Pharmacogenomics Exam 1
How many NADPH molecules are produced in the oxidative phase of the pentose phosphate pathway from Glucose-6-phosphate?
2 NADPH's
What is the name for a combination of alleles that are located on one chromosome and inherited together?
Haplotype
What process is used to show the RFLP pattern in a DNA sample?
Gel electrophoresis
What is the name for the most common allele and deviations?
"wild-type" or "reference"
How wide is a single DNA strand?
11 Angstroms
What are the steps of cloning a specific gene?
1. Cut plasmid and target DNA with the same restriction endonucleases. 2. Create Recombinant vector by ligating target DNA with plasmid. (Use DNA Ligase) 3. Transform cells by electroporation, or rapidly warming cells in CaCl2 for 0ºC to 40ºC 4. Lastly, amplify the gene by letting the cells grow.
Discribe the steps of PCR?
1. Heat to separate strands. 2. Add synthetic oligonucleotide primers and cool.
How many chromosomes are in humans?
23 pairs or 46 chromosomes in 'normal' somatic human cells. 22 pairs of 'autosomes'; one pair of sex chromosomes (X, Y)
Generally, in humans chromosomes are not visible under the microscope. But during S phase they double, and during M phase they condence to ____(number) chromosomes.
96 (46 doubled chromosomes.)
What is real time PCR?
A dye that only fluoresces when bound to the gene sequence of interest. As the PCR amplifies the number of copies of this gene of interest, the sample begins to fluoresce when enough of the copies are now available for study. Two different color dyes can be used at the same time to determine two different sequences, such as in heterozygous samples.
What type of mutation is caused by a mutation in a stop codon leading to a longer than normal protein?
A run on mutation
What is the Shine-Dalgarno sequence?
A short conserved nucleotide sequence upstream of the AUG start codon that serves to align the mRNA on the bacterial small ribosomal subunit. - AGGAGG
What disease is an autosomal dominant disorder caused by a defect in the FGFR3 gene? •Causes abnormal cartilage growth-plate differentiation and inefficient bony development - Dwarfism, short arms and legs, - 80% de novo, usually due to mutated sperm. - Risk increases with the age of the father.
Achondroplasia
SNPs in transcription factor binding sites or other regulatory gene regions can...
Affect concentration of protein - Also referred to as "expression" SNPs (eSNPs)
Describe the inheritance of an X-linked dominate trait if the father has it but the mother does not?
All of the daughters would receive the trait, and none of the sons would.
Which of the following is false? •Many genes encode for more than one protein. •Genes may encode for RNA which does not get translated into protein. •Processing and regulation of mRNA very complex.
All of them are true!
What is alternative splicing?
Alternative splicing is the ability of some genes to use various combinations of eons to create multiple proteins from one hnRNA transcript. This increase protein diversity and allows a species to maximize the number of proteins it can create from a limited number of genes. **This explains over 100,000 proteins from only 25,000 genes. *The Pro Opio Melano Cortin protein can be cut into numerous other functional proteins depending on which cell it is in.
Whet genetic test is able to determine fast or slow CYP metabolizers using PCR and a gene chip.
AmpliChip CYP450 Test
What disorder demonstrates Genetic imprinting and is described here? Intellectual and developmental delay, sleep disturbance, seizures, jerky movements especially hand-flapping, frequent laughter or smiling, and usually a happy demeanor. Mutation in proximal part of chromosome 15 coming from the mother(!!!) DNA methylation may explain this since maternal DNA is methylated differently than paternal. These affected genes tend to be in clusters with other affected genes. Paternal genes tend to increase fetal growth where maternal tend to decrease fetal growth.
Angelman syndrome
What are all of the different traits of X-linked disorders?
Associated with genes carried on X chromosome. Recessive disorders more common than dominant. Male offsprings of carrier mothers often affected. Female offsprings of carrier mothers often only carriers. Female offsprings affected if mother a carrier and father is affected. X-linked dominant disorders common in female offsprings. X-linked dominant trait from a father is transmitted to all female offsprings only, not to any male offsprings. Manifestation of X-linked dominant trait exaggerated in males.
What type of genetic inheritance do Huntington's disease and Marfan's disease follow?
Autosomal dominant
What type of inheritance/genes are described here? - Manifests even if only one copy of the allele is present - Males and females are affected in same ratio - Condition does not skip generations - Occurs with a 50% probability More common in structural protein genes (e.g. O.imperfecta) - Only one functional gene is not enough, both genes must be active. - Dominate negative affect
Autosomal dominant genes/inheritance
What type of genetic inheritance does sickle cell, cystic Fibrosis, and Tay-Sachs disease follow?
Autosomal recessive
What genetic markers are associated with hereditary breast cancer? By the age of 70-80 years - 55%-72% of women who inherit _________ variant will develop breast cancer - 45%-69% of women who inherit _________ variant will develop breast cancer
BRCA1 and/or BRCA2 mutations
What are some of the most common type II endonucleases used?
BamHI ClaI EcoRI EcoRV HaeIII HindIII HotI PstI PvuII Tth111I
What disorder is associated with snRNP's that is due to an AT replacing a GT at the 5' end of the first or second intron, or at the splice junction? Found in Eukaryotic cells and are similar to type II introns. Made from both independent RNA completed with proteins (not shown). AG AT mutation (!!!) ATP is needed for this process (!!)
Beta0-thalassemia
What type of mutations can cause both Frame Shift Mutations (non-sense mutations)?
Deletions or Additions
What is Prostate specific antigen (PSA) an example of? - Used to help diagnose patients with prostate cancer and to monitor for response to therapy during the treatment. *Used as an indicator of a biological state.
