Medical Genetics 4

Prenatal screening

method of determining the risk that the fetus will be born with abnormality during pregnancy → they cannot make definitive diagnoses (need diagnostic test to confirm diagnosis)

Non-invasive Prenatal Screening

o Prenatal Risk Assessment Screening

- 1st trimester screen

- 2nd trimester screen

o Obstetrical Ultrasonography

o DNA testing of the maternal blood sample

1st trimester screen

- blood test and ultrasound

- measure size of the clear space in the tissue of the back of the baby's neck (nuchal translucency)

• Thick neck → Trisomy 21 (Down)

• short neck → Trisomy 18 (Edwards)

2nd trimester screen

quad screen (blood test) to measure levels of 4 blood substances (markers) to determine risk of abnormalities in fetus

what does the quad screen require

accurate gestational aging w/ sampling at 16 to 20 weeks gestation (2nd trimester)

2nd trimester screen (Quad) sensitivity

Sensitivity: 81% accuracy (triple screen is 72% accurate)

2nd trimester screen markers

1) AFP

2) hCG

3) uE3/Estriol

4) Inhibin-A

AFP

alpha fetoprotein

- produced by yolk and liver

hCG

human chorionic gonadotropin

- hormone produced by placenta

estriol

estrogen produced by fetus and placenta

inhibin A

produced by placenta and ovaries

- commonly rising in down syndrome

quad screen interpretation of NTD

open neural tube defect (NTD)

- diffusing and rising AFP

quad screen interpretation of trisomy 18

falling AFP, uE3, and hCG

quad screen interpretation of down syndrome

falling AFP and uE3

rising hCG and inhibin A

Ultrasound can find abnormalities including:

- Down syndrome and Turner syndrome--abundant neck skin

- Edward syndrome- Short neck

- Patau syndrome- Microcephaly (small head)

invasive prenatal testing

o Amniocentesis

o Chorionic Villus Sampling (CVS)

amniocentesis

- amniotic fluid is drawn from mother's uterus

- prenatal genetic studies and assessment of fetal lung maturity

- evaluation of the fetus for infection, degree of hemolytic anemia, blood or platelet type, hemoglobinopathy, and NTD

when is amniocentesis done?

▪ Typically done at 15 - 16 weeks

▪ Can be done during 10-14 weeks → associated with higher fetal loss and complications

why is amniocentesis done?

Only done if mother has significant risk (i.e. abnormal ultrasound, family history, etc)

Chorionic Villus Sampling (CVS)

small sample of chorionic villus cells from placenta obtained for genetic testing during the first 10 weeks

- first choice procedure for testing done before 15 weeks gestation

why is a CVS done?

for any condition in which diagnostic cytogenetic, biochemical/molecular, or DNA analysis is possible

What are the advantages of invasive prenatal testing that are relevant to genetics?

- Fetal karyotype can be performed

- Gives high accuracy and specificity for genetic abnormalities in the fetus → 99.9% accurate

factors that should be taken into account for genetic disorders

1. Familial aggregation

2. Single-gene defects

3. Polygenic/multifactorial disorders

4. Familial dietary and behavior patterns

examples of single gene defects

- Locus heterogeneity (different genes-similar symptoms)

- Mosaicism

- Penetrance

- Genomic imprinting

Common adult-onset genetic diseases

Multifactorial

- Type 2 Diabetes

- Cardiovascular disease

- Cancers (i.e. Breast, Colon, Melanoma, etc.)

Common adult-onset genetic diseases occurence

usually random, not due to hereditary factors

o However, if two or more first-degree relatives the disease → genetic counseling/testing is recommended

o When two or more family members are affected → 2 - 5-fold increase in the risk for common adult-onset genetic diseases

Difficulties w/ Genetic Testing

o Genetic testing is expensive and may not be covered by insurance

o Patient may not be able to handle the test results regardless of positive or negative

Genetic Diabetic Syndromes

- Leukocyte antigen (HLA) alleles: the only ones that have a large genetic effect.

