Review of Mendelian geneticsReview of Mendelian genetics

Gregor Mendel analyzed the patterns of Gregor Mendel analyzed the patterns of inheritance of seven pairs of contrasting traits in inheritance of seven pairs of contrasting traits in the domestic pea plant. As an example pair:the domestic pea plant. As an example pair:

P1P1: He mated a plant that was : He mated a plant that was homozygoushomozygous for for round (round (RRRR) yellow () yellow (YYYY) seeds with one that was ) seeds with one that was homozygous for wrinkled (homozygous for wrinkled (rrrr) green () green (yyyy) seeds.) seeds.

F1F1: All the offspring were dihybrids, i.e., : All the offspring were dihybrids, i.e., heterozygousheterozygous for each pair of for each pair of allelesalleles ( (RrYyRrYy).).

All seeds were round and yellow, showing that All seeds were round and yellow, showing that the genes for round and yellow are the genes for round and yellow are dominantdominant. .

Mendelian genetics (2)Mendelian genetics (2)

F2F2: Mendel then crossed the RrYy : Mendel then crossed the RrYy dihybrids. dihybrids.

If round seeds must always be If round seeds must always be yellow and wrinkled seeds must yellow and wrinkled seeds must be green (linked genes), then this be green (linked genes), then this would have produced a typical would have produced a typical monohybridmonohybrid cross cross

But in fact, the F2s had seeds But in fact, the F2s had seeds with all combinations: with all combinations:

Round-yellowRound-yellow 9/169/16Round-greenRound-green 3/163/16Wrinkled-yellowWrinkled-yellow3/163/16Wrinkled-greenWrinkled-green 1/161/16

RYRY ryry

RYRY RRYYRRYY RrYyRrYy

ryry RrYyRrYy rryyrryy

Recombinants

Reco

mbin

ants

Percentage of recombinants = 50%

Mendel’s Rule of Independent AssortmentMendel’s Rule of Independent Assortment

The inheritance of one pair of factors (genes) is The inheritance of one pair of factors (genes) is independent of the inheritance of the other pair.independent of the inheritance of the other pair.

In other words, the percentage of recombinants is 50%In other words, the percentage of recombinants is 50% Today, we know that this rule holds only if one of two conditions Today, we know that this rule holds only if one of two conditions

is met: is met: – The genes are on separate chromosomesThe genes are on separate chromosomes

– The genes are widely separated on the same chromosome.The genes are widely separated on the same chromosome.

Mendel was lucky in that every pair of genes he studied met one Mendel was lucky in that every pair of genes he studied met one requirement or the other!!!requirement or the other!!!

In fact, the rule does not apply to many matings of dihybrids. In In fact, the rule does not apply to many matings of dihybrids. In many cases, two alleles inherited from one parent show a strong many cases, two alleles inherited from one parent show a strong tendency to stay together as do those from the other parent. tendency to stay together as do those from the other parent.

This phenomenon is called This phenomenon is called linkagelinkage. .

Genetic distance in centiMorgansGenetic distance in centiMorgans

The percentage of recombinants formed by F1 The percentage of recombinants formed by F1 individuals can range from 0-50%.individuals can range from 0-50%.

0% is seen if two loci map to the same gene.0% is seen if two loci map to the same gene.

50% is seen for two loci on separate 50% is seen for two loci on separate chromosomes (chromosomes (independent assortmentindependent assortment). ).

Between these extremes, the higher the Between these extremes, the higher the percentage of recombinants, the greater the percentage of recombinants, the greater the genetic distance separating the two loci. genetic distance separating the two loci.

The percent of recombinants is arbitrarily chosen The percent of recombinants is arbitrarily chosen as the genetic distance in as the genetic distance in centimorganscentimorgans ( (cMcM), ), named for the pioneering geneticist Thomas Hunt named for the pioneering geneticist Thomas Hunt Morgan. Morgan.

