Second Week of Notes Flashcards
Characteristics of Autosomal Recessive Disorders
o Phenotype is only expressed in homozygotes rr
Need to have both mutant alleles
o Males and females are usually equally affected
Does not target based on gender
o Horizontal Inheritance Pattern
-Normally see it across in siblings (they are rare unless there are carrier parents
Parents of an affected child are obligate carriers
o Recurrent risk for each unborn child is ¼ (both parents are carriers)
RR, Rr, Rr, rr (rr is 25%)
o The chance of unaffected siblings being a carrier is 2/3
Carrier =Rr
Only 3 unaffected made RR, Rr, Rr….. 2 of the three are carriers
Calculating Frequencies of AR Disorders (PRACTICE)
o Amount of an autosomal recessive disease 1/10,000
♣ This is the q^2
o Find the square root to get q
♣ 1/100 is the amount of q alleles there are
o Find the amount of carriers (the Rr)
♣ Find 2pq
♣ Rare diseases, just do 2q
• 2* 1/100= 2/100
o REMEMBER, when finding carriers for rare diseases
♣ 2pq~ 2q
• Carrier Frequency vs. Disease Frequency (Practice!!)
o Scotland 1/5,300 1/36 (2pq)
o Finland 1/200,000 1/250
Parental Consanguinity
• Parental Consanguinity The more affected children of an autosomal recessive disease, the more likely there is Parental Consanguinity (common ancestor or inbred
o If the two parents inherited the same mutant allele from a common ancestor, then the disease risk for their child
Much higher risk to have the carrier traits passed down in consanguinity
Compound Heterozygosit
Compound Heterozygosity: presence of multiple common mutant alleles of the same gene in a population. There are different mutant alleles
o Example: is an individual who carries two different mutant alleles of the same gene
♣ Bc// Bs (both of these are mutant alleles in hemoglobin)
• One is sickle cell, other is the hemoglobin C
Simple Heterozygotes
Simple Heterozygotes Have two different alleles, only one of them could be mutant
♣ Ba//Bs (one is normal, the other is mutant sickle-cell)
o Homozygots= Ba//Ba Bs//Bs (one healthy homozygous, other is mutant homozygous)
Phenylketonuria and it’s genetics
Phenylketonuria High phenylalanine in blood due to lacking a critical enzyme, phenylalanine hydroxylase. Will lead to mental retardation, hyperactivity and epilepsy. Caused by mutations for phenylalanine hydroxylase at chromosome 12. Treated by a low phenylalanine diet and possible neutral amino acid supplementation
Cause of Phenylketonuria
♣ High amount of Phenylalanine levels in the blood, due to the defective nature or lack of enzyme phenylalanine hydroxylase
• Phenylalanine Hydroxylase (PAH): Normally found in the liver, is used to turn phenylalanine Tyrosine
• Defects cause 98% of the diseases
Defect in Cofactor BH4 ( a cofactor for PAH) Need the cofactor B4 to bind to the phenylalanine hydroxylase enzyme (and for dopamine/serotonin)
• This causes 1-2% of the cases of Phenylketonuria
• Lacking BH4 Also leads to a loss of neurotransmitters such as dopamine and serotonin
Possible phenotypes from Phenylketonuria
High phenylalanine metabolites in urine, hyperactivity, mental retardation, epilepsy, microcephaly
Molecular defects in PAH The PAH gene is at chromosome 12q22-24. Most mutations in PAH are partial or complete loss-of-function alleles. PAH gene exhibits high allelic heterogeneity; over 400 alleles have been identified. Most PKU patients are compound heterozygotes (i.e. having two different mutant alleles of the PAH gene). Severity of phenotype varies and probably reflects compound heterozygosity
Phenylketonuria (PKU) Defects in BH4 synthesis and Recycle
♣ Defects in different enzymes that give rise to cofactor BH4 (BH4 is for the phenylalanine hydroxylase)
• Enzymes defected to build BH4: GTP-CH, 6-PTS
o Phenylketonuria (PKU) Screening
Detecting Phenylketonuria (PKU) and treating it
Phenylketonuria (PKU) Screening
-Mass Spectrometry(MS/MS) is the current method of choice for many newborn screenings including PKU. A mass spectrometer simultaneously sorts many molecules in a blood specimen by weight (mass) and size, and also measures the quantity of each molecule.
• Sorts molecules in a blood specimen by size, weight, and quantity.
• Fast detection and high sensitivity.
• Measures multiple molecules simultaneously.
Timing of Test: The sensitivity of PKU screening is influenced by the age of the newborn when the blood sample is obtained. Phenylalanine level is typically normal in PKU babies at birth because of normal PAH in maternal supply and increases progressively with the initiation of protein feedings during the first days of life. Early detection and treatment is crucial to prevent irreversible damage to the developing brain. However, if tested too early (within 1-2 days of birth), some affected children can be missed.
