Learning Objectives Week 2 Flashcards
Multifactorial Inheritance (characteristics of diseases and other traits that demonstrate multifactorial inheritance)
Multifactorial inheritance:
- increased risk to relatives, but no consistent pattern of inheritance with families. Many of these diseases have traits that aren’t explained by genotype, and different alleles at same gene can yield different severity. Multiple genes + environmental factors –>disease susceptibility. Made up of complex traits which:
- aggregate in families
- don’t follow simple modes of Mendelian inheritance
- are likely due to variants in multiple genes and non-genetic factors that interact
- don’t have a simple relationship between variant and trait in the population.
Multifactorial Inheritance
examples of diseases and other traits that demonstrate multifactorial inheritance
Not sure how important this is..
Examples from text:
1) Digenic Pigmentosa = patients heterozygous for EITHER a missense mutation in one gene or for null allele in another gene don’t develop disease; patients heterozygous for both mutations do develop.
2) Venous thrombosis = mutant allele of factor V (FVL) in which arginine glutamine more frequent in white people. Mutation in prothrombin gene (GA) also more prevalent in Whites. Use of oral contraceptives increase risk for thrombosis, independent of genotype at FVL and prothrombin. Having two of these factors (2 genetic, 1 environmental) raises risk for idiopathic cerebral vein thrombosis.
3) Hirschsprung Disease = HSCR inherited in Mendelian manner; due to mutations in RET gene (affects a tyrosine kinase receptor). Some families require that individual have both RET and GDNE mutation. HSCR = multifactorial disease that results from additive effects of susceptibility alleles at RET, EDNRB, and other loci.
4) Type 1 DM = MHC locus is a major genetic factor in type 1 diabetes. Association between HLA-DR3 and HLA-DR4, which can be subdivided into a dozen+ more alleles. VNTR polymorphisms in promoter of insulin gene itself and other SNPs can affect.
5) Alzheimer’s disease = age, gender, and family history = most significant risk factors. APOE locus = significant genetic factor. Genotype with at least one E4 allele found 2-3x more frequently among patients; patients with 2 E4 alleles have earlier onset (so E4 is a predisposing factor). E4 variant predisposes to a complex trait, but does not predestine anyone carrying allele to develop disease.
(Also, some cancers, IBD, asthma, schizophrenia, clefting, etc. demonstrate multifactorial inheritance).
Multifactorial Inheritance
(strategies used to determine the relative importance of genetic vs. non-genetic factors in contributing to the variation in a complex trait)
-Twin Studies
Twin studies:
-compare MZ to DZ twins. If it can be assumed that MZ and DZ twins are equally similar with respect to non-inherited factors, we can use this to estimate contribution of genetic vs. environmental variation of trait.
(Uses concordance rates. High CR = genetic variation contributes to variation in risk more than environment).
Can study MZ twins raised apart to study environment.
Multifactorial Inheritance
(he potential difficulties associated with quantifying the role of genetic factors in contributing to risk of disease at both the population level and the individual level)
-Risk of disease in relatives:
= risk of disease in affected sibs/risk in general population.
-Heritability (h2):
= proportion of variance in trait due to genetic variation.
High heritability = differences among people with respect to a trait (ex: blood pressure) can be attributed to differences in genetic makeup = more genetic variation.
Low heritability = low genetic variation; differences can be applied to the environment.
High heritability does NOT mean non-genetic factors aren’t important and vice versa.
Multifactorial Inheritance (characteristics of complex traits General)
- Incomplete penetrance
- Variable expressivity
- Heterogeneity
- (Presence of phenocopies)
Multifactorial Inheritance
(characteristics of complex traits)
-Incomplete penetrance
Incomplete penetrance:
-not everyone with predisposing variant develops disease
Example: Type I diabetes and MHC
Multifactorial Inheritance
(characteristics of complex traits)
-Variable expressivity
Variable expressivity:
-no two individuals with the same genetic variant have
exactly the same disease characteristics
Example: Maturity Onset Diabetes in the Young (MODY)
Multifactorial Inheritance
(characteristics of complex traits)
-Heterogeneity
Heterogeneity (2 definitions from powerpoint):
1) Different alleles in the same gene result in same trait
2) Different alleles in the same gene result in different traits
(from handout)
-allele and locus: The “same” disease can be caused by different
alleles at one location or by alleles at different locations in the genome
Example (allele): Cystic Fibrosis
Example (locus): Alzheimer Disease
Multifactorial Inheritance
(characteristics of complex traits)
-(Presence of phenocopies)
(Presence of phenocopies):
-Individuals who have the disease or trait for reasons
that are not primarily genetic even though clinical presentation mimics the more genetic version
Example: Thalidomide-induced limb malformation vs. genetically-induced
Multifactorial Inheritance (strategies used to determine the relative importance of genetic vs. non-genetic factors in contributing to the variation in a complex trait) -Adoption Studies
Adoption studies:
-compares similarity between biological siblings raised apart and adopted sibs.