Genetic recombinationGenetic recombination is due to the is due to the physical process of physical process of crossing-overcrossing-over

Mating occurs AFTER all of this

Genetic MapsGenetic Maps Chromosome maps prepared by Chromosome maps prepared by

counting phenotypes are called counting phenotypes are called genetic mapsgenetic maps..

Maps have been prepared for Maps have been prepared for many eukaryotes, including corn, many eukaryotes, including corn, Drosophila, the mouse, and Drosophila, the mouse, and tomato. tomato.

Controlled matings are not Controlled matings are not practicable in humans, but map practicable in humans, but map positions are estimated by positions are estimated by examining family trees examining family trees (pedigrees)(pedigrees)

A genetic map of chr. 9 of the A genetic map of chr. 9 of the corn plant (corn plant (Zea maysZea mays) is shown ) is shown on the right with distances in cM.on the right with distances in cM.

Note distances >50cM. How?Note distances >50cM. How?

ExampleExample Corn plants are scored for three traits:

C/c colored/colorless seedsBz/bz bronze/non-bronze stalkSh/sh Smooth/shrunken

The following F1 heterozygote self-crosses are performed:

What does the genetic map look like?

(C/c; Bz/bz) X (C/c; Bz/bz) 4.6 cM

(Sh/sh; C/c) X (Sh/sh; C/c) 2.8 cM

(Sh/sh; Bz/bz) X (Sh/sh; Bz/bz) 1.8 cM

Gather more data– now can the map be determined?

Problems with genetic mapsProblems with genetic maps Recombination frequency underestimates genetic distance Recombination frequency underestimates genetic distance

for larger distances, due to higher order cross-over events, for larger distances, due to higher order cross-over events, i.e. double and triple crossovers between markersi.e. double and triple crossovers between markersThis is overcome with 3 pt. mapping (homework)This is overcome with 3 pt. mapping (homework)

The probability of a crossover is not uniform along the The probability of a crossover is not uniform along the entire length of the chromosome. entire length of the chromosome. – Crossing over is inhibited in some regions (e.g., near the Crossing over is inhibited in some regions (e.g., near the

centromere). centromere).

– Some regions are "hot spots" for recombination (for reasons Some regions are "hot spots" for recombination (for reasons that are not clear). Approximately 80% of genetic that are not clear). Approximately 80% of genetic recombination in humans is confined to just one-quarter of our recombination in humans is confined to just one-quarter of our genome.genome.

In humans, the frequency of recombination of loci on most In humans, the frequency of recombination of loci on most chromosomes is higher in females than in males. Therefore, chromosomes is higher in females than in males. Therefore, genetic maps of female chromosomes are longer than genetic maps of female chromosomes are longer than those for males.those for males.

Genetic vs. physical mapsGenetic vs. physical maps The loci in The loci in genetic mapsgenetic maps are simply parts are simply parts

of the DNA molecule that create the of the DNA molecule that create the observed phenotype.observed phenotype.

Knowing the DNA sequence (or at least the Knowing the DNA sequence (or at least the ordering of contigs) directly gives the ordering of contigs) directly gives the order/spacing of genes. order/spacing of genes.

Maps drawn in this way are called Maps drawn in this way are called physical mapsphysical maps. .

As a very rough rule of thumb, As a very rough rule of thumb, 1 cM genetic distance ~ 1 MB of DNA. 1 cM genetic distance ~ 1 MB of DNA.

Applying genetic linkage to diseaseApplying genetic linkage to disease• Tries to find a common inheritance pattern Tries to find a common inheritance pattern

between a chromosomal region/marker and a between a chromosomal region/marker and a disease phenotypedisease phenotype

• Requires genotyping on large, multigeneration Requires genotyping on large, multigeneration pedigreespedigrees

• Coarse mapping with sparse markers <10 MbCoarse mapping with sparse markers <10 Mb

• At greater distances linkage generally does not At greater distances linkage generally does not occur due to frequent recombination eventsoccur due to frequent recombination events

• At lesser distances all loci are typically linked At lesser distances all loci are typically linked and thus are indistinguishable from one anotherand thus are indistinguishable from one another

Linkage analysis in a 3 generation pedigreeLinkage analysis in a 3 generation pedigree