- Insulin gene polymorphisms

- PTPN22 (protein tyrosine phosphatase non receptor type 22)

- Numerous common polymorphisms

Numerous common polymorphisms

- approximately 50, as of 2014

- weakly contribute to the risk for or protection from type 2 diabetes

- genes encode proteins that cause alterations in several pathways leading to diabetes, including pancreatic development, insulin synthesis, processing, and secretion; amyloid deposition in beta cells; cellular insulin resistance; and impaired regulation of gluconeogenesis

causes of type 2 diabetes

Monogenic causes: represent only a small fraction of cases

Commonly inherited polymorphisms: individually contribute only small degrees of risk for, or protection from, diabetes

Complex polygenic risk factors: results in most of the genetic risk for type 2 diabetes

Mass genetic screening programs require tests with what qualities?

require tests with high enough sensitivity and specificity to be cost effective

Population screening

the process of assessing the prevalence of a particular trait in the entire population or in a subgroup of the population

population screening criteria

▪ Prevalent and serious

▪ Can be influenced pre-symptomatically through lifestyle changes, screening, medications, or other risk-reducing interventions (i.e. Tay Sachs disease → significantly reduced)

• The condition has to be pre-symptomatic

▪ Identification of risk does NOT result in undue discrimination (insurance or employment) or harm

what are the increased risks in common adult-onset genetic disease when two or more family members are affected by the disease?

When two or more family members are affected → 2 - 5-fold increase in risk

reasons why family history is important for CVD

- understanding one's risk for CVD

- allows one to take preventative measures to lower the risk of CVD

Recurrence Risk Assessment:

o Autosomal Recessive: 25% x Penetrance (when both parents heterozygous)

o Autosomal Dominant: 50% x Penetrance (when both parents heterozygous)

o Multifactorial: 2% - 5% (for most)

▪ Ranges depending on disorder → some disorders/traits are associated with higher risks (i.e. 10% for hypospadias; 6% for bilateral cleft lip)

o Mitochondrial: accurate percentile figures cannot be given due to variable heteroplasmy among eggs → often the risk is quoted as "0-100%"

multifactorial risks

1. Severity of the defect

2. Gender of the affected individual (less commonly affected gender has greater recurrence risk)

3. Number of affected family members

risk of severity of the defect in cleft lip

Unilateral cleft lip has a recurrence risk of 4%

Bilateral cleft lip has a risk of 6%

risk of gender in pyloric stenosis

Pyloric stenosis is more common in males, therefore:

- An affected male has a recurrence risk for siblings of ~2-3%

- Affected female has a recurrence risk for siblings ~4-10%

risk of family members in spina bifida

Spina bifida has

- 0.3% recurrence risk if only one individual is affected

- 5% recurrence risk if there is one individual and one parent is affected"

Recurrence Risk: Breast Cancer

Autosomal Dominant

- Father's side has concerning family history

- If there is 50% chance that her father is a carrier → there is a 25% chance that she is carrier

- Penetrance is 50% → there is a 12.5%

chance that she shows the phenotype

o 50% x 25% = 12.5%

- Recurrence risk → 12.5%

miscellaneous issues in clinical genetics

- Recall of family history may be inaccurate

- Disease penetrance may be incomplete

- An allele (i.e. BRCA1) may cause variable malignancies

- Assumption (i.e. mendelian inheritance) may be incorrect

Traditional approach to genetic testing

- Patient identified by clinical history of familial disorder

- Pretest counseling for risks and benefits of analysis of specific genes and informed consent

- Mutational analysis

- If negative consider next most likely genes

- Posttest counseling and treatment implications for patient and family members

- Return to primary care physician for follow-up

Genetic testing in the era of next-generation sequencing

- Pretest counseling for risks and benefits of analysis of multiple genes (or whole exome) and informed consent

- Mutational analysis

- Interpretation of the findings by a physician in the context of the individual's personal and family medical history

- Posttest counseling and treatment implications for patient and family members

- Return to primary care physician for follow-up

Characterization of phenotype for Familial or sporadic genetic disorder if the gene is unknown?

Start: Pedigree analysis

- Linkage analysis

- Positional cloning

- Mutational analysis

then:

- Determine functional properties of identified mutations in vitro and in vivo

- Genetic counseling or Testing of other family members

- Treatment based on pathophysiology

Characterization of phenotype for Familial or sporadic genetic disorder if the gene is known or is a candidate gene?

