N323 - Genomics - Ward

Family History Public Health Initiative:

-Promotes the use of a FHH to reduce chronic disease burden; supports integration of FHH into EMR.

How can we apply the central dogma in single gene disorders? What are the potential strategies?

-Reduce the amount of substrate (ex.: PKU-reducing intake of chemical) -Replacing the protein (ex.: ERT (Enzyme replacement therapy) -replacing the enzyme in PKU) -Fix/Destroy the mRNA -Chaperone Therapy - Ex: Say in a missense mutation-a drug that bridges errors in mRNA so that the protein is produced properly -miRNA or siRNA

What are some of the issues in genetic testing?

-Social Justice --Lower detection rates in minority groups, variability of access, availability of prenatal testing and pregnancy termination -Unintended consequences and incidental findings -23&Me - Established by Anne Wojcicki and Sergey Brin (cofounder of Google) - DTC genetic testing for $100 ---Service Provided - created profit - also created biobank ---Found over 200 health-related variations ---Nov. 2013: FDA shut it down b/c analytically and clinically it wasn't validated to have intended use

What are the possible targets of DNA testing?

-Specific mutation analysis (most economic)(ex.:BRCA185delAG) -Specific whole genome sequencing (broad) -Broad panel of tests (Ashkenazi panel, prostate cancer panel) -Whole Exome Sequencing: ---Has variable resolution-SNP's to haplotypes to full base-by-base sequencing ---Problem is, this all only tells you the target you're looking for, doesn't reveal anything else.

What is alternative splicing and how does it affect protein formation?

-Splicing the RNA to make multiple proteins -A single gene can produce multiple proteins

What is epigenetic research?

-Whole genome methylation studies and it's association w/ gene expression (not DNA sequence) -Promising for cancer, especially, because the idea of shutting down oncogenes in cancer -Epigenetics counters the belief of genetic determinism and we need to use that in practice

Explain why sex chromosomes aneuploidies are better tolerated than autosomal aneuploidies.

-X inactivation -Small # of genes on Y chromosome

Translation:

-mRNA interacts w/ ribosomes in cytoplasm -Ribosomes read the sequence of mRNA bases -Each sequence of 3 bases (codon) codes for an amino acid ---AA's are the building blocks of proteins -Transfer RNA (tRNA) assembles the protein until the ribosome hits the "stop" codon

When does transcription NOT lead to translation? (Aka doesn't follow central dogma?)

-microRNAs & siRNAs are small 21-22 nucleotide length RNA sequences that stop RNA from producing protein after transcription before it reaches translation. -Degrades mRNA or suppresses translation in the cytoplasm

Haploid

1 copy of every chromosome - sex cells are haploid

What are the #1 and #2 risk factors for developing breast cancer?

1. Being a Woman 2. Age-the older they are, the more at risk they are. (>50 risk high)

Diagnostic Testing (Genetic Counseling)

1. CVS (Chronic Villus Sampling) - Samples placental tissue -Transabdominal or transcervical 2. Amniocentesis - needle inserted into amniotic fluid

The Human Genome Project 1. "Who's Genome IS the human genome?" 2. "How different are we from each other?

1. Everyone's b/c we are 99% identical 2. At the genome level, we are 99% identical. We have <1% of variation in us d/t SNPs that accounts for how we are all different.

10 facts to remember about cancer genetics:

1. Mutations in genes lead to abnormal proteins that can't do their job of preventing or stopping cancer 2. These mutations may occur in proto-oncogenes or in tumor suppressor genes 3. Genetic mutations that cause cancer can be acquired, inherited, or both 4. It takes more than one mutation to cause cancer 5. Genetic mutations in the APC gene may cause over growth of polyps sometimes leading to colon cancer. 6. HNPCC (Lynch Syndrome) is an autosomal mutation in genes that repair DNA sequences causing an elevated risk of colon cancer and endometrial cancer. 7. BRCA 1 & 2 are tumor suppressor genes 8. Mutations in BRCA1&2 increase the risk of breast and ovarian cancer. 9. An individual may inherit mutations in BRCA1/BRCA2 from either one's mother or father. 10. One clue to a hereditary linked cancer is the earlier onset of cancer (< age 50)

What type of variations are present in chromosomes?

1. Number -Aneuploidies 2. Structure -Deletions, duplications, insertions, rearrangements

Genotype DOES NOT always predict Phenotype - Why?

1. Outcome of mutations can be influenced by random processes. 2. Genetic variation in one generation can influence phenotypic traits in the next generation. 3. The environment experienced by one generation can influence phenotypic variation in the next generation.

Biopsy Results for Mito - 3 Stages

1. Profileration of mito 2. Enlarged, ineffective mito 3. Cell/organ death - heart, muscles, brain cells, or any high energy cells.

Proto-oncogenes -> Oncogenes

1. Proto-oncogenes: The group of genes that cause normal cells to become cancerous when mutated; mutations that results in increased expression, activity, and cell-cycle machinery. 2. Oncogene: Mutated version of a proto-oncogene that 'turns on' cell-cycle machinery. -GF, GF receptors, intracellular signaling molecules, transcription factors -Major target of cancer medications.

What are the 3 categories of cancer?

1. Sporadic: 75% of all cancers, occur at the age of onset expected for that specific cancer, d/t non-hereditary factors altering the DNA structure in a specific area of the body. 2. Familial: 10-15% of all cancers, occurs at the expected age in more than 1 close relative on the same side of the family, a combination of environmental and genomic influences. -Ex: SNP's and genes with low to moderate penetrance 3. Hereditary: 5-10% of all cancers, earlier age at onset than normally expected for a particular cancer, single gene mutation in the germline that predisposes individuals to developing certain cancers.

Diploid

2 copies of every chromosome - each cell has 2 copies of every gene.

Codominant:

2 different versions (alleles) of a gene can be expressed, and each version makes a slightly different protein -Both alleles influence the genetic trait or determine the characteristics of the genetic condition

DNA contains _____ - ______ thousands of genes

20,000-25,000

Trinucleotide Repeat:

3-base pairs in a DNA sequences that are repeated a number of times in a row

Nucleotide

A Base, sugar, and a phosphate -Arranged in 2 long strands that form a spiral called a double helix

Genetic Testing:

A Medical test that identifies changes in chromosomes, genes, or proteins to find changes associated with inherited disorders Purposes: -Screening, diagnosis, risk assessment (risk alleles), informing treatment decisions, monitoring therapy -May be done multiple times, wheras genotyping may only be done ONCE.

