Single Nucleotide Variants (SNVs) in Genetics
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Questions and Answers

What is another term for single nucleotide variants?

  • Chromosomal abnormalities
  • Gene mutations
  • Point mutations (correct)
  • Genetic disorders

    • How many types of SNVs are there?

  • Four
  • Eight
  • Six (correct)
  • Ten

    • What is the primary function of nucleotide excision repair (NER)?

  • Repairing small, non-helix-distorting lesions
  • Repairing helix-distorting damage (correct)
  • Repairing DNA methylation errors
  • Repairing base-base mismatches

    • What is the result of spontaneous deamination of 5-methylcyosine?

    <p>C&gt;T at CG dinucleotides</p> Signup and view all the answers

    What is an example of an exogenous mutational process?

    <p>Cigarette smoke</p> Signup and view all the answers

    What is the consequence of mutations in DNA repair factors?

    <p>Increased risk of disease</p> Signup and view all the answers

    What percentage of human malignant melanomas has the BRAF V600E mutation?

    <p>60%</p> Signup and view all the answers

    What is the position of the mutation in the gene BRAF that causes BRAF V600E?

    <p>1799</p> Signup and view all the answers

    What is a common outcome of unbalanced structural variants?

    <p>An overall gain or loss of DNA from the cell</p> Signup and view all the answers

    What is the purpose of chromosome painting?

    <p>To visualize structural variants in chromosomes</p> Signup and view all the answers

    What is the term for a type of balanced structural variant involving two chromosomes?

    <p>Reciprocal translocation</p> Signup and view all the answers

    What is a common characteristic of unbalanced structural variants and copy number variants?

    <p>They are frequently found in cancer</p> Signup and view all the answers

    What is the result of double-stranded DNA breakage?

    <p>The repair of DNA through homologous recombination or non-homologous end joining</p> Signup and view all the answers

    What is an example of a developmental disorder associated with unbalanced structural variants and copy number variants?

    <p>22q11.2 deletion syndrome</p> Signup and view all the answers

    What is the primary mechanism of repairing double-stranded DNA breakage in structural variants?

    <p>Non-homologous end joining (NHEJ) and homologous recombination (HR)</p> Signup and view all the answers

    What is the term for the process of sorting chromosomes into separate tubes, fluorescently labeling them, and hybridizing them onto a chromosomal karyotype?

    <p>Chromosome painting</p> Signup and view all the answers

    Which of the following is an example of an unbalanced structural variant?

    <p>22q11.2 deletion syndrome</p> Signup and view all the answers

    What is the result of unbalanced structural variants in the germline?

    <p>Developmental disorders</p> Signup and view all the answers

    What is the characteristic of balanced structural variants?

    <p>Do not lead to an overall gain or loss of DNA from the cell</p> Signup and view all the answers

    What is the outcome of unbalanced structural variants in cancer cells?

    <p>Copy number variants</p> Signup and view all the answers

    Which condition is commonly associated with trisomy 21?

    <p>Down syndrome</p> Signup and view all the answers

    What process often occurs in cancer cells resulting in tetraploid cells?

    <p>Endoreduplication</p> Signup and view all the answers

    What is the primary role of the spindle assembly checkpoint?

    <p>To ensure chromosomes are correctly attached to the spindle apparatus</p> Signup and view all the answers

    Which error commonly leads to aneuploidy during cell division?

    <p>Segregation errors</p> Signup and view all the answers

    What is a frequent cause of whole genome duplication in cancer cells?

    <p>Endoreduplication</p> Signup and view all the answers

    What is the primary difference between germline cells and somatic cells?

    <p>Germline cells are able to contribute to the next generation, while somatic cells are not.</p> Signup and view all the answers

    Which type of variation is more important for understanding inherited genetic disease?

    <p>Germline variation</p> Signup and view all the answers

    What is the primary consequence of somatic variation?

    <p>It can lead to cancer and ageing</p> Signup and view all the answers

    Which cell type is responsible for passing on genetic variation to the next generation?

    <p>Germline cells</p> Signup and view all the answers

    What is the main difference between germline and somatic variation?

