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  • Minocycline HCl br every gene annotation br annotation

    2019-10-07


    every gene annotation
    annotation annotation gene copy- fusion
    and and number breakpoint
    COSMIC query COSMIC query variation rebuilding
    get clinically relevant information
    final clinical report
    Abbreviations: CNA ¼ copy number alteration; COSMIC ¼ Catalogue Of Somatic Mutations In Cancer; INDEL ¼ insertion/deletion; SNV ¼ single nucleotide variant.
    Giorgio Corti et al
    Figure 4 The Final Report. A, The First Part of the Final Report Reviews General Information About the Patient, Along With Sample Characteristics and Next Generation Sequencing Technical Specifications. B, The Second Part Summarizes Overall Molecular Features of the Sample, Such as Tumor Mutational Burden, Microsatellite Status, and Ploidy. C, In the Third Part, Results From Each Module Used During the Bioinformatics Analysis are Reported in a Table Along With the Most Relevant Annotations. SNV and INDEL Minocycline HCl Reported Listing Genomic Position, COSMIC Occurrence, Variant Frequency, Amino Acid, and Nucleotide Changes. FUSION are Reported Listing the 2 Genes Involved in the Translocation Together With the Number of Supporting Reads. CNAs are Shown Through a Graphical Representation of the Entire Genome and a More Detailed Plot of the Individual Chromosome
    A
    B
    Report N°
    ADDRESSEE
    Date
    • Ordering Center • Oncologist / Pathologist • Date of request
    PATIENT
    ASSAY
    ID N° XXXXX
    Genomic Target WES Sequencer HiSeq2000
    Clinical Diagnosis mCRC
    Target size
    SPECIMEN (TUMOR)
    SPECIMEN (NORMAL)
    XXXXX
    XXXXX
    Sample type
    FFPE
    Sample type
    PBMC
    Tissue of origin
    colon
    Tissue of origin
    PBMC
    Date of delivery
    XXXX/XX/XX
    Date of delivery
    XXXX/XX/XX
    Date of collection
    XXXX/XX/XX
    Date of collection
    XXXX/XX/XX
    GENETIC CHARACTERIZATION
    Reference Genome
    Microsatellite status
    Ploidy level
    Ploidy 2N
    Tumor Mutational Burden
    Aneuploidy (% of regions)
    SNVs identified
    Gene information
    Variation description
    Annotations
    Symbol Name N aa Effect Frequency Coord. Supporting Accession COSMIC
    change change reads N°
    antigen p53 syn
    INDELs identified
    Gene information
    Variation description
    Annotations
    Symbol Name Type Length Effect
    Frequency
    Coord. Supporting
    Accession COSMIC
    reads
    Adenomatous
    Frame
    APC polyposis coli Del
    shift
    protein
    FUSIONs identified
    Gene 1 information Gene 2 information
    Variation description
    Symbol Name Symbol
    Name
    Supporting reads
    High affinity
    LMNA Prelamin-A/C NTRK1
    nerve growth
    factor
    receptor
    For research use only
    CNAs idenƟfied
    Gene informaƟon
    CN in sample 1 CN in sample 2
    VariaƟon
    CN
    SupporƟng
    SupporƟng
    Copy number
    Symbol Name
    Coord.
    CN
    reads
    reads
    variation
    ERBB2
    erb-b2 receptor
    tyrosine kinase 2
    For research use only
    Abbreviations: CNAs ¼ copy number alterations; COSMIC ¼ Catalogue Of Somatic Mutations In Cancer; FFPE ¼ formalin-fixed paraffin-embedded; INDEL ¼ insertion/deletion; mCRC ¼ metastatic colorectal cancer; PBMC ¼ peripheral blood mononuclear cell; QC ¼ quality control; SNV ¼ single nucleotide variant; WES ¼ whole exome sequencing.
    IDEA NGS Workflow
    the translocation occurs.49-51 Once a translocation is identified, it can be exploited to design patient-specific PCR probes and track the rearrangement in ctDNA in longitudinal plasma samples.51