Last Exam Flashcards
- ) In what manner are gain of function and loss of function mutations inherited?
- ) Exceptions to the loss of function (3)?
1.) Gain of function: Dominant inheritance.
Loss of function: Recessive inheritance.
2.) BRCA1/2, TP53, RB1.
L18, #7
Oncogenes are ________ versions of “_________,” which are part of ______________.
Oncogenes are abnormal versions of “proto-oncogenes,” which are part of normal cell function.
L18 #9
What types of modifications can convert a proto-oncogene into an oncogene (2)?
Modifications at either the structural level, or at the level of expression.
L18, #9
Oncogene formation is usually a ____________ mutation (________ of function).
autosomal dominant mutation (gain of function mutation).
L18, #9
Proto-oncogenes encode proteins essential for ___________.
Cellular growth control.
L18 #10
List the mechanisms of oncogene formation that result in the following:
- ) Abnormal (hyperactive) protein (3)
- ) Excess normal protein (3)
1.) Point mutation, chromosomal translocation, local DNA rearrangements (insertion, deletion, inversion or transposition).
2.) Gene amplification, chromosomal translocation, insertional mutagenesis.
L18 #13
What does RET proto-oncogene (10q11) encode for, and what is it normally activated by?
A receptor tyrosine kinase involved in neural crest development; normally activated by glial cell line-derived neurotrophic factor (GDNF).
L18 #16
What is the result of:
- ) RET point mutations (and where —> two places); leads to three things.
- ) Rearrangements of RET gene (two things)
1.) Point mutations in the Cys-rich extracellular domain and in tyrosine kinase domains of RET cause constitutive activation and lead to (a) multiple endocrine neoplasia (MEN 2A), MEN 2B, and familial medullary thyroid carcinoma (FMTC).
2.) Involved in papillary thyroid carcinoma (PTC), and lung adenocarcinoma.
L18 #16
What is activation by over-expression (mechanism?)
A phenomenon in which additional copies of a chromosomal segment are present in a cell.
-The extra copies of chromosomal regions contain proto-oncogenes.
L18 #17
- ) What is HER2 (what type of receptor is it)? What is it encoded by and where is it?
- ) What cancer is its amplification associated with and how?
1.) HER2 receptor = human epidermal growth factor receptor (a tyrosine kinase receptor).
-Encoded by ERBB2, a known proto-oncogene located in the long arm of human chromosome 17.
2.) Up to 200-fold amplification of HER2/neu in breast cancer has been observed.
L18 #17
- ) Over-expression of what receptor is associated with colorectal cancer?
- ) What cancer is deletion of this same receptor associated with?
1.) EGF receptor ( a protein-tyrosine kinase).
2.) Glioma
L18 #18
What type of point mutation in HER2 leads to breast cancer?
Valine to Glutamine point mutation.
L18 #18
What causes the following:
- ) Chronic Myelogenous Leukemia (CML)
- ) Burkitt Lymphoma
- ) Follicular Lymphoma
- ) Chronic Myelogenous Leukemia (CML): Translocation between chromosomes 9 and 22 leads to hybrid gene, Brc-Abl. Reciprocal translocation creates the Philadelphia chromosome
- ) Burkitt Lymphoma: Translocation between chromosomes 8 and 14 activates the expression of Myc gene.
- ) Follicular Lymphoma: Translocation involving chromosomes 18 and 14 leads to over-expression of the anti-apoptotic gene Bcl-2.
L18 #20
- ) What cell function is Ras-MAPK (a component of the Bcr-Abl signalling pathway) involved in?
- ) On which gene is it encoded?
1.) Activation of cell proliferation and survival.
2.) BCR
L18 #23
What portions of the Bcr-Abl signalling pathway are involved in inhibition of apoptosis (2)?
PI3-K/PKB-mediated and Bcl-xL-mediated pathways.
L18 #23
What portion of the Bcr-Abl signalling pathway is involved in focal adhesion?
Paxillin
L18 #23
- ) Describe the etiology of Burkitt lymphoma.
2. ) What other etiology is Burkitt associated with?
1.) 8:14 translocation —> Places the c-Myc gene (encodes a transcription factor) from chromosome 8 under control of Ig heavy chain promoters/enhancers on chromosome 14.
2.) Also associated with Epstein Barr virus (EBV) infection.
L18 #24
How is Epstein Barr virus (EBV) associated with cell proliferation and survival, and via what pathways (3)?
EBV induces the expression of a membrane protein called Latent Membrane Protein (LMP-1), which mimics an activated cytokine receptor (TNFR) to initiate cell proliferation and cell survival signals via: 1.) MAPK pathway 2.) PI3-K/PKB pathway 3.) NF-kB pathway L18 #25
Describe the etiology of follicular lymphoma
Translocation involving chromosomes 18 and 14 leads to over-expression of the anti-apoptotic gene Bcl-2.
• 14:18 translocation places the anti-apoptotic Bcl2 gene from Ch18 next to strong Ig heavy chain promoter on Ch14.
• Increased expression of Bcl2 promotes enhanced survival of B-lymphocytes.
Present in 100% of cases
L18 #26
By which mechanism does HPV cause cervical cancer? Explain.
Insertional mutagenesis: Accidental integration of viral DNA fragment into host chromosome.
• Causes unbalanced production of viral replication proteins.
• Viral replication proteins, E6 and E7, interfere with the normal function of host p53 and Rb proteins, respectively. —> E6/p53 and E7/Rb
L18 #29
Give two examples of insertional mutagenesis mediated by retroviruses (give the cancer and the retrovirus).
1.) Adult T-cell leukemia/lymphoma (caused by HTLV).
2.) Kaposi’s sarcoma (caused by HIV).
L18 #30
With respect to the cell cycle, define gatekeepers (two examples) and caretakers (three examples).
Gatekeeper: Regulate transition through the cell cycle.
-e.g. RB, p53.
Caretaker: Protect the integrity of the genome.
-e.g. BRCA, XP, MLH1/MSH2
L19 #5
Describe/define E2F, i.e. what is it necessary for?
A transcription factor required for transition from the G1 phase to the S phase.
L19 #6
Describe cell cycle regulation via Rb (two main steps).
1.) Active retinoblastoma protein (Rb) binds and sequesters E2F.
2.) Phosphorylation of Rb by G1-CDK inactivates Rb, causing it to release E2F, thus allowing progression to the S phase.
L19 #6
p53 is stabilized ONLY when __________, why?
there is DNA damage, because that is when ATM kinase becomes active.
L19 #7
Inhibition of Cdk results in ___________.
arrest of the cell cycle in G1 and G2.
L19 #7
Concerning p53, what does DNA damage lead to?
DNA damage leads to phosphorylation by ATM kinase and stabilization of p53.
L19 #7
p53 induces the expression of _______, which is a _______.
p53 induces the expression of p21, a Cdk inhibitor (CKI)
L19 #7
What is the role of tumor suppressor (TS) proteins?
To arrest cell cycle at restriction points and keep cell division in check.
-Also involved in DNA repair, chromosomal disjunction, and in apoptosis.
L19 #9
What is the typical inheritance pattern for mutations in tumor suppressor genes? Why?
Recessive, because they are loss of function mutations
L19 #9
- ) Define/describe loss of heterozygosity (LOH).
2. ) How are these mutations inherited in TS genes?
1.) When mutation of one allele leads to loss of the normal copy.
2.) In such instances, mutations in TS genes may be inherited in a dominant fashion.
L19 #9
What is often considered evidence for the existence of a tumor-suppressor gene?
Loss of heterozygosity (LOH)…WHY? I don’t know, sort it out.
L19 #10
Tumor suppressor gene mutations are inherited as if they are _______ ________ mutations, rather than _______.
Inherited as if they are autosomal dominant mutations, rather than autosomal recessive mutations.
L19 #10
List five types of TS proteins that are mutated in cancer, give examples.
- ) (1)
- ) (1)
- ) (3)
- ) (3)
- ) (1)
1.) Proteins that regulate a particular phase of the cell cycle, e.g. Rb protein in G1.
2.) Proteins that monitor checkpoints to arrest cell cycle, e.g. p53.
3.) Proteins that are components of growth-inhibitory signaling pathways, e.g. TGFβ receptor, NF1 protein, APC protein.
4.) Proteins that promote apoptosis, e.g. Fas, Bax, Apaf-1.