Oncogene

A gene that directs uncontrolled cell growth of cancer. Alterations can be inherited or caused by an environmental exposure to carcinogens.

Proto-Oncogenes

A gene with the potential to change into an active oncogene

A poor metabolizer of any active drug may require:

A lower dose

Point Mutations

A mutation affecting only one or very few nucleotides in a gene sequence -If the lateration in gene structure impairs health, it's a point mutation -Includes insertions and deletions -Gene Dysfunction -> Gene structure (variation in DNA sequence)

Amplification

A selective increase in the number of copies of a gene coding for a specific protein without a proportional increase in other genes. -Ex: Cancer cells

Haplotype

A set of DNA variations (SNPs) that tend to be inherited together d/t close proximity on the same chromosome

Mis-Match Repair Genes

A. Encode protein products that recognize specific mismatched nucleotides in DNA B. MSI: Microsatellite Instability -Result of impaired MMR (mismatch repair); evidence that MMR's are not functioning correctly -Microsatellites - repeated seqences of DNA C. MMR Mutation: HNPCC (Hereditary Non-Polyposis Colorectal Cancer - Lynch Syndrome) -HNPCC - increases risk of second cancer; colorectal, endometrial, ovarian, and gastric cancers

CNV (Copy Number Variance)

Abnormal # of alleles/genes -Results from insertions, deletions, and duplications in large segments of DNA

Indications for Prenatal Genetic Counseling

Advanced maternal age (>35), abnormal screening, abnormal NIPT (noninvasive prenatal testing), abnormal genetic testing, abnormal US (ultrasound), FHH w/ birth defect requiring surgery, mental retardation, chromosomal/genetic disorder, maternal rx/drug exposure, maternal diabetes, hx of 3+ miscarriages, consanguinity, pt requests invasive testing instead of blood screening

Exons

All the pieces of an individuals DNA that provides instructions for making proteins -Makes up 1.5% of human genome

DNA Hybridization

Allows us to check for mutations using fluorescent tags Step 1: Heat to separate strands Step 2: Add identical DNA strands w/ attached probes Step 3: Cool to allow renaturation of double stranded DNA If the pts DNA contains fluorescent probes, then we can identify the mutation

Diagnostic:

An individual-based test -Goal -> to reveal a diagnosis

Chromosomes

Are made up of DNA

A person w/ extra copies (more than 2) of a gene encoding 2C19 is at risk for:

Benzo ineffectiveness

2C19 metabolizes benzos, a 2C19 poor metabolizer is at an increased risk for:

Benzo toxicity

Targeted Testing:

Can range from narow to broad, testing for specific mutations or presence of certain genes

Polyploidy

Cells containing more than 2 paired SETS of chromosomes

Triploid

Cells w/ 1 additional SET of chromosomes, 3 copies of every chromosome - total of 69

Tetraploid

Cells w/ 2 additional SETS of chromosomes, 3 copies of every chromosome - Total of 92

Nonsense Mutation:

Change in 1 DNA base pair -Altered DNA signals cells to STOP building a protein

Missense Mutation (Conservative):

Change in 1 DNA base pair resulting in the substitution of 1 AA(Amino Acid) for another protein

Silent Mutation:

Change in the DNA, not the protein (No affect on health)

Insertion:

Changes in the # of DNA bases in a gene by ADDING a piece of DNA

Mutation Panels

Check for specific mutations or 'hot spots', rare mutations will not be detected

A SNP in a CYD gene might affect the:

Circulating Drug level -SNP may cause CYP enzymes not to metabolize drugs

Cosanguinity:

Close relationship or connections; being from the same kinship as another person -Increased risk of AR disorders (marrying 2nd cousins)

RN Roles/Responsibilities r/t FHH:

Collecting, depicting and interpreting -Conduct a family hx that recognizes genetic risks to identify current and future health px's -Analyze ASSESSMENT FINDINGS for genetic and genomic influences and risk factors -Identify clients who may benefit from specific genetic and genomic information and/or services BASED ON ASSESSMENT DATA -Know HOW AND WHEN to make a referral to a genetics professional.

Warfarin

Commonly prescribed anticoagulant, INR to monitor (Norm is 1.0) -Individualization of warfarin dosing is Standard of Care -Pharmacokinetics-CYP2C9 - metabolizing enzyme for Warfarin! ---Everyone has 2 alleles of the CYP2C9 ---10% dose variation d/t CYP2C9 genotype -----1-Wild Type -----2-40% reduced warfarin metabolism -----3-90% reduced warfarin metabolism -----4-Clinical Significance - higher risk of bleeds, high INR

Loss of function:

Complete loss of the protein

Epigenome:

Comprises all of the chemical compounds that have been added to the entirety of one's DNA (genome) as a way to regulate the activity (expression) of all the genes w/in the genome -Tightly wraps inactive genes, making them unreadable -Relaxes active genes, making them easily accessible -DOES NOT involve changes in DNA sequence -DOES affect gene expression -ARE affected by environmental factors (ex: diet, toxins, physical activity, stress) -CAN BE passed to new generations

Genetic Exceptionalism (ELSI):

Concept that genetic information is inherently unique and should be treated differently in law than other forms of personal or medical information.

Congenital vs. Hereditary

Congential: Not usually inherited, but born w/ it -Ex: FAS Hereditary: In your genes, inherited from parents

Centromere:

Constriction point on a chromosome that divides it into the short arm (p arm) and the long arm (q arm) -Helps describe the location of specific genes

Duty to Warn (ELSI):

Currently - recommended strategy is to educate/advise patients about the need to warn family members and document.