If biological sibling is more concordant with biological sib than adopted sib –> evidence for genetic variation.
(If opposite = evidence for environment.)
Genetic Testing (Define what constitutes a genetic test)
- 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.
Less Restrictive Definition:
-Many ‘tests’ provide information about genetic status/risk without directly testing DNA.
Genetic Testing
(Types of Genetic Tests)
-Genotyping
Genotyping:
Used to determine presence/absence of known genetic variant.
• General Uses and Indications: Used to identify sequence changes (mutations) in specific genes. In general you need the following:
o You must know or suspect a specific genetic diagnosis
o The gene must have been identified, and the disorder should exhibit little or no allelic heterogeneity. Genotyping is cost-effective when there are few variants; as the number of candidate variants, grows, sequencing quickly becomes cheaper.
• Can Diagnose: Previously-described mutations in known genes, polymorphic variants.
• Cannot Diagnose: The technique is very specific, assaying only the specific mutation(s) for which the test has been designed. The mutation(s) identified should represent the majority of causative mutations in the gene of interest, otherwise a negative result is uninformative.
Genetic Testing
(Types of Genetic Tests)
-Fragment Analysis
Fragment Analysis:
Sizing of PCR products by capillary electrophoresis or, historically, gel electrophoresis.
• General Uses and Indications: Used to identify mutations that are expected to differ in PCR amplicon size (e.g., insertions / deletions). In general you need the following:
o You must know or suspect a specific genetic diagnosis
o The gene must have been identified
o The expected mutation must be of a type expected to result in a larger or smaller amplicon than wild-type, and there must be no other size polymorphisms within the amplicon.
• Can Diagnose: Small-medium (1 to ~2000 nucleotide) deletion/insertions, repeat expansions.
• Cannot Diagnose: This technique will not detect sequence changes other than insertions/deletions.
Genetic Testing
(Types of Genetic Tests)
-Sanger Sequencing
Sanger Sequencing:
Widely used method of mutation detection based on Sanger-Gilbert method. Able to identify the genetic mutation causing many disease conditions.
• General Uses and Indications: Used to identify sequence changes (mutations) in specific genes. In general you need the following:
o You 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)
• 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
• 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.
Genetic Testing
(Types of Genetic Tests)
-Massively-Parallel Sequencing / Next-generation sequencing
Massively-Parallel/Nex Gen
Uses massively-parallel sequencing of individual DNA molecules and is likely to replace majority of Sanger DNA sequencing within a few years. Has been in clinical use since 2012. Powerful tool for identifying genetic etiology in difficult cases.
• General Uses and Indications: Used to identify sequence changes in a number of circumstances, but usually most powerful when there is significant genetic or allelic heterogeneity, or when the clinical diagnosis is uncertain. Used in limited by expanding fashion to identify copy-number changes and large deletions.
o You do not necessarily have to suspect a specific genetic diagnosis!! (although it’s helpful)
o The gene must have been identified
o The mutation must be detectable by analysis algorithm (sequence variants and small-moderate insertions/deletions are easy to detect, cytogenetic abnormalities less so)
o The mutation must be located in a region of the genome that is captured (promoter and deep-intronic regions are often omitted)
• 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 genes in highly heterogeneic diseases, or for clinical cases for which the diagnosis is uncertain.
• Cannot Diagnose: The technique is very powerful, but typically does not detect large repeat expansions (e.g., Fragile X, HD). This technique cannot easily detect large deletions/insertions, rearrangements, and most chromosomal abnormalities, although the technologies and algorithms are constantly improving.
Genetic Testing
Informative
Informative Genetic Test:
• An informative genetic test result is one where the information from a genetic test definitively diagnoses or excludes the disease in question. Put another way, an informative genetic test result is one that is reliably either a true positive or true negative result (ruling-in or ruling-out disease/risk, respectively).
