Lecture 1: Introduction to pedigree analysis

Transcription

1 Lecture 1: Introduction to pedigree analysis Magnus Dehli Vigeland NORBIS course, 8 th 12 th of January 2018, Oslo

2 Outline Part I: Brief introductions Pedigrees symbols and terminology Some common relationships Genetics Locus, allele, genotype, marker Mendelian inheritance Autosomal X, Y Part II: Pedigree likelihoods Motivation: Real-life problems Ingredients: Hardy-Weinberg equilibrium Mendelian transition probabilities Likelihoods by hand Computer algorithms

3 Outline Part I: Brief introductions Pedigrees symbols and terminology Some common relationships Genetics Locus, allele, genotype, marker Mendelian inheritance Autosomal X, Y Part II: Pedigree likelihoods Motivation: Real-life problems Ingredients: Hardy-Weinberg equilibrium Mendelian transition probabilities Likelihoods by hand Computer algorithms

4 Pedigrees: Symbols and terminology Founders: No parents included in the pedigree = male = female Nonfounders

5 Pedigrees: Symbols and terminology = male = female Consanguineous marriage

6 Pedigrees: Symbols and terminology Medical pedigrees: = affected = unaffected = carrier of disease allele

7 Alternative ways of drawing pedigrees Standard Simplified Directed acyclic graph

8 Outline Part I: Brief introductions Pedigrees symbols and terminology Some common relationships Genetics Locus, allele, genotype, marker Mendelian inheritance Autosomal X, Y Part II: Pedigree likelihoods Motivation: Real-life problems Ingredients: Hardy-Weinberg equilibrium Mendelian transition probabilities Likelihoods by hand Computer algorithms

9 Cousin relationships Full siblings First cousins Second cousins

10 Cousin relationships First cousins once removed

11 Half cousin relationships Half siblings (paternal) Half first cousins Half second cousins

12 Half cousin relationships

13 More complicated relationships Other: Double first cousins Quadruple half first cousins 3/4 siblings

14 Outline Part I: Brief introductions Pedigrees symbols and terminology Some common relationships Genetics Locus, allele, genotype, marker Mendelian inheritance Autosomal X, Y Part II: Pedigree likelihoods Motivation: Real-life problems Ingredients: Hardy-Weinberg equilibrium Mendelian transition probabilities Likelihoods by hand Computer algorithms

15 Genetics Human genome: Diploid 22 pairs of autosomes Sex chroms: X and Y Some important terms Locus Allele Genotype Genetic markers SNPs microsatellites

16 Locus, allele, genotype M F alleles A B locus genotype: A/B Homologous chromosomes LOCUS = a specific place in the genome, e.g. a base pair, a gene or a region ALLELE = any of the alternative forms of a locus GENOTYPE = the set of alleles carried by an individual at a given locus

17 Genetic markers Small parts of the genome which... have known position vary in the population are easy to genotype SNPs (single nucleotide polymorphisms) two alleles usual requirement: MAF > 1% = minor allele frequency very common in the genome (millions!) used in medical genetics CCGTTATATGGGC......CCGTTAGATGGGC......CCGTTATATGGGC......CCGTTATATGGGC......CCGTTAGATGGGC... STRs (short tandem repeats) = microsatellites consecutive repeats of 2-5 bases multiallelic: 5-50 alleles allele names: # repeats used in forensics...acg TTAG TTAG TTAG TTAG AAC.....ACG TTAG TTAG AAC.....ACG TTAG TTAG TTAG TTAG TTAG AAC..

18 Outline Part I: Brief introductions Pedigrees symbols and terminology Some common relationships Genetics Locus, allele, genotype, marker Mendelian inheritance Autosomal X, Y Part II: Pedigree likelihoods Motivation: Real-life problems Ingredients: Hardy-Weinberg equilibrium Mendelian transition probabilities Likelihoods by hand Computer algorithms

19 Mendelian inheritance: Autosomal (chromosomes 1-22) Example: autosomal marker with 3 alleles: A, B, C homozygous A/A B/C heterozygous A/B A/C A/B Probability of transmitting either allele: always 50% B/C

20 Mendelian inheritance: X-linked Example: X-linked marker with 3 alleles: A, B, C males are hemizygous A B/C A/C A/B C forced transmission from father to daughter A no transmisison from father to son

21 Mendelian inheritance: Y-linked Example: Y-linked marker with 2 alleles: A, B A B no transmission involving females B father-son forced

22 Assumptions throughout (most of) this course Diploid species No cytogenetic abnormalitites No de novo mutations COFFEE BREAK!