Biomarker
What gene is associated with cystic fibrosis (CF) codes for a protein that functions as a channel across the membrane of cells which produce mucus, sweat, saliva, etc.?
CFTR (Cystic fibrosis transmembrane conductance regulator)
Which CYP enzyme has multiple important variants that could effect metabolism of drugs?
CYP2C9
What is it called when there is a transfer of part of one chromosome to another? - May cause Schizophrenia, bipolar disorders, cancers.
Chromosomal translocations
What disorders are examples of uniparental disomy (UPD)?
Chromosome 15 disomy (Prader-Willie vs Angelman syndrom). Chromosome 11 (segment) disomy (Beckwith-Wiedmann syndrome). Cystic Fibrosis, when one parent is not even a carrier
Where in the chromosomes is the p53 gene located? - 53K molecular weight *Most cancer cells with p53 mutations show reduced sensitivity to chemotherapy and radiation.
Chromosome 17 short arm 17p13.1 - 7,661,779bp to 7,687,550bp -over 20kb long
What type of mutation is a change to the gene product that causes only a small effect such as switching a glutamate for an aspartate, both are acid amino acids.
Conservative Mutation
What is chromatin?
Contains DNA wrapped around histone proteins
What is the name for gene families - created through gene duplication? - Cytochrome P450 (CYP) superfamily that contains 56 putatively functional and over 50 pseudogenes.28-30CYP2D6, a gene that harbors numerous SNPs and small indels. - Duplications and multiplications of functional gene units contribute to increased activity and ultrarapid drug metabolism.
Copy Number Variation (CNV)
What are the major genes that are located on chromosome 21 and what effect do they have?
Cystathionine beta-synthase (CBS) - Catalyzes homocysteine to cystathionine - Homocysteine is metabolized faster using folate faster. PFK-1 - Rate controlling step of glycolysis. - Faster glycolysis
What disease is an autosomal Recessive disorder that is the 2nd most common autosomal recessive disorder in the world? - Occurs on Chromosome 7 - Defective chloride channel (1480 amino acids) - 1 in 25 of northern European ancestry has the trait - 1 in 3000 Caucasian newborns have the disorder. Carries of the mutant CFTR gene may confer partial resistance to Cholera, Typhoid and Tuberculosis. This has not been proven.
Cystic Fibrosis
What is the iron containing heme-protein with similar structure to myoglobin and hemoglobin that has enzymatic activity that oxidizes substrates including zenobiotics (drugs and toxins) and metabolites? •There are multiple alleles of this protein. •Absorbs light at 450nm.
Cytochrome P450
What enzymes are used to cut up DNA at specific locations and what are the different types?
DNA endonucleases Type II restriction endonucleases are used for these techniques. Type I and III endonucleases are not specific enough and are generally not used.
What enzyme used in recombinant DNA technology fills gaps in duplexes by stepwise addition of nucleotides to 3' ends
DNA polymerase I
What type of mutation occurs when a piece of DNA is abnormally copied one or more times?
Duplication mutation
Describe mtDNA
Each mitochondria has bacteria-like circular DNA. Interestingly, there may be more than one DNA per mitochondria. All the mitochondria in a cell would have very similar DNA, however, since mitochondria divide in a cell, there will be some genetic drift, thus there may be several polymorphisms of mitochondrial DNA in the same cell lines. *You can have more than one type of DNA in a mitochondria. (!!)
How was it first discovered that DNA is what carries all of our genetic information?
Early Experiments showed that the Genetic information is carried by a Phosphate containing molecule and not a sulfur containing molecule. Phosphorus is a permanent component of DNA, but only a transient component of Proteins. Sulfur is a permanent component of proteins (recall that cysteine and methionine are sulfur containing amino acids), but sulfur is not part of the structure of DNA. Therefore, DNA contains the genetic signal and not protein, even though there is more protein in the nucleus (histone proteins) than there is nucleic acid (DNA).
What disease is an X-linked recessive trait that is a lysosomal storage disease? - Defective alpha-galactosidase - Pan-ethnic - 1 in 3100 in Italy, 1 in 1500 in Taiwan.
Fabry disease
T or F: Only prokaryotic cells have enhancer and promoter regions upstream from genes.
False, Both Prokaryotic and Eukaryotic systems have Enhancer and Promoter regions. Not all genes have UP elements
T or F: Multigenic traits are actually fairly simple.
False, Multigenic traits are complex! Most human traits are multigenic (aka multifactorial). Disorders of single gene mutations are rare. Disorders of complex traits could result from mutations in one or more genes controlling that trait, resulting in a complex phenotype. Thus, even if the genes controlling a complex trait may segregate, the phenotypes do not segregate in a predictable fashion and may even appear to aggregate in a family. Individual risk calculation becomes very difficult!
T or F: Mutations in the region that codes for the Shine-Dalgarno sequences can increase protein synthesis for a gene. - The Shine-Dalgarno sequences is the place on the gene where the ribosome binds to.
False, Mutations in the region that codes for the Shine-Dalgarno sequences can DECREASE protein synthesis for a gene.
T or F: There are no evidence-based guidelines for detection of disease and treatments for some conditions based on family health.
False, There ARE evidence-based guidelines for detection of disease and treatments for some conditions based on family health. Ex. According to the American Diabetes Association one of the factors which increases the risk of prediabetes which can lead to diabetes mellitus 2 condition is: - Have a parent, brother or sister with diabetes
T or F: X-linked recessive traits are seen equally in men and women.
False, X-linked recessive traits rarely affect daughters but can on occasion.
