Lecutre 1: Chromosomal Abnormalities 1. Describe the molecular components of human chromosomes. 2.

Explain the mechanistic basis for congenital (condition present at birth) chromosomal abnormalities. 3. Name human diseases caused by chromosomal abnormalities and their karyotypes. 4. Define the terms provided in the "Basic Terminology" section of the notes. Lecture 2: Gene Functions 1. Describe the basic transcription machinery, the basic structure of genes (including promoters) and transcription units, and the basic mechanism of transcription in eukaryotes. 2. Discuss the roles of transcriptional activator proteins, enhancer elements, coactivators, and chromatin in regulation of eukaryotic transcription. 3. 3. Describe the cellular response (or signal transduction) pathway used by steroid hormones and list the major hormones which interact with members of the nuclear receptor family. 4. Explain why agonists promote gene activation by steroid receptors, but antagonists inhibit steroid receptor function. 5. Discuss the roles of steroid receptors and their agonists/antagonists in the etiology and/or treatment of breast cancer. Lecture 3: Gene Expression 1. Understand and be able to state the basic steps of mRNA processing 2. Understand how RNA processing can help regulate gene expression and stimulate biological diversity 3. Be able to explain how mistakes in RNA processing could lead to human disease Lecture 4: 1. Be able to describe the principle of mRNA translation and explain the degeneracy of the genetic code 2. Understand and be able to summarize the general steps of translation 3. Be able to explain how aberrant translation can play a role in human disease: * splicing mutations/frameshift changes 4. The role of nonsense-mediated mRNA decay * aminoglycoside antibiotics/deafness Lecture 5: DNA Replication 1. Identify therapeutic agents that affect DNA replication and the basis for their activity 2. Describe how defects n DNA repair and replication lead to common and rare diseases 3. Name diseases whose pathogenesis (cellular events and reactions and other pathologic mechanisms occurring in the development of disease) is related to inherited or acquired defects in DNA repair and replication 4. Define the terms provided in this handout Lecture 6/7: Mendelian Genetics 1. Interpret pedigree information and recognize Mendelian inheritance patterns 2. Explain Hardy-Weinberg equilibrium and apply it to solving problems relevant to genetic counseling 3. Define the terms provided in these handouts and recognize their clinical correlates 4. Illustrate general principles of Mendelian inheritance based on attributes of human disorders Lecture 8: Human Genome Projects 1. Cite the relative abundance of the different classes of sequences in the human genome discusses in this lecture 2. Explain basis for the observed differences in the genetic variation in different human populations 3. Recall the relative abundance of different classes of medically important sequence variants in a healthy persons genome 4. Define haplotypes and discuss their application in Genome Wide Association Studies 5. Explain the complex disease: common variant hypothesis and the results of GWAS studies relevant to the hypothesis Lecture 9: Epigenetics 1. Explain the term epigenetics and how it differs from genetics

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Epigenetics: mitotically or meiotically heritable alterations in phenotype that are not based on DNA sequence (for example DNA methylation and histone modification). Passes on what TYPE of cell a daughter cell should become. Epigenetics are similar (in one cell type) from person to person) powerful force in determining phenotypes and human disease. Mechanisms: DNA methylations, histone modifications, chromatic structure and nucleosomal positioning , non-coding RNAs, TF regulatory networks Explain the concepts of epigenetic writers, readers, erasers, remodelers, and insulators Writers: establish epigenetic mark Readers: interpret epigenetic mark Erasers: remove epigenetic mark Remodelers: shift nucleosomes about Insulators: separate epigenetic domains Define and give specific examples of the role of epigenetics in Mendelian disorders Inherited defects in epigenetic regulators: -ICF (Immunodeficiency, centromeric instability, facial anomalies syndrome: mutation in DNMT3B (DNA methylation writer) -Rett syndrome mutation in MECP2 (DNA methylation reader) -Kabuki Syndrome (MLL2 histone methylation writer) Monoallelic Gene Expression and Genomic imprinting only one of two homologous alleles are expressed (ex: X- inactivation, genomic imprinting) Uniparental disomy 2 copies of a chromosome from one parent and none from other -Angelman syndrome- 2 paternal copes if UBE3A mental retardation -Prader-Willi Syndrome 2 maternal copies -Bechwith- Wiedmann Syndrome 2 paternal of IGF2 Define and give specific examples of the role of epigenetics in cancer Systemic silencing or predisposition to silencing of MSH2 DNA repair gene predispose to colorectal cancer Epigenetic silencing of tumor suppressor genes found in many types of cancer Be aware of ongoing research of the role of epigenetics in other common diseases