DNA Replication vs. Central Dogma

DNA REPLICATION is how genetic info is passed from one cell to another -Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases ---This is critical when cells divide b/c each new cell needs to have an exact copy of the DNA present in the old cell Central Dogma: DNA ->RNA ->Proteins DNA: DNA->DNA Polymerase->New DNA + Old DNA

Proteins Role in Pharmacogenomics:

DNA-RNA-Protein -The sequence of AA in a protein is determined by the transcription of DNA to RNA and the translation of RNA to proteins. -Variation in gene structure, gene expression, or gene doses can lead to alterations in health by affecting the structure, shape, function, or amount of protein

How does SCD differ from TS via testing and morbidity/mortality?

Differ according to WHO Criteria: -Substantial prevalence/mortality -Natural history well characterized -Effective + Available treatment -Testing acceptable to population -Consensus on clinical guidelines -Screening = cost effective -High PPD, NPD, sensitivity, specificity.

Genetic Discrimination (ELSI):

Discrimination faced by an asymptomatic individual who has a genetic mutation. GINA -Protects against discrimination based on genetic info, in terms of health insurance and emploment, including: FHH, carrier testing, prenatal genetic testing, susceptibility/predictive testing, tumor analysis, other gene/mutation/chromosomal tests -GINA PROTECTIONS DO NOT APPLY IF A PATIENT ALREADY HAS A MANIFEST DISEASE. -Health insurers and employers cannot require/request genetic testing or use genetic info to make eligibility or premiums/employment-based decisions.

Biochemical Genetic Tests

Do not directly evaluate DNA but measure gene products - Enzymes, metabolites, hormones; Ex: Newborn Screening

Trisomy 21

Down's Syndrome

Trisomy 18

Edward's Syndrome - MODS (Multiple Organ Dysfunction Syndrome -Usually die w/in 6 days -SUPER TINY babies -These chromosomes have small # of genes so that extras are tolerated.

The gene VCORO1 affects warfarin:

Effectiveness

Tumor Suppressor Genes:

Encode proteins that inhibit cell proliferation -Repression of cell cycle -Initiation of apoptosis -Inhibition of metastasis -DNA repair

Genomic Imprinting:

Epigenetic 'marking' (methylation) and inactivation of a gene, w/ VARIATION IN PHENOTYPE according to parent of origin -Some traits are expressed when inherited only from father, and some only from mother -Factor that influences how some genetic conditions are inherited

Nondisjunction

Error in cell division results in reproductive cells (eggs and sperm) w/ an abnormal # of chromosomes

Trisomy 13

Extra Digits (Patau Syndrome)

Genetic "Red Flags"

F - Family hx positive G - Groups of congenital abnormalities E - Extreme presentation of common conditions N - Neurodevelopmental delay E - Extreme pathology (rare tumors, multiple cancers) S - Surprising lab balues

Explain the genomic instability associated w/ Fragile X Syndrome (Trinucleotide repeats, expansion, anticipation)

Fragile X Syndrome: Trinucleotide repeat (gene structure) in the FMR-1 gene on the X chromosome -Portion of chormosome X is dangling by a thread -Most common cause of learning disabilities in men b/c men don't shut off X ---Males usually more affected than females -More than 200 CGG repeats

Explain why some autosomal aneuploidies are less severe than others (concept of mosaicism):

Full Trisomy vs. partial trisomy (mosaic) -Full: Every cell has trisomy b/c it's present in every cell of embryo -Partial (mosaic): Not every cell in child has a trisomy - some have 3 chromosomes and some have normal amount

Genomics

GENOME: An organisms complete set of DNA including all of it's genes GENOMICS: The branch of molecular bio concerned w/ the structure, fxn, evolution, and mapping of genomes -All our DNA that is hardwired into our genomes yet influenced by environmental factors -Genome->Chromosome->Gene->DNA->RNA->Proteins

Aneuploidy

Gain or loss of chromosomes from the normal 46 -Occur d/t nondisjunction or translocation

Tumor Profiling

Gene expression profiles are used to see if chemotherapy would be beneficial; actual tissue is needed

What should our concerns be with gene replacement therapy?

Gene therapy in US brought to halt: -Bubble Boy - died at 12 y/o after receiving adenovirus from bone marrow transplant. -Guy w/ x-linked mosaic disorder - died few days after clinical trial of gene vector therapy -We need to look for best possible studies: Double Blind Randomized Clinical Controlled Trials (Double Blind RCC Trial's) - not commonly found.

GINA

Genetic Nondiscrimination Act -States that genetic testing is different than non-genetic testing; federal law that trumps all state laws.

Newborn Screening

Genetic Test - gene mutation w/ high penetrance (genotype predicts phenotype) -A positive screen needs to be confirmed with a diagnostic test -Rare, serious disorders w/ effective treatment that require immediate treatment; 21-50 recommended conditions; Ex's: Hearing, critical congenital heart disease -ELSI issues: mandated in all states but parents can opt out; false positives - as more tests are added to the newborn screening panel the rate of false positive increase; over diagnosis; what happens to the heel sticks afterwards?

Genetic Exceptionalism:

Genetic info is inherently different and should be treated differently than other forms of personal or medical information

Genotype:

Genetic make up of a person (lab tests look at genotype)

Family Health History (FHH):

Genetic test done to predict individuals risk for common complex disease.

Psuedogenes:

Genetically similar to fxn gene but doesn't express proteins and are often containing numerous mutations

GWAS Studies

Genome-wide association studies Process: -1000+ ppl w/ a particular disorder -1000) ppl known NOT to have the disorder -Compared differences (usually SNPs) Limitations: -Association studies (not causation) --Disease markers -Common variants (will miss rare mutations) Purpose: Looking at differences between genes

Explain genomic imprinting and how that concept related to Prader Willi & Angleman syndromes

Genomic Imprinting: Epigenetic 'marking' (methylation) and inactivation of a gene, w/ VARIATION IN PHENOTYPE according to parent of origin -Some traits are expressed when inherited only from father, and some only from mother -Factor that influences how some genetic conditions are inherited Prader Willi Anglman Syndromes: -Deletion OR inactivation of genes on 15p (loss of fxn) -If maternal gene is deleted/silenced = Angleman's Syndrome -If paternal gene is deleted/silenced = Prader Willi's Syndrome

