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Understanding the Basics of Genetic Understanding the Basics of Genetic Understanding the Basics of Genetic Understanding the Basics of Genetic Testing in Research Studies Testing in Research Studies

Understand the Basics of Genetic Testing [Read-Only] the Basics of GeneticUnderstanding the Basics of Genetic Testing in ... and Polymorphism ... Understand_the_Basics_of_Genetic_Testing

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Page 1: Understand the Basics of Genetic Testing [Read-Only] the Basics of GeneticUnderstanding the Basics of Genetic Testing in ... and Polymorphism ... Understand_the_Basics_of_Genetic_Testing

Understanding the Basics of GeneticUnderstanding the Basics of GeneticUnderstanding the Basics of Genetic Understanding the Basics of Genetic Testing in Research StudiesTesting in Research Studies

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Learning ObjectivesLearning ObjectivesLearning ObjectivesLearning Objectives

After this lecture, you should be able to describe some basic approaches to genetic research

discriminate between different kinds of genetic research baseddiscriminate between different kinds of genetic research based on whether genetic testing is involved based on its definition by New York State Law

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DefinitionsDefinitionsDefinitionsDefinitions

Locus: physical location of the entity that is responsible for the passing of traits from one generation to the next (i.e. where the “gene” resides)Gene mapping: enterprise of physical localization ofGene mapping: enterprise of physical localization of a trait locus to a definable chromosomal region

Linkage mapping: mapping relative to another locus with known “address” by observing how alleles at different loci segregateaddress by observing how alleles at different loci segregate (genetic distance)

Physical mapping: mapping by determining the actual physical separation between the trait locus and another locus with knownseparation between the trait locus and another locus with known “address” using molecular genetic techniques (physical distance)

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Human ChromosomesHuman ChromosomesHuman ChromosomesHuman Chromosomes

46 chromosomes/somatic cell22 pairs of autosomes1 pair of sex chromosomes (XX or XY)

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Gene MappingGene MappingGene MappingGene Mapping

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Chromosome StructureChromosome StructureChromosome StructureChromosome Structure

Double helix DNA to chromosomesGenes are located on DNA thereforeon DNA, therefore also on chromosomes

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MutationsMutationsMutationsMutations

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Why Bother with Gene Mapping?Why Bother with Gene Mapping?Why Bother with Gene Mapping?Why Bother with Gene Mapping?

Allow for gene identification

Diagnosis prognosis treatmentDiagnosis, prognosis, treatmentGenetic counseling

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Traditional Genetics ResearchTraditional Genetics ResearchTraditional Genetics ResearchTraditional Genetics Research

Begins with individuals with a rare trait (e.g. disease)

Investigate whether mutation(s) in specific gene(s) causes, or determine in a very strong manner, the trait status

Affected and/or unaffected (presymptomatic?) family members may be needed

E lExamples

Cystic fibrosis, sickle cell disease, Duchenne muscular dystrophyBRCA1 or BRCA2 in breast cancer predisposition

Correlate specific genetic changes with prognosis, complication or treatment response

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Subjects for Traditional Gene Mapping ResearchSubjects for Traditional Gene Mapping ResearchSubjects for Traditional Gene Mapping ResearchSubjects for Traditional Gene Mapping ResearchThose with a defined trait (e.g. confirmed clinical diagnosis)Those without the defined trait (e g control)Those without the defined trait (e.g. control)

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Human Genome Project (1990Human Genome Project (1990 –– 2003)2003)Human Genome Project (1990 Human Genome Project (1990 2003)2003)Technology developmentDefining human sequence variationsDefining human sequence variationsDefining gene functions (functional genomics)Sponsoring genome initiatives of other organisms (comparative genomics)(comparative genomics)Ethical, legal and social issues (ELSI)Improving bioinformatics and computational capabilitiesP l t i iPersonnel training

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The Human GenomeThe Human GenomeThe Human GenomeThe Human Genome3,000,000,000 bp / haploid genome46 nuclear chromosomes (23 pairs)46 nuclear chromosomes (23 pairs)Many mitochondrial chromosomes (16.5 kb each)~20 000 protein coding genes (<5% of human~20,000 protein-coding genes (<5% of human genome)Some genes exist as a single copy per haploid g g py p pgenome

Most genes for Mendelian disorders

Oth i t i lti l iOther genes exist in multiple copies

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The Human GenomeThe Human GenomeThe Human GenomeThe Human Genome

