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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 ppyolymorp hisms 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 ppyolymorp hisms 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, hyp ertension , 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 tra ditional 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
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