Introns

Get spliced out

HapMap Project

Goal was to define patterns across human genome and to provide a resource to identify gene variations involved in disease. -OUTCOME: - Frequency of haplotypes varied according to georgraphical ancestry ---More variation occurs w/in groups than b/w groups! ---90% variat. is found w/in groups, 10% variation found b/w groups

Autosomal Dominant Mutations Linked to Cancer

HNPCC (Lynch Syndrome) FAP (Polyps) BRCA 1 &2 (Breast/Ovarian) P53 familial mutations (tumor suppressor gene) Rb familial mutations (tumor suppressor gene)

Heterozygous

Having 2 different alleles for a single trait

Heterozygous:

Having 2 different alleles for a single trait

Euploid

Having an exact multiple of the haploid # of chromosomes (This is normal)

Homozygous

Having identical alleles for a single trait

Homozygous:

Having identical alleles for a single trait

Lynch Syndrome

Hereditary Nonpolyposis Colorectal Cancer ARF multiple cancers inlcuding: -COLORECTAL cancer, stomach cancer, small intestine, liver, gall bladder ducts, upper urinary tract, brain, skin, OVARIES, lining of uterus (ENDOMETRIUM), benign colyn polyps

Explain the genomic instability associated w/ Huntington's Disease (HTT) (Trinucleotide repeats, expansion, anticipation)

Huntington's Disease: Trinucleotide repeat (gene structure) -HTT gene on Chromosome 4p(short arm) -10-35 CAG repeats: normal genotype ---With expanded CAG segment, extra glutamines (G) may disable the huntintin protein causing neurogenerative disease -36-40 CAG repeats: May/may not develop HD ---100% penetrance ->40 Cag repeats: WILL develop HD ---100% penetrance -Autosomal dominant inheritance

Gain of function

Increase in protein's function

Pharmacogenomic Testing

Individual and population based to identify individual likely to have an increased/reduced response to particular drugs or increased/decreased risk of Adverse Drug Reaction; Ex: Warfarin, SSRI's

Prognostic Testing

Individual based to assess the likely outcome/course of a disease or to monitor therapy; ex: HER-2, tumor profiling

Presymptomatic Testing

Individual based to identify a genetic condition w/ high penetrance that will occur later in life, Ex: Huntington's, FAP

Carrier

Individual that carries a disorder but doesn't express it

Carcinogenesis (Week 16):

Initiation of Cancer formation - a multistep process -DRIVER mutation - Promotes Development of cancer -PASSIVE mutation - mutated by accident, "along for the ride"

1000 Genomes Project

International collaboration to: -Sequence DNA from 2500 ppl from 50 populations to look at SNP's, insertions, deletions, and duplications

HapMap

International scientific effort to identify/map/compare the genetic sequences of individuals to identify where SNP's COMMONLY occur -Purpose: Describe common patterns of human genetic variation (SNPs) that are involved in human health and disease

Autosomal:

Involves chromosomes 1-22 Dominant: -1 alternate copy to be expressed -Individuals w/ AD DISORDERS are usually heterozygous -Individuals w/ AD TRAITS can be homo- or heterozygous -Affected homozygous individual w/ AD inheritance = lethal -Ex: Huntington's disease Recessive: -2 copies to be expressed -Carriers = heterozygous; affected individual = homozygous -Ex: CF, sickle cell anemia

Null allele does what?

It does not make proteins.

What is recombinant DNA and what can we use it for?

It is 2 diff. organism's DNA that is hooked together (humans) to make DNA that can produce proteins that the target organism needs. Can make: -Insulin -HGH -Factor VIII -Epogen -TPA -FSH -HPV Vaccine Proteins

What is CYP2D6?

It is an ENZYME (which is a protein), a gene, a protein, and a mutation

Why is it important to let parents know if mutations are de novo or not? ex: The Kabuki Syndrome patients

It tells them there's nothing they could have done and it doesn't pose a risk for their future children.

CYP enzymes are responsible for drug metabolism and are built in the:

Liver

Monosomy

Loss of a Chromosome - always lethal --Exception: Turner's Syndrome (45,X) ----(Gonadal Dysfxn:short stature, swelling, broad chest, low hairline, low-set ears, and webbed necks)

p53 Tumor Suppressor Gene:

Makes tumor protein p53 that keeps cell division in control via growth, division and apoptosis, and prevents tumor formation. -Li-Fraumeni - mutations in p53 -Germline or acquired mutations

Mitochondrial Disease:

Maternal inheritance -mtDNA - mito itself is damaged (maternal inheritance) -nDNA - nucleus of the cell isn't working properly and communicating to the mitochondria (gues speaker's daughter's case)

Mitochondrial:

Maternal inheritance; fathers don't pass the disorder on -Males and females equally affected -mtDNA mutations effect neurons, brain, and skeletal/cardiac muscles

Prevalence:

Measurement of the % of people in a population who HAVE A CONDITION -How many people in the population AT THAT TIME, have the disease -Ex: What % of people have COPD?

Incidence:

Measurement of the % of people in a population who acquire a CONDITION. -How often something OCCURS Ex: What % of babies in the US are born w/ PKU? What % of ppl suffer from MI?

The gene CYPC29 affects warfarin:

Metabolism

Kinds of Mutations:

Missense mutations Nonsense mutations Frameshift mutations Point mutations CNV's Deletions Insertions Silent mutations Prepature stop codons Loss of Fxn Null Mutation Gain of Fxn

Treatment for Mito

Mito Vitamin Cocktail: Vitamin C and E - oxidation, B12, coQ10 - ubiquitol, creatinine

Protein

Molecules made up of AA's required for the structure, function, and regulation of the body's tissues and organs -Function: Antibody, enzyme, messenger, structural component, transport/storage

Issues w/ monogenic inheritance vs. multifacrotial (complex) inheritance.

Monogenic inheritance: Disorders of a single gene -Sometimes genotype doesn't predict phenotype d/t: --Penetrance --Variable expressibity -Often, single gene mutations aren't inherited -> denova mutations Multifactorial (complex) inheritance: Traits expressed only when a combo of genes AND certain environmental factors are present -Polygenic (multiple gene mutations) + environmental contribution -Common -Not dominant/recessive, but QUANTITATIVE ---Risk alleles, environmental modifiers, and thresholds ---Relative risk (RR) or odds ratio (OR) -Gene variants increase/decrease RISK for disease

Gene Patents:

More than 4,000 gene patents have been issued. -Exclusive rights to mutation analysis ---Limits research and competition Brings up the issue of "are any types of DNA patent-eligible?" Supreme court ruled on validity of Gene Patents: June 13, 2013.