>95% of DNA in the human genome does not code for proteins

intergenicIntragenicIntragenic

Most have unknown function

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Mutation and PolymorphismMutation and PolymorphismMutation and PolymorphismMutation and Polymorphism

MutationAny intrinsic change in DNA

Generally denotes deleterious changes

PolymorphismPresence in the general population of 2 or more alternative variantsvariants

Generally denotes “benign” variations

ABO blood groupsABO blood groupsImmunoglobulinsMinor variants in chromosome structureDNA l hiDNA sequence polymorphism

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DNA PolymorphismDNA PolymorphismDNA PolymorphismDNA Polymorphism

Short tandem repeat polymorphism (STRP)p p y p ( )Mini-satellite repeat polymorphism

Microsatellite repeat polymorphism

Single nucleotide polymorphism (SNP) Restriction fragment length polymorphism (RFLPRestriction fragment length polymorphism (RFLP

Copy number variants (CNVs)

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DNA PolymorphismDNA PolymorphismDNA PolymorphismDNA Polymorphism

Short tandem repeat polymorphism (STRP)p p y p ( )Mini-satellite repeat polymorphism

Microsatellite repeat polymorphism

Single nucleotide polymorphism (SNP)Restriction fragment length polymorphism (RFLPRestriction fragment length polymorphism (RFLP

Copy number variants (CNVs)

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Single Nucleotide PolymorphismSingle Nucleotide PolymorphismSingle Nucleotide PolymorphismSingle Nucleotide Polymorphism

One SNP in every 1,000 bp of the human DNA, yielding roughly 3 million SNPs scattered throughout the genomeAccounts for vast majority of DNA sequenceAccounts for vast majority of DNA sequence polymorphismSNP genotyping is highly automated

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DNA PolymorphismDNA PolymorphismDNA PolymorphismDNA Polymorphism

“Our genes are 99.9% identical”g0.1% x 3,000,000,000 bp = 3,000,000 base differences

~2,850,000 differences are in non-coding regions

~150,000 differences in coding regions

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DNA PolymorphismDNA PolymorphismDNA PolymorphismDNA Polymorphism

DNA polymorphisms may not be so benignp y p y gCollective effect of relevant DNA polymorphism may that combined effect similar to that a single mutation with strong effect

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Relative Risk by Gene MutationRelative Risk by Gene MutationRelative Risk by Gene MutationRelative Risk by Gene Mutation

skat

ive

Ri

Rel

a

Pop lation Freq enc

Turnbull C and Rahman N. Annu Rev Genomics Hum Genet 2008

Population Frequency

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DNA PolymorphismDNA PolymorphismDNA PolymorphismDNA Polymorphism

DNA polymorphisms may not be so benignp y p y gCollective effect of relevant DNA polymorphism may that combined effect similar to that a single mutation with strong effectAt the least, DNA polymorphisms provide a “genome signature” which can have significant implication of health and diseasesignificant implication of health and disease

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Modern Genomics ResearchModern Genomics ResearchModern Genomics ResearchModern Genomics Research

Use of whole genome data to study disease predisposition, causation, prognosis, complications and treatment responsesNew focus on common complex disordersNew focus on common complex disorders

Examples

Coronary heart disease, hypertension, diabetes, obesity, y , yp , , y,behavioral disorders, asthma

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Genetic Profiles or SignaturesGenetic Profiles or SignaturesGenetic Profiles or SignaturesGenetic Profiles or Signatures

Genetic analysis

Genetic database

Patient/subject population

analysis database

Statistical analysis and validation

Genetic Signature

Collection of clinical data

Clinical database

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Subjects for Modern Gene Mapping ResearchSubjects for Modern Gene Mapping Research

Phenotype status

Subjects for Modern Gene Mapping ResearchSubjects for Modern Gene Mapping Research

Affected or unaffected

Symptomatic, asymptomatic or presymptomatic

Genotype statusMutation(s)/polymorphism(s) present and sufficient to manifest the trait?the trait?

Mutation(s)/polymorphism(s) present but insufficient to manifest the trait, yet can be passed on to the next generation?