5.) Proteins that participate in DNA damage repair, e.g. NER proteins implicated in Xeroderma pigmentosum.
L19 #11
For the given inherited cancer, give the mutated tumor suppressor gene(s), and that genes function.
- ) Retinoblastoma (1)
- ) Li-Fraumeni syndrome (1)
- ) Colorectal cancer (due to familial polyposis) (2)
- ) Colorectal cancer (without polyposis) (3)
- ) Breast and/or ovarian cancer (2)
- ) Wilms’ tumor (2)
- ) Nerve tumors (including brain) (2)
1.) RB1 – Cell division, DNA replication, cell death.
2.) TP53 (p53) –Cell division, cell death, DNA repair.
3.) APC, DCC –Cell division, DNA damage, cell migration/adhesion, cell death.
-APC = Adenomatous polyposis coli; hence the “P” for colorectal cancer due to familial “P”olyposis.
4.) MLH1, MSH2, MSH6 –DNA mismatch repair, cell cycle regulation.
5.) BRCA1/BRCA2: Repair of double-stranded DNA breaks, cell division, transcription, cell death.
6.) WT1, WT2 –Cell division, transcriptional regulation.
7.) NF1, NF2 –RAS-mediated signal transduction, cell differentiation, cell division, developmental processes.
L19 #12
- ) Describe the effects on the eye of the hereditary and sporadic forms of retinoblastoma.
- ) Are either associated with other cancers?
1.) Hereditary form: Affects BOTH eyes (LOH).
Sporadic form: Affects ONE eye.
2.) Hereditary may also cause osteosarcoma, soft tissue sarcomas, and melanoma.
L19 #14
On what chromosome is the RB1 gene located?
Chromosome 13
L19 #14
What gene encodes p53 and on which chromosome?
TP53 gene on chromosome 17.
L19 #15
Mutagen vs Carcinogen?
Mutagen: Compound that causes a mutation.
Carcinogen: Compound that results in a cancer-causing mutation.
L19 #15
- ) What type of compound is benzo(a)pyrene considered?
2. ) What genes does it affect?
1.) Pro-toxin (requires metabolic activation to be dangerous).
2.) Causes mutations in genes such as TP53 via G to T transversion.
L19 #15
What is AFLATOXIN?
A fungal metabolite that is present as a contaminant in moldy grain and peanuts; also induces G to T transversions in TP53 gene
L19 #15
Benzo(a)pyrene and aflatoxin are considered carcinogens, why?
Because the mutations they cause lead to cancer.
L19 #15
What are two examples of cancers in which p53 fails to activate?
Li-Fraumeni syndrome and Ataxia telangectasia.
L19 #15
- ) What are the chances of developing breast cancer by age 50 if one mutant BRCA1 allele inherited?
- ) Both alleles normal?
1.) 60% by age 50.
2.) ≈ 2%
L19 #17
- ) Which tumor suppressor (TS) gene is implicated in familial adenomatous polyposis (FAP)?
- ) What is this an early event in?
- ) What does this gene regulate?
1.) APC
2.) An early event in the progression towards colon cancer.
3.) APC regulates the degradation of β-catenin (see reference in OneNote for role of β-catenin).
L19 #17
BRCA proteins are involve in DNA ____________.
Involved in DNA double-strand break repair.
L19 #17
What proteins are mutated in hereditary nonpolyposis colorectal cancer? What do they do?
MLH1/MSH2: DNA mismatch repair proteins.
L19 #17
What is the role of ATM? What cancers is it associated with?
ATM is a kinase that recognizes DNA double stranded breaks, and is associated with hereditary pancreatic cancers.
L19 #17
What is the function of APC protein?
APC = Adenomatous polyposis coli.
-Cytoplasmic protein that regulates degradation of β-catenin, which links the cytoplasmic portion of cadherins with the actin cytoskeleton.
L19 #18
What is the result of a loss of APC (3)?
1.) Accumulation of free β-catenin.
2.) β-catenin translocated to the nucleus.
3.) Increase in gene expression of Myc and cyclin D1 (which causes increased cell replication).
L19 #18
What is FAP? What is one typical clinical sign in FAP heterozygotes?
FAP = Familial Adenomatous Polyposis
-Numerous benign growths (adenomatous polyps) by the age of 20 (usually one or more polyps become malignant).
L19 #19
How do you prevent development of malignancies in FAP?
Colectomy (removal of colon).
L19 #19
What causes neurofibromatosis?
Loss of NF1 (encodes GAP) allows Ras (signal transducer; active when GTP-bound, promotes cell proliferation) to remain in its GTP-bound state for an extended period.
L19 #20
What is the inheritance pattern of Wilms tumor (nephroblastoma)? Gene?
Autosomal recessive – only 50% of individuals carrying a WT1 germline mutation develop nephroblastoma
L19 #21
More than 50% of all cancers exhibit mutations in the _______ gene at chromosome _______.
TP53 gene at chromosome 17.
L19 #15
List four pro-apoptotic proteins (aka ________).
aka Caretakers: Fas, FasL, Apaf-1, Bax
L19 #23
List one anti-apoptotic protein (aka _______). Which cancer is this increased in?
aka Oncogene: Bcl-2
Increased in Follicular lymphoma
L19 #23
Melanoma is associated with a(n) ________ mutation.
Apaf-1 mutation.
L19 #24
- ) What is the cause of autoimmune lymphoproliferative syndrome (ALPS) and what is the direct effect?
- ) What is the inheritance pattern?
- ) What are the phenotypic manifestations (3)?
1.) Mutation in either Fas or FasL; causes reduced apoptosis of lymphocytes.
2.) Autosomal dominant.
3.) Anemia (reduced RBCs), thrombocytopenia (reduced platelets), and neutropenia (reduced neutrophils).
L19 #24
Driver mutations may be identified by ____________.
Network Enrichment Analysis algorithm.
L19 #28
With regards to Autosomal Dominant inheritance pattern:
- ) What is the correlation between affected persons and parents?
- ) Gender?
- ) Transmission and gender?
1.) An affected person usually has at least one affected parent.
2.) Affects either sex.
3.) Transmitted by either sex.
L20 #7
- ) How many copies of a mutant allele is needed for phenotypic expression in an autosomal dominant disease?
- ) What chance does a child of an affected + unaffected parentage have of being affected?
1.) One copy of mutant allele disease gene is sufficient for expression of the disease phenotype.
2.) 50% chance of being affected.
L20 #8
How often does an autosomal dominant abnormal phenotype appear throughout the course of many generations?
Abnormal phenotype appears in EVERY generation.
L20 #10
- ) What is the inheritance pattern of Huntington disease?
- ) What is the genetic basis for Huntington disease?
- ) What are the functions of the gene (3)?
1.) Autosomal dominant
2.) Trinucleotide expansion (CAG) in the huntingtin (HTT) gene in chromosome 4.
3.) HTT may be involved in signaling, transport, and protection from apoptosis.
L20 #12
What physical damage results from Huntington disease? What is the result (physical-2, mental-2)?
Damage to corpus striatum —> Causes abnormal, involuntary writhing movements (chorea), loss of motor control.
-Behavior, mood, and personality changes; loss of thinking ability.
L20 #12
What is the definition of penetrance?
The proportion of individuals carrying a variant (mutation) of a gene that ALSO express the associated phenotype.
L20 #13
In Huntington disease, what is the correlation between the number of repeats and the age of onset? What term applies to this relationship?
More CAG repeats correlated with EARLIER age of onset – This is called “ANTICIPATION.”
L20 #13
The tendency for repeat expansion in Huntington disease is greater when disease if of ________ origin.
PATERNAL origin.
L20 #13
How do you determine the number of repeats in Huntington disease?
PCR amplify to determine the number of CAG repeats.
L20 #13
In Huntington disease, how many repeats are required for…
- ) Unaffected/normal
- ) Pre-mutation/unaffected
- ) Reduced penetrance
- ) Full penetrance/mutation
1.) 10-26 = Normal; unaffected.
2.) 27-35 = Pre-mutation; unaffected.
3.) 36-40 = Reduced penetrance; (+/-) affected.
4.) >40 = Full mutation/penetrance; affected.
L20 #13
- ) What is the inheritance pattern of Familial Hypercholesterolemia?