Mosaicism:

Mutation in a single cell w/in an early embryo -Some cells w/ mutation and some cells w/out genetic change

Denova (new) mutations:

Mutation that occurs after fertilization -Affected child has mutation in every cell w/ no family hx of disorder -Ex: Achondroplasia

X-linked disorders:

Mutations in genes on the X-chromosome; fathers can't pass to sons (b/c they get their X chromosome from their mother) -No male carriers -Sex-linked - gender DOES make a difference w/ recessive -Transmission in a family may cease if the affected father has no daughters -Most X-linked disorders are recessive -Daughters of affected fathers = obligate carriers Dominant: Females more frequently affected -Families w/ an X-linked dominant disorder usually have affected males and females in each generation -Ex: Fragile X Syndrome Recessive: Males more frequently affected -Families w/ x-linked recessive disorder often have affected males and females in each generation -Ex: Hemophilia

Hereditary/Germline mutations

Mutations passed from parent to child (mutation in every cell) -Ex: CF

Null Mutation

No functional protein is made at all

Wild type

Normal

Polymorphism

Normal variation in DNA -Happens in >1% of population -Responsible for many normal differences b/w people (Ex: Hair/eye color, blood type)

Acquired (somatic) mutations:

Occur in DNA of individual at some point during their life -Can be c/b environmental factors or if a mistake was made as DNA copies itself during cell division -CANNOT be passed from generation to generation -Ex: -Cancer

Uniparental Disomy:

Occurs when a person receives 2 copies of a chromosome, or part of a chromosome from ONE parent and NO copies from the other parent. -No effect on health or development -Factor that influences how some genetic conditions are inherited

Frameshift Mutation:

Occurs when the addition or loss of DNA bases changes the genes' reading frame -This changes the code for AA's resulting in a protein that's usually nonfunctional -Insertions, deletions, and duplications can be FSMs (Frameshift Mutations)

HER-2 Gene:

Oncogene of Breast Cancer - highly targeted by therapy (Herceptin)

The Architects of Cancer

Oncogenes Tumor Suppressor Genes

Tumor Suppressor Genes

P53 Rb APC MYH MMR Oncogenes: HER-2

How will the study of genomics help individualize health care?

PREDICT risk of complex disease STRATIFY risk (high, mod., high, low/population) INDIVIDUALIZE risk reduction (decrease modifiable risk factors) PERSONALIZE screening (early dx) Tailor INTERVENTIONS (to maximize outcomes) MONITOR outcomes

Mutations

Permanent change in the DNA sequence that makes up a gene

Translocation

Piece of 1 chromosome breaks off and attached to another -Balanced: -Only if there is no gain or loss of genetic material in a cell

Duplication

Piece of DNA abnormally copied 1 or more times

Screening:

Population-based to identify RISK -Must be followed by a diagnostic test -Ex.: TB, mammogram, pap-smear

Risk Factors for Breast Cancer

Primary: - Female gender - >50y/o - Prior Breast Cancer, atypical hyperplasia, carcinoma in situ -1st degree relative(s) w/ BC -BRCA1 or BRCA2 mutation Secondary: - Postmenopausal obesity - Early menarche, late menopause - 1st full term pregnancy >30 y/p - Chest radiation <35 y/o - Benign breast disease (w/ associated biopsies) Other: - Hormone replacement Therapy - Alcohol intake (>2 drinks/day)

Anticipatory Guidance (ELSI):

Proactive, developmentally-based counseling technique that focuses on the needs of the individual

Insulin is a:

Protein!

Histones:

Proteins that are tightly coiled by DNA -Important for DNA packaging and regulating gene expression

Public Health Philosophy vs. Genetics Philosophy - Everyone vs. Self:

Public Health Philosophy: -Based on Utilitarianism and Paternalism --Utilitarianism: The belief that a morally good action is one that helps the greatest number of people --Paternalism: The attitude or actions of a person, organization, etc., that protects people and gives them what they need but does not give them any responsibility or freedom of choice -Benefits to society outweigh individual rights (immunization, isolation) Genetics: -Based on self determinism and social justice (non-directive counseling, autonomous decision-making, individual rights)

DNA Methylation

Putting methyl groups on a promoter turn it off - so it can't make ore proteins -No methyls on promoter = gene is expressed -Reversible -Methylation patterns CAN BE COPIED WHEN DNA IS REPLICATED (so generation to generation)

RNA Testing

RNA is only present when genes are expressed - therefore can see if genes are turned on or off in specific tissues via an expressional profile; ex: Cancers

DNA Sequencing

Reads every base of the gene, does not pick up deletions or duplications

Penetrance:

Refers to the proportion of people w/ a particular genetic change (such as a mutation in a specific gene) who exhibits s/s of a genetic disorder -C/b combo of genetic, environmental, and lifestyle factors

Variable Expressivity:

Refers to the range of s/s that can occur in different people w/ the same genetic condition -c/b a combo of genetic, environmental, and lifestyle factors

Variants

Results from insertions, deletions, and duplications in large segments of DNA

Mercaptopurine

Rx used to treat ALL (Acute Lymphocytic Leukemia), IBS (Irritable Bowel Syndrome) -Toxic levels - bone marrow suppression, aplastic anemia -TPMT = metabolizing enzyme for Mercaptopurine Several SNPs associated w/ low TPMT activity resulting in high levels of Mercaptopurine -Heterozygous - WT/P - Metabolizes slowly -Homozygous - P/P - small or no clearance of drug -TPMT genotyping is now a standard of care

Anticipation:

S/S of some genetic conditions tend to become more severe and appear at an earlier age as the disorder is passed from one generation to the next

What are SNP's and how do they affect health and disease?