T or F: Once a De Novo gene mutation occurs it affects all cells.
False, is affects only some cells, but not all cells. - Could be associated with cancer
T or F: Regarding ethnic differences of the occurrences of sequence variations, variability within ethnic groups is substantial but can never be greater than the differences between ethnic groups or races.
False, variability within ethnic groups is substantial and CAN be greater than the differences between ethnic groups or races.
What is important to know for a risk assessment for genomic medicine?
Family Health History •Self-reported family history information also used for risk assessment for individual patients •Can be easily collected and added into electronic medical record •Can create report for patients, clinicians and decision support information for some conditions (e. g. breast, ovarian and colorectal cancer, venous thrombosis)
How does favism cause hemolytic anemia?
Fava beans inhibit glutathione reductase and release H2O2 causing oxidative damage to cells.
What were some of the early findings from the First Data Bases based on AA sequences? - Bioinformatics - Comparing AA of two different proteins. - Comparing same functional proteins from different organisms.
Genetic drift is more prevalent than natural selection Natural selection mostly works against deleterious mutations created by genetic drift. - Called: Conservative or Purifying selection
Describe trisomy X.
Female cells will inactivate one of their two X chromosomes (Barr bodies), so females with this syndrome generally inactivate both of their extra chromosomes. - Generally they don't look different than other females. Females with the condition may have menstrual irregularities. - Some experience an early onset of menstruation. - Rarely, some exhibit severe mental impairments - Increased risk of learning disabilities, delayed speech, deficient language skills, and delayed development of motor skills. Most medical professionals do not regard the condition a disability. However, such status can be sought by parents for early intervention treatment if mild delays are present.
What effects does trisomy 21 have on methotrexate? (!!!!!!) - Leukemia rates are higher in Down syndrome.
Folate uptake by the reduced folate carrier protein (RFC) is faster. - This also takes up methotrexate and thus methotrexate accumulates faster. - Toxicity in non-tumor cells is more profound, especially in the gut.(!!!)
What SNP causes nonsense mutations? - Lead to premature termination due to the generation of stop codons.
Frameshifts - insertions or deletions of one or two nucleotides in coding regions
1. What metabolic disorder is an X-linked recessive disease? - Mostly males get this from their mother that was either a carrier or had the disorder (2 copies of defective gene). - Females only get this if their father had the disorder and their mother was at least a carrier. 2. Estimated 400 million people have this globally. 3. Most common in Mediterranean, Middle East, Asia and Africa. 4. Gives partial protection against malaria.
G6PDD
What disease is an x-linked recessive condition that causes hemolytic anemia? - Triggered by fava beans, aspirin, quinine, antimalarial drugs, infections.. - Confers resistance to malaria
G6PDD
Autosomal dominant genes/inheritance can also result in ____________________________________ mutations, meaning it causes an increase in activity due to mutation - this protein acts to inhibit growth and now it inhibiting too much.
Gain-of function mutations (e.g. FGFR3)
Each segment of a DNA molecule that codes for one "gene product"
Gene
What is a DNA segment that contributes to phenotype/function? - In the absence of demonstrated function a __________ may be characterized by sequence, transcription or homology
Gene
At what phases in the cell cycle are genes expressed?
Gene Expression takes place at ALL other times, including S phase send that specific section of DNA is not replicating.
What effect occurs when the severity of dominant mutations increases through generations? - Increasing phenotype severity - Early onset of disease - Ex. Huntington's disease, Myotonic dystrophy, Fragile X
Genetic anticipation
What term associated with inheritance is means that the genetic defect differs when it comes from one parent verse another. **When it appears to be a sex linked disorder, but the error is on an autosomal chromosome.(??)
Genetic imprinting
What is the study of biological variation and principles governing the inheritance & maintenance of that variation?
Genetics
What source has online genomics educational materials? Has specific resources involved in clinical application of pharmacogenomics including: •Genetic counselors •Nurses •Pharmacists •Physician assistants •Physicians
Genetics/Genomics Competency Center (G2C2)
What is all genetic information in a cell defined as?
Genome
What is defined as: "A measurable DNA and/or RNA characteristic that is an indicator of normal biologic processes, pathogenic processes, and/or response to therapeutic or other interventions." Can be a measurement of a gene: •Expression •Function •Regulation
Genomic biomarker
What is defined as an emerging medical discipline that involves using genomic information about an individual as part of their clinical care (e.g. for diagnostic or therapeutic decision-making) and the health outcomes and policy implications of that clinical use? •Part of precision medicine •Use of information from the genome to guide clinical decision making
Genomic medicine
What disorder is caused by a tandem TA dinucleotide repeat in the TATAA element of the gene promoter of UGT1A1, of seven repeats (TA)7 instead of the wild-type (TA)6 causes hyperbilirubinemia?
Gilbert syndrome
What is the term describing the combination of alleles that are located on one chromosome and inherited together?
Haplotypes
What is a disorder of a single gene trait that is an inherited as an autosomal recessive trait? - 1 in 10 individuals are carriers - 1 in 250-400 individuals may manifest disease - Results in INCREASED gastrointestinal iron absorption and complications thereof. (!!!) Symptoms are rare in pre-menopausal women. Symptoms are rare in regular blood donors.
Hemochromatosis : HEFC282Y
What syndrome associated with cancer is described here? Caused by mutations in certain genes passed from parents Examples of these are: •Hereditary breast cancer •Hereditary ovarian cancer syndrome •Li-Fraumeni syndrome •Cowden syndrome •Lynch syndrome
Hereditary cancer syndrome
What foods can worsen Hemochromatosis?