Mutation(s)/polymorphism(s) absent

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Privacy and Confidentiality Issues in Privacy and Confidentiality Issues in Traditional Genetics ResearchTraditional Genetics ResearchTraditional Genetics ResearchTraditional Genetics Research

Additional concerns when genetic privacy is violated

Image within a group setting

I di i i tiInsurance discrimination

Job discrimination

S i l di i i tiSocial discrimination

Stereotyping

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How Do We Achieve Confidentality?How Do We Achieve Confidentality?How Do We Achieve Confidentality?How Do We Achieve Confidentality?

Genetic analysis

Genetic database

Patient/subject population

analysis database

Statistical analysis and validation

Genetic Signature

Collection of clinical data

Clinical database

The more SNPs are used, the more precise the genetic signature, but the more g g ,identifiable the sample becomes

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Game of 20 Questions?Game of 20 Questions?Game of 20 Questions?Game of 20 Questions?

Is it organic? YesDoes it move? YesIs it an animal? YesIs it a mammal? YesIs it human? YesIs this a professional? YesIs this person’s job really important? YesDoes this person save lives? YesDo most people think this person is mean? YesIs this person really knowlegeable? Yes

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Game of 20 Questions?Game of 20 Questions?Game of 20 Questions?Game of 20 Questions?

Is this person a scientist? YesIs this person a humanist? YesIs this person a writer? YesIs this person a politician? YesIs this person an administrator? YesIs this person a boss? YesIs this person a teacher? YesIs this person a hero? YesDoes this person wear a red cape? No

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Game of 20 Questions?Game of 20 Questions?Game of 20 Questions?Game of 20 Questions?

Is this person an IRB Chair? Yes

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A Simple Math ProblemA Simple Math ProblemA Simple Math ProblemA Simple Math Problem

Population in the world: 10,000,000,000What is the minimum number of SNPs needed to “define” each individual?

10 000 000 000 = 2x10,000,000,000 = 2x

X = 33.2

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SNP Profile: Privacy vsSNP Profile: Privacy vsSNP Profile: Privacy vs SNP Profile: Privacy vs

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ConundrumConundrumConundrumConundrum

Genetic association studiesRoutinely uses 400,000 SNPs

Routinely requires large study sample size

Routinely involve large amount of clinical and other private information

Trending towards public data sharing including clinicalTrending towards public data sharing, including clinical and genetic profile (but “anonymized” according to traditional criteria)

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Is It A Real Risk Now?Is It A Real Risk Now?Is It A Real Risk Now?Is It A Real Risk Now?

Obtain SNP profile from an individualSearch and match to accessible genetic database

Military

Prisoners and criminals

Publicly funded research

Obtain other clinical and private dataLoss of privacyCurrent risk is low due to protection of these genetic databases

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Is It A Real Risk In The Near Future?Is It A Real Risk In The Near Future?Is It A Real Risk In The Near Future?Is It A Real Risk In The Near Future?

Obtain SNP profile from an individualInfer sex, age, race and other health parameters from the SNP profileR t t diti l id tifi dRecreate traditional identifiers de novoLoss of privacyThi i k i lThis risk is real

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Could It Be a Risk In The Far Future?Could It Be a Risk In The Far Future?Could It Be a Risk In The Far Future?Could It Be a Risk In The Far Future?

Obtain SNP profile from an individualInfer facial appearance from the SNP profileRecreate appearance of individualRisk unknown

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Potential SolutionsPotential SolutionsPotential SolutionsPotential Solutions

Limiting access to database (“elite researcher”)“Electronically mutating” content of genetic database (“head in the sand”)E ll l bj t t t ll d i f dEnroll only subject totally open and informed about privacy issues (“information altruists”)Improving informed consent for genetic researchImproving informed consent for genetic researchChanging the public attitude about privacyEducation, education and educationEducation, education and education

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Genetic TestsGenetic TestsGenetic TestsGenetic Tests

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NYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & AmendmentNYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & Amendment

Definitions(a) "genetic test" shall mean any laboratory test of human DNA, chromosomes, genes, or gene products to diagnose the presence of a genetic variation linked to a predisposition to a genetic disease or disability in the individual or the individual`sgenetic disease or disability in the individual or the individual s offspring; such term shall also include DNA profile analysis. "Genetic test" shall not be deemed to include any test of blood or other medically prescribed test in routine use that has beenor other medically prescribed test in routine use that has been or may be hereafter found to be associated with a genetic variation, unless conducted purposely to identify such genetic variation.

