Introduction to Genetic Epidemiology

Transcription

1 e of Genetic Epidemiology Introduction to Genetic Epidemiology Dr. Christian Gieger & Dr. Rajesh Rawal e of Genetic Epidemiology Helmholtz Zentrum München

2 Key concepts concepts in in genetic genetic epidemiology epidemiology Key What is is genetic genetic epidemiology? epidemiology? What e of Genetic Epidemiology Epidemiology is defined as the study of the distribution and determinants of health related states and events in populations. Genetic epidemiology means different things to different people. We regard it as a discipline that focuses on the familial, and in particular genetic, determinants of disease and the joint effects of genes and non-genetic determinants. Appropriate account is taken of the biology that underlies the action of genes and the known mechanisms of inheritance.

3 Genetics for for genetic genetic epidemiology epidemiology Genetics Human Genome Genome Human e of Genetic Epidemiology The genome is the entirety of a human s hereditary information It is made up of DNA, which consists of a long sequence of nucleotide bases of four types: adenine (A), cytosine (C), guanine (G), thymine (T)

4 Genetics for for genetic genetic epidemiology epidemiology Genetics DNA and and RNA RNA DNA Under native conditions, in the nucleus of a cell, DNA is double stranded. Double-stranded DNA is replicated by breakage of the two strands and construction of a new complementary strand for each, resulting in two identical copies of the original. A single strand of DNA acts as a template for a complementary strand of RNA. This transcription RNA is similar to DNA, but thymine (T) is replaced by uracil (U). e of Genetic Epidemiology

5 Genetics for for genetic genetic epidemiology epidemiology Genetics Human Genome Genome Human e of Genetic Epidemiology The human genome is distributed among 46 chromosomes: 22 homologous pairs of autosomes and 1 pair of sex chromosomes The complete set is the diploid complement. One chromosome in each of the 22 homologous pairs is derived from the mother and one from the father.

6 Genetics for for genetic genetic epidemiology epidemiology Genetics e of Genetic Epidemiology Gametes (sperm and ova) are haploid. They contain only one member of each homologous chromosomal pair (for example, only one version of chromosome 14). All ova have chromosomal complement 23,X and sperm are either 23, X or 23,Y. When sperm and ova fuse to form a zygote, the diploid chromosomal complement is restored.

7 Genetics for for genetic genetic epidemiology epidemiology Genetics Genes Genes In certain regions of the DNA, which can be called genes, transcribed RNA encodes instructions that tell the cell how to assemble amino acids to make proteins. It is mainly through altered protein function that changes in the DNA sequence affect health and disease. e of Genetic Epidemiology

8 Genetics for for genetic genetic epidemiology epidemiology Genetics Haploid genome genome Haploid e of Genetic Epidemiology The two homologues will have the same sequence of genes in the same positions, but they will usually exhibit sequence variations at several loci and can therefore be distinguished. The haploid genome is about 3.3 billion bp. 99,9% of the genome of any two unrelated individuals is identical. About 3% of the genome consists of coding sequences, and there are 30,000 40,000 protein-coding genes.

9 Genetics for for genetic genetic epidemiology epidemiology Genetics Allele Allele If the DNA sequence at a given locus (often a gene) varies between different chromosomes in the population, each different version is an allele. If there are two alleles at a given locus, the allele that is less common in the population is the minor allele e of Genetic Epidemiology

10 Genetics for for genetic genetic epidemiology epidemiology Genetics Homozygote Homozygote e of Genetic Epidemiology An organism/cell is homozygous for a particular gene/locus when identical alleles of the gene/locus are present on both homologous chromosomes. An individual that is homozygous dominant for a particular trait carries two copies of the allele that codes for the dominant trait. This allele is called the "dominant allele" (e.g. the allele for purple flowers, which are dominant in pea plants). An individual that is homozygous recessive for a particular trait carries two copies of the allele that codes for the recessive trait. This allele is called the "recessive allele" (e.g. the allele for white flowers, which are recessive in pea plants).