High consumption of red meat or other foods rich in iron. Vitamin C increases iron uptake (!!!) *Manifestations occur in middle age because it takes a while to accumulate the excess iron.
How do hormones activate specific genes?
Hormones activate genes by binding to proteins associated with a gene. - Either Directly or via translocation.
What. disease usually starts between 30-50 years of age and starts with a lack of coordination, jerky dance-like movements? - Declines into dementia. - 90% Autosomal dominant, 10% de novo (!!!!!) - Defect in the CAG triplet repeat in the HTT gene that codes for the _______________ protein. - 4-15 in every 100,000 of mostly European descent. - Near 100% penetrant - Mutation tends to get worse with each generation, known as genetic anticipation.
Huntington's disease
What main role can pharmacogenomics have in treating patients? - 3 main things.
Identify responders and non-responders to drug therapies. Avoid adverse effects. Optimize the doses of medications.
What are all of the inherited gene mutations that are associated with causing Lynch syndrome?
Inherited mutations in genes that affect DNA mismatch repair including: •MLHL •MSH2 •MSH6 •PMS2 •EPCAM
What is an Indel?
Insertion or Deletion
What are introns and exons?
Introns: some internal segments of RNA that do not code for protein. Exons: parts of the transcript that remain and code for protein.
What trisomy condition occurs when males have an extra X chromosome? - The extra X chromosome is mostly inactivated (barr bodies). - Small testicles and reduced fertility - Some degree of language learning impairment may be present - Lanky, youthful build and facial appearance, - Gynecomastia
Klinefelter's syndrome XXY
What condition is a hereditary cancer predisposition syndrome? - Higher risk of developing cancer across several generations. - >50% of individuals develop cancer diagnosis before age of 30. - First reported in 1969 Can develop many different types of cancers including:(!!) •Osteosarcoma •Acute leukemias •Breast cancer •Brain cancer •Melanoma •Lung cancer •Colon cancer •Pancreatic cancer
Li-Fraumeni Syndrome
What hereditary condition is also called hereditary non-polyposiscolorectal cancer (HNPCC)? - Most common cause of hereditary colon/colorectal cancer Cancer develops at younger age (before 50) Increased risk of other cancers including:(!!) •Uterine (endometrial) •Stomach •Liver •Kidney •Brain •Skin cancers
Lynch Syndrome
What type of genetic inheritance is described here?
Manifests only in individuals homozygous for the allele •Must have two bad copies of the gene. Heterozygotes are only 'carriers', do not manifest condition. •This is why we call it recessive May appear to skip generation. Males and females are affected in same ratio. More common in functional protein genes (e.g. Sickle cell anemia). May show a range of effects due to other factors. Consanguinity increases probability of homozygosous offsprings.
What is a disorder of connective tissue? - Tend to be tall, thin, long limbs, fingers and toes, and have very flexible joints. - Complications involve the heart and aorta - Mutation in the FBN1 gene needed to make fibrillin. - 75% of cases are autosomal dominant(!!!) - 25% are de novo (new) mutations. - Treatment includes beta blockers, calcium channel blockers or ACE inhibitors - About 1 in 5000 to 10000 have ______, occurs equally in males and females.
Marfan syndrome
What gene mapping tool contains numerous genes covalently attached to a microarray plate. - RNA expressed at any point in time for a cell can be reverse transcribed with fluorescent probes. - Hybridization with the DNA on the plate will tell you which genes are being expressed in that cell at the time tested.
Micro-arrays
What is the possible cause of genetic anticipation of Huntingtons disease?
Microsatellite amplification! The Huntington protein is encoded by the IT15 gene. If a C-A-G region of the gene is amplified Huntington's disease occurs. Codes for a poly glutamine in the middle of the protein. The disease form tend to have between 36 and 120 repeats, with each generation getting larger (genetic anticipation).
What are repetitive sequences of DNA composed of 1 to 5 base pairs? - One of the most abundant classes of inter-genetic material - Generally very stable One form of a dinucleotide repeat has been shown to be unstable in some cancers - The number of repeats would change - Called microsatellite instability - Caused by a defective DNA mismatch repair system
Microsatellites
What repetitive DNA sequences may also be called short tandem repeats (STRs) or simple sequence repeats (SSRs), and minisatellites (>5 bp in length) constitute variable number tandem repeat (VNTR)?
Microsatellites
What type of SNPs cause AA to change
Missense mutations
What type of inheritance that is an exception to mendelian genetics is described here? - Mitochondrial DNA contains some mitochondrial protein genes. - Mitochondrial genome is inherited maternally, hence mutations affecting mitochondrial genes are inherited maternally. - All offsprings of affected female are affected irrespective of gender - Offsprings of affected male are not affected at all. - Heteroplasmy and extreme variations are common - Homoplasmy of either type is extremely rare
Mitochondreal inheritance
What is mtDNA?
Mitochondrial DNA. Each cell has multiple mitochondria (liver cells have over 1000 each).
Describe XYY Syndrome
Most often, the extra Y chromosome causes no unusual physical features or medical problems. - Increased risk of learning difficulties - IQ scores of 47,XYY boys average 10-15 points below their siblings, About 1 in 1,000 boys are born with a 47,XYY karyotype, most may never know they have it.
What does polycistronic mean?
Multiple genes from one strand, does this by shifting reading frame.
What gene mutation on the CFTR gene is tested for to indicate the use of Ivacaftor for treating CF?