• Newborns are tested first after birth and then again at their first pediatrician’s visit days later.
Guthrie test (aka Guthrie bacterial inhibition assay) for PKU was developed in the mid- 1960s. This test is based on the findings that phenylalanine inhibits the growth of the bacterium Bacillus subtilis and that such inhibition can be overcome by a high level of phenylalanine in the blood sample of a PKU baby.
o Phenylketonuria Treatment When treated early with low-phenylalanine diet, the mental retardation can be prevented. Phenylalanine is an essential amino acid and thus cannot be eliminated from the diet. The low-phenylalanine diet should be maintained throughout childhood and school years, and preferably the patient’s whole life. BH4-deficient PKU patients are treated with oral BH4, low-phenylalanine diet, and supplements (L-dopa and 5-hydroxytryptophan etc) to balance neurotransmitter levels.
Low-Phenylalanine Diet:
• From birth through childhood, and beyond
• For women, throughout child-bearing years
BH4 supplementation • Kuvan® : long-term safety and effectiveness?
Other treatments:
• Neutral amino acid supplementation
o Dietary supplementation with large neutral amino acids(LNAAs), with or without the traditional PKU diet is another treatment strategy. The LNAAs (e.g.leu,tyr,trp,met,his,ile,val,thr) compete with phe for specific carrier proteins that transport LNAAs across the intestinal mucosa into the blood and across theblood brain barrierinto the brain .
• Enzyme replacement therapy
• Gene therapy
o PKU: Maternal Effect
♣ Problem: Phenylketonuria women who are off low-Phe diet in pregnancy
• markedly increased risk of miscarriage.
• congenital malformations and mental retardation in babies.
Cause: elevated phenylalanine level in maternal circulation (due to being off diet)
• Prevention: maintain low-Phe diet for females with PKU throughout their child-bearing years.
1-antitrypsin deficiency (ATD)
1-antitrypsin deficiency (ATD) A disease where a protease inhibitor (Serpina1 gene) is inhibited, allowing the protease elastase run rampant, destroying connective tissue elastin in lungs, leading to lung emphysema and liver disease
Phenotype
ATD patients have a 20-fold increased risk of developing emphysema, with more severe symptoms among smokers. This disorder is late-onset, especially in non-smokers, but 80- 90% of deficient individuals will eventually develop disease symptoms. Many patients also develop liver cirrhosis and have increased risk of liver carcinoma due to the accumulation of a misfolded α1-AT mutant protein in the liver
Different conditions it leads to :
• Emphysema of lungs and lung disease
• Liver Cancer and Liver Cirhosis
Earlier and more severe symptoms in smoker (ecogenetics).
Mechanism of 1-antitrypsin deficiency (ATD)
α1-antitrypsin (ATT or SERPINA1) is made in the liver and secreted into plasma. SERPINA1 is a member of serpins (serine protease inhibitor), which are suicide substrates that bind and inhibit specific serine proteases. The main target of SERPINA1 is elastase, which is released by neutrophils in the lung. When left unchecked, elastase can destroy the connective tissue proteins (particularly elastin) of the lung, causing alveolar wall damage and emphysema.
♣ Deficiency in a1-antitrypsin protein (SERPINA1, AAT), a protease inhibitor
♣ SERPINA1 is a suicide substrate of the serine protease elastase.
• Elastase is released by activated neutrophils at the airway, destroying elastin in the connective tissues.
• It’s macrophages that release signals to summon neutrophils the neutrophils will release the Elastase
♣ ATD patients have an imbalance of elastase and SERPINA1 levels
ATD: Molecular Basis The SERPINA1 gene is on chromosome 14 (14q32.13). There are ~20 different mutant alleles, although the Z & S alleles account for most of the disease cases. The Z allele (Glu342Lys) encodes a misfolded protein that aggregates in the endoplasmic reticulum (ER) of liver cells, causing damage to the liver in addition to the lung. The S allele (Glu264Val) expresses an unstable protein that is less effective.
♣ ATD is caused by mutations in a1-AT (SERPINA1) gene.
♣ a1-antitrypsin (elastin inhibitor) is produced in the liver and transported to the lungs via the blood.
Three common M alleles encodes functional proteins.
• Z allele (Glu342Lys) is the most common mutant allele. (Glu at 342 is replaced by Lysine)
o Individuals with Z/Z genotype have ~15% of normal SERPINA1 level.
o The Z allele makes a protein that is not folded properly and tends to accumulate in the endoplasmic reticulum of liver cells, leading to liver damage.
