Week 7 - Cormier & Nelson Flashcards
1) Name the three types of Heterogeneity; give a brief description and example of each.
2) Name the three types of Heterogeneity that account for variation in clinical phenotype in several inherited disorders.
I) Types of Heterogeneity:
- o Allelic heterogeneity - one gene with more or less severe mutants;
- Ex: CF (CFTR gene has 1400 diff mutations = CF, different severities)
- Ex: PKU (PAH gene mutations)
- Also PKU (d/t PAH gene mutations)
- Locus heterogeneity - same disease, caused by different mutant genes;
- Ex: Retinitis pigmentosa (photoreceptor degeneration, manifested by >70 diff mut)
- Ex: Hyperphenylalanemias (PKU is in this category, but is not locus hetero.)
- Phenotypic heterogeneity – mutant in 1 gene causes different diseases
- Ex: Hirschsprung Disease (mutation in Ret gene - tyrosine kinase receptor gene)
- 1 mutation = no colonic ganglia dvlpmt →Narrowing of distal colon→ chronic constipation, dominantly inherited
- cancer of thyroid & adrenal glands (multiple endocrine neoplasia type 2A & 2B) dominantly inherited
- BOTH Hirschsprung disease & endocrine cancer
II) Clinical Phenotype Variation:
- allelic heterogeneity: diff alleles of the same gene cause varying disease severity; example of PAH
- locus heterogeneity: muts in different genes can yield same disease; for example, phenylalanemia
- modifier genes: people (even within families) with the same mut can present different phenotypes due to the presence of modifier genes; classic example is ApoE4, if you carry 1 or 2 alleles of ApoE4(worse than other Apo’s) you are more susceptible to a range of neurological and neurodegenerative disorders; common variants in genes can affect the onset & severity of a disease but don’t cause disease itself; ex. people with 1 or 2 copies of the E4 allele of ApoE are at a greater risk for Alzheimer Disease (AD)
PRACTICE PEDIGREES!!
What is a “Proband”
In pedigree analysis, “Proband” refers to a particular subject being studied or reported on. In pedigrees, the proband is noted with an arrow and the box (male) or circle (female) shaded accordingly.
4 Basic Patterns of Inheritance
- **Autosomal Dominant **
- Autosomal Recessive (AR)
- X-linked Dominant
- X-linked Recessive
Penetrance vs. Expressivity
*People w/ same disease-causing genotype have varying phenotypes… *
o Penetrance: *probability that a mutant gene will have a phenotypic expression *
• Reduced penetrance: when the expression of a mutant phenotype is less than 100%
o Expressivity: severity of exprsn of the phenotype among individuals with the same genotype
- Variable expressivity: when the severity of the disease differs in people who have the same genotype
- Ex: Neurofibromatosis (NF1) = pleiotropy, wide range of xprsn in tissues (café au lait spots, harmartomas on iris, tumors, neurofibromas on skin) phenotype depends on body location of NF1 mutation
- NF1 can randomly appear, then be passed on thru generations
Name & Describe 4 ALTERNATIVE Patterns of Inheritance
• Y-linked dominance
o ~20 genes on Y
• SRY genes most important – sex determining
o Inherited Y-linked disorders are rare, but dominant by definition
o Most involve various forms of infertility / reproductive abnormalities
o One form of male deafness is associated w/ Y
o Pedigree – Only affects males, every father to every son
• Mutational Mosaicism
o X-inactivation is one example
o Can occur in either the germline or somatic cells
• can form abnormal tissue/organ
o Seen in childhood cancers & developmental disorders
• Ex: Osteogenesis imperfecta, an AD disease that affects bone development
• both affected children have the same point mutation in a collagen gene
• father is unaffected and has no such mutation in his somatic cells
• mosaic for a new mutation in his germline
• Unstable Repeat Expansion Disorders / Premutation Alleles
o Mutation can change from one generation to the next
• premutation (no phenotype) → mild phenotype → more severe phenotype
o Unstable triplet repeat that can cause CNS diseases (AD, AR, X-linked)
• severity correlates w/ the length of the repeats
• ex: Huntington Disease, Fragile X, Myotonic Dystrophy, Friedrick Ataxia
• Maternal inherited mut Mitoch. genome:
o Segregation of mitochondria during cellular replication is random – some daughter cells can receive more mitoch than others
o Mother → all children!
• Some may not be as severe
o Father → No children
What is a “Haplotype” or “Haplotype Block”?
