Pharmacogenomic part 1
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Questions and Answers

What is a common outcome of chromothripsis in human malignancies?

  • Increased survival of non-transformed cells
  • Lower expression of oncogenes
  • Gene amplification leading to resistance to therapy (correct)
  • Complete eradication of cancerous cells

    • Which tumor suppressor gene is often lost prior to chromothripsis?

  • CDKN2A
  • TP53 (correct)
  • BRCA1
  • PTEN

    • In pancreatic cancer, which genetic alterations are commonly associated with chromothripsis?

  • Inactivation of the TP53 gene (correct)
  • Amplification of the BRAF gene
  • Mutation of the EGFR gene
  • Overexpression of the APC gene

    • What role do APOBEC enzymes play in cancer progression?

    <p>Formation of kataegis through mutating TpC dinucleotides (D)</p> Signup and view all the answers

    What defines kataegis in tumors?

    <p>Localized hypermutation particularly at TpC dinucleotides (A)</p> Signup and view all the answers

    What effect does chromothripsis have on non-transformed cells?

    <p>Leads to cell death in most instances (A)</p> Signup and view all the answers

    Which of the following is a hallmark of genetic changes due to chromothripsis?

    <p>Complex rearrangements leading to oncogenic gene fusions (A)</p> Signup and view all the answers

    In supratentorial ependymomas, chromothripsis specifically affects which chromosome?

    <p>Chromosome 11 (B)</p> Signup and view all the answers

    What may contribute to the varying rates of mutations among individuals?

    <p>Differing carcinogen exposures or neoplastic changes (D)</p> Signup and view all the answers

    Which mutational signature is linked to tobacco smoking and displays transcriptional strand bias?

    <p>Signature 4 (C)</p> Signup and view all the answers

    Which signature is associated with malignant melanoma and primarily exhibits C/T mutations?

    <p>Signature 7 (C)</p> Signup and view all the answers

    What characterizes Signature 6 in relation to DNA repair mechanisms?

    <p>It indicates microsatellite instability linked to defective DNA mismatch repair. (D)</p> Signup and view all the answers

    Which of the following indel signatures is linked to BRCA1 and BRCA2 mutations?

    <p>Signature 3 (A)</p> Signup and view all the answers

    Which mutation type represents a common outcome of bulky DNA adducts from tobacco smoke?

    <p>C/A mutations in transcriptionally active strands (C)</p> Signup and view all the answers

    What distinguishes Signature 15 from other mutational signatures?

    <p>It is also associated with stomach cancers. (C)</p> Signup and view all the answers

    Which process is particularly influenced by transcription-coupled nucleotide excision repair (NER)?

    <p>The efficiency of DNA damage and maintenance (C)</p> Signup and view all the answers

    What is the primary purpose of washing in the experimental protocol?

    <p>To remove unbound DNA and select for methylated DNA (A)</p> Signup and view all the answers

    Which step is NOT included in the library preparation for sequencing?

    <p>Digestion with methylation-sensitive enzymes (C)</p> Signup and view all the answers

    What is the role of methylation-sensitive restriction enzymes in MRE-SEQ?

    <p>To cut unmethylated regions while leaving methylated DNA intact (A)</p> Signup and view all the answers

    How does MeDIP-seq and MRE-seq complement each other?

    <p>One focuses on methylated regions while the other targets unmethylated regions (C)</p> Signup and view all the answers

    What is the significance of quality control checks using MeDIP-specific QC tools like MEDIPS?

    <p>To filter out low-quality reads and errors (A)</p> Signup and view all the answers

    What bioinformatic tool is used to detect unmethylated regions post sequencing?

    <p>Bismark (D)</p> Signup and view all the answers

    What is the first step in the MRE-seq protocol?

    <p>DNA extraction (B)</p> Signup and view all the answers

    Which genomic regions are primarily targeted by the MRE-seq method?

    <p>CpG islands, gene promoters, and regulatory regions (C)</p> Signup and view all the answers

    What is the primary role of DNA methylation in cellular processes?

    <p>Regulating transcription and maintaining epigenetic stability (A)</p> Signup and view all the answers

    Which of the following statements about 5-methylcytosine (5mC) is accurate?

    <p>It is a stable form of DNA modification with significant roles in development. (D)</p> Signup and view all the answers

    How does DNA methylation primarily influence chromatin structure?

    <p>By leading to a condensed chromatin structure (D)</p> Signup and view all the answers

    What characteristic is true regarding CpG islands (CGI) in the genome?

    <p>They are clusters of CpGs that are typically unmethylated and associated with active genes. (B)</p> Signup and view all the answers

    What is the function of DNA methyltransferases (DNMTs) in the genome?

    <p>They add methylation marks to cytosines in DNA. (C)</p> Signup and view all the answers

    Which of the following DNMTs is known as a canonical cytosine-5 methyltransferase?

    <p>DNMT1 (C)</p> Signup and view all the answers

    What is the relationship between m6A modifications and lung cancer?

