Genomics in Modern Medicine

Question 1

1. This is a technology that permits rapid interrogation of DNA, up to and including entire genomes, via massively parallel sequencing

Answer 1

NGS

Question 2

2. NGS are technologies that can rapidly interrogate DNA via

Answer 2

a. Massively parallel sequencing

Question 3

3. How many base pairs, genes, proteins does the human genome have?

Answer 3

a. 3.2 billion base pairs
b. 19,000 genes
c. 100,00 proteins

Question 4

4. Genetic variation can be based on what?

Answer 4

a. Size
b. Location
c. impact on a codon
d. Impact on the protein
e. Impact of the expression

Question 5

5. What is the human variation for genetics?

Answer 5

a. 0.5% = 16 million base pairs

Question 6

6. What are 3 different ways you can have DNA changes?

Answer 6

a. Single nucleotide variants
b. In-del
c. CNVs

Question 7

7. These are commonly found in the population

Answer 7

a. Single nucleotide variants aka SNPs

Question 8

8. These are single nucleotide variants that are commonly found in the population

Answer 8

SNP

Question 9

9. These account for 75% of all DNA changes

Answer 9

a. Single nucleotide variants

Question 10

10. These cause insertions and deletions of up to 50-100 nucleotides

Answer 10

a. In-del

Question 11

11. How often do In-del occur compared to Single nucleotide variants?

Answer 11

1/10

Question 12

12. These are the least frequent but affect the most nucleotides of all the DNA changes

Answer 12

CNVs

Question 13

13. How can you perform a sample preparation?

Answer 13

a. RNA/DNA isolation → library → genome → sequencing
b. RNA/DNA isolation → library → panel → enrichment → sequencing

Question 14

14. Each DNA fragment has what?

Answer 14

a. Sequencing primer
b. Adapters
c. Barcode

Question 15

15. When you have a gene panel from a library, what is required?

Answer 15

a. Enrichment

Question 16

16. This involves selecting specific regions of interest for sequencing using capture probes

Answer 16

Enrichment

Question 17

17. Sequencing by synthesis (SBS) incorporates what for sequencing?

Answer 17

a. Fluorescent nucleotides

Question 18

18. How many variants are in a ‘small panel’?

Answer 18

8000

Question 19

19. How many variants are in an ‘exome’?

Answer 19

300,000

Question 20

20. How many variants are in a ‘whole genome’?

Answer 20

a. 4,000,000

Question 21

21. Sensitivity and specificity for SNPs are

Answer 21

a. >99%

Question 22

22. Copy number variant detection is focused on what?

Answer 22

a. Exonic level deletion/duplication

Question 23

23. What genes are important for osteogenesis imperfecta?

Answer 23

a. COL1A1
b. COL1A2

Question 24

24. PLS3 variants cause what?

Answer 24

a. Opalescent teeth
b. Hypophosphatasia
c. Osteogenesis imperfecta

Question 25

25. These are inherited syndromes that can affect tooth development

Answer 25

a. Mineralization defects
b. Ectodermal dysplasias

Question 26

26. What genes affect mineralization defects?

Answer 26

a. PHEX
b. DMP1
c. FGF23

Question 27

27. What is the cause of hypo/oligodontia?

Answer 27

PAX9

Question 28

28. Amelogenesis imperfecta causes what?

Answer 28

a. Enamel defects

Question 29

29. Are children routinely (pediatric populations) screened for Amelogensis imperfecta?

Answer 29

NO

Question 30

30. What genes are associated with non-syndromic amelogenesis imperfecta?

Answer 30

a. AMELX
b. AMTN
c. ENAM

Question 31

31. (T/F) Amelogenesis imperfecta is NOT diagnosed clinically

Answer 31

False, it is

Question 32

32. How many genes are associated with NON-SYNDROMIC AI?

Answer 32

At least 18

Question 33

33. These permit a new way of molecular diagnosis

Answer 33

NGS