Mutation G551D in CFTR gene - Identified in CF cases which leads to impaired chloride channel function. Ivacaftor indicated for patients WITH the CFTR G551D mutation. Indicated in patients 6 years and older If genotype is unknown it is recommended to test for CF mutation to detect G551D mutation
What are chemical Changes to Nucleic Acid Bases? If not repaired, can cause a misreading of the genetic code during DNA replication. SNPs. -Variations that occur in less than 1% of the population.
Mutations
What can occur if a mutation affects the stop codon?
Mutations affecting the stop codon can also cause early stop mutations and run-on mutations.
When using genomic testing to diagnose essential thrombocytopenia, what marker is associated with causing an increased risk of that condition?
Mutations in JAK2 (V617F) - JAK2 mutations identified in about 50% of patients with essential thrombocytopenia.
What genomic mutations are associated with Li-Fraumeni Syndrome (LFS)?
Mutations in TP53 gene - About 70% of families with LFS will have a mutation in TP53 gene Mutations in CHEK2 gene also identified in some families with LFS
What are all of the ways that a De Novo gene mutation can occur? - New mutations that occurred in this individual.
Occurred during life - Affects only some cells, but not all cells. - Could be associated with cancer Occurred in germ cells prior to conception - Birth defect Inherited Occurred in a previous generation and was passed to the offspring.
What is the most common point mutation that can occur?
One of the MOST common mutations is a C to T mutation because of an added methyl!!!!!!!!!
What is the difference between orthologous and paralogous sequences?
Orthologous - Same protein in different species. (separated by a speciation event) - Ex. Hemoglobin alpha in both dogs and cats. Paralogous - Similar proteins in same species. (separated by a gene duplication event) - Ex. Hemoglobin alpha and myoglobin
What generally broad term is a model of healthcare that emphasizes the use of each individual's unique clinical, genetic, genomic and environmental information for disease prevention and treatment?
Personalized Medicine
What resource for pharmacogenomics is described here? •Repository for pharmacogene variation (!!) •Has information on haplotype structure and allelic variation. •Has resource to help with basic and clinical research. •Helps with interpretation of pharmacogenetic test results to direct precision medicine.
Pharmacogene Variation Consortium (PharmVar)
What is defined as a field of research that studies how a person's genes affect how that person responds to medications? - Part of precision medicine. Deals with influence of genetic variation on drug responses in patients by correlating DNA sequence variants or other biomarkers. Studies how this correlation affects medications: - Toxicity and/or - Efficacy
Pharmacogenomics
What online pharmacogenomic resource includes different information including: •Clinical guidelines •Drug labels •Potentially clinically actionable gene-drug associations and genotype-phenotype relationships *Collects, curates and disseminates information how human genetic variation can influence drug responses
Pharmacogenomics Knowledge Base (PharmGKB) - PharmGKB website www.pharmgkb.org
What resource for pharmacogenomics is described here? •Catalyzes and leads research in precision medicine. •Leads to discovery and translation of genomic variation which influence therapeutic and adverse drug effects. •Has educational resources such as: tools, implementation resources, competencies, research methods, etc.
Pharmacogenomics Research Network (PGRN)
What are all of the post-translational modifications that can occur?
Phosphorylations Other chemical modifications and cross-links Di-sulfide bonds Addition of Prosthetic Groups Proteolytic cleavage. Carboxylation Methylation
What is the evolutionary history of a molecule (such as a gene or a protein), or even a species and the relationship between such entities?
Phylogeny
What type of mutation are when only one base is changed?
Point Mutations (missense mutations)
What are the 2 types of mutations that can cause early stop mutations and run on mutations?
Points mutations as well as frameshift mutations.
What is a polymorphism and how is it different than a mutation?
Polymorphism - when two or more different phenotypes are present in a population. - Examples are hair color or blood types. - Occur at a frequency of at least 1%. Mutation - variation occurs less frequently than <1%
What disorder demonstrates Genetic imprinting and is described here? Hyperphagia and food preoccupations, as well as small stature and learning difficulties. - Mutation in proximal part of chromosome 15 coming from the father(!!!!)
Prader-Willi syndrome
What are the ways that pharmacogenomics can be used preemptively (proactive) and reactively?
Preemptive pharmacogenomic testing: - Patients are tested for many pharmacogenomic variants prior to developing need/indication for specific medications. Reactive pharmacogenomic testing: - Usually performed when a patient is experiencing adverse effects unexplained by dose or drug-drug or drug-disease interactions or... - When use of high-risk drug is anticipated and genotype is ordered due to start of therapy.
What drug should NOT be given to someone with G6PDD?
Primaquine (!!!!) (KNOW THIS ONE) Ascorbic acid Chloramphenicol Colchine Dopamine Acetaminophen Probenecid Quinine Streptomycin Sulfanilamide
How long does the promoter region span?
Promoter region spans -70 to +30
What is a biomarker of prostate cancer used for: •Detection •Classification •Prognosis
Prostate Specific Antigen (PSA) PSA levels 20-70 mg/mL especially useful for predicting prognosis of prostate cancer. PSA >70 mg/mL: plateau so not very useful.
What was the first noticed instance of genetic variants?
Pythagoras noticed 2500 years ago that some people had adverse reactions to eating fava beans and others did not. We now know that "Favism" is caused by a glucose-6-phosphate dehydrogenase deficiency, which is a genetically inherited trait. **Fava beans contains divicine. Divicine(!!!) and certain other drugs produce H2O2 which can cause a hemolytic anemia (massive destruction of RBC) in G6PD deficient individuals.
SNPs located in introns and exons can alter ________________ - Introns get expressed
RNA splicing
Crizotinib is a kinase inhibitor indicated for patients with NSCLC with anaplastic lymphoma kinase (ALK) or ________-positive identified by FDA-approved tests.