    <p>Germline variation is inherited, while somatic variation is not</p> Signup and view all the answers

    Study Notes

    Single Nucleotide Variants (SNVs)

    • Also known as "point mutations" or "substitutions"
    • If they occur in the germline and are variable within individuals in a population, they are often termed "single nucleotide polymorphisms" (SNPs)

    Types of SNVs

    • Two types are transitions (involving only purines or only pyrimidines respectively)
    • Four types are transversions (involving purines converting to pyrimidines or vice versa)

    Repair Pathways

    • Three cellular DNA repair pathways: nucleotide excision repair (NER), base excision repair (BER), and mismatch repair (MMR)
    • NER primarily repairs helix-distorting damage
    • BER mainly repairs small, non-helix-distorting lesions
    • MMR repairs base-base mismatches

    Causes of SNVs

    • Exogenous mutational processes: involve exposure to exogenous agents (e.g. cigarette smoke, ultraviolet (UV) light)
    • Endogenous mutational processes: derive from mutational activities within the cell (e.g. spontaneous deamination of 5-methylcyosine, causing C>T at CG dinucleotides)

    Effects of SNVs

    • Most SNVs have no effect on the cell
    • A small subset cause disease (e.g. 1799 T>A mutation in the BRAF gene, causing BRAF V600E, present in 60% of human malignant melanomas)
    • Mutations in DNA repair factors can cause disease by causing excessive accumulation of mutations (e.g. xeroderma pigmentosum)

    Structural Variants

    • Large-scale genomic rearrangements that lead to juxtaposition of previously unconnected DNA
    • Frequently involve double-stranded DNA breakage, which is repaired by homologous recombination (HR) or non-homologous end joining (NHEJ)

    Types of Structural Variants

    • Inter-chromosomal: involves two chromosomes
    • Intra-chromosomal: involves different parts of the same chromosome

    Balanced vs Unbalanced Structural Variants

    • Balanced: do not lead to an overall gain or loss of DNA from the cell
    • Unbalanced: introduce additional DNA or cause DNA to be lost from the cell, resulting in copy number variants

    Visualizing Structural Variants

    • Chromosome painting: sorting chromosomes into separate tubes, fluorescently labelling them, and hybridizing them onto a chromosomal karyotype

    Examples of Structural Variants

    • Philadelphia chromosome: a translocation between human chromosomes 9 and 22, frequently observed in chronic myeloid leukaemia, and an example of a reciprocal translocation (a type of balanced structural variant)
    • 22q11.2 deletion syndrome: an example of an unbalanced structural variant, associated with developmental disorders

    Clinical Significance

    • Unbalanced structural variants and copy number variants are frequently found in cancer
    • They can also be found in the germline, where they are frequently associated with developmental disorders

    Structural Variants

    • Large-scale genomic rearrangements that lead to juxtaposition of previously unconnected DNA
    • Frequently involve double-stranded DNA breakage, which is repaired by homologous recombination (HR) or non-homologous end joining (NHEJ)

    Types of Structural Variants

    • Inter-chromosomal: involves two chromosomes
    • Intra-chromosomal: involves different parts of the same chromosome

    Balanced vs Unbalanced Structural Variants

    • Balanced: do not lead to an overall gain or loss of DNA from the cell
    • Unbalanced: introduce additional DNA or cause DNA to be lost from the cell, resulting in copy number variants

    Visualizing Structural Variants

    • Chromosome painting: sorting chromosomes into separate tubes, fluorescently labelling them, and hybridizing them onto a chromosomal karyotype

    Examples of Structural Variants

    • Philadelphia chromosome: a translocation between human chromosomes 9 and 22, frequently observed in chronic myeloid leukaemia, and an example of a reciprocal translocation (a type of balanced structural variant)
    • 22q11.2 deletion syndrome: an example of an unbalanced structural variant, associated with developmental disorders

    Clinical Significance

    • Unbalanced structural variants and copy number variants are frequently found in cancer
    • They can also be found in the germline, where they are frequently associated with developmental disorders

    Cytogenetic Variation

    • Involves the gain or loss of one or more entire chromosome(s), leading to aneuploidy
    • Can be caused by segregation errors in the germline, resulting in conditions such as Down syndrome (trisomy 21)
    • Whole genome duplication can occur, leading to tetraploid cells, as well as additional aneuploidy, frequently in cancer cells
    • This can occur via a process of endoreduplication in cancer cells

    Cellular Checkpoints

    • The spindle assembly checkpoint is a mechanism that prevents aneuploidy
    • This checkpoint prevents progression through mitosis if chromosomes are not correctly attached to the spindle apparatus
    • If aneuploidy is observed, it indicates that these checkpoints have failed

    Germline and Somatic Cells

    • The body consists of two distinct cell types: germline cells and somatic cells.
    • Germline cells are gametes (sperm and egg cells) or their precursors.
    • Germline cells can pass their genetic variation to the next generation.

    Germline Variation

    • Germline variation occurs in germline cells and is inherited.
    • It is important for understanding inherited genetic disease.

    Somatic Cells

    • Somatic cells are the cells of the body that cannot contribute to the next generation.
    • All cells except for germ cells are somatic cells.

    Somatic Variation

    • Somatic variation is "private" to the individual body and cannot contribute to the next generation.
    • It is important in cancer and possibly in ageing.

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    Description

    This quiz covers single nucleotide variants, also known as point mutations or substitutions, including types of SNVs and their characteristics.

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