Genetic Testing and Counseling

Question 1

Affected individuals should not be grouped on a pedigree chart. True or false?

Answer 1

True

Question 2

A standard pedigree should cover 3 generations and include what other individuals?

Answer 2

Proband: First affected individual in the family who brought the family to medical attention (not necessarily the same as the consultand/patient/participant)
Consultand: The person seeking genetic services
1st degree relatives
2nd degree relatives
3rd degree relatives

Question 3

-Horizontal pattern of inheritance
-number of males =number of females affected
-consanguinity
These are all characteristics of which mode of inheritance?

Answer 3

autosomal recessive

Question 4

If individual has a sibling affected with an AR disorder, the risk of that person being a carrier is?

Answer 4

2/3

Question 5

• Vertical pattern of inheritance
• Number of males = number of females affected
• Male to male transmission
• Every affected child has an affected parent
• Penetrance and Variable Expressivity

These are all characteristics of which mode of inheritance?

Answer 5

Autosomal Dominant

Question 6

• Only males affected, related through carrier females
• No male to male transmission
• Lyonization leading to affected females
• Apparent male to male transmission
• 2/3 carrier risk for mother of isolated case if condition is reproductively fatal

These are all characteristics of which mode of inheritance?

Answer 6

X-linked recessive

Question 7

• Vertical Pattern
• All daughters of affected males are affected, but none of the sons
• Number of females > number of males
• No male to male transmission
• Often fatal in males

These are all characteristics of which mode of inheritance?

Answer 7

X-linked Dominant

All Daughters of affected males are affected
The males give the Y to the males.

Question 8

All the related men in the pedigree will have this disorder through what type of inheritance?

Answer 8

Y linked inheritance

• No known diseases linked to the Y chromosome
• Unlikely since women do not have any Y-linked genes and are normal

Question 9

• Vertical pattern
• Number of males = Number of females
• All affected females’ children are affected (none of affected males)

These are all characteristics of which mode of inheritance?

Answer 9

Mitochondrial

Question 10

What is the difference between screening and diagnostic?

Answer 10

Screening
identifies those at risk for a particular outcome
usually requires further evaluation to get final answer

Diagnostic
provides confirmed result that an individual has a medical condition of interest or genetic anomaly
may be of limited informativeness

Question 11

You would use 23 ACOG/ACMG mutation panel or expanded panel to screen for?

Answer 11

cystic fibrosis during prenatal testing

Question 12

You would use hemoglobin electrophoresis to screen for?

Answer 12

Hemoglobinopathies

Question 13

First trimester and second trimester screening typically examine for what?

Answer 13

looking at analytes in maternal serum

Question 14

When the cells of the placenta go through apoptosis, they release their DNA and go through the area around them and get into maternal serum. So there are fragments of fetal DNA in maternal serum that are generally degenerated pretty quickly. We can isolate and identify which chromosome that chromosome belongs to. It could either be suspected to be the mom or the fetus. What does this cell free DNA screening screen for?

Answer 14

fetal aneuploidy
microdeletions
autosomal dominant mutations

Question 15

Why do false positives occur when screening for complex disease risk in multifactorial conditions such as diabetes, heart disease, and cancer?

Answer 15

we’re looking at the piece of the elephant
you’re only going to access what you’re looking at
So you are not looking at the whole picture

False positives, false negatives, detection rates, and predictive values need to be taken into account

Question 16

What are the common disease tested for in individuals of Ashkenazi Jewish ethnicity?

Answer 16

Tay-Sachs
Canavan
Familial Dysautonomia

Question 17

Important concept with carrier screening:
-controlling who has children together to reduce children with Tay-Sachs for example

Does this decrease the gene frequency for diseases like Tay-Sachs?

Answer 17

can decrease the disease frequency but does NOT decrease the gene frequency because these carriers can still mate with other individuals

Question 18

There’s so much admixture in America!! What are the typical screenings for:

• African Americans
• West Africans
• Hispanic
• Italian
• Caucasian
• Ashkenazi Jewish
• French Canadian
• Mennonite/Amish

Answer 18

Hemoglobinopathy (SS, SC, beta thalaseemia)

• African Americans 1/12
• West Africans 1/6
• Hispanic 1/100
• Italian 1/20-1/30 for beta thalaseemia

Cystic Fibrosis
-Caucasian 1/25

Tay-Sachs Disease

• Ashkenazi Jewish 1/30
• French Canadian 1/30

Maple Syrup Urine Disease
-Mennonite/Amish 1/20

Question 19

Sequential screening (a combo for the first and second trimester) for maternal biomarkers can determine risk for Trisomy 21 and 18 by what concentrations of what?