23 Outline Part I: Brief introductions Pedigrees symbols and terminology Some common relationships Genetics Locus, allele, genotype, marker Mendelian inheritance Autosomal X, Y Part II: Pedigree likelihoods Motivation: Real-life problems Ingredients: Hardy-Weinberg equilibrium Mendelian transition probabilities Likelihoods by hand Computer algorithms

24 Questions related to pedigrees with genotypes Will my child have the disease? Is NN the true father? Brothers or half brothers? Is NN related to this family? How? Predict the missing genotype?

25 Questions related to pedigrees with genotypes D/N? D Disease locus: alleles D and N Will my child have the disease?

26 Questions related to pedigrees with genotypes /13 -/- 13/18 11/18 Suppose: 11 is common 18 is rare Who is the true father?

27 Questions related to pedigrees with genotypes Brothers or half brothers?

28 Questions related to pedigrees with genotypes 12/14 32/40 7/11 6/21 11/14 32/40 13/13 6/25 12/16 34/40 7/7 12/21 11/16 32/41 7/13 6/25 Is this woman related to the family?

29 Questions related to pedigrees with genotypes A/B A/A A/A?/? A/B A/B Can we predict the missing genotype?

30 Common to all of these: The need to calculate probabilities P( genotypes pedigree, marker info, allele freqs,.. ) Called the likelihood of the pedigree.

31 Ingredients for likelihood computations founder probabilites A/B A/A transition probabilities A/A -/- A/B A/A untyped individuals

32 Ingredient 1: Founder probabilities Suppose the allele frequencies are: P A = p P B = q What are the frequencies of the genotypes AA, AB, BB? Under certain assumptions, the alleles can be treated as independent: P(AA) = P A P A = p 2 P BB = P B P B = q 2 P AB = P AB or BA = pq + qp = 2pq two possible orderings!

33 The Hardy-Weinberg principle Assumptions: A p B q infinite population random mating no selection AA AB BB no mutations no migration A p B q Hardy (1908): Shows «... using a little mathemathics of the multiplication table kind»: p 2 2pq q 2 AA AB BB allele freqs are unchanged from generation to generation after 1 generation the genotype freqs stay unchanged A p B q P AA = p 2 P AB = 2pq P(BB) = q 2 HW equilibrium p 2 AA 2pq AB q 2 BB

34 p AA = p 2 p AB = 2pq p BB = q 2 assuming HWE Allele frequencies Genotype frequencies always p = p AA p AB q = p BB p AB

35 Ingredient 2: Transition probabilities P(g child g parents ) Easy - follows directly from Mendel's laws! A/A -/- A/B child parents A/A AB BB AA AA AA AB AA BB AB AA AB AB AB BB BB AA BB AB BB BB 0 0 1

36 Example 1 2 A/A A/B 3 A/B L = P g 1, g 2, g 3 = P g 1 ) P(g 2 ) P(g 3 g 1, g 2 = P AA P AB P AB parents = AA AB) = p 2 2pq 0.5 = p 3 q assuming HWE!

37 Example on X A 1 2 A/B B/B A/B B 6 B/B L = P genotypes pedigree, p, q contribution from each individual = p 2pq q 2 1 = 0.5 p 2 q 3

38 Ingredient 3: How to deal with untyped individuals Solution: Sum of all possible genotypes for the untyped 1 2 A/A -/- 3 A/B P g 1, g 3 = P(g 1, g 2, g 3 ) = P g 1 ) P(g 2 ) P(g 3 g 1, g 2 g 2 g 2 = P(AA) P(AA) P AB AA AA) + P(AA) P(AB) P AB AA AB) + P(AA) P(BB) P AB AA BB) = p 2 p p 2 2pq p 2 q 2 1 = p 3 q + p 2 q 2 = p 2 q p + q = p 2 q

39 Pedigree likelihood: General formula Given: pedigree with n individuals k members are genotyped: g 1, g 2,, g k Then: founders non-founders P g 1,..., g k = G 1 G 2 G n P g 1 P g j P g j+1 par P g n par If everyone is typed: Only one term easy G i = set of possible genotypes for individual i Number of terms grows exponentially in #(untyped) but clever algorithms exist!

40 Computer algorithms for pedigree likelihoods Elston-Stewart algorithm a peeling algorithm linear in pedigree size! A/B A/A A/A -/- A/A Lander-Green based on inheritance vectors hidden Markov model best choice with many linked markers small/medium pedigrees only A/B

41 Software R/paramlink R environment Elston-Stewart general likelihoods, inbreeding, simulation ++ Familias GUI for forensic applications Elston-Stewart handles mutations, HW deviations, ++ MERLIN command line program Lander-Green medical applications: multipoint linkage