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Genetics and genomes > W12LECT - Genomics in dental medicine > Flashcards

W12LECT - Genomics in dental medicine Flashcards

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Biology 101 flashcards
1
Q

Amelogenesis imperfecta
1. What are the features of Amelogenesis imperfecta?

A

1/ X – Dominant
2/ Tooth enamel formation problem

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2
Q

Amelogenesis imperfecta
1. What are the features of Amelogenesis imperfecta?

A

1/ X – Dominant
2/ Tooth enamel formation problem
3/ Genes affected”
- AMELX; Xp22.3-1; amelogenin
- ENAM; 4q13.3; enamelin (5%)

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3
Q

How do we find mutation is in the patient?

A
  • collect DNA of the patients
    – isolate it from blood
  • collect medical data of the patients
  • analyze the pedigree
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4
Q

What is the use of Sequencing?

A
  • find a new mutation in a specific area
  • search for SNPs, small insertions, deletions, duplications
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5
Q

How do we perform Genotyping by sequencing?

A

1/ The sequence of nucleotides and the corresponding signal strength is analyzed.
2/ Color-coded chromatograms facilitate evaluation.
3/ on the chromatogram only one nucleotide specific signal is shown in homozygotes (for a nucleotide).
4/ on the chromatogram two nucleotides specific signals (which are a little decreased) can be seen in heterozygotes
homozygous (C/C)

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6
Q

What is the result of Genotyping by sequencing?

A
  1. New SNV in a specific area
  2. A deletion was found in some patients
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7
Q

What are the features of Genotyping by Sanger sequencing

A
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8
Q

What are the 2 Methods for the genomic backgrounds of diseases?

A
  1. Wet laboratory methods (classical methods, lab experiments)
  2. in silico methods (analyze data, bioinformatics)
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9
Q

What are the 2 Methods for the genomic backgrounds of diseases?

A
  1. Wet laboratory methods (classical methods, lab experiments)
  2. in silico methods (analyze data, bioinformatics)
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10
Q

What are the features of In silico methods?

A
  • (Re) analysis of data from on-line databases
  • Lots of online software
  • Discovering new genes (APOA5)
  • Meta-analyzes (joint analysis of several previous studies)
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11
Q

What are the 2 Genomics methods for studying the genetic background of disease?

A
  1. Hypothesis-driven approaches
  2. Hypothesis-free approaches
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12
Q

How do we perform In silico methods?

A
  • alleles or genotypes of markers (e.g.: SNPs, microsatellites), are determined in patients vs. in controls
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13
Q

Association studies
1. Association is a statistical statement
=> What is this statement?

A
  1. The specific allele significantly more likely to occur WITH a specific phenotype
  2. This means:
    – case-control method, we examine the presence of the selected (candidate) genevariant
    – whether it is more common in patients, than in healthy controls
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14
Q

Genetic markers
1. What is a genetic marker?

A

A genetic marker is usually a sequence variation with a known location on a chromosome that can be used to identify individuals, with a relative high chance to differentiate between different alleles on homologous chromosomes.

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15
Q

Genetic markers
2. What are examples of genetic markers?

A
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16
Q

How should Microsatellite detection be?

A
17
Q

Examples of using STR as markers
1. How do we use STR as markers in Prenatal diagnosis?

A

5-6 STR markers/chromosome

18
Q

How do we Use SNP/SNV as markers

A

They are only biallelic, but much more than STR >300 million vs. ≈ 30,000
Easier to detect

19
Q

Give an example of Using SNP/SNV as markers?

A
  • Genes predisposing for numerical differences in teeth are searched
  • 21 SNPs were genotyped in 13 genes by PCR-RFLP Patients: 159 congenital hypodontia or oligodontia Controls: 185 fully healthy, wisdom tooth also
  • frequency of SNPs were compared in patients and controls
    => result: CHDH gene deficiency affects the number of teeth
20
Q

What is the method that measures Whole genome gene expression?

A

microarray
e.g.: 44k chip: measures the expression of 44,000 mRNAs simultaneously.

21
Q

What is the role of DNA microarray?