S allele (Glu264Val) makes unstable SERPINA1 protein. o Individuals with S/S genotype has 50-60% of normal SERPINA1 level.
1-antitrypsin deficiency (ATD) Treatment and
effects of smoking on ATD
antitrypsin deficiency (ATD) treatment:
Two approaches of delivering human SERPINA1 to the pulmonary epithelium are being studied: intravenous infusion and aerosol inhalation.
♣ Inhaled bronchodilators and inhaled steroids
♣ O2 therapy and possibly lung replacement
♣ In the future: Enzyme Replacement Therapy and Gene therapy are possibilities
1-antitrypsin deficiency (ATD) and Smoking:
Ecogenetics (Ecogenetics) Smoking accelerates the onset of emphysema in ATD patients. Tobacco smoke damages the lung, prompting the body to send more neutrophils to the lung for protection. More neutrophils release more elastase, causing more severe lung damage. (Dont have α1-antitrypsin to inhibit elastase)
Tay-Sachs Disease (GM2 gangliosidosis type I)
Tay-Sachs is an inherited disorder that progressively destroys neurons in the brain and spinal cord. The most common form of T-S is an early-onset, fatal disorder apparent in infancy. T-S infants appear normal until the age of 3-6 months, when early symptoms such as muscle weakness, decreased attentiveness, and increased startle response appear. As the disease progresses, the T-S children experience symptoms of neurodegeneration including seizures, vision and hearing loss, diminishing mental function, and paralysis. An eye abnormality called “cherry-red spot” is a characteristic of T-S. Children of T-S usually live only till 3-4 years of age.
T-S is caused by a defective α subunit; only HexA activity is affected. Sandhoff disease is caused by a defective Hex A and defective Hex B, leading to defective Hexosaminidase A and B
Phenotype A fatal genetic disorder in children that causes progressive destruction of the central nervous system.
-T-S babies start to develop neurological deterioration around 3 - 6 months of age, and die by 2 - 4 years.
First signs - muscle weakness and a startle response at sudden sound.
Advanced Symptoms: Loss of voluntary movement, muscle seizure, mental retardation, vegetative state
Biochemical defects of Tay-Sachs disease T-S is a lysosomal storage disease. Inability to degrade GM2 ganglioside results in up to 300-fold accumulation of this sphingolipid inside swollen lysosomes in neurons of the central nervous system. A defective hexosaminidase A (HexA) needed for in metabolizing GM2 is responsible for T-S. HexA is a heterodimer of αβ, which are encoded by the HEXA and HEXB genes, respectively. Although HexA is a ubiquitous enzyme, the impact of T-S is primarily in the brain where most of GM2 ganglioside is synthesized.
T-S is a lysosomal storage disorder with (>300x) accumulation of GM2 ganglioside in the lysosome.
• GM2 ganglioside is primarily synthesized in neurons of the brain and a componentof neuron cell membrane.
♣ T-S patients are unable to degrade GM2 ganglioside because of a defective hexosaminidase A.
• Hexosaminidase A consists of two subunits: a and b, which are encoded by the HEXA and HEXB genes, respectively.
o T-S patients usually have mutations in the HEXA gene.
• Mutations in HEX B causes Sandhoff disease (GM2 gangliosidosis II),a similar lysosomal storage disorder.
Sandhoff disease
Sandhoff disease (GM2 gangliosidosis type II) presents the same neurological symptoms as T-S. Sandhoff disease patients have defects in both genes Hexosaminidase A and Hexosaminidase B (HexB) • T-S is caused by a defective α subunit; only HexA activity is affected. Sandhoff disease is caused by a defective Hex A and defective Hex B, leading to defective Alpha and Beta units in Hexosaminidase A • The α subunit gene HEXA and the β subunit gene HEXB reside on chromosomes #15 and #5, respectively.
GM2 ganglioside degradation requires three proteins
The first two proteins are the hexosaminidase A and the hexosaminidase B (the two proteins that enzymatic degrade GM2 ganglioside
GM2A Need this protein to recognize the ganglioside and bring it the hexosaminidase A and B complex for degradation
• If GM2A is defective, can lead to lysosome storage disease
GM2A
GM2A Need this protein to recognize the ganglioside and bring it the hexosaminidase A and B complex for degradation
• If GM2A is defective, can lead to lysosome storage disease
Recognize The effects of Tay-Sachs and Sandhoffs Disease
Tay-Sachs is caused by a defective α subunit; only HexA gene activity is affected.