- ) What is the primary genetic defect in familial hypercholesterolemia?
- ) What are the results and consequential predispositions?
- ) What is the result if heterozygotic for this condition?
1.) Autosomal dominant
2.) Mutations in the LDLR gene in chromosome 19.
3.) Elevated blood LDL levels, predisposing to coronary artery disease (CAD) at a young age.
4.) Reduced number of functional LDL receptors.
L20 #15
What are four outward physical manifestations of familial hypercholesterolemia?
1.) Thickened achilles tendon
2.) Cholesterol deposits in soft tissues leading to xanthelasmas, xanthomas, and arcus cornealis.
L20 #15
What is the definition of locus heterogeneity?
Where mutations in different genes result in the same phenotype.
L20 #17
- ) What is the inheritance pattern of HNPCC?
2. ) What is the primary genetic defect in HNPCC (aka ________). Give four genes and their associated chromosome.
1.) Autosomal dominant
2.) Hereditary Non-Polyposis Colon Cancer (HNPCC), aka Lynch Syndrome.
1˚ genetic defect: Mutations in mismatch repair genes —> MLH1 (Ch3), MSH2 (Ch2), PMS1 (Ch2), and PMS2 (Ch7).
1322, 1227 - in alphabetical order, L to S
L20 #17
In HNPCC, what other type of cancer (besides colon cancer) is there a high probability of developing?
Endometrial cancer.
L20 #17
- ) What is the inheritance pattern of Postaxial Polydactyly.
- ) What is the primary genetic defect in Postaxial Polydactyly and what does it encode for?
- ) What is the consequence of mutation?
1.) Autosomal dominant
2.) Mutations in the GLI3 gene in chromosome 7 —> Encodes for a TF involved in shaping/patterning of many organs and tissues during development.
3.) Extra fingers or toes.
L20 #18
What are two variations that may be exhibited in postaxial polydactyly?
1.) May exhibit reduced penetrance.
2.) May exhibit variable expressivity (i.e. extra digit may vary from a small skin tag to a fully formed digit).
L20 #18
- ) What is the inheritance pattern of achondroplasia?
- )What is the primary genetic defect in achondroplasia?
- ) What does the gene encode for?
- ) Consequences of mutation (5)?
1.) Autosomal dominant
2.) Mutations in FGFR3 gene in chromosome 4.
3.) FGFR encodes for a transmembrane tyrosine kinase receptor that binds fibroblast growth factor.
4.) Bone growth disturbances —> short limbs relative to trunk (normal-sized torso), prominent forehead, flattened nasal bridge, and redundant skin folds in arms and legs.
L20 #19
What is the most common source of achondroplasia mutations? What is the mutation?
≈ 75-88% of cases due to NEW (de novo) MUTATIONS, while ≈ 12-25% are inherited from an affected parent.
MUTATION = Gly —> Arg substitution (380)
L20 #19
- ) What is the inheritance pattern of Marfan syndrome?
- ) What is the primary genetic defect in Marfan syndrome?
- ) What does the gene encode for?
- ) What type of mutation is observed in the most severe phenotype?
- ) What type of effect is observed in certain phenotypes? Describe.
1.) Autosomal dominant
2.) Mutations in FBN1 gene in chromosome 15.
3.) Encodes for fibrillin in connective tissue; affects the deposition of elastin.
4.) Missense mutations.
5.) Dominant negative effect: Mutant fibrillins bind to and disable normal fibrillins.
L20 #21
What is the definition of pleiotropism?
When a single gene affects a number of phenotypic traits in the same organism. These pleiotropic effects often seem to be unrelated to each other.
•Mutations in a single gene results in defects in several organ systems (multiple phenotypes)
•Multiple phenotypic effects of a single gene.
L20 #38
What organ systems can be affected by Marfan syndrome (3)? Give examples of each.
1.) Ocular: Myopia, displaced lens (ectopia lentis).
2.) Skeletal: Tall stature, unusually long and slender limbs, scoliosis, hypermobility of joints.
3.) Cardiovascular: Mitral valve prolapse, dilatation of the ascending aorta.
L20 #22
Concerning Autosomal Recessive Inheritance of Disease:
- ) An affected person is usually born to ________ parents.
- ) Parents of an affected person are usually ______________.
- ) Parental _________ increases the incidence.
- ) Which sexes do they affect?
1.) Unaffected parents.
2.) Asymptomatic carriers.
3.) Consanguinity.
4.) Affects either sex.
L20 #25
- ) What is the zygosity of each parent in autosomal recessive diseases?
- ) Affected individual?
- ) After birth of an affected individual, each subsequent child has a ___% chance of being affected.
1.) Each parent is a heterozygote (carries altered allele of gene).
2.) Affected individual is a homozygote (requires two copies of mutant gene to be affected).
3.) 25% chance
L20 #26
If an autosomal recessive phenotype appears more than once within a family, between which family members does it occur?
Usually occurs between siblings of proband (affected individual); NOT in parents, offspring, or other relatives.
L20 #28
- ) What is the inheritance pattern for cystic fibrosis?
- ) What is the primary genetic defect?
- ) Most common location of mutation?
- ) What is the function of the mutated gene/protein?
1.) Autosomal recessive
2.) Mutations in cystic fibrosis transmembrane conductance regulator (CFTR) gene –chromosome 7.
3.) ∆F508 is the most common.
4.) CFTR protein functions as a chloride channel, important for salt and water balance – affects multiple organs (e.g. lungs, pancreas).
L20 #31
What is the normal base pair length of CFTR gene on PCR? Abnormal?
Normal = 63 bp
Abnormal = 60 bp
L20 #33
- ) What is the inheritance pattern of classical phenylketonuria (PKU)?
- ) What is the primary genetic defect in classical phenylketonuria (PKU)? What is the function of the gene?
- ) Result?
- ) What causes the associated hypopigmentation?
- ) Dietary treatment, i.e. limitations (1), supplementation (5)?
1.) Autosomal recessive
2.) Mutations in phenylalanine hydroxylase (PAH) gene, chromosome 12. PAH responsible for conversion of Phe to Tyr
3.) Complete or near complete deficiency of enzyme activity.
4.) Hypopigmentation due to lack of Tyr
5.) Limiting dietary Phe, along with supplementation of Tyr, Trp, and branched-chain amino acids (Leu, Ile, Val).
Mnemonic —> TT-LIV
L20 #34, p.16 njp
Give two diseases that exhibit pleiotrophy. What is their inheritance pattern?
1.) Marfan syndrome (FBN1 mutation): Autosomal dominant.
2.) Phenylketonuria – PKU (PAH mutation): Autosomal recessive.
L20 #38
What genetic disorder is often the result of a new mutation?
Achondroplasia –Affected person may be the first person in the family with the condition.
L20 #36
- ) What is the definition of locus heterogeneity? Give example of genetic disease that exhibits this.
- ) Mutations in which genes cause a predisposition for this disease (4)?
1.) Same phenotype caused by many different genes.
e.g. Hereditary Non-Polyposis Colorectal Cancer (HNPCC).
2.) Mutations in mismatch repair genes —> MSH2, MLH1, PMS1, and PMS2.
L20 #38
If all (or almost all) affected individuals are males, and the affected individual does not have an affected parent, what is the inheritance pattern of the disease?
X-linked recessive.
L20 #43
If an individual has a disease that does not exhibit male-to-male transmission, what other familial inheritance pattern must be observed to confirm the disease inheritance as X-linked?
All daughters of an affected male must also be affected.
L20 #43
What is the Lyon Hypothesis?
One of the X chromosomes in females is randomly inactivated early in embryonic development.
L21 #5, p.17 njp
Mutations in how many genes are associated with X-linked disorders?
300 genes
L21 #6
What is the term of zygosity used for the X chromosome in males? Why?
HEMIzygous: Because only one X chromosome and, therefore, cannot be hetero- or homozygous.
L21 #6
Define manifesting heterozygote
When a female has one mutant copy of an X-linked gene and shows signs of an X-linked recessive disorder.
-A female heterozygous for an X-linked disorder in whom, because of non-random X inactivation, the trait is expressed clinically, although usually not to the same degree of severity as in hemizygous affected males.
L21 #7, p.1108 TT
Give four characteristics of the X-linked recessive pattern of inheritance (e.g. who is affected, parents of affected individual, mother of affected individual, transmission).