• haplotypes (short for haploid genotypes): any combination of alleles, loci, or markers on the same chromosome that are inherited together
CHARACTERISTICS:
- o not really mendelian, it’s a subtle susceptibility to a disease
- o think of it as a “block” of genes/markers that are usually inherited all on the same chrom
- • sets of SNPs (haplotypes) have more statistical power to identify disease genes and regions
Know the in’s and out’s of Prader-Willi and Angelman Syndrome:
- Presentation
- Susceptibility
- Allele function
- Maternal vs. Paternal imprinting
- snRNAs (SNORD 116 & UBE3A)
- Mosaicism in imprinting
Prader-Willi and Angelman Syndrome
• Dvlpmntal mental retardation – childhood
• Area of genome with PW/A is a hotspot for deletions/recombo
• Only 1 fxn allele = functional hemizygous
o Anything that leads to loss of fxn of the one allele (loss of chrom, deletion, mut, etc.) will give rise to either PWS or AS
o PWS and AS usually deleted together
• P-W = maternally imprinted, if mutation occurs in the expressed allele (from father), no gene product is made, PWS
o Caused by small nucleolar RNA (snoRNA – noncoding), loss of this gives rise to PWS
o Not due to a gene/protein
• A = Paternally imprinted, mutation occurs in expressed allele (from mother), results in AS
o Is due to a gene/protein
snRNAs – made w/PWS exprsn, act in silencing UBE3A
Deletion of snRNAs = exprsn of UBE3A
Due to snRNA deletion *snoRNA is a type of snRNA – major causative snRNAs (especially SNORD116)
Imprinting Errors can affect PWS and AS
• Imprinting can go wrong… if imprinting is not erased (to be re-imprinted for gametes) then imprinting could occur on both copies of chroms – equal to a deletion.
• Or, failure to imprint – no imprinting results in more xprsn of a gene (increase in dosage)
• Or, mosaicism in imprinting – imprint gets lost during meiosis
• Can be tied to diseases, cancer
• PWS – see example B
• AS – see example C, D
Describe the “success story” and mechanism associated with BCR-ABL translocation
Cytogenetics in Cancer
• cytogenetic changes common in advanced cancers
• aneuploidy is the most common
• translocations can disrupt tumor suppressor genes or activate oncogenes
• BCR-ABL = Philadelphia chromosome in chronic myelogenous leukemia (CML) is a classic example
o 9-22 translocation
o Leads to overxprsn of tyr kinase in hematopoetic cells → leukemia
o Detected by FISH
Down’s Syndrome:
- What is Down’s syndrome?
- What are the associated risk factors?
- What is the rate among women >45?
- What is the risk of recurrence?
- What is the likelihood a woman >45 with one Down’s child will have another?
- What Micro RNA’s & genes associated?
- What is XIST?
• Trisomy 21, lethal in 75% of fetuses; most common chrom birth defect: 1/800; • trisomy 21 usually caused by meiotic non-dysjunction in meiosis I; disease likely caused by increased gene dosage
• rate inc. to 1/15 in women over 45
• 8-fold (1/100) risk of recurrence
o If a woman 45 or older has one down’s child already, her 1/15 chance (8 fold risk of recurrence) = 50% chance
5 miRNAs on chr. 21 that are overexpressed in DS patients o two of these, **miR-155 and miR-802** were shown to downregulate the expression of a methyl binding protein **(MECP2)** on a diff chrom o MECP2 (binds to methyllated cytosines) which causes overxprsn of **CREB1 and MEF2C,** implicated in the CNS and other phenotypes of DS
XIST: controls genetic dosing of XXX–> Counts and Silences the extra copy
Describe the tests/results associated with the following Maternal Screening Phases (with particular focus on Down’s Syndrome):
- Non- Invasive Tests (4)
- Invasive Tests (3)
- Prenatal Strategy for DS
• NON-INVASIVE TESTS
1) Maternal Serum Screening (double, triple, quad)
• first trimester: βHCG (free β-human chorionic gonadotropin) increase in DS; PAPP-A (pregnancy associated plasma protein-A) decrease in DS
• second trimester: can detect alpha-fetoprotein (AFP), unconjugated estriol (uE3), inhibin and human chorionic gonadotropin (HCG)
• depressed levels of AFP (& uE3) and elevated levels of HCG and inhibin A are associated with DS
• increased levels of AFP are associated with neural tube defects such as open spina bifuda
*• can have slight overlaps of values in ranges of disease vs normal (ex: AFP) – makes determining risk based on just 1 factor nearly impossible *
2) Ultrasound
3) Radiography
4) MRI
INVASIVE TESTS (IF NEEDED)
*1-3% risk of miscarriage
- *chorionic villus sampling**: biopsy of tissue from the villous area of the chorion, can occur 4-5 weeks before amniocentesis
- *amniocentesis:** removal of amniotic fluid transabdominally by syringe; fetal cells are cultured for diagnostic tests (FISH – can look for aneuploidy)
- *cordocentesis:** removal of fetal blood from the umbilical cord, more often used when other methods have failed or are ambiguous
• Prenatal Testing Strategy for Down Syndrome
