Understanding the Basics of Genetic Understanding the Basics Of

Understanding the Basics of Genetic Testing in Research Studies Learning Objectives

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

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

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 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 segregate (genetic distance)

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

46 chromosomes/somatic cell

22 pairs of autosomes

1 pair of sex chromosomes (XX or XY) Gene Mapping

Chromosome Structure

Double helix DNA to chromosomes

Genes are located on DNA , therefore also on chromosomes

Mutations Why Bother with Gene Mapping?

Allow for gene identification

Diagnosis, prognosis , treatment

Genetic counseling Traditional 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

ElExamples

Cystic fibrosis, sickle cell disease, Duchenne muscular dystrophy BRCA1 or BRCA2 in breast cancer predisposition Correlate specific genetic changes with prognosis, complication or treatment response Subjects for Traditional Gene Mapping Research

Those with a defined trait (e.g. confirmed clinical diagnosis)

Those without the defined trait (e .g . control) Human Genome Project (1990 – 2003)

Technology development Defining human sequence variations Defining gene functions (functional genomics) Sponsoring genome initiatives of other organisms (comparative genomics) Ethical, legal and social issues (ELSI) Improving bioinformatics and computational capabilities PltiiPersonnel training

The Human Genome

3,000,000,000 bp / haploid genome

46 nuclear chromosomes (23 pairs)

Many mitochondrial chromosomes (16.5 kb each)

~20, 000 protein-coding genes (<5% of human genome)

Some gggpyppenes exist as a single copy per haploid genome Most genes for Mendelian disorders Other genes exi st i n multi pl e copi es The Human Genome

>95% of DNA in the human genome does not code for proteins intergenic Intragenic Most have unknown function Mutation and Polymorphism

Mutation Any intrinsic change in DNA

Generally denotes deleterious changes

Polymorphism Presence in the general population of 2 or more alternative variants

Generally denotes “benign” variations

ABO blood groups Immunoglobulins Minor variants in chromosome structure DNA sequence po lymorp hism DNA Polymorphism

Short tandem repppypeat polymorphism ( STRP) Mini-satellite repeat polymorphism

Microsatellite repeat polymorphism

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

Copy number variants (CNVs) DNA Polymorphism

Short tandem repppypeat polymorphism ( STRP) Mini-satellite repeat polymorphism

Microsatellite repeat polymorphism

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

Copy number variants (CNVs) Single Nucleotide Polymorphism

One SNP in every 1,000 bp of the human DNA, yielding roughly 3 million SNPs scattered throughout the genome

Accounts for vast majority of DNA sequence polymorphism

SNP genotyping is highly automated DNA Polymorphism

“Our genes are 99.9% identical” 0.1% 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 DNA Polymorphism

DNA ppyolymor phisms may not be so benig n

Collective effect of relevant DNA polymorphism may that combined effect similar to that a single mutation with strong effect Relative Risk by Gene Mutation sk tive Ri aa Rel

PoplationFreqencPopulation Frequency

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

DNA ppyolymor phisms may not be so benig n

Collective effect of relevant DNA polymorphism may that combined effect similar to that a single mutation with strong effect

At the least, DNA polymorphisms provide a “genome signature” which can have significant implication of health and disease Modern Genomics Research

Use of whole genome data to study disease predisposition, causation, prognosis, complications and treatment responses

New focus on common complex disorders Examples

Coronary heart disease , h ypertension, diabetes, obesity, behavioral disorders, asthma Genetic Profiles or Signatures

Genetic Genetic analysis database

Statistical Patient/subject Genetic analysis and population Signature validation

Collection of clinical Clinical data database Subjects for Modern Gene Mapping Research

Phenotype status Affected or unaffected

Symptomatic, asymptomatic or presymptomatic

Genotype status Mutation(s)/polymorphism(s) present and sufficient to manifest 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 Privacy and Confidentiality Issues in Traditional Genetics Research

Additional concerns when genetic privacy is violated Image within a group setting

IdiiitiInsurance discrimination

Job discrimination

SildiiitiSocial discrimination

Stereotyping How Do We Achieve Confidentality?

Genetic Genetic analysis database

Statistical Patient/subject Genetic analysis and population Signature validation

Collection of clinical Clinical data database

The more SNPs are used, the more precise the ggg,enetic signature, but the more identifiable the sample becomes Game of 20 Questions?

Is it organic? Yes

Does it move? Yes

Is it an animal? Yes

Is it a mammal? Yes

Is it human? Yes

Is this a professional? Yes

Is this person’s job really important? Yes

Does this person save lives? Yes

Do most people think this person is mean? Yes

Is this person really knowlegeable? Yes Game of 20 Questions?

Is this person a scientist? Yes

Is this person a humanist? Yes

Is this person a writer? Yes

Is this person a politician? Yes

Is this person an administrator? Yes

Is this person a boss? Yes

Is this person a teacher? Yes

Is this person a hero? Yes

Does this person wear a red cape? No Game of 20 Questions?

Is this person an IRB Chair?

Yes A Simple Math Problem

Population in the world: 10,000,000,000

What is the minimum number of SNPs needed to “define” each individual? 10, 000, 000, 000 = 2x

X = 33.2 SNP Profile: Privacy vs Conundrum

Genetic association studies Routinely 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 clinical and genetic profile (but “anonymized” according to traditional criteria) Is It A Real Risk Now?

Obtain SNP profile from an individual

Search and match to accessible genetic database Military

Prisoners and criminals

Publicly funded research

Obtain other clinical and private data

Loss of privacy

Current risk is low due to protection of these genetic databases Is It A Real Risk In The Near Future?

Obtain SNP profile from an individual

Infer sex, age, race and other health parameters from the SNP profile

Recrea te traditi onal id entifi ers de novo

Loss of privacy

This ri sk i s real Could It Be a Risk In The Far Future?

Obtain SNP profile from an individual

Infer facial appearance from the SNP profile

Recreate appearance of individual

Risk unknown Potential Solutions

Limiting access to database (“elite researcher”)

“Electronically mutating” content of genetic database (“head in the sand”)

ElllEnroll only subj bjtttllect totally open and difd informed about privacy issues (“information altruists”)

Improving informed consent for genetic research

Changing the public attitude about privacy

Education, education and education Genetic Tests NYS Civil Rights Law 79-1 & 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 `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 been or may be hereafter found to be associated with a genetic variation, unless conducted purposely to identify such genetic variation. “Genes and Gene Product ” NYS Civil Rights Law 79-1 & 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 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 has not resulted in any symptoms of such disease or disorder. NYS Civil Rights Law 79-1 & 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`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 been or may be hereafter found to be associated with a genetic variation, unless conducted purposely to identify such genetic variation. NYS Civil Rights Law 79-1 & Amendment

2. (a) No person shall perform a genetic test on a biological sample 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) 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 a positive test result for that disease or condition serves as a predictor of such disease......

NYS Civil Rights Law 79-1 & Amendment

…..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 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 than five thousand dollars or by imprisonment for not more than ninety days or by both such fine and imprisonment NYS Civil Rights Law 79-1 & Amendment

Gene discovery Candidate gene approach

Genome-wide approach (GWAS)

Non-gene discovery Needs genotyping for eligibility

Needs genotyping for data analysis and stratification

RNA profiling