Genetic testing

Question 1

examples of less restrictive definitions

Answer 1

biochemical tests (amino aids, organic acids as in phenylketonuria or maple syrup urine disease),
enzyme activity assays (Gaucher disease),
protein electrophoresis (sickle cell disease),
lipid levels (familial hypercholesterolemia),
X-rays (achondroplasia), ultrasound (polycystic kidney disease,
hypertropic cardiomyopathy), sweat chloride test (cystic fibrosis),
skin examination (albinism), medical history,
family history, etc.

Question 2

biochemical tests could test for

Answer 2

(amino aids, organic acids as in phenylketonuria or maple syrup urine disease)

Question 3

enzyme activity assays test for

Answer 3

(Gaucher disease)

Question 4

protein electrophoresis test for

Answer 4

sickle cell disease

Question 5

lipid levels (test for

Answer 5

familial hypercholesterolemia)

Question 6

X-rays test for

Answer 6

achondroplasia

Question 7

ultrasound can test for

Answer 7

polycystic kidney disease,

hypertropic cardiomyopathy

Question 8

sweat chloride test can test for

Answer 8

cystic fibrosis

Question 9

skin examination can test for

Answer 9

(albinism)

Question 10

genetic testing definition

Answer 10

Analyzing an individual’s genetic material to determine predisposition to a particular health condition or to confirm a diagnosis of genetic disease.

Examining a sample of blood or other body fluid or tissue for biochemical, chromosomal, or genetic markers that indicate the presence or absence of genetic disease.

Question 11

CHROMOSOMAL ANALYSIS:

General Uses and Indications:

Answer 11

Suspected abnormality of chromosome number or structure
(deletion, insertion, rearrangements). Frequently obtained from pregnant women > 35 years (amniocentesis or chorionic villus sampling), from patients with congenital abnormalities (dysmorphisms, structural organ defects, mental and/or growth retardation), from families with multiple miscarriages and/or fertility problems, and directly from certain cancer biopsies.

Question 12

CHROMOSOMAL ANALYSIS:

can diagnose

Answer 12

aneuploidies (abnormal chromosome number),

chromosome deletions,

duplications, and

insertions of moderate to large size

(>3,000-5,000 kb / 3-5 Mb), and rearrangements.

Question 13

chromosomal analysis cannot diagnose

Answer 13

single gene deletions, point mutations, small deletions, duplications, and insertions, methylation defects, trinucleotide repeat abnormalities.

Question 14

FISH general use and indication

Answer 14

Used to diagnose deletions, some translocations, and abnormalities of copy number. Often used to detect cytogenetic changes that are at or beyond the limits of resolution obtained by high-resolution chromosomal analysis. FISH for duplications works
better on cells in interphase than metaphase (metaphase the chromatin is very compact)

Question 15

FISH can diagnose

Answer 15

recognized microdeletion syndromes,
recognized chromosomal rearrangements (in cancers), and
gene copy numbers (cancers).

Also useful in diagnosing anueploidies (e.g.
trisomy 13, 18, 21) in the prenatal setting.

Question 16

FISH cannot diagnose

Answer 16

deletions,
rearrangements that are not specifically tested for (i.e. FISH probes are specifically designed for each condition).

FISH is not always able to detect duplications of
gene regions.

Point mutations and small deletions cannot be diagnosed with this approach.

Question 17

examples of micro deletions that FISH can detect

Answer 17

Cri-du-chat, Smith-Magenis,

DiGeorge (22qdel),

Williams syndrome,

Wolf-Hirschhorn,

Prader-Willi syndrome,

Angelman syndrome.

Question 18

Microarray: expression array

Answer 18

Used to test the RNA expression
of genes (i.e. which genes are turned ‘on’ or ‘off’). 
These are semi-quantitative and test the activity of genes (see figure) rather than just the presence or absence of a gene or genetic variant (expression arrays). 

These have a small, but likely growing role, in oncology.

Question 19

Chromosomal Microarray Analysis (CMA):

Answer 19

These
have a big role in clincal genetics currently. These
look for chromosomal DNA losses and gains (so called ‘deletion/duplication’ studies). Sometimes this is also called array comparative genomic hybridization (aCGH) analysis.

Question 20

General Uses and Indications of CMA:

Answer 20

CMA has become fairly standard for looking for small genomic deletions/insertions.

superior method to looking for chromosomal gains than losses than traditional chromosomal analysis because the resolution of the CMA is vastly superior to chromosomal analysis.

The probe size used these days is between 100-200 Kb so they can pick up smaller changes than can be appreciated by chromosome analysis.

Currently, some labs use >~200 Kb for deletions and >~400 Kb for duplications.