- start with non-invasive 1st and 2nd trimester screening in combination; ultrasound plus βHCG and PAPP-A in the 1st trimester, followed by AFP, uE3, inhibin, and HCG in the 2nd trimester; this results in ~95% detection rate for DS
- positive non-invasive test results justify confirmative invasive testing, e.g., amniocentesis/FISH
- availability of genetic and reproductive counseling
Name some examples of Ecogenetics discussed in class
*o Ex: α1-AT polymorphisms, lactase def., ADH def., G6PD deficiency and fava beans *
Alpha-Antitrypsin:
- ZZ genotype make only 15% of normal AAT protein and are susceptible to diseases
- allele freq vary by ethnicity with Z frequency highest in Caucasians (especially Danes)
- AAT, smoking, and Survival
- ZZ non-smokers have much higher survival than ZZ smokers
- AAT variants (Z) also increase risk of liver disease
Heterozygous Advantage: Sickle Cell Anemia
• β-globin locus (sickle cell anemia)
o thalassemia and sickle cell anemias
o βS allele frequency is 5% in A-A, higher in some pops in sub-Saharan Africa
o people who are heterozygous for βS allele are resistant to malaria
o βS - deleterious allele maintained in a pop b/c when hetero, inc. reproductive fitness = heterozygous advantage
Allelic vs. Genotypic Frequency
Allele Frequency (gene frequency) = percentage of allele in a population
• problem of defining a population – US genetically mixed!
• determining the allele frequency from a genotype frequency (remember we are diploid organisms)
o just count the alleles:
o Ex: if a population has 20 AA, 10 Aa, and 5 aa –
• 2(20A) + 10A = 50A
• 2(5a) + 10a = 20a
• 70 total, each are a fraction (50/70 and 20/70)
• NOTE: p+q=1
Genotype Frequency = proportion of indiv in a pop that have a genotype (homo, hetero)
• not as easy since the distribution of alleles between homozygotes and heterozygotes may not be known
Hardy-Weinberg Law - helps determine carrier frequency/gene mapping in pop and mutation rates
p2 + 2pq + q2 (comes from punnet sq)
Which pop is in HW equilibrium?
o Pop. AA Aa aa
X 0.25 0.50 0.25 (q = 0.5) – correct
Y 0.10 0.74 0.16 (q = 0.4) – incorrect for p & 2pq
Z 0.64 0.27 0.09 (q = 0.3) – incorrect for p & 2pq
List the 9 Cellular/Biochemical Disease Classifications, and give an example for each.
Enzyme Defects
• enzymes contain critical regions that can be disrupted by mutations
o PKU - relatively common defect in newborns that is tested for at birth
o PKU is an example of defect that occurs in one tissue (liver & kidney) but where the phenotype is manifest elsewhere (brain)
Defect in Lysosomal Storage
• increases in tissue mass, common cause of neurodegeneration and other CNS problems
• heterogenous group of ~ 40 genetic disorders, caused by muts in lysosomal enzymes, aut recessive
o ex: Tay-Sachs disease, a buildup of GM2 ganglioside sphingolipids, mutation in hexA gene
• ubiquitously expressed, mutant phenotype in brain (retina spot with white area around it)
• Tay-Sachs 100 times more prevalent among Ashkenazi Jews; carry a mutant hexA allele
• homozygous infants are normal until 3-6 months, then neuro problems begin, death between 2-4 years
Defects in Protein Trafficking
• many proteins are post-tln modified (add sugars, signals for trafficking)
• ex: I-cell disease, no M-6-P tag for lysosome enzymes, sent out of cell instead
Defect in Co-Factor Metabolism
• ex: α1-AT, co-factor in interactions with environmental factors like cigarette smoke
Defects in Receptor Proteins
• ex: LDL-R- which is responsible for binding & internalization of LDL & cholesterol
• hypercholesterolemia is an autosomal dominant disorder (hemidominant – heterozygotes also have some symptoms) arising from LDLR defects, and is common familial disease more severe in homozygotes
Defects in Transport
• classic example is cystic fibrosis (CF), an autosomal recessive disease
• CF caused by F508 mut in the CFTR gene - chlorine channel in the apical membrane of epithelial cells
Defects in Structural Proteins
• example: DMD an X-linked recessive disease, mut in the dystrophin gene; causes progressive muscle deterioration from childhood on, leading to death by late teens; currently untreatable but gene therapy trials are underway
o dystrophin has two functions: maintains muscle-membrane integrity, linking actin skeleton to the ECM; and it maintains synaptic junctions in the brain
• 1/3 of DMD arise from new mutations b/c of the size of the gene & because of higher mut rates in sperm
• carrier mothers have no clinical manifestations but often show elevated creatine kinase levels
Neurodegenerative Defects
• Alzheimer’s disease - 1st degree relatives have a 38% risk of AD and 10% of AD is familial (clusters of disease in certain families)
• triplet repeat expansion disorders, including Huntington disease
Mitochondrial Disorders
• mitochondria encode either tRNA or oxidative P proteins
o high mut rate
• mitochondrial diseases found in tissues with high energy demands: CNS and muscle
• maternally inherited, affected males cannot pass on a mitochondrial disorder
• mosaicism
What is genetic mapping?
