Genetic testing Flashcards
examples of less restrictive definitions
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.
biochemical tests could test for
(amino aids, organic acids as in phenylketonuria or maple syrup urine disease)
enzyme activity assays test for
(Gaucher disease)
protein electrophoresis test for
sickle cell disease
lipid levels (test for
familial hypercholesterolemia)
X-rays test for
achondroplasia
ultrasound can test for
polycystic kidney disease,
hypertropic cardiomyopathy
sweat chloride test can test for
cystic fibrosis
skin examination can test for
(albinism)
genetic testing definition
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.
CHROMOSOMAL ANALYSIS:
General Uses and Indications:
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.
CHROMOSOMAL ANALYSIS:
can diagnose
aneuploidies (abnormal chromosome number),
chromosome deletions,
duplications, and
insertions of moderate to large size
(>3,000-5,000 kb / 3-5 Mb), and rearrangements.
chromosomal analysis cannot diagnose
single gene deletions, point mutations, small deletions, duplications, and insertions, methylation defects, trinucleotide repeat abnormalities.
FISH general use and indication
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)
FISH can diagnose
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.
FISH cannot diagnose
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.
examples of micro deletions that FISH can detect
Cri-du-chat, Smith-Magenis,
DiGeorge (22qdel),
Williams syndrome,
Wolf-Hirschhorn,
Prader-Willi syndrome,
Angelman syndrome.
Microarray: expression array
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.
Chromosomal Microarray Analysis (CMA):
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.
General Uses and Indications of CMA:
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.
Microarray can diagnose
aneuploidies,
unbalanced chromosomal rearrangements,
chromosome deletions and
duplications > 200 Kb and 400 Kb, respectively.
Microarray cannot diagnose
Deletions/Duplications below the resolution of CMA,
nucleotide mutations,
balanced chromosomal rearrangements.
DNA sequencing
general uses and indications
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)
DNA sequencing can diagnose
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
DNA sequencing cannot diagnose
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.
NextGen DNA Methodology:
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).
Allelic Heterogeneity refers to
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)
allelic heterogeneity example:
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).
genetic heterogeneity
multiple genes (when mutated) associated with the same phenotype
genetic heterogeneity example
Hypertrophic cardiomyopathy (HCM) is an autosomal dominant disease caused by mutations in at least 10 different genes. HCM shows both allelic and genetic heterogeneity.
a genetic test which cannot completely account for
all possible allelic and genetic heterogeneity
in a particular disorder can lead to non-informative results.
genetic tests are not
solely restricted to DNA based tests
Chromosome analysis is useful for identifying ______
aneuploidies, like trisomy 21
also suitable for large structural changes like duplication, deletion, rearrangements
chromosome analysis resolution
3-5 Mb
high resolution chromosomal analysis can be used for
WAGR syndrome
interstitial deletion of 11p13
FISH can be used for
PAX6 locus in child with WAGR and normal chromosomes
FISH is
very specific
when you don’t know the diagnosis, consider a ____ test
genomic
aniridia without pax6 should use
DNA sequence analysis
DNA sequencing is now
workhorse technique for many single gene defects
• Can detect novel mutations • May miss larger deletions
diagnostic testing
patients with signs or symptoms of genetic disease
–> positive genetic test result confirms diagnosis
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, _______
‘confirmational’.
test results can diagnose the underlying and current disease.
predictive testing
pts with no signs or symptoms of genetic disease
–> positive genetic provides estimate of future disease risk
predictive testing. Patients has some ______
underlying ‘risk’ of disease (based on family history or ethnic background). The genetic test result further classifies the risk of a future disease
Genetic testing can be ______ or can be used in ______ capacity
diagnostic or
predictive in capacity
________ is an important concept when a genetic test is normal (negative test)
Informativity
– Some ‘negative’ results are truly negative (and exclude diagnosis/risk)
– Other ‘negative’ results are non-informative (and do NOT exclude diagnosis/risk)