Genetic Testing
Non-informative
Non-informative Genetic Test:
• A non-informative genetic test result usually refers to a situation where the genetic test result is normal, but it is not possible to definitively exclude disease/disease risk. A non-informative genetic test result leaves open the possibility that an underlying pathogenic mutation exists, but was missed/not detected by the test.
• A genetic test which cannot completely account for all possible allelic and genetic heterogeneity in a particular disorder can lead to non-informative results.
(•When considering ‘informativity’ ask yourself, how confident you are in your result (does a ‘positive’ result really mean disease/elevated risk and does a ‘negative’ result really mean no disease/no elevated risk). If the answer is ‘no’ then you may be dealing with a non-informative test result.)
Genetic Testing
(how allelic heterogeneity and genetic heterogeneity can affect the performance of genetic tests.)
-Allelic Heterogeneity
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)
o Example: Cystic fibrosis is an autosomal recessive disease caused by mutations in one gene, CFTR. Over 1,500 different mutations have been reported. Cystic fibrosis shows allelic heterogeneity but is genetically homogenous (e.g. NO Genetic Heterogeneity).
Genetic Testing
(how allelic heterogeneity and genetic heterogeneity can affect the performance of genetic tests.)
-Genetic Heterogeneity
Genetic Heterogeneity:
Mutations in multiple gene associated with the same phenotype
o 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.
Genetic Testing
(how allelic heterogeneity and genetic heterogeneity can affect the performance of genetic tests.)
-Pleiotropy
Pleiotropy:
Mutations in a single gene can cause multiple disorders
o Example: Mutations in COL1A1 can cause Ehlers-Danlos syndrome, infantile cortical hyperostosis, or osteogenesis imperfecta
Turner Syndrome
Clinical Presentation
Karyotype:
-45, XO.
-CVS issues = bicuspid aortic valve, coarctation of aorta, hypertension, prolonged QTc syndrome, partial anomalous pulmonary venous connection, persistent left SVC.
-Eye = inner canthal folds, ptosis, blue sclera.
Skeletal system: cubitus valgus, short 4th metacarpal/tarsal, short stature, scoliosis.
-Ear = sensorineural hearing loss, conductive hearing loss, chronic otitis media.
-Neck = web neck, low hairline, cystic hygroma.
-Learning = difficulty in math, visual spatial skills, and low non-verbal scores.
Poor breast development, shield-shaped thorax, widely spaced nipples, brown nevi, no menstruation.
-Endocrine = hypothyroidism and gonadal dysgenesis.
Turner Syndrome
challenges across life span
Infertility, stature, sexual development, concerns regarding health and aging.
Turner Syndrome
Pitfalls of medical culture in dealing with affected patients
Secret keeping and not telling patients full truth causes patient depression, isolation, mistrust, and handling the diagnosis poorly themselves. Difficulty communicating an infertility diagnosis (insensitive, not at all empathetic), perceived negative experiences with physicians (inappropriate humor, too rushed).
Autosomal Recessive (common characteristics of disorders that are of autosomal recessive inheritance.)
AR disorders have phenotypes expressed only in people with 2 mutant alleles of same gene (males and females equally affected). It displays horizontal inheritance; parents of affected child are obligate carriers. Recurrence risk is ¼ for each unborn child; probability of an unaffected sibling being a carrier is 2/3. Majority of mutant alleles present in carriers (not patients), and certain ethnic groups have higher frequencies of mutant allele (high-risk groups). Parental consanguinity causes increased incidence (but if subgroups tend to marry within their group, chances also increase because there was a common ancestor with the allele).
Autosomal Recessive (Calculate allele frequency and carrier frequency of a given autosomal recessive disease when provided with the disease frequency, and vice versa)
Frequency of disease = q2. Find q, find p 2pq = carrier frequency.
Autosomal Recessive
Allelic heterogeneity
Allelic heterogeneity:
– presence of multiple mutant alleles at the same gene
Autosomal Recessive
Compound heterozygote
Compound heterozygote:
– one who has two mutant alleles at the same gene.
Autosomal Recessive
Parental consanguinity
Parental consanguinity:
-if one’s parents share a common ancestor
Autosomal Recessive
High-risk groups
High-risk groups:
-– ethnic group in which a mutant allele/autosomal recessive disease occurs with higher frequency. Marrying within ethnic group increases chances of producing kid homozygous for condition.
Autosomal Recessive
Phenylketonuria PKU
Phenylketonuria (PKU):
- high Phe in blood
- high Phe metabolites in urine
- Hyperactivity
- epilepsy
- mental retardation
- microcephaly
Autosomal Recessive (biochemical deficiencies in PKU patients and the appropriate treatments)
- Defects in PAH (phenylalanine hydroxylase) =98% of people.