Lecture 10:Mitochondiral Lecture 11: Gene Therapy 1. Understand why gene therapy can be called DNA as a drug 2. Describe basic principles of retroviral vectors 3. Explain why HSC are a good target for certain gene therapies 4. Understand that gene therapy can be more than just a treatment for genetic diseases, but also infectious disease (HIV) and cancer 5. Describe challenges facing this field of medicine Lecture 12: Forensic Uses of DNA 1. Discuss common forensic DNA techniques including short tandem repeats, mitochondrial DNA, Ychromosomes STRs, restriction length polymorphism a. Short tandem repeats DNA region with short repeat units of 2-6 bp. i. Steps: 1. Extract DNA 2. Quantify 3. Amplify using PCR with florescent proteins 4. Capillary Electrophoresis of sample recording using argon laser 5. If math present, calculate probability of math occurring by chance ii. Number of repeats at each loci vary In people (receive one copy from mom and one from dad), many different alleles iii. FBI uses 13 STR core as a standard panel 1. 12 autosomal, 1 on either x or y chromosome ( amelogenin) b. Mitochondrial DNA i. The DNA found in mitochondria the energy-producing organelles of cells is often analyzed to trace evolutionary pathways. Mitochondrial DNA (mtDNA) has a high "substitution" or mutation rate, compared with other sites in our genome. ii. mtDNA is transmitted only from mother to child, and can be inherited intact over thousands of generations.

1. Mutations in the mtDNA sequence can be used to reconstruct the maternal lineage of populations. assed through the egg of the mother at fertilization. egg has about 50,000 mitochondria whereas the sperm have just a few, and those that do enter the egg are actually destroyed, so mitochondria and their DNA are inherited exclusively from the mother. iii. Typing results are expressed as differences from a standard sequence (the Anderson sequence) iv. Highly degraded samples contain more mtDNA than nuclear DNA v. mtDNA more variable than nuclear DA so exclusions may vi. The entire mtDNA genome is inherited as a single locus, so it varies less between individual c. Y chromosomes STRs i. The Y chromosome is passed only from father to son, and can be used to trace the evolutionary histories of men. The Y chromosome is more than 50 million DNA base pairs long and has 220 genes. ii. Mutations at particular locations on the Y chromosome can be used to reconstruct the paternal lineage of populations. iii. Used in sexual assault cases, or in paternity cases where alleged father is not available iv. Can type a male relative who is paternally related to the alleged father d. Restriction length polymorphism i. Steps: 1. Digest DNA with restriction enzymes 2. Separate fragments by length using electrophoresis 3. Transfer DNA to a membrane (Southern blot) 4. Hybridize membrane to a labeled DNA probe ii. Technique is obsolete because it is very time consuming and requires a lot of sample 2. Explain calculations based on Hardy-Weinberg Equilibrium a. Assumptions for a population to be in Hardy-Weinberg equilibrium i. Population is infinitely large ii. Mating is random iii. Population is free from effects of migration iv. There is no natural selection v. No mutations occur b. For a population in equilibrium with two genes occurring at frequencies p and q i. Probability of a homozygote is p2 or q2 ii. Probability of a heterozygote is 2pq iii. When you have multiple alleles, you multiply the probabilities iv. 3. Give case examples of forensic uses of DNA a. Identify unknown sample i. Locard Principle: every contact leaves a trace b. Molecular autopsy: cause of death i. Long QT syndrome in sudden cardiac death or unexplained drowning ii. Cytochrome p450 mutations in drug toxicity, iii. Alpha-tropomyosin in hypertrophic cardiomyopathy iv. hereditary thrombophilia (protein C deficiency) in pulmonary embolism c. Paternity testing d. Missing persons/mass disasters e. Military uses f. Convicted felon database i. Data housed in CODIS (Combined DNA Index System) which is a standardized system of 13 STR loci g. Historical investigation Lecture 13: Genomes and Medicine 1. Discuss strengths and limitations of genetic testing in adults 2. Describe the technological basis for non-invasive fetal genome sequencing