11 Genetics for for genetic genetic epidemiology epidemiology Genetics Heterozygote Heterozygote e of Genetic Epidemiology An organism/cell is heterozygous for a particular gene/locus when two different alleles occupy the gene/locus's position on the homologous chromosomes. If the trait in question is determined by simple (complete) dominance, a heterozygote will express only the trait coded by the dominant allele and the trait coded by the recessive allele will not be present. In more complex dominance schemes the results of heterozygosity can be more complex.

12 Genetics for for genetic genetic epidemiology epidemiology Genetics Genotype Genotype e of Genetic Epidemiology The genotype is the genetic constitution of a cell, an organism, or an individual (i.e. the specific allele makeup of the individual) Genotyping is the process of elucidating the genotype of an individual with a biological assay. Techniques include PCR, DNA sequencing, and nucleic acid hybridization to DNA microarrays.

13 Genetics for for genetic genetic epidemiology epidemiology Genetics Genetic variants variants Genetic e of Genetic Epidemiology The DNA sequence may vary between two versions of the same chromosome in several ways. Today, the most important structural classes are microsatellites and single nucleotide polymorphisms (SNPs). Microsatellites consist of multiple repeats of a short sequence (typically 2 8 bp) In microsatelites alleles are differentiated by the number of repeats (eg, CA12 indicates 12 CA repeats in a row). Microsatellites are highly variable and most people are heterozygous at any given locus. Coding regions tend not to contain microsatellite sequences.

14 Genetics for for genetic genetic epidemiology epidemiology Genetics Single nucleotide nucleotide polymorphisms polymorphisms (SNPs) (SNPs) Single e of Genetic Epidemiology SNPs represent variation in a single nucleotide (MAF > 1%). The different variants of the SNP are the alleles. The number of known SNPs in the human genome is 1.5x10 7 out of 3x109 bp (every ~200 bp) Usually the SNP is not causal for a disease but due to linkage disequilibrium the loci can be inferred. Although individual SNPs might carry limited information, their ease of typing and large number means that they are widely used in genetic epidemiology.

15 Genetics for for genetic genetic epidemiology epidemiology Genetics SNP and and Haplotype Haplotype SNP e of Epidemiology DNA sequence 1 differs from DNA sequence 2 at a single base-pair location (a?/? polymorphism) Haplotype: the ordered allele sequence on a chromosome CACC A C C C T C C A TCCA

16 Genetics for for genetic genetic epidemiology epidemiology Genetics SNP arrays arrays of of Affymetrix Affymetrix SNP e of Epidemiology

17 Genetics for for genetic genetic epidemiology epidemiology Genetics Structural variants variants Structural e of Epidemiology

18 Genetics for for genetic genetic epidemiology epidemiology Genetics Haplotype definition definition Haplotype e of Epidemiology Chromosom F...AAATACCTCTTATCCCGGTT... Chromosom M...AAATTCCTCTTATGCCGGTT... Only + Strand of the DNA (5-3 ) is shown ROCHE Genetic Education

19 Genetics for for genetic genetic epidemiology epidemiology Genetics Haplotype definition definition Haplotype e of Epidemiology Chromosom F...AAATACCTCTTATCCCGGTT... Chromosom M...AAATTCCTCTTATGCCGGTT... SNP1 A/T Haplotype 1 SNP2 SNP3 T/T C/G A T----- C (on chromosom F) Haplotype 2 (on chromosom M) T T----- G

20 Genetics for for genetic genetic epidemiology epidemiology Genetics Genotype -Haplotype -Haplotype Genotype e of Epidemiology Genotype: Locus specific information for a homolog pair of chromosomes, e.g. SNP. A genotype has no natural order. Haplotype: The allelic configuration along a single chromosome is called a haplotype. It contains chromosome specific information of multiple consecutive loci. A haplotype can reconstructed from a set of genotypes by applying statistical inference methods.