SNP's are single nucleotide polymorphisms -Most common type of genetic variation -Each SNP represents a difference in a nucleotide ----Ex: SNP may replace the nucleotide cytosine (C) w/ Thymine (T) -Can be used to track the inheritance of disease genes w/in families -May help predict individuals response to certain drugs, susceptibility to environmental factors (toxins), and risk of developing a particular disease. -These variations are found in the DNA b/w genes that are associated w/ disease -Most SNP's have no effect on health or development ---BUT, they may play direct role in disease by affecting the gene's fxn.

What kind of genetic test is a Family Health History? (Screening vs. Diagnostic)

Screening - applied to populations to identify people at risk for health alterations -It is a genetic test as well

Promoter:

Section of DNA located apart from the gene that turns it on/off (expression)

Whole Exome Sequencing:

Sequences ~1.5% of DNA (exons) -Much less financially than whole genome sequencing ($1000 or more)

Next Generation Sequencing

Sequencing many genes simultaneously for mutations

Epigenetic Research:

Study of the whole genome and methylation and expression. Promising for cancer research.

Transitional Research:

Takes an average of 17 years for only 14% of new scientific discoveries to enter every day clinical practice - 'from bench to bedside' -T0 - Basic and animal research -T1 - Discovery of potential health application ---Most $$$ goes to T0 and T1 -T2 - From health application to practice guidelines -T3 - From practice guidelines to clinical practice -T4 - Health practice to population health impact

Protein Testing

Tests gene products; ex: Protein microarrays, Western blots

Sensitivity:

The ability of a test to detect a POSITIVE result -100% means no false negatives -Want to avoid false positives -Important for screening tests

Specificity:

The ability to detect NEGATIVE results -100% is no false positives -Important for diagnostic testing

Specificity:

The ability to exclude the condition; how often the test is negative when the mutation is not present; most important for diagnostic testing

Sensitivity:

The ability to identify the condition; how often the test it positive when the mutation is present; most important for screening tests

Central Dogma

The flow of information from: DNA->RNA->Proteins -2 Major steps: Transcription and translation = gene expression

Genetic Determinism

The idea (usually misconceived) that "DNA is destiny" and that it overlooks the environmental contribution to disease.

Base Pair:

The info in DNA is stored as a code made up of 4 chemical bases: Adenine (A), Guanine (G), Cytosine(C), and Thymine(T): A-T, C-G

Carcinogenesis:

The mutation of the genetic material of normal cells, which upsets the normal balance between proliferation and cell death; the initiation of cancer formation -Acquired, inherited, or both -Theory of Carcinogenesis: Initiation, promotion, progression -Chemical: Direct acting vs. indirect-acting (must be metabolized to activated metabolic form) -Physical: UV light, asbestos -Viral: DNA & RNA; viruses house mutated genes (viral oncogenes - potential to cause cancer) -Bacterial: H. Pylori

Phenotype:

The physical manifestation of an inherited trait or disease (what you see)

Karyotype:

The picture of the human chromosome lined up in pairs

Trisomy

The presence of an extra chromosome (3) -Exceptions: Chromosomes 21, 18, 13 b/c they are compatible with Y. --X Chromosome is shut off (extra) --Y Chromosome is small so it's tolerable

Genetic Counseling:

The process of helping ppl understand/adapt to implications of the diseasel interpretation of family and medical histories to assess chance of disease occurence or recurrence, education about inheritance, testing, management, prevention, resources and research, and couseling to promote informed choice and adaptation to risk or condition.

Public Health Genomics:

The responsible and effective translation of genome-based knowledge for the benefit of population health. -Monitor health, diagnose health problems, inform people, mobilize community partnerships, develop policies and plans, enforce regulations, link people to services, assure a competent Public Health workforce, evaluate services, research to solve health px's.

Population Risk:

The risk of an individual given their family history or other circumstances, as compared to that of the affected population.

Genetics

The study of heredity and the variation of inherited characteristics -Has a narrow focus on single gene disorders

What is comparative genomics?

The study of how humans are related to other species, i.e. mice/rats, snakes, fish, dogs -Observe differences/similarities in how genes are expressed. -Observe differences/similarities in phenotype AND genotype.

Pharmacogenomics

The study of the genetic determinism to human variation in response to pharmaceuticals, both in terms of drug efficacy (therapeutic effects) and adverse drug effects -Pharmacokinetics - metabolism, absorption, excretion, transport systems! -Pharmacodynamics - Drug transporters, receptors, and when the drug binds to the receptor -Proteins are responsible for cellular activities in pharmacodynamics and kinetics! -Pharmacogenetics - based on observations

B2 receptor:

There are 2 common variants (SNPs) - one having a positive response to B2 agonists and one having a poor response - one individual has 2 copies (alleles) of each

Carrier Testing (Genetic Counseling)

To determine if the pt/partner is a carrier of a genetic disease -Recessive conditions only -Negative testing concludes that their chance is reduced not eliminated -Ex: Single gene panels - one gene, many mutations, sequencing, Next Generation Sequencing

TCGA - The Cancer Genome Atlas

Tumor profiling across carcinogenesis -They look at all the diff. types of tumor cells and track genomic instability.

APC (Adenomatous Polyposis Coli) gene:

Tumor suppressor gene -Makes APC protein that prevents uncontrolled growth of cells, controls division, how often a cell divides, how it attaches to other cells in a tissue, and whether a cell moves w/in or away from a tissue -Acquired or inherited mutations -FAP (Familial Adenomatous Polyposis) - More severe polyposis -AFAP (Attenuated Familial Adenomatous Polyposis) - Less severe polyposis

BRCA1 & 2

Tumor suppressor genes -Produce proteins used to repair DNA w/ double-stranded breaks present. -Mutations can be inherited from mother or father ---Increases Breast Cancer risk, early onset, AD -Autosomal Dominant mutations-each child has 50/50 chance-if a man in the family has breast cancer we WILL test for this mutation.

ACCE Evaluation Model:

Used to evaluate data on genetic tests; considers the 4 characteristics: A. Analytic Validity: Ability to accurately and reliably measure the genotype of interest; population dependent - lab focused -Does the test identify the genotype? C. Clinical Validity: Ability to detect or predict the associated phenotype (disorder) - what the lab is telling you about the patient -Analytic validity, clinical sensitivity and specificity, penetrance -Does the test predict the phenotype? C. Clinical Utility: Clinical usefulness; does it make a difference in health outcomes? -Analytic/clinical validity and real-world usefulness -Ex: Does BRCA testing reduce morbidity and mortality for women? -Does testing improve health outcomes? E. ELSI (Ethical Legal and Social Implications) -Confidentiality, privacy, discrimination, stigmatization, consent, ownership of samples, patenting, reporting requirements, etc.