a. Non invasive fetal genome sequencing takes advange of the fact that 13% of ell free DNA in plasma of pregnant female is fetal in origin b. DNA is sequenced and computational alanlzy required to discrimbate between the sequences derived from mother and fetus c. False positives are common 3. Cite genotype-specific therapies for Mendelian disorders a. Missense Mutation therapy point mutation causing change in one amno acid i. CFTR G551d reaches cell surface but defective chloride transport ii. Ivacaftor potentiates CFTR channel activity by binding to protein b. Nonsene Mutations convert codon to a premature stop codon, which causes nonsense mediated decay i. CF and Duchenne Muscular Dystropy (DMD) ii. Nonsense suppressor therapies: drugs that promote the read through of stop codons iii. PTC124 binds ribosome to promote read through and prevent NMD Only increases read through by a little bit c. Frameshift mutation therapies: insertion or deletion of base pairs, to shift reading frame and eventually produce a premature stop codon i. Duchenne Muscular dystrophy (DMD) X linked recessive disorder that results in progressive weakening and loss of muscle funticon Caused by mutations in DMD gene (dystrophin) DMD exons are deleted or duplicated (huge protein) Dystrophin: stabilizes and links the muscle fiber cytoskeleton the membrane and renders muscles fibers more resistance to mechanical strength ii. Exon skipping terapy chemically modified antisense oligonucleotide (AO) binds to and masks specific splice junctions Goal is to alter splicing so that mutant exons are removed while persevering the correct open reading frame Produces truncated but partially functional protein d. Chronic myelogenous leukemia (CML) therapies i. Philadelphia chromosome present in cancer cells reciprocal translocation between chromosomes 9 and 22 ii. Produces a bcr-abl fusion gene that produces unregulated tyrosine kinase leads to CML iii. Imatinib blocks the tyrosine kinase activity of bcr-abl and results in decreased cancer growth iv. 4. Recognize and recall examples of pharmacogenomic applications in cancer therapies a. Pharmacogenomics studies how all of the genes (the genome) can influence responses to drug. Pharmacogenomics is the study of how genes affect a persons response to drugs. This relatively new field combines pharmacology (the science of drugs) and genomics (the study of genes and their functions) to develop effective, safe medications and doses that will be tailored to a persons genetic makeup. b. Pharmacokinetic effects - the movement and change of drugs in the body over a period of time. Genetic variation in processes involved in the absorption, distribution, metabolism, or elimination of a drug can result in changes in drug availability. genetic polymorphisms lead to variations in the levels or concentrations of drugs or their metabolites at the site of action. i. Ex . Colorectal cancer: Treated with Irinotecan (topoisomerase inhibitor) ii. UGT1A1 processes active metabolites of irinotecan iii. seven TA dinucleotide repeats instead of six repeats in the promoter region of UGT1A1 less UGT1Ai enzyme produced lower enzyme activity decreased rate of drug metabolism (more active metabolite floating around) more toxicity iv. Rate of toxic effects associated with irinotecan (diarrhea and myelosuppression) is increased in patients with seven TA dinucleotide repeats c. Phmacodynamics and Drug Response, the study of the biochemical and physiological effects of drugs and the mechanisms of their actions. Genetic variation in drug targets can cause measurable differences in the response of an organism to a drug. Data in this category document that the biological or physiological response to a drug varies, and that this variation can be associated with the variation of one or more genes. This variation is often measured at the whole-organism level.