1.) Mainly affects males.
2.) Affected males are usually born to unaffected parents.
3.) The mother is normally an asymptomatic carrier and may have affected male relatives.
4.) NO MALE-TO-MALE TRANSMISSION in the pedigree. Transmission occurs from an affected male THROUGH FEMALES to an affected grandson and/or great-grandson
L21 #8, p.251 TT
- ) What is the inheritance pattern of Duchenne Muscular Dytrophy (DMD)?
- ) What causes Duchenne Muscular Dystrophy (DMD)?
- ) What is the result (3)?
- ) What is the early diagnostic indicator? Explain.
1.) X-linked recessive
2.) Caused by mutations in dystrophin (DMD) gene in the X chromosome.
3.) (a) Degeneration of muscle fibers (normal fiber replaced by fat and connective tissue; seen as pseudohypertrophy of calf muscles), (b) presence of chronic inflammatory cells, (c) heart and respiratory muscles affected and eventually fail (usual cause of death by age 25).
4.) Creatine kinase released by muscle may be 20-fold higher.
L21 #13
What is the best method to detect location of mutation in individuals with Duchenne and Becker muscular dystrophy?
Multiplex PCR.
L21 #14
- ) What is the role of G6PD (2)?
- ) What are the effects of G6PD deficiency (2)?
- ) What is the G6PD deficiency inheritance pattern?
1.) (a) Regulated step in PPP/HMP shunt, (b) Protects RBCs from effects of reactive oxygen species (ROS).
2.) (a) Causes RBC destruction (hemolysis), (b) Results in hemolytic anemia.
3.) X-linked recessive.
L21 #15, p.18 njp
- ) What mutation causes hemophilia A?
- ) What are five consequences?
- ) What is the inheritance pattern?
1.) Caused by mutations in Factor VIII (F8) gene.
2.) Fibrin formation affected, prolonged bleeding from wounds, bruising, hemorrhages in joints and muscles, intracranial bleeding with head trauma.
3.) X-linked recessive.
L21 #18-19
What is the term for an inability to perceive green colors? red?
Green: Deuteranopia
Red: Protanopia
L21 #20
The degree of red and green color perception depends on where the ________ occurs within the genes during ________.
Crossing over occurs within the genes during meiosis.
L21 #22
Which genes encode for the proteins that allow (a) Green color vision, and (b) Red color vision?
(a) Green: OPN1MW (opsin-1 medium-wave-sensitive).
(b) Red: OPN1LW (opsin-1 long-wave-sensitive).
L21 #20
Give four examples of X-linked recessive disorders
1.) Duchenne muscular dystrophy
2.) G6PD deficiency
3.) Hemophilia A
4.) Color blindness
L21 #23
What is the pattern of inheritance for the offspring of X-linked dominant affected males?
All daughters affected, no sons affected (i.e. no male-to-male transmission).
L21 #26
Describe how X-linked dominant disorders affect the sexes/offspring differently (4).
-Affects either sex, but more females than males (because there are more possible situations in which a female can be affected).
-Females are often more mildly and variably affected than males (due to random X inactivation and the fact that males have only one X chromosome).
-Affected female + Normal male = 50% chance of affected son or daughter.
-Affected male + Normal female = All affected daughters, no affected sons.
L21 #26
- ) What is the pattern of inheritance for Rett syndrome?
- ) What is the cause of Rett syndrome?
- ) What is the function of the mutated gene? What do the mutations do?
- ) What is the inheritance pattern?
- ) What is the manifestation in affected males?
1.) X-linked dominant.
2.) Mutations in the MeCP2 (methyl CpG binding protein 2).
3.) To bind methylated cytosines and mediate gene silencing. Mutations allow improper activation of many genes which are methylated and should normally have been silenced
-Thus, Rett syndrome is a DNA methylation disorder.
4.) X-linked dominant.
5.) Affected males are miscarried (male lethal).
L21 #30
- ) What is the pattern of inheritance for Fragile X Syndrome?
- ) What is the cause of Fragile X Syndrome?
- ) Give the normal and abnormal versions (# of repeats).
- ) On Southern blot, how many kb for the normal gene and gene with full mutation.
1.) X-linked dominant
2.) Trinucleotide repeat expansion (CCG) in the 5’ UTR of the FMR1 gene.
3.) Normal = 6-50 repeats, Abnormal > 200 repeats (due to duplication).
4.) Normal = 5.2kb, Full mutation = 5.7kb
L21 #32
- ) Define “skewed X inactivation.” When/how does it occur?
2. ) What is the medical significance?
1.) Occurs when the inactivation of one X chromosome is favored over the other, leading to an uneven number of cells with each chromosome inactivated.
2.) This is of medical significance due to the potential for the expression of disease genes present on the X chromosome that are normally not expressed due to random X inactivation.
-i.e. Mutation is present, but individual is phenotypically normal due to inactivated chromosome.
L21 #34
Define “manifesting heterozygote”
A female heterozygous for an X-linked disorder can potentially manifest the disease phenotype IF all of active X chromosome happen to be the one carrying the gene with disease-causing mutation, Xm.
-A female heterozygous for an X-linked disorder in whom, because of random X inactivation, the trait is expressed clinically, although not usually to the same degree of severity as in hemizygous affected males (p.1108 TT)
L21 #35
Microdeletions in which gene regions (3) are observed in males with azoospermia (AZF), i.e. no measurable levels of sperm in semen?
DAZ, DDX3Y, and USP9Y genes.
L21 #39
Define the pseudoautosomal region (PAR) of the Y chromosome.
Region that shares homology with regions on X chromosome and is used for pairing with X chromosome during meiosis.
Site of recombination with X chromosome
L21 #39
Segment of the X and Y chromosome, located at the most distal portion of their respective p and q arms, at which crossing over occurs during male meiosis.
•Traits due to alleles at pseudoautosomal loci will appear to be inherited as autosomal traits despite the physical location of these loci on the sex chromosomes.
p.1117 TT
Define the sex-determining region of the Y chromosome (SRY), i.e. what does it encode for?
Encodes for testis-determining factor (TDF) that triggers testes formation.
L21 #39
What occurs in the gonads during development when the Y chromosome is present and absent?
Y chromosome present: The SRY encoding for TDF increases the transcription factor SOX9, which promotes the development of the testes and, subsequently, male internal/external genitalia.
Y chromosome absent: Absence of Y chromosome = absence of TDF/SRY = No male genitals = Female internal/external genitalia.
L21 #40
- ) What are two disorders of sexual development (and their genotypes) caused by SRY gene and sex reversal? What is a characteristic of both?
- ) How do they occur?
1.)
i.) Incomplete masculinization (XY female).
ii.) Virilization (XX male).
Both exhibit ambiguous genitalia
2.) When errors occur during meiosis where crossing over occurs outside of the PAR region –it is likely to involve the SRY gene since it is relatively close to the PAR (see image on L21 #41). If the SRY gene does cross over to the X chromosome – potential for XX males and XY females
L21 #41
What is the consequence of an absent, mutated, or non-functioning SRY gene?
Female sex differentiation pathway proceeds.
L21 #42
What Y-linked gene mutation causes hearing loss? What is the transmission pattern?
DFNY1 gene mutations cause hearing loss –Transmission is EXCLUSIVELY male-to-male (i.e. Holandric transmission –gene occurring on the Y chromosome).
Mnemonic —> Hearing loss = Deaf = DF in NY = DFNY1
L21 #43
What type of transmission pattern likely reflects mitochondrial inheritance?
If transmission occurs through affected mothers and NEVER through affected sons.
L21 #44
- ) What is a complex disease?
- ) What is the inheritance pattern?
- ) In complex diseases, the influence of risk factors is ______.
- ) Interaction of ________ and _________ confer both ________ and _________.
1.) A common disease with a complex inheritance pattern.
2.) Tend to cluster in families, but do not follow classic Mendelian inheritance patterns.
3.) Additive
4.) Interaction of genetic and environmental factors confer both susceptibility and protection.
L22 #4
What are the two ways in which the final phenotype of a complex disease can be classified? Describe.
1.) Qualitative –i.e. present or absent.
2.) Quantitative –height, weight, body mass, etc.
L22 #6
- ) Explain the threshold model for complex diseases.
2. ) In a graphical representation, what portion of the curve represents the number of individuals affected?