- Defects in PAH cofactor, B4 = 1-2% of people (B4 also cofactor for Tyr and Trp hydroxylases).
- Generally mutations in PAH due to LOF alleles; PAH has high allelic heterogeneity (means many PKU patients will be compound heterozygotes).
- For defects in PAH – low Phe diet, generally throughout life.
- For defects in B4 = low Phe diet and meds for NT balance.
Autosomal Recessive
maternal PKU and its treatment
Pregnant PKU women must remain on low-Phe diet while pregnant because otherwise have higher risk of miscarriage or giving birth to children with malformations and mental retardation, regardless of their genotypes.
Autosomal Recessive (newborn screening procedures for PKU and importance of the timing of the test)
Newborn screening by mass spectrometry (can also use Guthrie test, a bacterial inhibition assay). Detection must be within first few days of life to prevent irreversible brain damage, but not within first 2 days because some children can be missed. Sometime within first 2 weeks.
Autosomal Recessive (alpha 1-Antitrypsin Deficiency (ATD)) -clinical features of α1-antitrypsin deficiency and the influence of environmental factors on the expression and severity of the disease (ecogenetics)
Generally presents with later onset (goes under-diagnosed), common in N. Europeans (1/2500). Increased risk of developing emphysema, liver cirrhosis/cancer (due to accumulation of misfolded α1AT protein in liver).
Ecogenetics = earlier and more severe symptoms in smokers. Smoking accelerates onset of emphysema because smoke damages lung, prompting body to send more neutrophils increased elastase release.
Autosomal Recessive (Which enzyme is the primary target of α1-antitrypsin)
α1AT (aka SERPINA1, a serine protease inhibitor) inhibits the elastase enzyme whose main target is elastin. Elastase binds elastin in connective tissue and digests it. In ATD, there is a defect in SERPINA1 so there’s an increase in elastase and thus an increase in tissue damage in the lungs (alveolar wall damage and emphysema).
Autosomal Recessive (two most common mutant alleles that cause ATD and the severity of different allelic combinations. Why do some ATD patients have liver failure?)
- M alleles encode functional proteins.
- Z allele (Glu–> Lys) most common mutant allele–> Z/Z genotype = 15% normal SERPINA1 level. Z allele makes protein that isn’t folded properly and accumulates in ER of liver cells (= liver damage).
-S allele (Glu–>Val) makes an unstable SERPINA1 protein, so S/S genotype has 50-60% normal protein level.
-Z/S genotype = compound heterozygote = 30-35% normal SERPINA1 activity and may develop emphysema.
Treat by either delivering protein via intravenous infusion or aerosol inhalation.
Autosomal Recessive
Tay-Sachs Disease (T-S)
T-S:
fatal genetic disorder that causes progressive destruction of CNS.
Autosomal Recessive (biochemical defects in Tay-Sachs disease and why the brain is the major target)
TS = lysosomal storage disorder with accumulation of GM2 ganglioside, which is synthesized primarily in the brain accumulates in lysosomes of neurons. Patients can’t degrade GM2 because of defective Hexosaminidase A enzyme (which has an alpha and beta subunit encoded by HEXA and HEXB genes TS patients have mutation in HEXA on C15).
Autosomal Recessive (Compare similarities and differences between Tay-Sachs disease, Sandhoff disease and the AB variant of Tay-Sachs disease)
TS = Type I GM2 gangliosidosis. Mutation in HEXA gene on C15 defect in alpha subunit protein in HexA enzyme (which is made of an alpha and beta unit). (HexB enzyme is normal.)
Sandhoff = Type II = same clinical presentation but occurs due to mutation in HEXB gene on C5 causes defects in HexA and HexB enzymes.
AP variant of TS = rare form of TS. HexA and HexB enzymes both normal, but still get GM2 accumulation because of defect in GM2-AP (activator protein) which is responsible for facilitating interaction between lipid and HexA enzyme.
Autosomal Recessive
(Know the high-risk group for Tay-Sachs disease and the available methods for carrier screening and prenatal screening in the high-risk population)
Ashkenazi Jews = 100-fold higher risk for TS (1/3600), whereas general is 1/360000. (Certain French Canadian communities, Amish in PA, and Cajuns of LO, too.)