i. Ex: Non-small cell lung cancer: EGF normally binds EGFR to promote cell growth, but mutations causes out of control growth ii. Treat with Gefitinib which is a kinase inhibitor blocks kinase activity of EGFR effectively shuts down the cancers ability ot replicate quickly iii. Nonsmall-cell lung cancer tumors with activating mutations in the EGFR tyrosine kinase domain are more sensitive to Gefitinib treatment. These are somatic mutations acquired during tumorigenesis iv. tumor genome plays a critical role in the response to gefitinib since the sensitivity of nonsmall-cell lung cancer to this drug is enhanced by activating mutations in the kinase domain of the gene encoding epidermal growth factor receptor v. Tumor EGFR encoding activating mutations within the kinase domain results in enhanced tumor sensitivity to Gefitinib 5. Describe drug rescue and drug repurposing efforts for rare disorders a. NCATS initiative: find novel drug therapies for rare diseases b. Drug rescue: involves small molecules and biologics whose development was abandoned before the could be approved by FDA i. rescuing a drug that wasnt deemed effective for its intended purpose but was deemed safe for human use c. Drug repurposing: involves small molecules and biological approved to treat a disease or condition to see if the are safe and effect ive for treatingother disease i. repurposing a drug that is already used in practice but it is hoped that it can be used to treat another disease as well Lecture 14: Genetics Counseling 1. Define genetic counseling and integration into different clinical settings a. The process of helping people understand and adapt to the medical, psychological and familial implications of the genetic contributions to disease b. Goal: to promote informed choices and adaptation to the risk or condition c. Integration in medicine i. Family Planning/Prenatal: risk for genetic disease ii. Pediatric: failure to thrive, developmental delays iii. Adult: predisposition to adult onset 2. Describe three psychosocial considerations relevant to genetic testing and disease a. Prenatal and preconception testing i. Chronic sorrow refers to the difficulty resolving the sense of loss that comes from the birth of a child with a syndrome or congenital defect. Also, can refer to the loss associated with terminating a pregnancy. b. Pediatric i. Impact on child 1. Self-image 2. stigmatization ii. Impact on parents 1. Shame and guilt 2. Interpersonal relationship strain iii. Impact on siblings 1. Deprivation of paternal attention 2. Fear and embarrassment c. Adult i. Impact on patient 1. Fear of disease development 2. Image of self ii. Impact on family 1. Survivor guilt - refers to the guilt experienced by an individual who tests NEGATIVE for a known family mutatio 2. Unified-divided front against disease iii. Availability of treatment iv. Insurability v. Reproductive issues and family planning 3. Define ELSI and GINA

a. ELSI Ethical, Legal, and Social Implications arising from the Human Genome Project Major point: privacy and confidentiality i. Fairness in the use of genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others. ii. 2. Privacy and confidentiality of genetic information. iii. Psychological impact and stigmatization due to an individual's genetic differences. iv. Reproductive issues including adequate informed consent for complex and potentially controversial procedures, use of genetic information in reproductive decision making, and reproductive rights. v. Clinical issues including the education of doctors and other health service providers, patients, and the general public in genetic capabilities, scientific limitations, and social risks; and implementation of standards and quality- control measures in testing procedures. vi. Uncertainties associated with gene tests for susceptibilities and complex conditions (e.g., heart disease) linked to multiple genes and gene-environment interactions vii. Conceptual and philosophical implications regarding human responsibility, free will vs. genetic determinism, and concepts of health and disease. viii. Health and environmental issues concerning genetically modified foods (GM) and microbes. ix. Commercialization of products including property rights (patents, copyrights, and trade secrets) and accessibility of data and materials. b. GINA Genetic Nondiscrimination Information Act, passed in 2008 i. Genetic discrimination refers to concerns about being treated differently by an employer or insurer because an individual has a genetic condition or are at risk of having an inherited disorder. ii. GINA Does: 1. Prohibits the use of genetic info to determine eligibility or to adjust premiums/contributions 2. Prohibits employers from firing, refusing to hire, or from other workplace discriminations based on genetic info iii. GINA Does Not: 1. Mandate coverage for any particular test or treatment 2. Prohibit medical underwriting based on current health status 3. Cover life, disability, or long-term care insurance 4. Apply to members of the military 4. Discuss one pro and one con to the clinical integration of next generation sequencing a. Personalized risk assessment b. Creates potential to address risk c. For some, less anxiety and stress d. Possibility to alert and involve other at-risk family members e. Lecture 15: Newborn Screening Lecture 16: Problem Sovling