Molecular diagnostics in Medicine Flashcards Preview

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Flashcards in Molecular diagnostics in Medicine Deck (33)
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1

Types of genetic tests (hint: screening to diagnose and predict prognosis)

"screening to diagnose and predict prognosis"

Screening Test

Diagnostic test (e.g. CF)

Predictive test (e.g. BRCA/cancer)

Prognostic test (cancers)

 

2

Test characteristics (2 categories)

APSS (technical)

Accuracy

Precision

Sensitivity

Specificity

(clinical/patient related)

Clinical Validity

Clinical Utility

Personal Utility

3

Clinical validity

Accuracy of disease prediction/how well test predicts disease

4

Clinical utility

Usefulness of test results treatment/patient management

5

Personal utility

Effect of test results on patient (patient's life basically)

6

Categories of etiologies

Point mutations

Copy number changes

Repeat expansions

Epigenetic changes

7

Point mutation types

Frameshift

Missense (conservative vs nonconservative)

Nonsense

Silent

8

Conservative vs Nonconservative missense mutations

Conservative - results in AA change; new AA resembles WT AA in function (so no functional difference)

Non-conservative - results in AA change; new AA functionally different from WT AA (gain or loss of function)

9

Types of Copy number changes

Aneuploidy; Translocation

Microdeletion/duplication (e.g. CF = loss of 1 bp)

Gene gain/loss

Exon gain/loss

10

Repeat expansion types and locations

Trinucleotide expansion (CGG) or Dinucleotide

Located within gene, promoter or intron

11

Epigenetic changes

Methylation of CpG islands

12

Molecular diagnostic techniques 

"RFLP e sequence"

"Microsatellites methylate ASO's"

RFLP

Sequencing

Microsatellite analysis

Methylation testing (via Southern)

Allele-specific oligonucleotide

RFLPing the sequence!!

Microsatellites methyl8 ASO's!!

13

Point mutation genetic test used

RFLP (SNP type)

Sequencing

14

Test for repeat expansions

Microsatellite analysis

15

Test for methylation

Southern Blot

16

Test for copy number changes

Microarray

Multiplex ligation-dependent probe amplification

17

Multiplex ligation dependent amplification

Essentially, PCR with 2 primers >> 

each w/ probe on one end>>

If mutated sequence = amplification but wrong size

If no mutation = amplification + right size

18

Next generation sequencing types

Targeted gene panels

Exome sequencing (highest coverage) [coding regions only]

(Whole) Genome sequencing

19

3 false negative scenarios

20

Sequence interpretation

21

Down Syndrome etiologies

22

Tests for DS

23

Test to order for DS

24

Fragile X Syndrome etiology

25

Tests for Fragile X Syndrome

26

Which test would you order for Fragile X?

Trinucleotide repeat analysis

27

Intepret the Southern Blot below of Fragile X patients. Give reasons for each intepretation.

28

Prader Willi Syndrome etiologies

29

PWS testing

30

Why would you choose methylation testing for PWS and not any of the other tests?

 

MLPA and FISH will only detect gain/loss of genetic info

Microarray won't detect UPD

UPD analysis won't detect deletion