Genomics in Modern Medicine

Question 1

What is the gold standard of genetic testing?

Answer 1

Sanger PCR

Question 2

What does sanger PCR do?

Answer 2

Gene by gene, exon by exon sequencing

Question 3

What are the downfalls of sanger PCR?

Answer 3

• Time consuming
• Limited to known genes/regions

Question 4

What is next generation sequencing (NGS)?

Answer 4

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

Question 5

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

Answer 5

Decreasing cost and comparatively rapid results

Question 6

How many base pairs in the human genome?

Answer 6

3.2 billion base pairs

Question 7

How many nucleotides in the human genome?

Answer 7

6.4 billion

Question 8

How many genes in the human genome?

Answer 8

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

Question 9

How many proteins does the human genome encode?

Answer 9

100,000

Question 10

What is the normal human variation?

Answer 10

0.5% or 16 million base pairs

Question 11

What can genetic variation be?

Answer 11

Size
Location

Question 12

What can genetic variation impact?

Answer 12

• Impact on a codon
• Impact on the protein
• Impact on expression

Question 13

What is the least frequent genomic variant?

Answer 13

structural change (ex: whole chromosomes)

Question 14

What is the most frequent genomic variant?

Answer 14

SNV

Question 15

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

Answer 15

karyotype
aCGH
SNP array
gemonic sequencing

Question 16

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

Answer 16

SNV
In-del
CNV

Question 17

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

Answer 17

75%

Question 18

Single nucleotide variants are found in 1 in every ________ nucleotides

Answer 18

100-300

Question 19

Insertions and deletions include up to _____ nucleotides

Answer 19

50-100

Question 20

In-del occur _____ as often as SNV

Answer 20

1/10

Question 21

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

Answer 21

90%
*harder to detect b/c so small

Question 22

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

Answer 22

CNVs

Question 23

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

Answer 23

enrichment

Question 24

What step is required for all genome sequencing?

Answer 24

library

Question 25

What are the steps for whole genome sequencing?

Answer 25

- RNA/DNA isolation - library - genome - sequencing

Question 26

What are the steps for a small section genome sequencing?

Answer 26

- RNA/DNA isolation - library - panel - enrichment - sequencing

Question 27

What is the goal of library preparation?

Answer 27

add primers and barcodes to identify individuals

Question 28

What is shotgun sequencing?

Answer 28

fragmenting DNA during library preparation

Question 29

Each DNA fragment has what when library is completed?

Answer 29

* Sequencing primer * Adapters * Barcode

Question 30

What is enrichment?

Answer 30

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

Question 31

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

Answer 31

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

Question 32

How does sequencing works?

Answer 32

* Fluorescent nucleotides are incorporated one at a time * Lasers excite the fluorescence, which is read by the instrument

Question 33

What is variant detection?

Answer 33

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

Question 34

What are the steps in the variant detection process?

Answer 34

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

Question 35

What is the variant count for a typical small panel?

Answer 35

8000

Question 36

What is the variant count for a typical exome?

Answer 36

300,000

Question 37

What is the variant count for a typical whole genome?

Answer 37

4,000,000

Question 38

What is the sensitivity and specificity for SNPs?

Answer 38

>99%

Question 39

What does next generation sequencing (NGS) allow for?

Answer 39

diagnosis of atypical presentations that would not have otherwise be considered

Question 40

What are examples of inherited syndromes that affect tooth development?

Answer 40

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

Question 41

What is amelogenesis imperfecta?

Answer 41

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

Question 42

How many genes associated with non-syndromic amelogenesis imperfecta?

Answer 42

at least 18

Question 43

What is the prevalence range of ameologenesis imperfecta?

Answer 43

1/700 to 1/14,000

Question 44

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

Answer 44

* Amelogenin * Amelotin * Enamelin

Question 45

What are common barriers to genetic testing in dentistry?

Answer 45

* Identified a need for more education * Justification of testing * Changing landscape (Patients will ask for it)

Question 46

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

Answer 46

NGS