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“Genes and Gene Product”“Genes and Gene Product”Genes and Gene ProductGenes and Gene Product

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NYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & AmendmentNYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & Amendment

Definitions(b) "genetic predisposition" shall mean the presence of a variation in the composition of the genes of an individual or an individual`s family member which is scientifically or medically identifiable and which is determined to be associated with anidentifiable and which is determined to be associated with an increased statistical risk of being expressed as either a physical or mental disease or disability in the individual or having offspring with a genetically influenced disease, but which hasoffspring with a genetically influenced disease, but which has not resulted in any symptoms of such disease or disorder.

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NYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & AmendmentNYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & Amendment

Definitions(a) "genetic test" shall mean any laboratory test of human DNA, chromosomes, genes, or gene products to diagnose the presence of a genetic variation linked to a predisposition to a genetic disease or disability in the individual or the individual`sgenetic disease or disability in the individual or the individual s offspring; such term shall also include DNA profile analysis. "Genetic test" shall not be deemed to include any test of blood or other medically prescribed test in routine use that has beenor other medically prescribed test in routine use that has been or may be hereafter found to be associated with a genetic variation, unless conducted purposely to identify such genetic variation.

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NYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & AmendmentNYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & Amendment

2. (a) No person shall perform a genetic test on a biological sample taken from an individual without the prior writtensample taken from an individual without the prior written informed consent of such individual…..(b) Written informed consent to a genetic test shall consist of written authorization that is dated and signed and includes at least the following: (1)that is dated and signed and includes at least the following: (1) a general description of the test; (2) a statement of the purpose of the test; 2-a. a statement indicating that the individual may wish to obtain professional genetic counseling prior to signing the informed consent. (3) a statement that a positive test result is an indication that the individual may be predisposed to or have the specific …(4) a general description of each specific disease or condition tested for; (5) the level of certainty that adisease or condition tested for; (5) the level of certainty that a positive test result for that disease or condition serves as a predictor of such disease......

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NYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & AmendmentNYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & Amendment

…..a general description of the test; (2) a statement of the purpose of the test; 2 a a statement indicating that thepurpose of the test; 2-a. a statement indicating that the individual may wish to obtain professional genetic counseling prior to signing the informed consent. (3) a statement that a positive test result is an indication that the individual may bepositive test result is an indication that the individual may be predisposed to or have the specific …(4) a general description of each specific disease or condition tested for; (5) the level of certainty that a positive test result for that disease or condition serves as a predictor of such disease......5. Penalties. (a) Any person who violates the provisions of subdivision two or three of this section shall be guilty of a violation punishable by a civil fine of not more than one thousand dollars. (b) Any person who willfully violates the provisions of subdivision two or three of this section shall be guilty of a misdemeanor punishable by a fine of not more thanguilty of a misdemeanor punishable by a fine of not more than five thousand dollars or by imprisonment for not more than ninety days or by both such fine and imprisonment

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NYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & AmendmentNYS Civil Rights Law 79NYS Civil Rights Law 79--1 & Amendment1 & Amendment

…..a general description of the test; (2) a statement of the purpose of the test; 2 a a statement indicating that thepurpose of the test; 2-a. a statement indicating that the individual may wish to obtain professional genetic counseling prior to signing the informed consent. (3) a statement that a positive test result is an indication that the individual may bepositive test result is an indication that the individual may be predisposed to or have the specific …(4) a general description of each specific disease or condition tested for; (5) the level of certainty that a positive test result for that disease or condition serves as a predictor of such disease......5. Penalties. (a) Any person who violates the provisions of subdivision two or three of this section shall be guilty of a violation punishable by a civil fine of not more than one thousand dollars. (b) Any person who willfully violates the provisions of subdivision two or three of this section shall be guilty of a misdemeanor punishable by a fine of not more thanguilty of a misdemeanor punishable by a fine of not more than five thousand dollars or by imprisonment for not more than ninety days or by both such fine and imprisonment

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Genetic TestingGenetic TestingGenetic TestingGenetic Testing

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Designs for Studies with Genetic TestingDesigns for Studies with Genetic TestingDesigns for Studies with Genetic TestingDesigns for Studies with Genetic Testing

Gene discoveryCandidate gene approach

Genome-wide approach (GWAS)

Non-gene discoveryNeeds genotyping for eligibility

Needs genotyping for data analysis and stratification

RNA profiling

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