Can determine enzyme activity by running enzymatic activity assay (distinguish between HexA and HexB because HexA inactivated by heat). Carrier screening has 97% accuracy among Jewish population because they have lower HexA enzymes levels in blood.
Can perform enzyme test on amniotic fluid cells to perform prenatal screening. Can also do DNA testing, which is able to detect 95% of Ashkenazi Jew carriers and 50% of carriers otherwise. DNA test will miss some carriers.
Hemoglobinopathies
(Describe the layout of the α- and β-globin gene clusters and the switch between different forms of hemoglobin (Hb) during development. Explain the function of the locus control region (LCR).))
HbA = adult Hb = α2β2 tetramer with 2 alpha and 2 beta chains. . Alpha and alpha-like genes on C16; beta and beta-like genes on C11. 2 copies of alpha, but one copy of beta.
alpha cluster = zeta-aplha2-alpha1 (zeta only expressed embryonically)
beta cluster = epsilon-gammaG-gammaA-delta-beta
Embryonic Hb’s = Hb Gower 1 (zeta2-epsilon2); Hb Gower 2 (alpha2-epsilon2); Hb Portland (zeta2-gamma2)
Fetal Hb’s = HbF (alpha2-gamma2)
Adult Hb’s = HbA (alpha2-beta2; 95%); HbA2 (alpha2-delta2; 3.5%) (and ~1% HbF)
Turn off zeta and epsilon, turn on alpha and gamma during embryogenesis. Turn off gamma and turn on beta and delta around time of birth. HbF is better to bind O2 at placenta because has higher affinity for O2 and low pO2 than HbA. This switches after birth.
Homotetramers are poor O2 carriers and precipitate inside RBCs.
LCR = located at most upstream region of each cluster; makes physical contact of promoter and regulatory regions of globin genes to influence expression. Deletion of LCR of beta cluster beta-thalassemia
Hemoglobinopathies
(Describe the mutations that cause sickle cell anemia and hemoglobin C disease and their consequences. Know the DNA diagnosis method of the sickle cell disease mutant allele)
These are structural variants (qualitative hemoglobinopathies) that affect globin polypeptide properties without affecting its synthesis.
Sickle cell anemia (HbSS) more common in African descent (10% = carrier frequency). Glu6Val mutation HbS less soluble in low-O2 environment polymerizes into long fibers sickle shaped RBC.
HbCC = milder form of anemia caused by Gly6Lys less soluble, Hb forms crystals
both are auto recessive. Compound heterozygotes have milder anemia than sickle cell.
Diagnose sickle cell using PCR, southern blot, and RFLP (MstII restriction enzyme). Cut site is mutated in sickle cell = get different sized products between normal and HbS. Can also diagnose by electrophoresis of Hb protein (separate protein based on charge since different AA substitutions will affect that).
Hemoglobinopathies
(Know the six possible genotypes of α-globin locus, their clinical phenotypes, and the geographical distributions of α-thal-1 (–) and α-thal-2 (α-) alleles))
*Alpha-thalassemia = low alpha-globin, beta and gamma globin present in excess and precipitate. Usually caused by deletion of alpha-globin genes.
*αα/αα = 100% alpha-globin level = normal αα/α- = 75% alpha-globin level = silent carrier
- αα/– = α-thal-1 = 50% alpha globin level = α-thalassemia 1 trait = common in SE Asia; caused by deletion of both copies of alpha globin genes. Heterozygotes have mild anemia.
- α-/α- = α-thal-2 = 50% alpha globin level = α-thalassemia 2 trait = common in Africa, Mediterranean, and Asia; due to deletion of one of alpha globin genes. Mild anemia. Heterozygote = αα/α- = silent carrier.
- α-/– = 25% alpha globin level = severe anemia = HbH disease (5-30% of hemoglobin is HbH, β4, which precipitates in blood) = a-thal-1/a-thal-2. SE Asia.
- –/– = 0% alpha-globin level = fetal death/hydrops fetalis (ϒ4) – SE Asia.
Hemoglobinopathies
(Understand the following concepts about β-thalassemias)
-thalassemia majors
Show high allelic heterogeneity = lots of compound heterozygotes.
-thalassemia majors – severe anemia, thinning bone cortex, enlarged liver and spleen. Consist of β0 (no Hb detected) and β+ (some β expression) homozygotes?
Hemoglobinopathies
(Understand the following concepts about β-thalassemias)
-thalassemia minor
clinically normal, carriers of one beta-thalassemia allele. Consist of β0 and β+ heterozygotes (slightly more expression)