1.) In multifactorial disorders, there is a threshold (of genetic and environmental factors), above which a person will develop the multifactorial disorder.
2.) The area under the curve to the right of the threshold line.
L22 #7
Give five examples of common human, adult-onset diseases with complex pattern of inheritance.
*1.) DM Type II
*2.) Alzheimer disease
3.) Arthritis
4.) Asthma
5.) Cancer
L22 #8
Give five examples of common human congenital malformations with complex patterns of inheritance.
1.) Cleft lip-palate
2.) Congenital hip dislocations
3.) Congenital heart defects
4.) Pyloric stenosis
5.) Neural tube defects
L22 #8
Describe complex diseases in terms of the following:
- ) Number of genes involved to cause disease phenotype.
- ) Frequency
- ) Mendelian pattern of inheritance?
- ) Recurrence rate
1.) Many genes involved to cause the disease phenotype.
2.) Common frequency
3.) No Mendelian pattern of inheritance.
4.) Low recurrence rate.
L22 #10
Describe single gene diseases in terms of the following:
- ) Number of genes involved to cause disease phenotype.
- ) Frequency
- ) Mendelian pattern of inheritance?
- ) Recurrence rate
1.) One gene involved to cause disease phenotype.
2.) Rare frequency
3.) Follows Mendelian pattern of inheritance
4.) High recurrence rate
L22 #10
What are four way that genetic and environmental factors associated with complex diseases are identified? Explain.
1.) Familial risks: Incidence of a disorder in relatives compared with the incidence in the general population.
2.) Twin studies: What is the incidence in monozygotic twins compared with dizygotic twins?
3.) Adoption studies: What is the incidence in adopted children of the disorders which their biological parents had (same genetic background, but different environment)?
4.) Population and migration studies: What is the incidence in people from the same ancestry group when they move to a different geographic area (helps to identify the effect of the environment on the disease).
L22 #12
What does the following information tell us about the influences on complex diseases among adopted children:
- ) Increased frequency with adopted family.
- ) Increased frequency in biological family.
1.) Strong evidence for environmental influence in developing the disease.
2.) Strong evidence for genetic contribution to disease.
L22 #13
For 1st degree family relationships, give the type(s) of family members, and % of genes in common.
Parents, siblings, children —> 50% genes in common.
L22 #15
For 2nd degree family relationships, give the type(s) of family members, and % of genes in common.
Aunt, uncle, niece, nephew, grandparents/grandchildren, and half-siblings —> 25% genes in common.
L22 #15
For 3rd degree family relationships, give the type(s) of family members, and % of genes in common.
First cousins, great grandchildren/-parents, great aunt/uncle/niece/nephew —> 12.5% genes in common.
L22 #15
The more closely related two individuals are, the more _______ they have in common.
Alleles.
L22 #16
What type of relation have the same alleles in every locus?
Monozygotic twins.
L22 #16
Why do complex diseases cluster in families?
Because relatives of an affected individual are more likely to have disease-predisposing alleles in common.
L22 #16
- ) What is the formula for Relative risk ratio (λr)?
- ) What does it mean if λr >1?
- ) What does it mean if λr = 1?
1.) λr = (Prevalence of disease in relatives of affected person/Prevalence of disease in the general population)
2.) λr > 1 means a relative is more likely to develop the disease than any individual in the population.
3.) λr = 1 means that a relative is NO MORE LIKELY to develop the disease than any individual in the population.
L22 #16
- ) What is the definition of Concordance?
2. ) What is the Rate of Concordance?
1.) When two individuals in a family share a trait or have the same disease.
2.) Proportion of pairs of individuals (e.g. twins) who share a trait or have the same disease.
L22 #18
What % of genes and environment do monozygotic (MZ) and dizygotic (DZ) twins share?
1.) Monozygotic: Identical genotype (and gene expression patterns); usually share same environment.
2.) Dizygotic (two eggs fertilized by two sperm): Share 50% of genes; usually share same environment.
L22 #18
What is the meaning of the following:
- ) 100% concordance in MZ twins.
- ) less than 100% concordance in MZ twins.
1.) Strong evidence that genotype alone is sufficient to develop disease, e.g. sickle cell disease (all genetic).
2.) Strong evidence that non-genetic factors (e.g. environment) play a role in the disease.
L22 #19
What does the “Common disease-Common variant theory” state? What does it suggest?
That susceptibility alleles confer moderate risk and occur at relatively high frequency in the population (>1%).
-Suggests that association studies in large cohort populations (e.g. unrelated individuals sharing the common disease) will be fruitful —> Look for segregation of disease with a particular genotype.
L22 #24
- ) What is the definition of Genetic Association?
2. ) What method of genomic analysis is used in this study?
1.) Correlation between SNPs/genotype/haplotype, and phenotype.
2.) SNPs have facilitated this type of study; use of SNP microarray.
L22 #24
Carriers of Type II DM risk variants are more likely to:
- ) Fail which therapy as opposed to another?
- ) Require what?
- ) What two genes are commonly associated with risk variants for Type II DM? What is their significance?
1.) Fail sulfonylurea therapy than metformin.
2.) Require/are more likely to be on insulin than diet alone.
3.) (i) TCF7L2: Associated with “open chromatin sites,”’ i.e. regions that are bound by regulatory factors; identified important role of intergenic SNPs. (ii) SLC30A8: encodes for β-cell zinc transporter (ZnT-8) crucial for insulin secretion.
L22 #26-28
Explain the biologic significance of SNPs in intergenic DNA segments in Type II DM (i.e. genes involved and consequences).
TCF7L2 gene associated with “open chromatin sites” –Regions that are bound by regulatory factors.
-High-risk T allele associated with greater enhancer activity, increased transcription of TCF7L2 (5-fold in individuals with Type II DM compared to controls
L22 #27
Explain the pathway (w/ associated genes) and its associated genetic variant that causes an insulin secretory defect.
SLC30A8 gene encodes for β-cell zinc transporter, ZnT-8, which is expressed exclusively in pancreatic islet cells.
-Zn transporter localized in membranes of secretory vesicles that transport Zn from cytoplasm into insulin secretory vesicles;provides Zn to allow for insulin storage and secretion.
-Variant encodes for an Arg to Trp change in position 325, which causes an insulin secretion defect.
L22 #26
- ) What is the definition for “recurrence risk?”
- ) What is the usual recurrence risk for:
a. ) Autosomal dominant traits
b. ) Autosomal recessive traits
1.) The chance that an inherited disease that is present in a family will recur in that family, affecting another person orpersons.
2.)
a.) Autosomal dominant = 50%
b.) Autosomal recessive = 25%
L23 #25
In X-linked recessive disorders, how is the disorder transmitted between successive generations?
A disorder is transmitted from an affected male through FEMALE obligate carriers (unaffected daughters) of the following generation (meaning the expressed disorder effectively “skips” a generation) to grandsons and great-grandsons of the aforementioned affected male.
i. e. Transmitted from an affected male through females to an affected grandson and great-grandson (if the daughter of an obligate carrier, herself and obligate carrier, transmits the disorder to her son).
p. 252 TT
What is the definition of Pharmacogenetics?
The study of how the variations in a targeted gene or groups of functionally related genes affect individual’s responses to drug therapy.
L24 #6
What is the definition of Pharmacogenomics?
Refers to the sum of all relevant genetic information affecting drug therapy.
-Is a much broader investigation of genetic variations at the level of the genome.
L24 #6
Concerning the Human Genome:
- ) How many nucleotides?
- ) ≈ How many protein-coding genes?
- ) How many proteins?
- ) Where do the majority of differences between individuals in their genomes occur?
- ) ≈ one in how many nucleotides do people differ in their genome?
1.) 3 billion
2.) ≈ 21,000
3.) ≈ 100,000
4.) SNPs
5.) 1 in every 1,000 nucleotides
L24 #7
What is the overall purpose of the phase I and phase II reactions of drug metabolism? What happens in each phase?
Phase I and II: Makes drugs more polar and, therefore, more easily excreted by the kidneys.
-Phase I: Oxidation and reduction.
-Phase II: Conjugation reaction.
L24 #11
Which enzymes of phase I (2) and phase II (1) drug metabolism reactions are associated with genetic variations that alter drug effects?
Phase I: CYP2C9, CYP2D6
Phase II: TPMT
L24 #12
Describe the four different kinds of drug metabolizers.