Punnett Squares:

Used to predict recurrence risk in monogenic inheritance

Carrier Testing

Usually individual-based but may target populations to establish carrier status for autosomal or X-linked recessive conditions in asymptomatic individuals. -Commonly used in reproductive decision making; ex: Tay Sachs, CF

Whole Genome Sequencing:

Variable Resolution!!! - Can range from SNPs to haplotypes to full base-by-base DNA sequencing. -Utlized in rare diseases (GWAS targets common variants) -Charcot-Marie-Tooth - discovered variations in candidate genes of certain diseases by doing this.

Pharmacodynamics - VKORC1

Warfarin Drug Target (binds) -20-25% dose variation d/t VKORC1 genotype Common variants that affect warfarin response: ---G-Wild Type ---A-Variant 'warfarin sensitive' ---Genotype frequency varies according to ancestry -Other variations in warfarin response: Age, sex, weight, unknown factors

Message of Race Lecture:

We are all 99.6% identical at the DNA level.

Deletion:

When a chromosome breaks and genetic material is lost - Throws off reading frame

Chromosomal mosaicism

When an individual has 2 or more CELL POPULATIONS w/ a different chromosomal makeup

Premature Stop Codon:

When read, signals the ribosomes that translation is to stop and ends protein formation

Gene Expression

Whether/to what degree gene is "turned on" -When a gene is expressed, it is transcribed -Largely determined by -epigenetic effects-

Histone Modification:

Wrapping the gene too tightly to be exposed and transcribed -Can alter availability of genes for trascription

Single Gene Disorders

"Mendelian"(Monogenic) disoders -When a mutated single gene is known to cause a disease; predictable Ex's: SCA(Sickle Cell Anemia), SCD(Sickle Cell Disease), CF(Cystic Fibrosis), Fragile X Syndrome, MD(Muscular Dystrophy), HTT (Huntington's Disease)

What should be the 7th Medication right?

"The right drug for the right genome"

Based on the karyotype, what are some of the expected features of individuals with TURNER SYNDROME:

(45,X)(Single Dose) -Short stature, lack of ovarian development/early ovarian failure, webbed beck, low posterior hairline, elbow changes, normal intelligence, no secondary sexual development (no puberty)

Based on the karyotype, what are some of the expected features of individuals with KLINEFELTER SYNDROME:

(47,XXY) (Gene Dose) -Tall, feminized body shape, small testes, gynecomastia (breast development), low sperm count, lack of secondary sexual characteristics, sometimes learning disabilities

Based on the karyotype, what are some of the expected features of individuals with POLYSOMY Y:

(47,XXY)(Gene Dose) -Male, tall, bad acne, increased testosterone, prone to violence

Multifactorial Disorder

(Complex)(Genomic) -Traits expressed only when a combo of genes AND certain environmental factors are present -Gene Variants increase/decrease RISK of disease Ex's: Heart disease, diabetes, obesity

Gene Structure

(Variation in DNA Sequence) -Alteration in gene function occurs b/c of an alteration in gene structure -Point mutations, indels (insertions, deletions), repeats -SNP's and CNV's most common -Ex's: Fragile X Syndrome, HTT(Huntington's Disease)

Gene Number

(Variation in Dose) -Alteration in gene dosage, c/b the loss of a functional allele -CNV**(Insertions, deletions, duplications) -Ex's: Trisomy 13,18,21; monosomy, cancers

Gene Function

(Variation in Expression) -Alteration b/c of a gene mutation that affects gene function -Epigenetic Effects -Ex: Diabetes

It's possible it's mito if:

---Increased lactic acid ---Increased ammonia ---3 or more organs affected.

Facts about Mito:

-1:200 prevalence in population but only 1;10,000 dx -Under-diagnosed -Multiple-organ failure -No biological markers (blood draws) - only symptoms are used to diagnose

Review the common myths of dominance in terms of alleles:

-A dominant CONDITION is one in which the phenotype is expressed w/ only one altered allele. -A dominant ALLELE is one that causes a particular phenotype regardless of it's homolog.

What are the benefits of a FHH?

-Accessible -Noninvasive (no needles, gloves, etc) -Reliable (demonstrated sensitivity/specificity) -Inexpensive -Efficacious (30-40% of population has significant FHH) -Produces quantifiable risk (OR, RR) -Informs individualized interventions to mitigate risk ---PRIMARY PROMOTION -> Preventative ---SECONDARY PROMOTION -> Early screening ---TERTIARY PROMOTION -> Treatment

How do SNP's differ from mutations?

-Alteration in gene structure = alteration in gene sequence -Single letter (base) variations: ---If they're NOT associated w/ health alterations, they're called SNP's ---If they ARE associated w/ health (impairs health) they're called point mutations

How do various diseases differ in genetic/environmental components?

-Anything other than genes affecting a disease is environmental -9/10 leading causes of mortality have genetic + environmental components

Why is an individual w/ an AD condition presumed to be heterozygous for the disorder?

-B/c w/ AD conditions, you only need 1 copy of the mutated gene for the disorder to be expressed (the other copy can be normal)

What do genes encode?

-Before we learned that 1 gene can encode multiple proteins -Sometimes genes don't do a thing, these are called pseudogenes -Sometime's it's not protein produced, it's RNA (miRNAs, siRNAs, and regulatory RNAs)

How do mutations affect health?

-By changing the order of AA's and therefore the shape and therefore the fxn of the protein.

How does an error in DNA/Mutations ultimately affect health?

-Changes that affect the structure of chromosomes can cause px's w/ growth, development, and function of the body's systems. -When a mutation alters a protein, it can disrupt the normal development or cause a medical condition.