    <p>m6A modifications activate multiple signaling pathways associated with lung cancer. (C)</p> Signup and view all the answers

    Why is the symmetrical presence of CpG methylation important?

    <p>It allows post-replicative maintenance of DNA methylation patterns. (B)</p> Signup and view all the answers

    What role does TET2 play in inflammatory regulation?

    <p>It helps regulate inflammation in various genes. (A)</p> Signup and view all the answers

    What mechanism is primarily used for demethylation of the paternal genome after fertilization?

    <p>A combination of passive dilution and TET3-mediated active modification. (B)</p> Signup and view all the answers

    Which statement correctly describes histone properties?

    <p>Histones are positively charged proteins that bind tightly to negatively charged DNA. (D)</p> Signup and view all the answers

    What distinguishes the non-catalytic roles of TDG from its catalytic ones?

    <p>Non-catalytic roles are less understood but oppose the catalytic functions. (B)</p> Signup and view all the answers

    What condition is associated with aberrant demethylation?

    <p>Cancer development. (C)</p> Signup and view all the answers

    How is the maternal genome primarily demethylated post-fertilization?

    <p>By passive dilution only. (A)</p> Signup and view all the answers

    What role does active DNA demethylation play in embryonic stem cell maintenance?

    <p>It contributes to cellular differentiation processes. (D)</p> Signup and view all the answers

    What phenotypic differences can arise in progeny with epigenetic defects between different parental genotypes?

    <p>Variation in embryonic lethality and growth defects. (D)</p> Signup and view all the answers

    What does CAB-seq primarily produce for analysis in genomic regions?

    <p>A comprehensive 5caC-specific methylation map (C)</p> Signup and view all the answers

    Which tools are used for identifying changes in 5caC levels during comparative studies?

    <p>methylKit or EdgeR (C)</p> Signup and view all the answers

    What role does 5caC serve in the context of DNA demethylation?

    <p>It marks regions of active demethylation. (C)</p> Signup and view all the answers

    What is a key advantage of long-read sequencing in epigenomic studies?

    <p>It allows detection of modifications without chemical treatment. (C)</p> Signup and view all the answers

    Which of the following is NOT part of the general steps in long-read sequencing?

    <p>Sample Decontamination (D)</p> Signup and view all the answers

    In bioinformatics workflow, what does the tool Minimap2 primarily focus on?

    <p>Alignment and error correction (D)</p> Signup and view all the answers

    Which of the following modifications can be detected through methylation analysis in long-read sequencing?

    <p>5mC and 5hmC (A)</p> Signup and view all the answers

    What insight does mapping 5caC provide regarding gene regulation?

    <p>It uncovers active regulatory elements and gene dynamics. (A)</p> Signup and view all the answers

    Study Notes

    Gene Ontology (GO)

    • GO is a database for systematic analysis of gene function.
    • It integrates genomic, biochemical, and phylogenetic information.
    • KEGG and Reactome are types of gene set enrichment analysis (GSEA), often used for functional analysis.
    • A GO annotation connects a gene product to a GO term using relations from the Relation Ontology (RO).
    • Each annotation is independent.

    Key Components of a GO Annotation

    • Gene product: A protein, miRNA, tRNA, or other gene product.
    • GO term: The specific Gene Ontology term linked to the gene product.
    • Reference: Usually a PMID, DOI, or GO reference.
    • Evidence code: Describes the type of evidence supporting the annotation.
      • Manually-curated if reviewed by an expert.
      • Automated if not manually reviewed.

    Semantics of a Standard GO Annotation

    • Molecular Function: The gene product's molecular activity.
    • Biological Process: Pathways and processes the gene product contributes to.
    • Cellular Component: Where in the cell the gene product acts.

    PANTHER

    • Protein ANalysis THrough Evolutionary Relationships Classification System
    • Provides functionally-annotated gene families and phylogenetic trees.
    • Includes subfamily, ortholog, paralog, function, and pathway information.

    KEGG

    • Database for systematic analysis of gene functions.
    • Contains over 19 sub-databases of genomic, biochemical, and phylogenetic information.

    Reactome

    • Open-source knowledge base of biomolecular pathways.
    • Organizes biological processes into reactions, entities, networks, and pathways.
    • Uses reaction entities (nucleic acids, proteins, complexes).

    GeneCodis

    • API and web-tool for enrichment analyses
    • Supports gene and protein nomenclature from NCBI and Ensembl.
    • Includes regulatory elements like TFs and miRNAs.
    • Contains annotations for 14 different organisms.

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    Pharmacogenomics 2-1 PDF

    Description

    Explore the intricate relationship between chromothripsis and cancer in this quiz. Test your knowledge on genetic markers, mutational signatures, and the impacts of chromothripsis on various tumor types, including pancreatic cancer and ependymomas. This quiz covers essential concepts regarding tumor suppressor genes and their role in malignancies.

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