ROS1 positive
What are reference SNPs that are catalogued by the NCBI?
RefSNPs (rs)
What enzymes are used to chop up ("restrict") foreign DNA? They generally don't work on methylated DNA. The cell's own DNA is generally not cut up by these endonucleases because the endonucleases don't enter the nucleus or mitochondria.
Restriction Endonucleases
What enzymes used in DNA fingerprinting are used to chop up ("restrict") foreign DNA.? - They generally don't work on methylated DNA. - The cells own DNA is generally not cut up by these enzymes.
Restriction Endonucleases
What are RFLP's?
Restriction fragment length polymorphisms - Differences in the fragment lengths of the genes from different individuals that were cut by the same enzyme. - For any one DNA and one restriction enzyme, there is a unique pattern. That is the RFLP.
Complementary DNA (cDNA) is made from an mRNA strand and what enzyme?
Reverse Transcripase.
Where can ribosomes be found?
Ribosomes are found in cytoplasm, rER, mitochondria and chloroplasts.
What term refers to when two sequences that came from the same ancestral sequence?
Sequence Homology
What condition is an autosomal recessive disease caused by a Glu to Val mutation at beta 6 - GAG to GTG, chromosome 11p15.5 - 4.4 million people - 43 million have the trait
Sickle Cell
How is High-Resolution Melt Curve Analysis used for gene mapping?
Since A=T and C=G have different binding strengths, it takes more heat to melt DNA that has more C=G to separate double strand to single strand) DNA. Using a fluorescent dye to detect double helix, as the DNA separates, the fluorescence decreases. If there is a SNP, the melting curve will shift slightly, indicating that there is a SNP (sequence variation).
What is an SNP?
Single nucleotide is changed to another at a particular position within a genome. - Approximately 1 SNP per 1,000 base pairs, or >3 million per genome. - Triallelic, meaning that T or A can be found instead of the wild-type G (G > T/A).
What are snRNP's and what is their function?
Small nuclear ribonucleoproteins, they function as part of a spliceosome.
What type of SNPs cause no AA change?
Synonymous or silent SNPs
What type of SNPs are sequence variations that allow discrimination of the different haplotypes? Genotype information of a _____ SNP indirectly provides information regarding all other SNPs that are statistically linked to it. (!!!)
Tag SNPs
Describe the DNA sequencing process. - Sanger Method
Take a DNA segment and add a portion to 4 different test tubes. Add to each -Mixture of all 4 dNTP -A different ddNTP at a lower concentration -Add DNA polymerase Using radioactive ddNTP's and x-ray film. Then run a gel electrophoresis and look at where all of the differ lines end up for each base.
________________ or ends of chromosomes are important in DNA replication.
Telomeres
What online pharmacogenomic resource is a project between PharmGKB and the Pharmacogenomics Research Network (PGRN)? •International consortium with goal to address main barrier to implementation of pharmacogenetic testing in the clinic which is difficulty in translating genetic laboratory test results into actionable prescribing decisions for affected drugs. *Creates, curates, and posting freely available, peer-reviewed, evidence-based gene/drug clinical practice guidelines
The Clinical Pharmacogenetic Implementation Consortium (CPIC)
What website is the most useful for interpreting genetic variations.
The NCBI website
What is the largest pharmacogenomics consideration a pharmacist must make?
The largest genetic difference within the human population is the difference between males and females. Generally -Estrogen is not given to men -Testosterone is not given to women
What type of genetic inheritance does Leber's syndrome, Leigh Syndrome, and mitochondrial myopathy follow?
They are mitochondrial disorders so they are spread from mothers to all children. (Regardless of gender)
What is the difference between topoisomerase I and II?
Type I - break one strand and change linking number by 1 Type II - break both strands and change linking number by 2
What is a repeat expansion?
Type of SNP that is caused by repeated sections of DNA increase the number of repeats.
What is the proposed mechanism that is responsible for genetic anticipation?
Triplet repeat expansion
Patau syndrome, also known as trisomy ____ and trisomy D. Patau syndrome affects approximately one in 10,000 live births.
Trisomy 13
What trisomy condition is described here? Clenched hand and overlapping fingers: index finger overlaps third finger and fifth finger overlaps fourth finger, characteristically seen in trisomy ___. The syndrome has a very low rate of survival, resulting from heart abnormalities, kidney malformations, and other internal organ disorders.
Trisomy 18 (Trisomy E or Edwards syndrome)
What are examples of trisomys?
Trisomy 21 : extra copy chromosome 21- Down's syndrome. Trisomy 13 : extra copy of chromosome 13- severe retardation, death. Trisomy18 : extra copy of chromosome 18 - microcephaly Trisomy X : extra copy of X chromosome in females : behavioral defects XXY : extra copy of X in males : sterility, gynacomastia XYY: extra copy of Y in males : hyperactivity
T of F: Southern blot analysis and long-range polymerase chain reaction (PCR) may only yield information regarding the presence or absence of the gene, but NOT how many copies are present.
True
T or F: In genomic medicine, family health history is included in risk assessment.
True
T or F: Mismatch repair enzymes are able to recognized the original strand and differentiated it from the newly synthesized strand.
True
T or F: All mitochondria genes code for mitochondrial proteins, however, most mitochondrial proteins are coded for in the nucleus.
True!!!
T or F: During development, male cells will methylate a DIFFERENT set of genes than female cells.