Question 21

Microarray can diagnose

Answer 21

aneuploidies,
unbalanced chromosomal rearrangements,
chromosome deletions and

duplications > 200 Kb and 400 Kb, respectively.

Question 22

Microarray cannot diagnose

Answer 22

Deletions/Duplications below the resolution of CMA,

nucleotide mutations,

balanced chromosomal rearrangements.

Question 23

DNA sequencing

general uses and indications

Answer 23

Used to identify sequence changes (mutations) in specific genes.
In general you need the following:
oYou must know or suspect a specific genetic diagnosis
o The gene must have been identified
o The mutation must be detectable by sequencing (deletions, insertions, rearrangements
are not always found by sequencing)
o The mutation must be located in a region of the gene that is actually sequenced
(promoter and deep-intronic mutations often missed by commercial tests)

Question 24

DNA sequencing can diagnose

Answer 24

Mutations in known genes (mutation can be previously reported or can be novel),

polymorphic variants, small (1 to ~100 nucleotide) deletion/insertions.

Ideal for looking at the
sequence of a known disease gene

Question 25

DNA sequencing cannot diagnose

Answer 25

The technique is very specific, assaying only the region of the gene(s) for which the test has been designed.
Frequently, many clinical genetic tests do NOT routinely sequence all parts of a gene (e.g. promoters, introns).
This means that although the approach is often very specific, clinical sensitivity is frequently below 100% (this is an important concept to understand).
This technique cannot easily detect larger deletions/insertions, rearrangements, and most chromosomal abnormalities.

Question 26

NextGen DNA Methodology:

Answer 26

Uses massively-parallel sequencing of individual DNA molecules and is likely to replace PCR based DNA sequencing within a few years (and is actually already in clinical use as of early 2012).

Question 27

Allelic Heterogeneity refers to

Answer 27

the fact that multiple mutations in a particular gene (or at a particular loci) can cause disease. (Allelic heterogeneity in the research setting can also refer to
the present of multiple non-pathogenic polymorphisms within a gene)

Question 28

allelic heterogeneity example:

Answer 28

Cystic fibrosis is an autosomal recessive disease caused my mutations in one gene,
CFTR.
Over 1,000 different mutations have been reported.
Cystic fibrosis shows allelic heterogeneity but is genetically homogenous (e.g. NO Genetic Heterogeneity).

Question 29

genetic heterogeneity

Answer 29

multiple genes (when mutated) associated with the same phenotype

Question 30

genetic heterogeneity example

Answer 30

Hypertrophic cardiomyopathy (HCM) is an autosomal dominant disease caused by
mutations in at least 10 different genes. HCM shows both allelic and genetic heterogeneity.

Question 31

a genetic test which cannot completely account for

Answer 31

all possible allelic and genetic heterogeneity

in a particular disorder can lead to non-informative results.

Question 32

genetic tests are not

Answer 32

solely restricted to DNA based tests

Question 33

Chromosome analysis is useful for identifying ______

Answer 33

aneuploidies, like trisomy 21

also suitable for large structural changes like duplication, deletion, rearrangements

Question 34

chromosome analysis resolution

Answer 34

3-5 Mb

Question 35

high resolution chromosomal analysis can be used for

Answer 35

WAGR syndrome

interstitial deletion of 11p13

Question 36

FISH can be used for

Answer 36

PAX6 locus in child with WAGR and normal chromosomes

Question 37

FISH is

Answer 37

very specific

Question 38

when you don’t know the diagnosis, consider a ____ test

Answer 38

genomic

Question 39

aniridia without pax6 should use

Answer 39

DNA sequence analysis

Question 40

DNA sequencing is now

Answer 40

workhorse technique for many single gene defects

• Can detect novel mutations • May miss larger deletions

Question 41

diagnostic testing

Answer 41

patients with signs or symptoms of genetic disease

–> positive genetic test result confirms diagnosis

Question 42

Diagnostic testing if the disease diagnosis is already suspected on clinical grounds then test is ______.

If the symptoms are present, but clear diagnosis is unknown, _______

Answer 42

‘confirmational’.

test results can diagnose the underlying and current disease.

Question 43

predictive testing

Answer 43

pts with no signs or symptoms of genetic disease

–> positive genetic provides estimate of future disease risk

Question 44

predictive testing. Patients has some ______

Answer 44

underlying ‘risk’ of disease (based on family history or ethnic background). The genetic test result further classifies the risk of a future disease

Question 45

Genetic testing can be ______ or can be used in ______ capacity

Answer 45

diagnostic or

predictive in capacity

Question 46

________ is an important concept when a genetic test is normal (negative test)

Answer 46

Informativity

– Some ‘negative’ results are truly negative (and exclude diagnosis/risk)
– Other ‘negative’ results are non-informative (and do NOT exclude diagnosis/risk)