Sandhoff disease is caused by a defective Hex A and defective Hex B, leading to defective Alpha and Beta units in Hexosaminidase A
If the GM2AP activator is defective, then you cant bring Ganglioside to the hexosaminidase
Screening for Tay-Sachs disease:
o Enzymatic activity assay: both HexA and HexB enzymes are present in the serum. Their activities can be distinguished in such assays because only HexA is inactivated by heat.
o Carrier Screening: primarily among Ashkenazi Jewish population, the enzyme test has 97% accuracy because carriers have lower HexA enzyme levels in the blood.
o Prenatal screening: the enzyme test can also be performed on cultured amniotic fluid cells to detect T-S fetus when both parents are known to be carriers. Notably, this screening has reduced the number of T-S cases by about 95% over the past 30 years.
o DNA testing: The tests currently available can detect about 95% of carriers in the Ashkenazi Jewish population and about 60% of carriers among non-Jewish individuals. Therefore, some carriers will be missed by DNA test alone.
Complex Traits
Complex Traits—> Multifactorial Inheritance
o For a large portion of diseases there are multiple genetic components and environmental components
o Complex traits aggregate in families
Need to distinguish between clustering in families due to genetic factors and those due to shared environmental factors
o Epidemiologic twin, adoption, and immigration studies used
-Each measure of genetic contribution needs to be interpreted carefully, but as a group can provide compelling evidence for genetic contribution to trait.
Concordance
Usually means the presence of the same trait in both members of a pair of twins. However, the strict definition is the probability that a pair of individuals will both have a certain characteristic, given that one of the pair has the characteristic.
o For example, twins are concordant when both have or both lack a given trait
o A twin study compares the concordance rate of identical twins to that of fraternal twins. This can help suggest whether a disease or a certain trait has a genetic cause
Twin Studies
o Compare monozygotic to dizygotic twins
If twins raised together and assume same degree of similar environment, then differences in concordance rate between mono- and dizygotic twins likely due to genetic factors
- Monozygotic Twins Share 100% of the same genetic code
- Dizygotic Twins Shares roughly 50% of the same genetic code
Twin studies provide a potential means of overcoming this problem. Monozygous (MZ) twins are identically matched for DNA sequence, age, and gender, and perhaps closely matched for environmental exposures. Dizygous (DZ) twins on average share 1/2 of their DNA sequences, but may be about as closely matched for other factors as are MZ twins. If it can be assumed that MZ and DZ twins are equally similar with respect to noninherited factors, then twins can be used to get an estimate of the relative contribution of genetic vs. environmental variation to the trait.
Compare Monozygotic twins raised apart
If twins raised apart and assume had different environments, then similarities in trait (high concordance rates) likely due to genetic factors.
• Share 100% same genetics, different environments with Environment 1 and Environment 2
o Adoption Studies
Compare similarity between biological siblings raised apart and adoptive siblings
• If biological sib 2 more concordant with biological sibling than adopted sibling, then have evidence for genetic component as opposed to environmental component.
o This means that despite being in a different environment, the biological twin 2 is more concordant with biological sibling 1 traits are genetic component
Risk of Disease in Relatives
o Can compare the frequency of disease in relatives of patients to see if higher than in general population
o Risk of disease in sibling/ risk of disease in general population= Risk of disease in relative
♣ Risk in general population ~ 0.4%
♣ Risk to sibs of type 1 diabetes patient ~ 6%
o S ~ 15 for type 1 diabetes.
Heritability
Heritability—> Proportion of variance in trait that is due to genetic variation (compared to non-genetic variation)
o The Heritability of a trait is the proportion of total variance in a trait that is due to variation in genes. A high heritability implies that differences among individuals with respect to a trait
♣ such as blood pressure in a population can be attributed to differences in the genetic makeup.
The key to interpreting heritability estimates is to remember that we’re talking about and describing variation in BOTH genetic factors AND non-genetic factors.
♣ If one (alleles or environment) doesn’t demonstrate much variability, then it doesn’t have much potential to explain variability in a trait.
o ***Implication: A high heritability does not imply that non-genetic factors are not important. A low heritability does not imply that environment is not important.
Allele and Locus Difference
Locus is that point on chromosome where the trait or gene is situated. Gene is found at a certain locus. Homologous chromosomes have same genes at the same locus but have different alleles. Gene mapping is used very commonly to determine locus in a certain biological trait. Hence, locus is a maker of DNA. Locus is usually referred as a chromosome marker. It could be called as a gene but it is used specifically to locate the position of chromosome on the gene. Single allele can be found on one single loci and that is what makes it distinct.
Characteristics of Complex Traits
Contains one or more of the following:
♣ Incomplete Penetrance= phenotype does not always show
♣ Variable Expressivity= different ranges/types of expression with the phenotype
♣ Heterogeneity – allele and locus
• The trait exists on different locuses or allels throughout the genome (on different chromosomes)
♣ Presence of phenocopies