Samenvatting Genes & Genomes

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Samenvatting - Genes & Genomes

  • 1 Week 1

  • What is this weeks theme?
    Pedigrees and disease inheritance
  • 1.1 Lecture

  • Name some important reasons why genetic diagnoses are important
    Have an explanation, limiting diagnostic circuit, providing treatment, prognosis, information about the disease etc.
  • What does consanguineous mean?
    'having the same blood' or in short a common ancestor
  • What is a pedigree?
    A family tree showing symbols to visualise generations, sexes and whether or not being affected by a familiar disease
  • In what order are family members drawn in a pedigree?
    First the patient, partner, children, parents, siblings, nieces/nephews, grandparents/grandchildren, aunts/uncles, cousins etc. Later the partners family may also be included
  • How does one recognise dominant inheritance?
    Many family members having similar symptoms on one side of the family
  • What is genotype-phenotype correlation?
    The correlation between specific mutations and their phenotype. For example knowing that mutations in bp 0-150 have effect X and mutations in bp 150-300 have effect Y etc.
  • What are mosaic mutations?
    Dominant mutations that are not somatic in parents, but do occur in newborns. These have occured in oocytes or sperm cells, meaning they have effect after fertilisation.
  • What level of dominance do most mosaic mutations have?
    These are usually dominant mutations
  • How does one recognise recessive inheritance?
    Affected children are usually born to unaffected parents. Both parents are carriers, 2 carrier parents have a 25% chance to have an affected child
  • What is a specific feature of X-linked recessive inherited diseases?
    Mostly boys are affected, females can be carriers
  • Why is it possible for women to have some symptoms of X-linked recessive diseases?
    Due to the Lyon hypothesis, which states that each cell inactivates one of the X-chromosomes randomly. So roughly 50% of their tissue has an effective mutation
  • How can mosaic mutations play a role in X-linked diseases?
    These diseases can develop through mosaic mutations in the germline cells, meaning this mutation only occurs in oocytes
  • How does mitochondrial DNA pass on from parents to children?
    Mostly from the mother, since oocytes have the most mitochondria
  • How can symptoms vary between different patients suffering from diseases caused by mitochondrial DNA mutations?
    These depend on the number of affected mitochondria in the oocyte. Each oocyte has multiple different mitochondria, if someone suffers from this disease, the percentage of affected vs healthy mitochondria may differ, meaning that the symptoms differ.
  • What does multifactorial inheritance mean?
    Diseases caused by a multitude of factors, including genetics and environmental
  • What is a polygenic disease?
    A disease caused by mutations in multiple genes
  • What risks do family members have on the topic of multifactorial inheritance diseases?
    Usually only very close relatives have an extra risk. Since these are the only ones with both similar genetic and environmental factors
  • How does a threshold work with multifactorial diseases?
    Usually there are multiple factors and a minimum of a specific amount is required for seeing symptoms. This amount is a threshold
  • What does reduced penetrance mean? Name an example
    When a mutation is inherited, but this person does not have symptoms. For example BRCA mutations raise the risk of breast cancer, but not every person with the mutation does get breast cancer
  • What is a phenocopy?
    Copy of the phenotype, so meaning that different diseases result in the same phenotype
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Laatst toegevoegde flashcards

What is the main gain of using long read sequencing?
It is easier to detect large inversions and indels because you cover the entire gene in one read
What is so special about nanopore machines?
They can sequence a lot of DNA at the same time, but the machines are the size of a USB drive
What is nanopore sequencing?
There is a tiny pore in a surface, so small that only one nt can go through it. A motor protein is attached to the DNA, which runs the DNA through the pore. An electric current flows over the surface, which changes depending on what base is in the pore, this way a large DNA molecule can be sequenced very precisely and extremely fast.
How does 3rd gen sequencing work using light signals?
A tiny hole is built in a surface, there is a single polymerase in this pore. A single DNA molecule is run through the pore, with each base, a licht signal is show to see the nt that has been built in. This pore is so small that only the nucleotide in the polymerase is visible, so during duplication the DNA is sequenced
What is the main difference between NGS and third generation sequencing?
3rd gen uses a single molecule and long reads
How does one detect duplications in sequence viewers?
When the coverage of some parts is very high
How does one detect deletions in a sequence viewer?
When the coverage of certain parts of the reference genome is very low, one can at least see something is wrong
For what purpose can coverage be used?
Finding out if someone is heterozygous for a particular variant
After obtaining all reads, what is the next step, what extra part of information is obtained in this step?
Mapping all reads to the reference genome using a sequence viewer like IGV. Here one can see the coverage of each base separately to find the complete and correct sequence
How can one find SNP's or SNV's from the massive amounts of data obtained from NGS?
Using variant callers