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Growth and Development > Genomics in Modern Medicine > Flashcards

Genomics in Modern Medicine Flashcards

1
Q

What is the gold standard of genetic testing?

A

Sanger PCR

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2
Q

What does sanger PCR do?

A

Gene by gene, exon by exon sequencing

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3
Q

What are the downfalls of sanger PCR?

A
  • Time consuming
  • Limited to known genes/regions
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4
Q

What is next generation sequencing (NGS)?

A

Technologies that permit rapid interrogation of DNA, up to and including entire genomes, via massively parallel sequencing

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5
Q

What are the benefits of next generation sequencing (NGS)?

A

Decreasing cost and comparatively rapid results

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6
Q

How many base pairs in the human genome?

A

3.2 billion base pairs

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7
Q

How many nucleotides in the human genome?

A

6.4 billion

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8
Q

How many genes in the human genome?

A

19,000 genes (1-2% of the genome)

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9
Q

How many proteins does the human genome encode?

A

100,000

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10
Q

What is the normal human variation?

A

0.5% or 16 million base pairs

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11
Q

What can genetic variation be?

A

Size
Location

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12
Q

What can genetic variation impact?

A
  • Impact on a codon
  • Impact on the protein
  • Impact on expression
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13
Q

What is the least frequent genomic variant?

A

structural change (ex: whole chromosomes)

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14
Q

What is the most frequent genomic variant?

A

SNV

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15
Q

What are the ways to test/view the human genome for variants?

A

karyotype
aCGH
SNP array
gemonic sequencing

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16
Q

What are the order of most to least frequent: in-del, CNV, SNV?

A

SNV
In-del
CNV

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17
Q

Single nucleotide variants account for about ___ percent of all DNA changes?

A

75%

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18
Q

Single nucleotide variants are found in 1 in every ________ nucleotides

A

100-300

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19
Q

Insertions and deletions include up to _____ nucleotides

A

50-100

20
Q

In-del occur _____ as often as SNV

A

1/10

21
Q

____% of In-del are 1-10 nucleotides in length (very short)

A

90%
*harder to detect b/c so small

22
Q

What DNA change is the least frequent but large, so affect the most nucleotides?

A

CNVs

23
Q

What step must you do if you want to sequence a panal instead of the whole genome?

A

enrichment

24
Q

What step is required for all genome sequencing?

A

library

25
Q

What are the steps for whole genome sequencing?

A
  • RNA/DNA isolation
  • library
  • genome
  • sequencing
26
Q

What are the steps for a small section genome sequencing?

A
  • RNA/DNA isolation
  • library
  • panel
  • enrichment
  • sequencing
27
Q

What is the goal of library preparation?

A

add primers and barcodes to identify individuals

28
Q

What is shotgun sequencing?

A

fragmenting DNA during library preparation

29
Q

Each DNA fragment has what when library is completed?

A
  • Sequencing primer
  • Adapters
  • Barcode
30
Q

What is enrichment?

A

Involves selecting out specific regions of interest for sequencing using capture probes

31
Q

Why would you sequence a small chunk instead of the whole genome?

A
  • Pooling allows for samples to be mixed together before enrichment
  • Allows for more sequencing of targeted regions
  • Decreases costs and time per sample
32
Q

How does sequencing works?

A
  • Fluorescent nucleotides are incorporated one at a time
  • Lasers excite the fluorescence, which is read by the instrument
33
Q

What is variant detection?

A

the analysis of sequence data to find the differences between an individual’s DNA and the human reference genome

34
Q

What are the steps in the variant detection process?

A
  1. Sequence alignment
  2. Candidate variant identification
  3. Consensus calling
  4. Characterization
35
Q

What is the variant count for a typical small panel?

A

8000

36
Q

What is the variant count for a typical exome?

A

300,000

37
Q

What is the variant count for a typical whole genome?

A

4,000,000

38
Q

What is the sensitivity and specificity for SNPs?

A

> 99%

39
Q

What does next generation sequencing (NGS) allow for?

A

diagnosis of atypical presentations that would not have otherwise be considered

40
Q

What are examples of inherited syndromes that affect tooth development?

A
  • Mineralization Defects (PHEX, DMP1, FGF23)
  • Ectodermal dysplasias
  • Hypo/Oligodontia (PAX9)
  • Enamel defects such as Amelogenesis Imperfecta (ENAM)
41
Q

What is amelogenesis imperfecta?

A

Several forms of autosomal dominant enamel dysplasia
- Enamel hypoplasia or hypocalcification

42
Q

How many genes associated with non-syndromic amelogenesis imperfecta?

A

at least 18

43
Q

What is the prevalence range of ameologenesis imperfecta?

A

1/700 to 1/14,000

44
Q

What were the 3 genes that had variants related to amelogenesis imperfecta?

A
  • Amelogenin
  • Amelotin
  • Enamelin
45
Q

What are common barriers to genetic testing in dentistry?

A
  • Identified a need for more education
  • Justification of testing
  • Changing landscape (Patients will ask for it)
46
Q

___ permits a new way of molecular diagnosis via panels, exomes, and genomes

A

NGS

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