Answer 19

Trisomy 21: low AFP, high hCG, low uE3, high Inhibin A

Trisomy 18: unchanged AFP, very low hCG, low uE3, unchanged inhibin A

AFP=alpha-fetoprotein
uE3= unconjugated estriol
hCG= human chorionic gonadotropin

Question 20

The following describes what type of analysis?

Isolation of chromosomal fragments from maternal serum
Fetal cells are primarily from the trophoblast
Identify chromosomal origin through massive parallel shotgun sequencing
Available after 10 weeks, although fetal fraction has to be over 4% for testing to be valid
Negatively affected by maternal obesity
Detection rates close to 99%

Answer 20

Cell free DNA analysis
(non-invasive prenatal screening)

The detection risks are pretty high (detection rates close to 99%)
It is NOT diagnostic.

• Used to determine sex aneuploidies
• can get information about the mom from these tests (tumors of cancer in pregnant woman)

Question 21

What is the only way to look at chromosomal aberrations and what is the limitation?

Answer 21

karyotype: you can see 700 – 1200 bands, deletions and duplications, >4.0 Mb, translocations, ring chromosomes, marker chromosomes, and other chromosome aberrations
limitation: cannot see specific gene deletions because its too small

Question 22

What type of screening would you use to screen or diagnose cystic fibrosis, sickle cell, or deletion/duplication in Duchenne Muscular Dystrophy? What are the limitations?

Answer 22

Single gene/specific mutation testing

CFTR gene for cystic
beta-globin gene for sickle cell
deletions in dystrophin gene for DMD

Appropriate when one or a few genes/alleles are responsible for majority (~> 90%) of phenotype
Works great if you know the gene of cause

locus heterogeneity: could have one phenotype caused by many of those genes

Question 23

A couple can have pre-natal testing by obtaining cells from the fetus than aminocytes in skin cells? Do you want to karyotope or do a single gene sequencing?

Answer 23

would be risky to do testing on the fetus
need to do testing on son to determine amniocentesis

Was genetic testing done on son?
If not, then testing cannot be done prenatally – have to establish mutation in proband

Question 24

What is flourescence in-situ hybridization (FISH)?

Answer 24

use probes that are made of DNA that will stick to a specific area of the chromosome and light up
can use probes for 18, 21, and 13

So can detect for down syndrome
can detect translocations (different markers on the same chromosome)

You have to know what you’re looking for.

Question 25

How can FISH be misleading at times?

Answer 25

Ultrasound examination, 20 weeks
Cleft lip
Ventricular septal defect
Polydactyly
Suspicious of trisomy, most likely 18
Amniocentesis elected, FISH ordered
Normal, two signals for 21, 13, 18, and X
7 days later, standard chromosome result
Deletion of 18q21.2 – 22.3
Aneuploidy FISH probe covers 18p11.1 – q11.1

Can be misleading as the probe is sticking to a part of the 18 not the entire chromosomal 18. 18q was deleted.

Question 26

What testing should you use to test for deafness, mental disability, seizures, ataxia, and autism (phenotypes associated with multiple genes)?

Answer 26

Multi-gene panel testing:
Testing individually for genes would be too costly and time consuming
Usually sequencing, deletion/duplication analysis – depends on established mutation types

Limitation: Variants of unknown significance (VUS)
Mutations in genes that don’t fit known phenotype
Possibly lead to redefinition of well-established condition

Question 27

Most of the genetic studies of disease are done in those with the disease. So you are limited by the the genes of defect that are detected in these individuals.

Answer 27

Color cancer gene (MSH16) in breast cancer individual

was looking for BRCA1

Question 28

What is the first line test for seizures and autism?

What is the first-tier testing for patients with unexplained developmental delay, mental retardation, multiple congenital anomalies, and autistic spectrum disorder?