1.) Ultra-rapid metabolizers (UM): Individuals who have multiple copies of an active gene.
2.) Extensive metabolizers (EM): Individuals who have two normal genes and metabolize a drug normally.
3.) Intermediate metabolizers (IM): Individuals who have one active and one non-active allele for the same gene.
4.) Poor metabolizers (PM): Individuals with a non-functional or less functional gene that metabolize a drug very slowly.
L24 #13
- ) What is Tamoxifen for?
- ) What is the prodrug and active drug?
- ) Genetic variations in which enzyme(s) influence the extent of metabolism and clinical outcome?
1.) Estrogen receptor positive breast cancer.
2.) Prodrug = Tamoxifen, Active drug = Endoxifen.
3.) CYP2D6
L24 #15
- ) What is the drug 6-mercaptopurine (6-MP) used for?
- ) Reduced function in which gene increases the toxicity of 6-mercaptopurine (6-MP)?
- ) Rate the three genetic polymorphisms of this gene from most active to least active.
1.) 6-MP is a chemotherapy drug used to treat acute lymphocytic leukemia.
2.) Thiopurine methyltransferase (TPMT)
3.) Wild type (wt/wt) = Most active
-Heterozygous wild type/variant (wt/v) = Intermediate activity
-Homozygous variant (v/v) = Least active
L24 #19
- ) What is the target protein of Warfarin?
2. ) How would you manipulate the dosage of a patient with less of this target?
1.) VKORC1 (Vitamin K recycling factor 1): Blocked by Warfarin to cause anticoagulant effect.
2.) Patients with less VKORC1 should get LESS Warfarin because they are more sensitive to the drug.
L24 #31
- ) What is the effect of Warfarin on poor metabolizers?
- ) What enzyme is responsible for metabolism of Warfarin to its inactive form?
- ) How would their dose differ from that of an effective metabolizer?
1.) Poor metabolizers have good efficacy with Warfarin, but this could result in Warfarin build-up and potential toxicity.
2.) CYP2C9
3.) Decrease the dose.
L24 #31
- ) What is the most active form of Warfarin?
2. ) What role does CYP2C9 play in the Warfarin pathway?
1.) S-Warfarin (100x more activity than R-Warfarin).
2.) Warfarin metabolizer, converts S-Warfarin to the inactive form, 7-OH Warfarin.
L24 #31
- ) What accounts for the fact that Warfarin doses can significantly differ from patient-to-patient?
- ) Rank the dosage level from highest to lowest based on the three VKORC1 genotypes (AA, GG, and GA).
1.) Dose depends on level-of-function of drug metabolism enzyme (CYP2C9), as well as the amount of drug target protein (VKORC1). Both of which can vary widely among patients due to their genotypes.
2.) GG = highest dose, GA = intermediate dose, AA = Lowest dose.
L24 #32
- ) When is amniocentesis used?
- ) What three general things is it used to evaluate?
- ) What are seven diagnostic tests performed on amniocentesis?
1.) 15-20 wks of gestation
2.) Fetal chromosome and genome analysis, in addition to [AFP].
3.) [AFP] for NTDs, fetal karyotype (FISH), genome analysis, enzyme measurements, fetal lung maturity tests, AF bilirubin, PCR for pathogens.
L25 #11-12, p.33 njp
- ) When is Chorionic Villus Sampling (CVS) performed?
- ) Performed to assess _________ (__-__ days).
- ) Risk of pregnancy loss similar to _______ with ________ approach.
- ) What is a major advantage of CVS compared to amniocentesis?
- ) Drawback compared to amniocentesis?
1.) 10-13 weeks
2.) Performed to assess fetal karyotype (7-10 days)
3.) Similar to amnio with transabdominal approach.
4.) Major advantage compared to amniocentesis is that CVS allows the results to be available at an early stage in pregnancy, thus reducing the period of uncertainty and allowing termination, if it is elected, to be performed in the first trimester.
5.) Not able to measure [AFP] and, thus, cannot evaluate for NTDs.
L25 #13, p.707 TT
What are two limitations that apply to chorionic villus sampling (CVS)?
1.) No amniotic fluid, thus, NTDs cannot be assessed (via [AFP]) – NTD requires AF or maternal serum alpha-fetoprotein levels (MSAFP).
2.) 1% of samples yield ambiguous results due to chromosomal mosaicism, follow up amnio is required.
L25 #15
- ) When is fetal blood sampling performed? What else is it called (2)?
- ) Indications (3)
- ) What type of diagnostic assessment can it rapidly provide and how long does it take?
1.) after 20 weeks —> aka cordocentesis or percutaneous umbilical blood sampling (PUBS).
2.) Fetal anemia, thrombocytopenia assessment, and fetal karyotype (KT) determination (e.g. cases of mosaicism after amnio or CVS).
3.) Rapid fetal karyotype (KT) in 24-48 hours.
L25 #16
- ) What is preimplantation genetic diagnosis (PGD), what does it allow for?
- ) What diagnostic tests can be done (3)?
1.) Testing of embryos during in vitro fertilization (IVF) for the purpose of selecting unaffected embryos for transfer to the uterus. Allows couples at high-risk for a specific genetic disorder in their offspring to avoid pregnancy termination
2.) PCR (for single gene disorders), FISH, chromosomal microarray (CMA).
L25 #17
Describe the two techniques used of preimplantation genetic diagnosis (PGD) and their timeframe.
1.) Blastomere biopsy: Single cell removed THREE DAYS after IVF, when embryo is 8-16 cells.
2.) Blastocyst biopsy: Five trophectoderm cells removed 5-6 days after IVF, when blastocyst has developed.
L25 #18
- ) Describe Cell-Free Fetal DNA (cfDNA) screening and timeframe.
- ) What type of screening is it?
- ) What type of diagnostic test is used?
1.) After 7 weeks gestation, maternal serum contains free fetal DNA derived from placental trophoblasts.
2.) Highly accurate, noninvasive prenatal screening (NIPS) for common autosomal and sex chromosome aneuploidies.
3.) cfDNA isolation followed by high-throughput sequencing.
L25 #19
- ) cfDNA is a _______, _________ screening for common _______ and _________.
- ) Not a _____ test; provides a _________.
- ) What should be done if abnormal?
1.) cfDNA is a highly accurate, non-invasive screening for common autosomal and sex chromosome aneuploidies.
2.) Not a definitive test; provides a risk assessment.
3.) If abnormal, invasive diagnostic testing should be done to confirm results.
L25 #20
- ) On which tissues is cytogenic analysis used?
- ) What does it detect and how?
- ) Limitations (3)?
1.) Any tissue containing cells capable of dividing is suitable.
2.) Conventional G-banding of metaphase chromosomes detect aneuploidies and large structural changes
3.) Cells must be cultured, doesn’t ID microscopic defects.
L25 #23
The speed of results in cytogenic analysis is related to what? Give two examples with timeframe.
Speed of results is related to how quickly the cells can grow in culture.
1.) Fetal blood cells = 24-48 hours.
2.) Amniotic fluid cells or Cultured chorionic villi = 7-10 days.
L25 #23
What are the three steps to cytogenic analysis?
1.) Colcemid treatment + harvest.
2.) Hypotonic treatment (allows cell membrane to stretch, but not to break) + fixation.
3.) Metaphase spreading + DNA staining.
L25 #24
- ) Describe Cytogenic Analysis by FISH
- ) Give timeframe and what it’s performed on.
- ) What does it provide information on?
1.) Rapid method for screening fetal cells for common aneuploidies (chromosomes 13, 18, 21, X, and Y).
2.) Can be done in 1-2 days on interphase nuclei (no culture).
3.) Only provides information on the chromosome or gene of interest.
L25 #25
According to the ACOG (American College of Obstetricians and Gynecologists), what test should be done when structural anomalies are detected on US?
- ) When is it indicated?
- ) Describe the level of genetic information given.
- ) What can it ID?
- ) Limitations (2)?
Chromosomal Microarray Analysis (CMA)
1.) Indicated when structural anomalies are detected on US.
2.) High resolution (yields more information than conventional karyotyping).
3.) Can ID chromosomal aneuploidy, as well as lesions too small to be detected by karyotyping.
4.) Limitations: Detects Variants of Unknown Significance (VUS), as well as adult onset diseases.
