Genomics in Modern Medicine

Question 1

“Genomic medicine is a new, structured approach
to (3)
that prominently features next-generation
sequencing and analysis.”

Answer 1

disease discovery, diagnosis and management

Question 2

Progression of Testing (4)

Answer 2

• Sanger PCR
  
  • Gene by gene, exon by exon sequencing
• Multiplexing can accommodate small panels
• Time consuming
• Limited to known genes/regions

Question 3

Building on Sanger: Human 
Genome Project (4)

Answer 3

• Public group consisted of ~20 international labs
• ~$2.7 billion (under budget!)
• Private Group-Celera Genomics
• Took 13 years for the first draft!

Question 4

NGS =

Answer 4

Technologies that permit rapid interrogation of DNA,
up to and including entire genomes, via massively parallel
sequencing
• Technology took shape in early 2000s

Question 5

NGS emphasizes a distinction from initial approaches that

involved sequencing

Answer 5

of one DNA strand at a time.

Question 6

Decreasing cost and comparatively rapid results are creating
a paradigm shift in genetics; particularly in

Answer 6

monogenic

disease.

Question 7

Genetic variation (5)
Human Variation 0.5% = --- million base pairs!

Answer 7

Size
Location
Impact on a codon
Impact on the protein
Impact on expression 

16

Question 8

Relationship of (2) of 
human genomic variants

Answer 8

frequency and size

Question 9

Single nucleotide variants
• Common:
• Rare:
• Account for about –% of all DNA changes
• Found in about – in every 100 to 300 nucleotides

Answer 9

found in >1% of population aka SNPs (can be advantageous/silent/risk associated)

<1% of population (all of the above + pathogenic)

75
1

Question 10

In-del (3)

Answer 10

• Insertions and deletions of up to 50-100 nucleotides
• Occur 1/10th as often as SNV
• 90% are 1-10 nt in length

Question 11

CNVs (1)

Answer 11

• Least frequent but large so, in total, affect the most nucleotides

Question 12

Sample Preparation For NGS (4)

Answer 12

• While there are subtle differences between tests, all samples undergo library prep
• The goal of library preparation is add primers and barcodes to identify individuals
• Process involves fragmentingDNA
• “Shotgun Sequencing”

Question 13

• Each DNA fragment has: (3)

Answer 13

• Sequencing primer
• Adapters
• Barcode

Question 14

Whole Genome

• Ready for —!

Answer 14

sequencing

Question 15

Gene Panel requires —

Answer 15

Enrichment

Question 16

Enrichment

• Involves selecting out

Answer 16

specific regions of interest for sequencing

using capture probes

Question 17

Cost and time considerations (3)

Answer 17

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

Question 18

Sequencing Instrumentation (3)

Answer 18

• 1 Novaseq
• 1 NextSeq 2000
• 2 MiSeqs

Question 19

1 Novaseq

Answer 19

• 66 genomes in 3 days

Question 20

2 MiSeqs

Answer 20

• 96 PgX samples in ~30 Hours

Question 21

6 Sequel IIe

Answer 21

• 1 genome = 90hrs (1 instrument)

Question 22

Illumina Chemistry uses

Answer 22

Sequencing by Synthesis (SBS)

Question 23

Fluorescent nucleotides are incorporated

Answer 23

one at a time

Question 24

— excite the fluorescence, which is read by the instrument

Answer 24

Lasers

Question 25

skipped | Bioinformatics (3)

Answer 25

``` • Sample preparation and sequencing are only a small part of the process • Critical need for Bioinformatics • Utilize custom and commercial software solutions ```

Question 26

``` Small Panel (571 genes) • --- ```

Answer 26

8000

Question 27

Exome | • ---

Answer 27

300,000

Question 28

Whole genome | • ---

Answer 28

4,000,000

Question 29

Sensitivity and Specificity for SNPs are >---% (NA12878)

Answer 29

99

Question 30

Reliably detect In-dels up to --bp | • Read length --

Answer 30

40 | 2x150

Question 31

Copy Number Variant detection is continually improving | • Focus on

Answer 31

exonic level deletion/duplications

Question 32

Next Generation sequencing allows for

Answer 32

diagnosis of atypical presentations that | would not have otherwise be considered

Question 33

ACMG recommends analysis of 73 genes (2)

Answer 33

* Primarily cancer and cardiovascular syndromes | * Report results back in pediatrics!`

Question 34

Genomes offered clinically since 2015 (2)

Answer 34

* Only 4 findings were reported in first 80 cases | * APOB, PMS2, RYR1, and TNNT2

Question 35

Inherited syndromes that affect tooth development (2)

Answer 35

* Mineralization Defects (PHEX, DMP1, FGF23) | * Ectodermal dysplasias

Question 36

Hypo/Oligodontia | • ---

Answer 36

PAX9

Question 37

Enamel defects | • ---

Answer 37

Amelogenesis Imperfecta (ENAM)

Question 38

CPGM has sequenced over --- DNA samples | • Continually increasing

Answer 38

13,000

Question 39

Clinical and research testing for --- disease

Answer 39

Mendelian

Question 40

Average Diagnostic Rate of ~---%

Answer 40

30

Question 41

Amelogenesis Imperfecta (3)

Answer 41

• Several forms of autosomal dominant enamel dysplasia • At least 18 genes associated with non-syndromic AI • Prevalence ranges from 1/700 to 1/14,000

Question 42

Several forms of autosomal dominant enamel | dysplasia (2)

Answer 42

• Enamel hypoplasia or hypocalcification

Question 43

At least 18 genes associated with non-syndromic | AI, including: (3)

Answer 43

* AMELX (Amelogenin) * AMTN (Amelotin) * ENAM (Enamalin)

Question 44

skipped Queried public databases for variants in three genes • CPGM- --- samples in public warehouse • gnomAD- ~--- genomes and exomes

Answer 44

7365 145,000 None were referred for a primary dental concern • Limited to predicted loss of function variants with a MAF<1%

Question 45

``` Analysis of 3 genes identified 95 variants • Amelogenin = --- variants • Amelotin = --- variants • Enamelin = --- variants • Estimated prevalence of ~1/527 • Unrecognized disease? • Non-penetrance/variable expressivity ```

Answer 45

7 20 68

Question 46

Amelogenesis Imperfecta is diagnosed clinically | • Clinical impact? (2)

Answer 46

* Earlier and more frequent screening | * Novel treatments

Question 47

Common Barriers (3)

Answer 47

``` • Identified a need for more education • Justification of testing • Changing landscape • Patients will ask for it ```

Question 48

--- permits a new way of molecular diagnosis | • Panels, ES, GS

Answer 48

NGS