Genomics in Modern Medicine Flashcards
1
Q
- This is a technology that permits rapid interrogation of DNA, up to and including entire genomes, via massively parallel sequencing
A
NGS
2
Q
- NGS are technologies that can rapidly interrogate DNA via
A
a. Massively parallel sequencing
3
Q
- How many base pairs, genes, proteins does the human genome have?
A
a. 3.2 billion base pairs
b. 19,000 genes
c. 100,00 proteins
4
Q
- Genetic variation can be based on what?
A
a. Size
b. Location
c. impact on a codon
d. Impact on the protein
e. Impact of the expression
5
Q
- What is the human variation for genetics?
A
a. 0.5% = 16 million base pairs
6
Q
- What are 3 different ways you can have DNA changes?
A
a. Single nucleotide variants
b. In-del
c. CNVs
7
Q
- These are commonly found in the population
A
a. Single nucleotide variants aka SNPs
8
Q
- These are single nucleotide variants that are commonly found in the population
A
SNP
9
Q
- These account for 75% of all DNA changes
A
a. Single nucleotide variants
10
Q
- These cause insertions and deletions of up to 50-100 nucleotides
A
a. In-del
11
Q
- How often do In-del occur compared to Single nucleotide variants?
A
1/10
12
Q
- These are the least frequent but affect the most nucleotides of all the DNA changes
A
CNVs
13
Q
- How can you perform a sample preparation?
A
a. RNA/DNA isolation → library → genome → sequencing
b. RNA/DNA isolation → library → panel → enrichment → sequencing
14
Q
- Each DNA fragment has what?
A
a. Sequencing primer
b. Adapters
c. Barcode
15
Q
- When you have a gene panel from a library, what is required?
A
a. Enrichment
16
Q
- This involves selecting specific regions of interest for sequencing using capture probes
A
Enrichment
17
Q
- Sequencing by synthesis (SBS) incorporates what for sequencing?
A
a. Fluorescent nucleotides
18
Q
- How many variants are in a ‘small panel’?
A
8000
19
Q
- How many variants are in an ‘exome’?
A
300,000
20
Q
- How many variants are in a ‘whole genome’?
A
a. 4,000,000
21
Q
- Sensitivity and specificity for SNPs are
A
a. >99%
22
Q
- Copy number variant detection is focused on what?
A
a. Exonic level deletion/duplication
23
Q
- What genes are important for osteogenesis imperfecta?
A
a. COL1A1
b. COL1A2
24
Q
- PLS3 variants cause what?
A
a. Opalescent teeth
b. Hypophosphatasia
c. Osteogenesis imperfecta
25
25. These are inherited syndromes that can affect tooth development
a. Mineralization defects
b. Ectodermal dysplasias
26
26. What genes affect mineralization defects?
a. PHEX
b. DMP1
c. FGF23
27
27. What is the cause of hypo/oligodontia?
PAX9
28
28. Amelogenesis imperfecta causes what?
a. Enamel defects
29
29. Are children routinely (pediatric populations) screened for Amelogensis imperfecta?
NO
30
30. What genes are associated with non-syndromic amelogenesis imperfecta?
a. AMELX
b. AMTN
c. ENAM
31
31. (T/F) Amelogenesis imperfecta is NOT diagnosed clinically
False, it is
32
32. How many genes are associated with NON-SYNDROMIC AI?
At least 18
33
33. These permit a new way of molecular diagnosis
NGS