L25 #26, p.724 TT
What are three problems that arise in Prenatal Chromosome Analysis?
1.) Pseudomosaicism (occurrence of a cytogenically abnormal cell that arose after the tissue was put into culture; generally considered to be artifactual and of no clinical signififance –p.1118 TT).
2.) Culture failure
3.) Unexpected adverse findings
L25 #27
- ) Describe Massively Parallel Sequencing using cell-free fetal DNA including timeframe.
- ) Who is it recommended for?
- ) What are its clinical applications (3)?
1.) After 7 weeks gestation, cfDNA released from trophoblast can be detected in maternal serum.
Sequence fetal DNA using Massively Parallel Sequencing (a non-invasive prenatal screening –NIPS)
2.) Not recommended for the general population because not enough genetic counsellors to handle a large burden, thus, only recommended for women at high risk for having a child with Down’s syndrome.
3.) Rh genotype, gender determination, detection of autosomal trisomies.
L25 #28
- ) What do Biochemical Assays for Metabolic Diseases detect?
- ) When must they be used?
1.) Detects abnormalities caused by any mutant allele that has a significant effect on protein function.
2.) May be the only option if the causative mutation in the family is unknown.
L25 #31
What are two major drawbacks of Fetal DNA and Fetal Genome Analysis?
1.) When the disorder in the patient is due to a mutation different from the one being sought, i.e. you must know what it is you’re looking for.
2.) May not be predictive of clinical presentation in disorders characterized by variable expressivity (e.g. neurofibromatosis type 1, mitochondrial disorders).
L25 #31, p.729 TT
- ) What causes NTDs and when?
- ) What three conditions does it result in?
- ) When and how do you screen for NTDs?
1.) Failure of the neural tube to close by the 27th day after conception.
2.) Anencephaly, encephalocele, spina bifida.
3.) Screening at 15-20 weeks (2nd trimester) utilizing maternal serum α-fetoprotein (MSAFP)
L25 #33
- ) Where is α-fetoprotein synthesized and where is it abundant in the fetus (3)?
- ) In NTDs, where is α-fetoprotein found (2)?
1.) Fetal yolk sac, GI tract, and liver –abundant in the fetal serum.
2.) Amniotic fluid and maternal serum.
L25 #36
During which weeks is α-fetoprotein highest in the fetal plasma, amniotic fluid, and maternal serum?
-Highest in fetal plasma and amniotic fluid at 10 weeks.
-Highest in maternal serum at ≈ 30-40 weeks.
L25 #37
- ) How are the results of screening for NTDs expressed?
- ) What is the formula?
- ) What is an abnormal result?
- ) What are results adjusted for (6)?
1.) Results expressed as Multiple of the Median (MoM)
2.) MoM = (Patient [MSAFP] / Median [MSAFP])
same gestational age (which means what???)
3.) Abnormal = 2.0 –2.5 MoM
4.) Maternal weight, race, IDDM (???), multiples, gestational age, and fetal viability.
L25 #38
- ) An association has been made between low MSAFP values and __________.
- ) Overall risk of this increases ≈ 2.5x at what maternal age?
- ) All women who present for prenatal care before ____ weeks should be offered screening.
1.) Down syndrome
2.) Maternal age > 35 years old
3.) 20 weeks
L25 #40
What are the Approaches to aneuploidy studying during:
- ) 1st trimester – ____ wks (3)
- ) 2nd trimester –____ wks (4)
- ) Integrated screening
- ) 1st trimester (11-14 wks): Ultrasound (US) of nuchal translucency (NT), and two maternal serum metabolites —> β-hCG and PAPP-A).
- ) 2nd trimester (15-20 wks): Quadruple screen –MSAFP, β-hCG, unconjugated estriol, inhibin A.
3.) Integrated screening: Combined 1st and 2nd trimester screening.
L25 #41
How is nuchal translucency seen? What is it an indicator of?
Nuchal translucency seen on fetal ultrasound (US); predictive of increased risk for Down syndrome.
L25 #42
What are the three definitive parameters in 1st and 2nd trimester screening tests that would give a definitive diagnosis of Down syndrome (trisomy 21)? Indicate which trimester.
1st trimester: Elevated hCG (decreased in trisomies 13 and 18).
2nd trimester: Elevated hCG, elevated Inhibin A (only seen in trisomy 21).
L25 #43
Which parameters used in 1st and 2nd trimester screening tests (4) are seen uniformly increased or decreased among the three major trisomy disorders (trisomy 13, 18, and 21)? Indicate whether increased or decreased and which trimester they are observed.
1.) Nuchal translucency (NT), 1st trimester: Increased
2.) PAPP-A, 2st trimester: Decreased
3.) uE3, 2nd trimester: Decreased
4.) AFP, 2nd trimester: Decreased
L25 #43
Which parameter used in 1st and 2nd trimester screening tests is indicative of a neural tube defect (NTD); increased or decreased, and during which trimester?
Increased AFP during the second trimester (15-20 weeks).
L25 #43
What is the new aneuploidy screening modality and what is the method?
Non-invasive prenatal screening testing (NIPS), through sequencing of cell-free DNA (cfDNA) in maternal plasma.
L25 #44
- ) ______ and ________ are essential before prenatal genetic testing.
- ) What is the function of this (what what ISN’T)?
- ) What are three key aspect of this role?
1.) Genetic counseling and informed consent.
2.) To provide information to support decision-making –NOT to dictate course of action
3.) Accurate diagnosis, communication, and non-directive presentation of options.
L25 #47
In which ethnic groups is cystic fibrosis (an autosomal recessive disease) seen with increased frequency (4)?
Non-hispanic white, Ashkenazi Jewish, Native American (Zuni, Pueblo).
L25 #48
Genetic counseling must address which SIX aspects (first three related to providing information, second three related to providing support)?
1.) Risk of affected fetus
2.) Consequences of condition
3.) Procedure-related risk
4.) Waiting for results
5.) Need for repeat procedure
6.) Possible inconclusive results
L25 #49
- ) Concerning PKU with allelic heterogeneity, how much residual enzyme activity must be present in order for high dose BH4 to increase enzyme activity? What enzyme?
- ) Which drug that acts as cofactor/coenzyme supplementation also requires the same residual enzyme activity? What does it act as?
1.) at least 12.5% residual phenylalanine hydroxylase (PAH) enzyme activity.
2.) Sapropterin dihydrochloride (Kuvan) —> tetrahydrobiopterin (BH4) cofactor
-Effective in some PKU patients (requires 12.5% residual PAH enzyme activity).
L26 #10
A.) Concerning G6PD deficiency, what four things must one avoid? —> Three drug classes (1, 2, 1) and one food.
B.) What is the overall goal of these restrictions?
A.)
1.) Antimalarial drugs: Primaquine, but not chloroquine or quinine.
2.) Antibiotics: Sulfamethoxazole, chloramphenicol.
3.) Antipyretics: Acetanilide, but not acetaminophen.
4.) Fava beans.
Triple A, F (AAA-F)
B.) Substrate reduction
L26 #7
What dietary manipulations must be made in the case of PKU (3)?
Restrict Phe, supplement with branched-chain AAs (Leu, Ile, Val), supplement with Tyr and Trp.
LIV–TT
L26 #9
What dietary changes must be made in the case of Ornithine Transcarbamoylase Deficiency (OTC) (2)?
Protein restriction, citrulline supplementation
L26 #9
- ) Give an example of cofactor/coenzyme supplementation in manipulation of metabolism and what it’s for.
- ) It’s efficacy is conditional on what?
1.) Sapropterin dihydrochloride (KUVAN) – BH4 cofactor effective in some PKU patients.
2.) Requires at least 12.5% residual enzyme activity.
L26 #10
Define diversion in the context of manipulating metabolism to treat metabolic enzyme deficiencies, give an example.
Diversion: Facilitates excretion and/or production of less toxic products –e.g. seek to mobilize NH3 excretion in individuals with OTC deficiency.
L26 #11
Give two examples of depletion in the context of metabolic manipulation.
Direct removal of a compound
1.) Use of apheresis to remove LDL from the circulation in patients with homozygous familial hypercholesterolemia (Apheresis: a medical technology in which the blood of a donor or patient is passed through an apparatus that separates out one particular constituent and returns the remainder to the circulation).