21 Genetics for for genetic genetic epidemiology epidemiology Genetics Phenotype Phenotype e of Epidemiology Phenotype will be used interchangeably with trait to refer to a measurable characteristic of an individual that is not itself a genotype. This definition includes binary disease states (qualitative trait; e.g. presence or absence of asthma) and quantitative characteristics (quantitative trait; e.g. systolic blood pressure).

22 SNP and and Haplotype Haplotype SNP Exercise Exercise e of Epidemiology How many SNP are in these sequences? What are the alleles of these SNPs? Which genotypes has the person at these SNPs? How many homozygote and heterozygote genotypes are in sequence? What are the haplotypes?

23 Genetics for for genetic genetic epidemiology epidemiology Genetics Exercise Exercise e of Epidemiology Explain the following terms: 1. Diploid and haploid 2. Gene, allele, genotype, haplotype 3. Heterozygote and homozygote What is the genotype frequency and minor allele frequency (MAF) of the following sequence of N=12 genotypes: T/C,T/T,T/C,T/C,T/T,T/T,T/C,C/C,C/C,T/T,T/C,T/C

24 Hardy-Weinberg Equilibrium Equilibrium Hardy-Weinberg The Hardy-Weinberg model describes a mathematical relationship that allows the prediction of the frequency of offspring genotypes based on parental allele frequencies Godfrey Hardy ( ) The Hardy-Weinberg model predicts that allele frequencies will not change from one generation to the next, i.e., it is an equilibrium or non-evolutionary model Wilhelm Weinberg ( )

25 Hardy-Weinberg Model Model Hardy-Weinberg If the frequency of an allele frequency (A) = p, and the frequency of the other allele at the locus frequency (B) = q (= 1-p), then the next generation will have: The frequency of the AA genotype = p 2 The frequency of the AB genotype = 2pq The frequency of the BB genotype = q 2 p2 + 2pq + q2 = 1

26 Hardy-Weinberg Example Example Hardy-Weinberg At the MN blood group locus the frequency of the M allele (p) equals 0.4 and the frequency of the N allele (q) equals 0.6, the offspring in the next generation will have: The frequency of the MM genotype = p2 = (0.4)2 = (0.4) x (0.4) = 0.16 The frequency of the MN genotype = 2pq = 2 x (0.4) x (0.6) = 2 x (0.24) = 0.48 The frequency of the NN genotype = q2 = (0.6)2 = (0.6) x (0.6) = 0.36

27 Hardy-Weinberg Requirements Requirements Hardy-Weinberg Static allele frequencies in a population across generations assume: 1. Random Mating 2. No Mutation (the alleles don't change) 3. No Migration or emigration (no exchange of alleles) 4. No Genetic Drift (infinitely large population size ) 5. No Selection (no selective pressure for or against any traits )

28 Random Mating Mating Random The frequency of mating between males of one genotype and females of another should be equal to the product of the two genotype frequencies Example: The frequency of the AA genotype in males is 0.7 and in females is also 0.7, then about half of all matings (0.7 x 0.7 = 0.49) should be between AA males and females If the frequency of mating is much different from the prediction, (how much different can be projected by a Chi-square test) then there is some deviation from random, and the Hardy-Weinberg model will not be accurate

29 Assortative Mating Mating Assortative If substantially more than half of the matings are between AA males and females, this would be an example of positive assortative mating Positive assortative mating is the occurrence of mating between similar individuals at higher than random frequencies, resulting in more homozygotes than the Hardy-Weinberg model predicts

30 Positive Assortative Assortative Mating Mating Positive As with most mammals, humans tend to mate with like individuals, particularly for visible or noticeable traits: Trait Spouse correlation I.Q Ear lobe length 0.40 Waist circumference 0.38 Height 0.28

31 Mutation Mutation Mutation, the alteration of genetic material, is the source of all truly new variability in the genome Mutation has a very small influence on changes in allele and genotype frequencies from one generation to the next Primarily important for the occurrence of new alleles

32 Gene Flow Flow and and Genetic Genetic Drift Drift Gene Gene Flow, the intermarriage or mixing between populations, has the effect of altering allele and genotype frequencies so that the two (or more) populations involved come to resemble each other in terms of genetic frequencies. An infinite population size eliminates the chance or random influences on gene frequencies from one generation to the next which are especially significant in small populations.