True, For this reason during fertilization, the father's DNA and the Mother's DNA will be expressed slightly differently in the offspring. •Prader-Willi syndrome is due to missing DNA on Chromosome 15 from the father. •Angleman syndrome is due to missing DNA on Chromosome 15 from the mother.
T or F: Some proteins have multiple subunits from multiple genes.
True, Hemoglobin has an alpha and a beta gene. Plus a gamma gene expressed during development and a delta gene that upregulates at high altitude.
T or F: There are many variants of G6PDD?
True, there is more than one variant of G6PDD. Mediterranean is the most common variant.(!!) G6PD-Mediterranean. 1. Isoform B 2. Ser188Phe (C->T at 563)
T or F: Medication labels may include different information on genomic markers.
True. •Drug exposure and clinical response variability •Risk for adverse effects of medications •Genotype-specific dosing •Mechanism of action •Polymorphic drug target and disposition genes •Trial design features
What tumor marker is elevated in ovarian cancer with higher levels in more advanced disease? •71.4% in stage I ovarian cancer •80.0% in stage II ovarian cancer
Tumor marker CA-125
What term is used to describe when there is inheritance of both chromosomes of a homologous pair from the same parent and non from the other? - May be entire chromosomes or segments of chromosomes - Caused by nondisjunction during zygotic divisions - Most occurrences result in no phenotypical anomalies. - rare recessive disorders can be passed from one parent
Uniparental disomy (UPD)
What are VNTRs?
Variable Number Tandem Repeats!! Distinct nucleotide sequences that everyone has in different numbers
Describe the nomenclature of the CYP enzymes.
Variants are distinguished by asterisks* - variant labeled *1, in most cases, represents the reference gene also referred as "wild-type." HUMAN - in upper case CYP2D9 Mouse - example:, cyp2d9
What exceptions to mendelian genetics is described here? - X/Y chromosomes contain genes not related to sex determination - How is XX dose tolerated by females of a species? Genetic inactivation of one of the X chromosomes to equalize gene dosage associated - Occurs very early in life (embryonic stage) - Inactivation is random, differing in each embryonic cell - Wide implications for X-linked disorders
X-inactivation and Lyon Hypothesis
What type of genetic inheritance do fragile X syndrome and Rett syndrome follow?
X-linked dominant - more common in females (Fathers to daughters)
What type of genetic inheritance does Hemophilia, Fabry disease, G6PPD, and Lesch-Nyhan follow?
X-linked recessive - more common in males(!)
What type of heredity disease is favism? - Patients are almost exclusively male - Confers protection against malaria caused by Plasmodium falciparum
X-linked recessive hereditary disease
What type of genetic inheritance does Swyer syndrome and Y chromosome infertility follow?
Y-linked - exclusively in males
Is variation good in genetics?
Yes (mostly) - Variation is essential for survival. - Some variation may be disadvantageous. - Some variation may be advantageous. - Some variation may be neutral.
A genomic biomarker can be a measure of gene? a) Expression, function, and regulation b) Expression and function but not regulation c) Expression and regulation but not function d) Function only
a) Expression, function, and regulation
What is the name for variable forms of the same gene?
allele
What is the use of computational methods to analyze the sequences, structures, and expression of biological molecules?
bioinformatics
Some highly repetitive DNA (aka Satellite DNA) is associated with specific chromosomal regions such as __________________.
centromeres
DNA synthesis takes place in what manner?
semi-conservatively
Which DNA base residues can be methylated to 5-methyl ______________? •The methylated ___________________ re found in GC rich areas called GC islands which are commonly near the promoter regions of a gene. •Generally, this will decrease transcription of that gene. •Ex. The globin genes are more extensively methylated on non-erythroid cells. •This is a common during fetal development.
cytosines
Pharmacogenomics is: a) Also sometimes called pharmacogenetics b) Defined as a field of research that studies how a person's genes affect how that person responds to medications c) Part of precision medicine d) All of the above
d) All of the above
Ivacaftor is indicated for patients with cystic fibrosis who have which of following mutation in CFTR gene? a) V600E mutation b) V600K mutation c) G551E mutation d) G551D mutation
d) G551D mutation
What agent used to block further replication of DNA strand? - No oxygen at either carbons 2 or 3.
ddNTP analog
Mutations of the AUG sequence would ________________ protein synthesis.
decrease
Incidence of congenital malformations is __________________ if parents are first cousins to about 3-5%. - This is called Consanguinity(!!!!!)
doubled Consanguinity for 3rd cousins is generally no higher than for any two other unrelated parents. -This is not true in isolated communities that have increased levels of inbreeding.
Membrane bound proteins are commonly linked to _____________.
farnesyl
Many VNTRs are located in _______________ regions without an apparent function
intergenic Can also occur within a gene. -Ex. the dominant trinucleotide repeat disorder Huntington disease. (<29 CAG repeats normal, >35 repeats are affected by the disease.
What is a type of skin cancer that is described here? - About 10% of all people with melanoma have a family history of the disease. - Risk of ____________ is increased if one or more of first-degree relatives (e.g. parents, brothers, sisters, or children) has had _____________.
melanoma
The most common DNA sequence within a population, is commonly called the wild type. - DNA sequence variations, as compared to the wild type are referred to as _____________________. -Variations that occur in more than 1% of the population
polymorphisms
What base pair mutation causes sickle cell anemia?
rs334(T;T) - Normal is A:A
If the newly synthesized DNA has a different base than the original strand had due to a mutation induced change or a simple mismatch that was not repaired, this is known as a _______________________________________.
single nucleotide polymorphism (SNP)
During translation, t-RNA's bind to specific _________________________>
triplet codons.