Transcription:

-DNA->mRNA->Cytoplasm -mRNA carries info from DNA into the cytoplasm

Public Health Genomics Initiative - EGAAP (Evaluation of Genomic Applications in Practice and Prevention):

-Develop a systematic process for assessing evidence regarding validity and utility of rapidly emerging genetic tests for clinical practice -> evaluating genetic tests for clinical practice -Uses the ACCE model - Analytic Validity, clinical validity, clinical utility, ELSI -PICO - Population, intervention, comparison intervention, outcome

MYH Gene

-Encodes a base excision repair protein that functions to repair oxidative DNA damage -Ex: CG -> oxidative stress -> OC -> repair replaces O w/ G -> GC -It's AR ---MAP (MUTYH-Associated Polyposis)

Molecular Genetic Tests

-Examines DNA or RNA or proteins - Central Dogma -Qualitative (structure) or Quantitative (amount) -Can examine whole genome, whole exome, specific genes, specific mutations -Can detect SNPs, mutations, nucleotide sequence, gene expression (active, not active), epigenetic patterns (which promoters are methylated, which histones are tightly wrapped)

Cytogenic Tests

-Examines number or structure of chromosomes -Karyotypes - only find large problems, FISH - using fluorescent probes

Biobehavioral Research - Multiplex Study:

-Explored whether knowledge about risk factors affects motivation to improve health behaviors.

Alleles

-Forms of the same gene w/ small differences in their sequence of DNA bases -These small differences contribute to each person's unique physical features

What are the 3 reasons for Gene Dysfunction?

-Gene Structure (Sequence) -Gene Function (Expression) -Gene Number (Dose)

ELSI Issues (Review):

-Genetic Exceptionalism -Privacy/Indentifiability of genetic information -Informed consent -Preventing genetic discrimination -Role of race and mistrust in genomic research and Health Care -Avoiding disparity in genomic Health Care -Risks/Benefits of genetic testing, therapies, research ---Incidental findings, effects on families, social justice -Genomic education of HCPs and the public -Genomic repositories (biobanks) -Gene patents -Policy development and implementation of genomic Health Care

Management of Mito:

-Goal - to maintain health and reduce symptoms/keep them from getting worse -Give mito pts D5W - Glucose for mitochondria - NOT LACTATED RINGERS! -Anticonvulsants, antiviotics - treats infection, immunizations

Predictive (Susceptibility Testing)

-Individual based to identify mutations that increase a person's risk of developing disorders with a genetic basis; usually mutlifactorial conditions, risk prediction, ex: Alzheimer's, BRCA, Lynch -DTC (Direct-to-Consumer)

Prenatal Testing

-Individual or population based in order to identify fetus w/ genetic disease. -Screening or diagnostic; may be standard of care d/t family history or mother --i. Ex: Screening - Triple or quad testing --ii. Ex: Diagnostic - amniocentesis

Diagnostic Testing

-Individual-based to establish genetic diagnoses in a patient with clinical indications/signs and symptoms -We do if: Positive screening test, positive family history

What do nurses need to be competent in genetics/genomics?

-Knowledge -Attitude -Skills

Cytochrome P450 Enzyme System

-Metabolized 60% of Rx drugs (substrate) and excretes it -Made in the liver -Possible genetic variation - change in the protein - change in the enzyme function - more or less available drug in circulation Drug Metabolizer Categories - CYPD26 Mutations: -Poor -Intermediate -Extensive (wild type/normal) -Ultrarapid -Varies according to ancestry but is not derived through ancestry -Keep in mind prodrug and active drug effects

Sickle Cell Disease:

-Missense mutation (single nucleotide change resulting in a codon that codes for a different AA), AR!, Most common inherited blood disorder in the US. -Mutations cause anbnormal Hb - Sickled RBCs die prematurely and get stuck in small blood vessels. ---Homozygous - Sickle Cell Disease ---Heterozygous - Sickle Cell Trait

Colorectal Cancer Red Flags

-Multiple colorectal adenoma -Colorectal Cancer < 50 y/o -Endometrial cancer < 50 y/o -Two or more HNPCC-related cancers in an individual or family

Race: The Power of an Illusion

-No genetic markers are present that define race -Genes for complex traits (like athletic performance) are not present -Sickle cell - not a racial trait, d/t having ancestors that lived in areas of malaria -85% of human variation is present between any 2 individuals w/in a population

Screening Testing (Genetic Counseling)

-Not Invasive -Blood Draw or US -Voluntary -Designed to determine risk -False + and - -Information only, not for cure or therapy -Weighs maternal age heavily into the calculation, results can be skewed if the pt is very young/old.

Inherited Diseases

-Passed from parent to child -Some disorders that affect multiple family members are caused by gene mutations, which are inherited.

Sources of Human Genetic Variation:

-Polymorphisms - SNPs or mutations (variations in DNA seq) -Copy Number Variants - variants in gene dose, < or > 2 alleles of a particular gene -Variation in gene expression - degree to which a gene is making protein

NHANES (National Health and Nutrition Examination Survey) Collaborative Genomics Project:

-Population-based survey assessing the health and nutritional status -Viewed SNPs and connecting them to genetics and disease today

What are the neurobehavioral phenotypes?

-Prader-Willi (Deletion) --Insatiety, temper, obsessiveness, difficulty relating w/ peers. -Williams (Deletion) ---Hypersocial - loquacity, unusual friendliness, lack of social inhibitions, prolonged gaze, musicality -Angleman (deletion) ---Early and persistant smiling, parozysmal/contagious laughter, hyperactivity, restlessness, enjoy slapstick humor -FMR1 Mutations (Fragile X - Expanded TNR) ---Hyperactivity, anxiety, phobias, social withdrawal, autistic features

Identify proband and who in a pedigree is a first, second, and third degree relative.

-Proband: First affected individual in a family who brings a genetic disorder to the attention of the medical community -1st degree relative = parents, children, brothers, sisters -2nd degree relative = grandparents, aunts/uncles, nieces/nephews, grandchildren -3rd degree relative = first cousins

Codeine -> Morphine

-Prodrug administered in an inactive form, must be metabolized in order to be utilized -CYPD26 degrades codeine and turns it into it's active form of Morphine ---Ultra rapid metabolizers - possible toxic level ---Poor metabolizers - low pain relief