33 Selection Selection Selection causes changes in allele and genotype frequencies from one generation to the next due to differential reproductive success of individuals with different genotypes Example: If individuals with genotype AA consistently have twice as many offspring as individuals with AB and BB genotypes, the frequency of the A allele will increase and eventually, everyone will have the AA genotype

34 Use of of Hardy-Weinberg Hardy-Weinberg Equilibrium Equilibrium Use Significant difference between the known and calculated genotypic frequencies population is not in Hardy-Weinberg Equilibrium one of the five conditions is not met for the locus in question

35 Linkage disequilibrium disequilibrium (LD) (LD) Linkage LD analysis reveals a possible co-segregation and the nonrandom association of alleles across two or more linked polymorphic loci due to lacking recombination events.

36 Measuring LD LD between between sequence sequence variants: variants: Measuring D and and R² R² D D The higher D, the less recombinations in earlier generations separated the two loci Independent of allele frequencies R2 The higher R2 the stronger is the correlation between genotypes of to loci Dependent on allele frequencies!!!

37 Calculating D D Calculating B b A pab pab pa. a pab pab Pa. P.B P.b 1 D explains the raw difference in frequency between the observed number of AB pairs and the expected number: D = pab*pab pab*pab D' is a scaled D: If D > 0: D = D / min(pa.*p.b, p+b*pa.) If D < 0: D = D / min(pa.*p.b, p.b*pa.)

38 Calculating D D Calculating B b A a D = pab*pab pab*pab = 0.2 D = D / min(pa.*p.b, p.b*pa.) = D / min(0.5*0.4, 0.6*0.5) = 0.2 / 0.2 = 1 Perfect LD between A and B D = 1

39 Example: Calculating Calculating R² R² Example: B b A a R² is the squared correlation coefficient between the markers R² = [D / pa. * pa. * p.b * p.b R² = [0.2 / ]² 0.5 * 0.5 * 0.6 * 0.4 ]² = [0.2 / 0.24]² = [0.83]² = 0.69 D = 1 But correlation is not perfect r2 < 1

40 LD map map LD

41 How far far does does LD LD go? go? How Generally, we observe with the increase of physical distance also decrease of LD Although: LD can be very weak over short distances but sometimes stretching over more than 100 kb or even 1 Mb LD varies between chromosomal regions and population LD is not predictable from one region to another

42 Utility of of LD LD in in association association studies studies Utility If I m a causal variant, what is relevant to my detection in association studies is how well correlated I am with one of the SNPs or haplotypes examined in the study. Regions of high LD (D ) are regions with low recombination. Regions of high r² design regions of highly correlated SNPs identification of sets of SNPs that suffice to detect the genetic variation in the gene (tag SNPs)

43 Genetic epidemiological epidemiological research research methods methods Genetic e of Epidemiology Handbook of Statistical Genetics (John Wiley & Sons) Fig.28-1

44 Genetic epidemiological epidemiological research research methods methods Genetic Flow of of research research Flow Disease characteristics: Familial clustering: Genetic or environmental: Mode of inheritance: Disease susceptibility loci: Disease susceptibility markers: e of Epidemiology Descriptive epidemiology Family aggregation studies Twin/adoption/half-sibling/migrant studies Segregation analysis Linkage analysis Association studies

45 e of Epidemiology THE END