A
  • It measures DNA or uses DNA as a part of its detection system.
  • In each of the spots in this array, a known DNA sequence or gene is orderly arranged.
22
Q

What are the features of sequencing 2nd generation (New generation, ie NGS = next generation sequencing or short-read sequencing, massively parallel sequencing)?

A
  • NGS (next generation sequencing)
  • Advantage: The majority of genetic variations can be detected
  • Disadvantage: difficult to evaluate (too many data)
23
Q

What are the examples of sequencing 2nd generation (New generation, ie NGS = next generation sequencing or short-read sequencing, massively parallel sequencing)?

A
  1. Exome sequencing: for monogenic diseases
  2. RNA-seq: gene expression measurement
  3. Bisulfite sequencing: methylation pattern
  4. Sequencing of pathogens
  5. Metagenomics: determination of the microbiome 55
24
Q

Explain WES (whole exome sequencing) vs. WGS (Whole genome sequencing)

A
  1. Genome > 3 billion bp; >15 million bp difference vs reference
    genome
  2. Exome: 1.2 % of the genome; ≈180.000 exons
  3. Majority of monogenic diseases are caused by mutations in protein coding regions (exons)
25
Q

What are Advantages of Exome
Sequencing?

A
  1. Majority of monogenic diseases are caused by mutations in protein coding regions (exons)
  2. Provides a cost-effective alternative to whole-genome sequencing (4–5 Gb of sequencing per exome compared to ≈90 Gb per whole human genome)
  3. Produces a smaller, more manageable data set for faster, easier analysis compared to whole-genome approaches
  4. Cheaper, easier to interpret
26
Q

What are weaknesses of Exome sequences?

A

In ≈70% of patients in whom there was a high degree of pre-test suspicion for a monogenic rare diseases, exome sequencing provides no molecular diagnosis.

27
Q

What are the reasons of Exome sequences?

A
  1. Mutations in non-coding regions: RNA genes (underrepresented); regulatory regions (enhancers, promoters, introns)
  2. Mosaicism
  3. Short read sequencing is not good in detecting indels (small and large insertion-deletions), copy-number variations (CNVs), and chromosomal rearrangements
  4. Epigenetics
28
Q

What are the 2 Methods for identification of larger deletions or inversions?

A
  1. MLPA: Multiplex ligation-dependent probe amplification (see in practice)
  2. Long range sequencing (third generation sequencing) creating ten thousand to a hundred thousand bases) length DNA
    sequences.
    - Nanopore sequencing
    - PacBio sequencing
29
Q

What are the Advantages of third generation, long read sequencing?

A

“long-read sequencing harbors the potential to deliver near-perfect genome analysis in the
future and long-read optical mapping may replace almost all karyotyping, FISH, and CNV- microarray assays in routine diagnostics.”

30
Q

What is the Possible role of epigenetic regulation in diseases?

A
  1. MZ twins with identical pathogenic mutation in WAS gene
  2. Discordant phenotypes:
    - X-linked thrombocytopenia (XLT)
    - More severe Wiskott-Aldrich syndrome-like (WAS; OMIM 301000) phenotype
  3. Researchers found that the sibling with a more aggressive phenotype showed a DNA hypermethylation compared to the brother with XLT.
31
Q

What is the mechanism of Detection of methylation pattern: whole-genome bisulfite sequencing (WGBS)?

A
  1. In bisulfite conversion cytosine is converted to uracil using sodium bisulfite, while 5-methylcytosine (5-mC) remains intact.
  2. After PCR uracil becomes thymine
  3. Comparison of the bisulfite-treated and non-treated by sequencing. Where cytosine remained cytosine, it was methylated.
32
Q

What are Shortcomings of animal models?

A
  1. Similar diseases can have different pathomechanisms
  2. At genomic levels the differences are larger (junk regions).
  3. Homologous genes with different functions
33
Q

What are features of Genetically modified animals?

A
  1. „KO” animals:
    – Disease models can be developed with inactivating genes
    – Study of gene functions
  2. Transgenic animals: disease models, gene functions
  3. In vivo gene modification, see CRISPR/Cas9
34
Q

Give the Summary: Methodology

A

Genetics and genomes (19 decks)

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