Start: Pedigree analysis

- Mutational analysis

then:

- Determine functional properties of identified mutations in vitro and in vivo

- Genetic counseling or Testing of other family members

- Treatment based on pathophysiology

Risk factors for myocardial infarction

- Older age (> 60 Year old)

- Male

- Smoking

- Hypercholesterolemia

- Hyperhomocysteinemia (high homocysteine, a toxic blood amino acid that is elevated when intakes of vitamins B2, B6, B12 and folic acid are insufficient)

- Diabetes

- High blood pressure

- Obesity

- Stress occupations

Clinical Laboratory Improvement Act

CLIA

Guidelines to improve quality of lab services:

- Benefits of a quality management system approach

- Factors to consider before introducing a new test

- Establishment and verification of test performance specifications

- Total laboratory testing process that consists of preanalytic, analytic, and postanalytic phase

- Confidentiality of patient information and test results

- Personnel qualification, responsibilities, and competency

DNA Testing and types

most commonly performed by DNA sequence analysis for mutations

o PCR, Next-generation DNA sequencing, DNA chips (microarray)

o Cytogenetics (big change), aCGH (unbiased detection), FISH (confirmation or detection if site is known), or Southern Blotting

Protein Truncation Tests (PTTs)

detects mutations causing premature termination of a polypeptide

o cDNA (in vitro translation) gel analysis

o most commonly for analyses of large genes with significant genetic heterogeneity (i.e. APC gene implicated in colon cancer)

Predictive Genetic Testing types

two types

o Pre-symptomatic testing

o Predisposition testing

Pre-symptomatic testing

applies to diseases where a specific genetic alteration is associated with a near 100% likelihood of developing the disease (i.e. Huntington's Disease)

o It is the performance of a genetic test on an asymptomatic individual at risk for a condition in order to determine whether the person has inherited the disease-causing mutation

Predisposition testing

predicts a risk for disease that is less than 100% (i.e. apolipoprotein E allele E4)

o This is a genetic test that provides information about a person's susceptibility to a disease

Indications for Genetic Counseling

o Advanced maternal (> 35) or paternal (> 50) age

o Consanguinity (incest)

o Previous history of a child with birth defects or genetic disorder

o Personal or family history suggestive of a genetic disorder

o High-risk ethnic groups; known carriers of genetic alterations

o Documented genetic alteration in a family member

o Ultrasound or prenatal testing suggesting genetic disorder

Monosomies are more ____ than trisomies

deleterious

Complete monosomies are generally not? with the exception of?

viable (except monosomy X)

which trisomies are viable?

Complete trisomy are viable for chr. 13, 18, 21, X, and Y

Phenotype in partial aneusomies depend on?

▪ size of the unbalanced segment

▪ if imbalance is monosomic or trisomic

▪ the regions of the genome affected

▪ which genes are involved

types of Inversion

▪ Paracentric

▪ Pericentric

paracentric inversion

- relatively rare

- found after infertility, miscarriage, and/or abnormalities

• Body eliminates them (most don't survive) → if they do survive (viable), then the viable form is heritable

pericentric inversion

larger changes with increased risks

• Most survive (are viable) → offspring may be affected due to unbalanced chromosome

genetic testing ethic concerns

o how test results may impact the patients relationship with family, friends, offspring, etc.

o Genetic discrimination: genetic information may be used by insurers to deny, limit or cancel health insurance or may be used by employers to discriminate in the workplace

Genetic Information Nondiscrimination Act (GINA)

Protects Americans against discrimination based on their genetic information when it comes to health insurance and employment (2008)

Health Insurance Portability & Accountability Act

HIPAA:

▪ Federal law that requires patient authorization for the release of medical information

Hemochromatosis is an example of?

Reduced penetrance: 1/3 do not show phenotype

Hemochromatosis

(1 in 200 homozygous among Northern European):

- HFE gene deficiency

- Too much iron being absorbed from the gastrointestinal tract

- Complications are potentially preventable

- 1/3 do not show phenotype (Reduced penetrance)

- Recommendation: Phenotypic screening → genetic testing

Transcription Therapy

- a genetic intervention strategy

- prevents gene expression of genes implicated in disease through direct intervention in the transcription process

Gene Transfer

- a genetic intervention strategy

introduction of genetic material into cells to:

1. compensate for abnormal genes

2. to make a beneficial protein

siRNA or RNAi

- a genetic intervention strategy

use of RNA (21-23 nucleotides long) to degrade mRNA and prevent it from being translated into protein

mutation protein trapping

a genetic intervention strategy

Protein/Enzyme Replacement

- a genetic intervention strategy

replacement proteins/enzymes are given to patients who suffer from chronic conditions resulting from enzyme deficiencies or malfunction