Describe Linkage Analysis.
A way to characterize the genetic basis for a phenotype within a given family. Does not require knowledge of sequence.
A genetic map indicates the relative position of genes (defined by fxn) shown by linkage analysis
• linkage analysis determines whether two genes/loci/markers, are near one another, estimated by the frequency that they are transmitted together during meiosis
• 2 genetic loci are linked if they are transmitted together more often than expected. the closer two genes or markers are to each other the less likely they will be separated during meiotic recombo
o Far apart: recombo likelihood = nonrecombo likelihood (50%) unlinked
o Close: nonrecombo likelihood > recombo likelihood (less than 50%) linked
What is Recombination frequency?
How long is 1 centiMorgan, and how is it derived?
If a Genetic Marker is recombined independently from the disease gene (AKA, no longer detected on same chromosome as disease gene) in only 1/25 progeny, how close is the marker to the disease gene?
Recombination frequency (θ) is the frequency with which a single chromosomal crossover will take place between two genes during meiosis. The recombination frequency will be 50% when two genes are located on different chromosomes or when they are widely separated on the same chromosome. This is a consequence of the law of independent assortment. The law of independent assortment always holds true for genes that are located on different chromosomes, but for genes that are on the same chromosome, it does not always hold true. When two genes are close together on the same chromosome, they do not assort independently and are said to be linked. Whereas genes located on different chromosomes assort independently and have a recombination frequency of 50%, linked genes have a recombination frequency that is less than 50%.
A centiMorgan corresponds to appx 2MB of genetic sequence separation. It is quantified by 1% of observd Recombination Frequency between two genes on a chromosome.
1/25 = 4% = 4cM. This independent recombination event is rare, because the marker and gene are located very close together on the same chromosome.
Compare Linkage Equilibrium and Disequilibrium
•**Linkage Equilibrium = **freq of the marker alleles and the disease alleles correspond,
o For example, if a marker locus (A, a) has allele frequencies of A = 0.7, a = 0.3, then disease gene linked to “A” in 70% of affected families and to “a” in 30% of affected families.
Linkage Disequilibrium = Frequencies vary
Indicates that the allele marker is very close to the disease gene (how the CF gene was cloned)
o Linkage Disequil is when 2 genetic loci, across the pop as a whole, are found together more often than expected, non-random association
• haplotypes (such as SNP haplotypes) can be in equilibrium or disequilibrium.
How might you map a single-gene (monogenetic) trait?
Give an example of a monogenetic trait and how it was initially mapped.
Mapping Primarily Single-Gene Trait Genes
• Easier to map than complex diseases – linkage analysis
• special considerations: reduced penetrance and variable expressivity
• polymorphic markers can be used in families, including linkage analysis of SNPs and SNP haplotypes
• Ex: SNP haplotypes to map a monogenic disease gene
o Ehlers-Danlos VIII disease is a rare aut dominant disorder involving a collagen defect
o initially mapped to chr. 12 in families (used LOD), one large fam permitted mapping of SNP haplotypes
o causative gene has not been identified yet
o Ex:linkage analysis for primarily single-gene diseases in families
• enroll families: either very large families (e.g., Nancy Wexler with Huntington’s Disease) or many small families (e.g., CF)