In genetic and genetic medicine, ____________ is the RULE rather than the exception in the living world.
variation
Explain the protocol for DNA fingerprinting.
•Add an equal portion of the DNA sample to one or more test tubes. •Add only one of the restriction enzymes (of your choice) to each tube. A different restriction enzyme can be used for each tube to obtain a different set of restriction fragments. •Digest the DNA into restriction fragments by giving enough time for the enzyme to digest the DNA. •Add glycerol to make sample dense, so it sinks to the bottom of the well when put on the electrophoresis gel. •Add dye so you can see where the sample is when you add it to the electrophoresis gel. The dye is negatively charged and will move with the smallest DNA fragments. Separate the DNA fragments by electrophoresis Through other experiments, you need to know which fragment contains the gene you plan to clone.
Describe the process of extracting DNA.
•Break cells open with SDS (and lysozyme if bacterial cells are used). •Slowly add cold ethanol or isopropanol to the top of the water and the DNA will precipitate at the interface of the two layers (don't shake or the alcohol will dissolve into the water layer). •Slowly spool a glass rod in the solution and the DNA fibers will wrap around the rod.
What were the main historical events involved with the development of pharmacogenomics?
•Charles Darwin •Gregor Mendel •Watson and Crick - discovery of DNA structure •Human Genome Project - Completed 2003 - First completed sequence of human genome Two decades preceding the "Age of Pharmacogenomics" •Discovered mechanisms of variation in drug responses. •Isolated and characterized polymorphic hepatic cytochrome P450. - "Reverse genetics" - identification of atypical amino acids helped to identify mutations at the DNA and mRNA level which lead to different drug responses. •Candidate gene association studies helped to identify clinical importance of: - Genetic polymorphism of proteins involved in drug disposition. - Protein targets which mediate pharmacodynamics responses to drugs. "Age of Pharmacogenomics" •In 2003 FDA started efforts to increase visibility of pharmacogenetic information in drug labels. •Started to encourage pharmaceutical industry to include investigations about genetic influences on drug responses during drug development studies. •At the present time many drugs have in drug package inserts information about germline or somatic gene variants (e.g. polymorphism, mutations, etc.) •In 2007 established the International Serious Adverse Events Consortium (SAEC). •Global, nonprofit partnership between FDA, pharmaceutical companies and academic institutions. •Goal to identify and validate genetic markers which can help identify who is at risk of serious adverse drug events (SAEs).
What is the ultimate goal of Pharmacogenomics?
•Correlate the different pharmacological responses to variations in DNA sequences. •The simplest differences would be individual SNP's.
The increased risk for melanoma due to family history may be attributed to what factors?
•Family lifestyle of frequent sun exposure •Family tendency to have fair skin •Certain gene mutations run in families •Combination of the above mentioned factors
In order to apply clinical pharmacogenomics, what must you understand first?
•How genetic variations impact pharmacokinetic and pharmacodynamics properties of a medication in specific disease states and patient populations •Molecular pathways •Influence of different factors such as age, sex, diet, pathophysiologic conditions, current medication, and their relationship with specific genetic variability
What are all of the challenges in with implementing genomics in clinical practice?
•Limited evidence •Conflicting interpretation of benefit and value •Limited access to genomic medicine expertise and testing •Lack of standards for genomic applications •Understanding by patients, clinicians, public - Need more education for patients, clinicians and public. •Lack of research funding and reimbursement.
Data from 1000 Genomes Project suggests that there are 20-40 millions of small nucleotide polymorphisms (SNPs) in the human genome which may lead to explanations of: 1. 2. 3.
•Mechanisms of underlying disease susceptibility •Disease progression •Different responses to drugs
What areas of medicine is genomic medicine had major application in so far?
•Oncology (use of genomic markers for screening, diagnostics and treatments) •Infectious disease •Pharmacology •Some rare and undiagnosed diseases
With regard to pharmacogenomics, Pharmacists are distinctively positioned to lead interprofessional efforts for developing processes for what processes?
•Ordering •Reporting and •Interpreting pharmacogenomic tests
What are all of the functions that pharmacists can have in clinical pharmacogenomics?
•Promoting optimal use and timing of pharmacogenomic tests. •Interpreting clinical pharmacogenomic test results. •Educating other pharmacists and other health care professionals, patients, and public. •Participating in research and different pharmacogenomic networks. •Recommending and/or scheduling pharmacogenomic testing. •Communicating pharmacogenomic-specific drug therapy recommendations to health care teams. •Pharmacists with specialized training in pharmacogenomics should have different specific functions in clinical pharmacogenomics such as: - Developing pharmacogenomic-specific clinical support systems in the electronic health record (EHR) systems. - Developing processes and education materials. - Developing institutional guidelines. •Contributing to evaluation and implementation of clinical pharmacogenomic testing. •Promoting collaborative relationships among different health care professional involved in drug therapy to improve appropriate use of pharmacogenomics tests in order to optimize drug therapy for patients. •Being involved in pharmacogenomics research.
What are all of the possible improvements in medication-related outcomes that can occur as a result of pharmacogenomics?
•Reduction in suboptimal clinical outcomes •Decrease costs of treatments •Improved adherence to medications •More appropriate choice of medications •Decreased length of treatment •Better patient safety
What all can genomic medicine can help with?
•Risk assessment •Early disease detection and disease diagnosis •Selecting optimal therapy - Pharmacogenomics •Disease prognosis •Disease monitoring
What are the potential strategies for increasing cost-effectiveness of genomic screening?
•Target screening to high-risk populations. •Focus on chronic diseases. •Limit screening to diseases with high prevalence.