2.) Use of phlebotomy to decrease iron overload in patients with hereditary hemochromatosis.
L26 #16
Give an example of small molecular therapy in order to increase amount of functional protein. Which disorder is it used for?
Vitamin B6 for pyridoxine-responsive homocystinuria –Only if there is residual enzyme activity
L26 #18
Define High Throughput Screening. What is it used for?
Test/assay a large number of potential compounds at the same time (use of automaton/robotics). Used to evaluate small molecules for small molecule therapy.
L26 #18
- ) 11% of known genetic mutations are _________. What do they result in?
- ) What treatment can be used to rectify this type of mutation?
- ) What is the ultimate result?
1.) Nonsense mutations –results in a premature stop codon.
2.) Small molecule therapy: small molecules encourage misreading of stop codon by tRNA during translation.
3.) Results in a functional protein.
L26 #19
- ) What disorder does ATTR stand for and what is its pattern of inheritance?
- ) What mutations does it result in (i.e. in what product and what does the product do)?
- ) What is the result?
- ) What is the current common treatment?
- ) What is an experimental drug treatment?
1.) Transerythrin-mediated amyloidosis (ATTR): Autosomal dominant disorder.
2.) Missense mutations in transerythrin (produced mainly in the liver), which transports retinol and thyroxine.
3.) Results in deposition of amyloid in peripheral nerves and heart = Neuropathy and cardiomyopathy.
4.) Liver transplant
5.) Patisiran (an RNAi).
L26 #25
What is the principal behind Induction of Exon Skipping, i.e. what does it use and what is the result? What is it being used to treat experimentally?
Use of antisense oligonucleotides to result in an in-frame mRNA.
-Used to treat Duchenne Muscular Dystrophy.
L26 #26
- ) Concerning modification of somatic genome by transplantation, what does a liver transplant treat?
- ) What is this mode of therapy called?
1.) Treatment of transerythin-mediated amyloidosis
2.) Serves as a mode of “gene replacement therapy” —> The organ serves as the mode of gene replacement.
L26 #27
- ) What are iPSCs?
2. ) What are they used for?
1.) Induced pluripotent stem cells.
2.) Can be taken from a patient in need of a transplant and induced to form the organ tissue and the organ itself.
L26 #28, p.549 TT
- ) How are hematopoietic stem cells and mesenchymal stromal cells harvested (three steps)?
- ) What is this used to treat (2)?
1.) Bone marrow aspirate —> Apheresis of growth factor-mobilized hematopoietic stem cells (HSC) —> HSC infused into patients.
2.) Hereditary blood disorders, lysosomal storage diseases.
L26 #31
Give 5 genetic diseases for which stem cell transplants have been beneficial —> three general groups (1, 2, 1)
1.) SCID
2.) Lysosomal storage diseases (Hurler syndrome)
3-4.) Hereditary blood disorders —> Thalassemias, sickle cell disease
5.) Osteogenesis Imperfecta (OI) —> Mesenchymal stromal cells for OI.
L26 #31
- ) What is umbilical blood a source of (2)?
2. ) What are the advantages (3) and disadvantages (1)
1.) Hematopoietic stem cells and mesenchymal stromal cells.
2.) Advantages: Faster availability, 1-2 HLA (human lymphocyte antigen) mismatches out of six tolerated (i.e. better toleration of mismatches), lower incidence and severity of acute graft versus host. Essentially, less of an immune response
Disadvantages: Limited/lower number of hematopoietic stem cells.
L26 #32
- ) What are iPSCs? (i.e. where are they derived from, moral issues?)
- ) How are they used?
1.) Induced pleuripotent stem cells: Derived from somatic cells, not subject to moral and ethical issues surrounding hESCs (human embryonic stem cells).
2.) Direct reprogramming of somatic cells using transcription factors to make tissue/organ of choice.
L26 #33
- ) What is the basic concept of “Modification of Somatic Genome by Somatic Gene Therapy?”
- ) How is it done?
1.) Introducing normal genes into somatic cells.
2.) Introduce genes via viral vectors
L26 #34
What are the characteristics of an ideal viral vector (5)?
1.) Adequate gene carrying capacity
2.) Undetectable by the immune system
3.) Efficiently/sufficiently correct the disease phenotype
4.) Long duration of expression
5.) Safe to administer
L26 #35
- ) For treatment of adenosine deaminase deficiency (ADA), what is used as a vector for gene therapy?
- ) What are three alternative treatments for ADA?
1.) Retrovirus used as a vector.
2.) BM transplant (matched donor), RBC transfusion from healthy donors, enzyme replacement therapy.
L26 #37
- ) What is the main goal of CRISPR/Cas9? What is this process called? What is the future possibility for CRISPR?
- ) How does it correct a mutant gene?
- ) Where can this process take place that makes it so useful? Example?
1.) To modify sequences in the genome in a site-specific (targeted) manner. Possibility of permanently curing disease
2.) Creates a double-strand break (endonucleases), and repairs using homology-directed repair.
3.) Can be done in vivo, e.g. Genetic editing works in mice with Duchenne muscular dystrophy —> DMD gene mutation is corrected and dystrophin expressed in muscles.
L26 #44-45
Drugs exert their effects by interacting with _________.
Specific target proteins.
L24 #24
Anti-asthma drug _______ decreases airway inflammation by inhibiting the enzyme _______, which is encoded by the gene _______.
Zileuton, 5-lipoxygenase, ALOX5
L24 #26
- ) ____________ in the promoter region for ALOX5 result in the expression of different amount of target protein.
- ) There must be _________ to get an ALOX5 enzyme with the highest activity.
1.) Variable Number of Tandem Repeats (VNTRs)
2.) Five tandem repeats
L24 #27
- ) Ultrasonography allows detection of structural fetal anomalies associate with which three types of genetic disorders? Give examples of each.
- ) Multiple fetal abnormalities increase the likelihood of a ___________ fetus.
1.)
i.) Single-gene disorders: OI.
ii.) Multifactorial disorders: NTDs, congenital heart defects.
iii.) Specific syndromes: Down and Turner syndrome.
2.) Chromosomally abnormal fetus.
L25 #9
What are three methods by which evaluation for possible NTDs can be conducted?
- ) Maternal serum alpha-fetoprotein (MSAFP) screening.
- ) Amniocentesis for amniotic fluid alpha-fetoprotein (AF-AFP).
- ) Ultrasonography (US).
p. 707 TT
Most of the mutations that cause cancer are _______.
Sporadic (75-80%)
L18 #5
Oncogenes may be introduced by _____ or ______.
DNA or RNA viruses.
Week 8 review, #4
- ) What three types of mutations activate oncogenes to produce abnormal (hyperactive) proteins?
- ) What three types of mutations activate oncogenes to produce excess normal protein?
- ) Point mutations, chromosomal translocations, local DNA rearrangements.
- ) Gene amplification, chromosomal translocations, insertional mutagenesis.
p. 1 njp
- ) What does the Ras gene encode for?
2. ) Point mutations in Ras gene result in what?
1.) Encodes for GTPase protein.
2.) G-protein locked into active position (GTP-bound form, i.e. blocks hydrolysis of GTP).
Infection with cancer that mutates Ras causes UNCONTROLLED GROWTH (transformation)
L18 #15
How is Bcr-Abl signaling related to cancer (2), i.e. how does it survive/proliferate and avoid apoptosis?
1.) Activation of cell proliferation and survival via the Ras-MAPK pathway.
2.) Inhibition of apoptosis via PI3-K/PKB and Bcl-xL-mediated pathways.
L18 #23
Inhibition of CDK by ______, a _______ (aka ____), results in arrest of the cell cycle in ____ and ____.
Inhibition of CDK by p21, a CDK inhibitor (aka CKI), results in arrest of the cell cycle in G1 and G2.
L19 #7
Mutations in tumor suppressor (TS) genes cause a ___________ in these proteins.
Loss of function
L19 #9
List four tumor suppressor (TS) genes. What type of mutation occurs in TS genes that imparts an autosomal dominant inheritance pattern upon them?
- ) TP53
- ) RB1
- ) BRCA1
- ) BRCA2
* Loss of heterozygosity (LOH)*
Rett syndrome is a _________ (not a pattern of inheritance) disorder observed mainly in _________.
DNA methylation disorder observed mainly in females.
L21 #30
