In The Name of GOD Genetic Polymorphism M.Dianatpour MLD,PHD

Terminology Locus Allele

Polymorphism Allele frequency more than 1% Rare Variant Allele frequency less than 1%

Genetically Differences The difference in sequence of DNA between two unrelated human is 1/1000 nucleotide About 1/2500 in coding sequences About 1/500 in noncoding and intergenic sequences

This small differences in DNA sequence among individuals is responsible for the genetically variability Disease No phenotypic effect Phenotypic variability

Phenotypic variability in: Anatomy Physiology Dietary intolerance Response or adverse reaction to medication (pharmacogenetics) and (individualized medicine) Susceptibility or resistance to infections Susceptibility or resistance to some diseases Even variability in peresonality traits ( art, sport,…)

There is not a correlation between allele frequency and the effect of the allele on health Often, but not always: Rare variants May be cause illness Common variants Increase susceptibility to. diseases Most common variants No known phenotypic effect

Site of polymorphic change Between genes or in introns Coding sequences Regulatory region of genes

Types of polymorphic variations Single nucleotide polymorphism (SNP) Insertion-Deletion polymorphism (Indel)

SNP The most common polymorphism Usually have two allele ACCTGCACTT ACCTGCGCTT 1/1000 base so 3000,000 differences between any two human genome The total SNP among all humans: about 10,000,000

SNP 10% of the most frequent SNPs were chosen as the markers for high-density mapping Many researches on the significance of SNPs for health Altering of disease susceptibility rather than direct cause of a disease

INDELs Multi allelic polymorphism Due to variable number of tandem repeat of a segment of DNA Two types of Indel polymorphism: Microsatellite Minisatellite

Microsatellite Microsatellite or Short Tandem Repeat (STR) Tandem repeats of 2-8 nucleotide,commonly 2,3or 4 nucleotide CACACA….CA CAACAACAA….CAA AAATAAATAAAT….AAAT

Microsatellite Repeated between 1 to a few dozen times Different alleles of a STR are the result of different number of the repeat So STR polymorphism has many allele and most of peoples are heterozygote CAACAACAA paternal allele CAACAACAACAACAA maternal allele

Microsatellite STR alleles can be genotyped by determining the size of PCR product Tens of thousands of STR loci are known along the human genome

Minisatellite Tandem repeat of various number(handreds to thousands) of a DNA sequence Usually nucleotide Variable Number Tandem Repeat(VNTR)

ACCGTAGGTCACGTG

Minisatellite Too many alleles The most informative polymorphism No two unrelated individuals are likely to have the same allele

RFLP Restriction Fragment length polymorphism Restriction enzymes

DNA Finger Printing Some common probes can detect several VNTR polymorphism loci around the genome

STR markers are detected by PCR VNTR markers by southern blot 13 different STR marker for DNA finger printing (CODIS)

Monozygotic twins Paternity tests Forensic medicine Linkage analysis Gene mapping

Copy Number Polymorphism CNPs : Variation in number of copies of larger segments ranging from 200 bp to 2Mb May have only two allels(0 or 1 copy) or multiple alleles (0,1,2,3 or more copies) Array Comparative Genome Hybridization(Array CGH)

Polymorphism in Proteins We are heterozygote for about 20% of loci determining structural or enzymatic polypeptide Biochemical Individuality Different response to environmental, dietary, pharmacological and …..

Medical Significant Polymorphism ABO Blood group Rh Blood group Blood transfusion, Transplantation and Hemolytic disease of the newborn MHC Transplantation and association to some diseases

ABO Blood group Locus on Ch. 9 3 Alleles A,B and O A and B are Codominant O is Recessive A: N-acetyl galactosamin transferase B: galactosyl transferase O: Frame shift mutation(1 nucleotide deletion)

ABO Blood group ABO Typing Serologic Genityping Technical difficulties in serologic typing, Forensic or paternity tests

ABO compatibility in transfusion and Transplantation

Rh Blood group Ch.1 According the expression of RhD antigen on RBC Rh- : homozygot for a non functional allele of RhD gene Transfusion and Hemolytic disease of the newborn

MHC Large cluster of genes on short arm of Ch.6 Class I and II genes encode cell surface proteins Critical role in immune response

MHC Many handreds of different alleles of the HLA I and II The most highly polymorphic loci in the human genome

MHC Typing Serologic Genotyping For example 24 different DNA sequence variant in HLA-B27 allele HLA-B2701, HLA-B2702, HLA-B2703, …

Inheritance Haplotype: The set of HLA alleles at Class I and II loci on chromosome, together form a Haplotype Alleles are codominant Each parent has two haplotype and express both of them These loci are very close, so the entire haplotype transmitted to child 25% chance that two sibs inherit matching HLA

Linkage Disequilibrium Example: HLA-Ax allele freq. = 0.15 HLA-By allele freq. = 0.20 =0.03 Actual freq. = 0.18 Low rates of Recombination Natural Selection Founder Effect

HLA and Disease Association Ankylosing Spondylitis Association with HLA-B27 Allele freq. in normal population= 9% Allele freq. in patients= 95% Risk of developing AS is 150 times more in HLA-B27(+) than HLA-B27(-) person Important note: Only 5% of HLA-B27(+) develop the disease

Cause of HLA and Disease Association Unknown Critical role in immune response Auto immune diseases Linkage Disequilibrium Disease gene is near to MHC genes like 21-hydroxylase gene and HFE gene

Susceptibility to Infection Example CCR5 gene a cell surface cytokine receptor Also can act as entery point for HIV ΔCCR5 a 32 base pair deletion leads to non functional gene Homozygotes for ΔCCR5 are resistant to HIV infection

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