
  • Targeted Locus Amplification (TLA): A Novel Next Generation Sequencing (NGS) Technology to Detect New Molecular Markers and Monitoring Minimal Residual Disease (MRD) in Mantle Cell and Follicular Lymphoma

    Genuardi E et al. (2017)                                                                                                            

    A.O.U. Citta della Salute e della Scienza di Torino, Azienda Ospedaliera SS Antonio e Biagio e Cesare Arrigo, Cergentis, Clinica Humanitas/Gavazzeni, University of Modena e Reggio Emilia & University of Torino

  • Personalized Medicine in Lymphoma: Tailoring Treatment According to Minimal Residual Disease

    Dogliotti I & Ferrero S (2017)                                                                                                            

    A.O.U. Citta della Salute e della Scienza di Torino & University of Torino

  • Spectrum of genetic variants of BRCA1 and BRCA2 in a German single center study

    Meisel C et al. (2017)                                                                                                            

    DKFZ, Medical Genetic Center Munich, National Center for Tumor Diseases (NCT), TU Dresden, University Kiel

  • Activating ESR1 Mutations Differentially Impact the Efficacy of ER Antagonists

    Toy W et al. (2016)                                                                                                                             

    AstraZeneca, Memorial Sloan Kettering Cancer Center, University of Chicago & University of Illinois at Urbana Champaign

  • Mechanisms of Therapy Resistance in Patient-Derived Xenograft Models of BRCA1-Deficient Breast Cancer

    Ter Brugge P et al. (2016)                                                                                                            

    Bellvitge Biomedical Research Institute Barcelona, Curie Institute, ICREA, Institute of Cancer Research London, The Netherlands Cancer Institute, University of Barcelona & University Medical Center Utrecht

  • Sequencing Structural Variants in Cancer for Precision Therapeutics

    Macintyre G et al. (2016)                                                                                                            

    University of Cambridge & VU University Medical Center

  • Guidelines for cytogenetic investigations in tumours

    Hastings RJ et al. (2015)                                                                                                            

    Charles University Prague, CHUV, Great Ormond St Hospital, Gustave Roussy, Hospital del Mar, Institute of Genomic Medicine, Oslo University Hospital, Ospedale di Circolo-Polo Universitario, Our Lady's Children's Hospital, Oxford University Hospitals NHS Trust, Radboud University Medical Center, St James's Hospital, University of Cagliari, University of Groningen, University Hospital Ghent, UZ Leuven, VU University Medical Center

  • Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping

    De Vree PJP et al.  (2014)                                                                                                                             

    Cergentis, Erasmus Medical Center, Ghent University, Hubrecht Institute-KNAW, Leiden University Medical Center, The Netherlands Cancer Institute, Radboud University Medical Center, University of Amsterdam, University of Groningen, University Medical Center Utrecht & VIB

  • Webinars
  • Applications and principles of TLA-based complete gene sequencing and haplotyping

     

  • Whole genome coverage plots generated with TLA and standard capture. The obtained sequencing coverage is much wider for proximity ligated samples than for standard targeting procedures, which enables the robust detection of structural variants.
  • Detection of NTRK fusion in colorectal cancer samples (together with Tom van Wezel). A TPM3-NTRK1 fusion was clearly detectable from the TLA data, while the NTRK3 locus is unaffected.
  • ALK fusions are frequently resulting from large inversions on the same chromosome. TLA results give a robust and clear view on the exact nature of the DNA rearrangement. Sample 1 has a straight inversion resulting in an EML4-ALK fusion and the reciprocal ALK-EML4 fusion. Sample 2 has an inversion with a large deletion, causing an EML4-ALK fusion and a reciprocal fusion product further downstream.
  • Whole genome coverage plots generated with TLA and standard capture. The obtained sequencing coverage is much wider for proximity ligated samples than for standard targeting procedures, which enables the robust detection of structural variants.
  • Detection of NTRK fusion in colorectal cancer samples (together with Tom van Wezel). A TPM3-NTRK1 fusion was clearly detectable from the TLA data, while the NTRK3 locus is unaffected.
  • ALK fusions are frequently resulting from large inversions on the same chromosome. TLA results give a robust and clear view on the exact nature of the DNA rearrangement. Sample 1 has a straight inversion resulting in an EML4-ALK fusion and the reciprocal ALK-EML4 fusion. Sample 2 has an inversion with a large deletion, causing an EML4-ALK fusion and a reciprocal fusion product further downstream.

TLA enables

  • Detection of all SVs and small mutations
  • Analysis on FFPE, gDNA and cells
  • Multiplexing to detect all relevant mutations in a single DNA-based test
  • SV breakpoint detection for personalised MRD and ctDNA test development
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For Research Use Only.Not for use in diagnostic procedures.