Answer 28

You can use comparative genomic hybridization (Microarray) which does NOT look at sequences and cannot pick up a balanced translocation

can find very small deletions or duplication you cannot see through karyotype

Use a microarray containing over 2.67 million probes
Average interprobe distance is 1150 base pairs
Flourophore-tagged DNA from the patient is applied to the microarray

Question 29

What is the limitation of whole genome/exome sequencing?

Whole Exome Sequencing
Sequencing of the component of the genome that predominantly encodes protein
About 1% of genome

Answer 29

Insufficient capture of some exons
No triplet repeat, large deletions or duplications, translocations,
or inversions are detected

Question 30

When determine rish of child having sickle disease, need to determine CARRIER risk and the risk of child getting it.

Answer 30

African American male carrier risk 1/12
Darla had a son with sickle from another man so we know she is an obligate carrier 1/1= 100%
Chance of having sickle cell child 1/4

so
1 x 1/12 x 1/4= 1/48

Question 31

32 y.o. African-American G4P3003 woman referred for routine ultrasound at 19 weeks. Patient relayed son was diagnosed with Wiskott-Aldrich syndrome (X-linked recessive). Formal genetic counseling session was declined, but patient said she wanted testing for the fetus. What test should be done?

Answer 31

Amniocentesis offered and performed

for 16 weeks and up

Chorionic Villus Sampling (10 – 13 weeks)

Question 32

WAS gene encodes for WAS protein, WASp, which is expressed in non-erythroid hematopoietic cells

Numerous described mutations alter function or expression of protein

Causes a spectrum of hematopoietic disorders with predominant effects of platelets and lymphocytes
Wiscott-Aldrich syndrome – absent WASp
X-linked thrombocytopenia (XLT) – residual WASp
X-linked severe congenital neutropenia (XLN) – gain of function mutations

Answer 32

Wiscott-Aldrich syndrome

Eczema
Microthrombocytopenia
Severe and recurrent infections

Question 33

Nucleic acid probes hybridized to unique chromosomal DNA sequences

Label probes with a fluorescent dye, which is visible under a specific wavelength of light

Used on metaphase chromosomes fixed on slides or cells in anaphase

Results in 24 – 48 hours

Purpose:
detect microscopic deletions (using probe that attaches to a specific sequence at a known loci)

Visualize obvious chromosome anomalies, including aneuploidy

Does not provide information on point mutations or other small genetic aberrations

What is this technique?

Answer 33

FISH

Question 34

19 y.o. G1P0 Mexican  woman
Ultrasound examination, 20 weeks
Cleft lip
Ventricular septal defect
Polydactyly

This is indicative of what condition? What test should you use to confirm?

Answer 34

Trisomy 18 (Edward’s Syndrome)

Amniocentesis elected, FISH ordered
Normal, two signals for 21, 13, 18, and X

7 days later, standard chromosome result
Deletion of 18q21.2 – 22.3
Aneuploidy FISH probe covers 18p11.1 – q11.1

FISH detects microscopic deletions (using probe that attaches to a specific sequence at a known loci)

Question 35

25 y.o. female diagnosed with breast cancer
Highly suspicious for BRCA1 or BRCA2 mutation

Do a single gene sequencing/ Specific mutation testing/ Panel testing: Negative for mutations in those genes

What test should you use next?

Answer 35

Expanded panel

Mutation in MSH6, a low penetrant gene associated with Lynch syndrome

Question 36

Severe IUGR and persistently small for age
Prolonged NICU stay
Retinopathy, hypercalcemia, hypothyroidism, astigmatism
Poor enunciation and articulation

Prenatal indications – in place of karyotyping
One or more major structural anomalies on ultrasound
If prenatal diagnosis is being done for other reasons (AMA, etc), if preferred instead of karyotype
Fetal demise or stillbirth

Intrauterine growth restriction (IUGR) is defined as a failure of the fetus to attain its pre-determined growth potential.

Which test should you do?

Answer 36

Indications for Comparative genomic hybridization (Microarray)

Large mosaic interstitial duplication of most of 2p 46, XX,der(2)dup(2)(p25.2;p16.3)del(2)(p25.2) (13) /
46,XX(7)
Overlap with well described full trisomy 2p (severe MR, hypertelorism, prominent forehead, other dysmorphisms