Solid red indicates the disease phenotype; dot means carrierThe gel is the result of RFLP analysis—note variants 1 and 2Is this a recessive or dominant gene? Autosomal or sex linked?What is the penetrance? This is Pr(disease phenotype | disease genotype)

Autosomal dominant linkageAutosomal dominant linkage

RFLP: 1/1 2/2

1/2 2/2

1/2 1/2 2/2 2/2 2/2 2/2 1/2 2/2 2/2

DiseaseNo DiseaseDisease: D/D d/d

d/dD/d

D/d D/d d/d D/d d/d d/d D/d d/d d/d

Computing a Log Odds (LOD) scoreComputing a Log Odds (LOD) score

From the last slide: 3 affected offspring carry RFLP1, while 1 affected and 5 unaffected offspring do not carry it.

If the two loci (RFLP1 and the disease gene) are unlinked, the probability of the above observation is (0.5)9 = 0.002

If the two loci are in fact linked and the chance of crossover is 10% (called the recombination fraction), the probability of the observed pattern of disease is (0.9)8(0.1)1 = 0.04

For each individual we are computing:

Pr(D|Model) = Pr(disease state | RFLP1 state ^ linkage)

Pr(D|Random) = Pr(disease state | RFLP1 state ^ non-linkage)

Computing a LOD scoreComputing a LOD score

In the prev. example the LOD score is In the prev. example the LOD score is loglog1010(0.04 / 0.002) = 1.3(0.04 / 0.002) = 1.3

A LOD > 3.0 is generally considered significantA LOD > 3.0 is generally considered significant

Alternatively, Alternatively, parametric parametric analysis models modes analysis models modes of inheritance (domnt,recssv,x-linked,etc.)of inheritance (domnt,recssv,x-linked,etc.)

children children

children

children

RDMD

RD

MDLOD

)|Pr(log)|Pr(log

)|Pr(

)|Pr(log10

Table of LOD scoresTable of LOD scores

Recombination Fraction (%)Recombination Fraction (%)

00 1010 2020 3030 4040

Family AFamily A 2.72.7 2.32.3 1.81.8 1.31.3 0.70.7

Family BFamily B -∞-∞ 1.01.0 0.90.9 0.60.6 0.30.3

TotalTotal -∞-∞ 3.33.3 2.72.7 1.91.9 1.01.0

If recombination fraction is unknown, optimize this If recombination fraction is unknown, optimize this parameterparameter

Box 12.1 from Primrose and Twyman

Linkage Linkage disdisequilibrium (LD) mappingequilibrium (LD) mapping

• Also looks at common inheritance but in Also looks at common inheritance but in populations of unrelated individuals – No populations of unrelated individuals – No pedigrees requiredpedigrees required

• Fine mapping with dense markers at least Fine mapping with dense markers at least every 60 kbevery 60 kb

• Beyond this distance loci are generally in Beyond this distance loci are generally in linkage equilibriumlinkage equilibrium

• Also called Association MappingAlso called Association Mapping

• Typically, used to obtain a finer-grained map Typically, used to obtain a finer-grained map after coarse mapping by linkage analysisafter coarse mapping by linkage analysis

Quantifying association with Quantifying association with contingency tablescontingency tables

DD dd

11 oo11 oo33

22 oo22 oo44

o1/(o1+o2)

o2/(o2+o4)Relative risk =

Observed o Expected e

DD dd

11 R1*C1/R1*C1/(R1+R2)(R1+R2)

R1*C2/R1*C2/(R1+R2)(R1+R2)

22 R2*C1/R2*C1/(R1+R2)(R1+R2)

R2*C2/R2*C2/(R1+R2)(R1+R2)

C1 C2

R1

R2

e

eo 22

Linkage and LD analysis in tandemLinkage and LD analysis in tandem

Figure 12.2 from Primrose and Twyman

LD mapping elucidates our LD mapping elucidates our evolutionary originsevolutionary origins

In Northern European populations, LD In Northern European populations, LD extends for ~60kbextends for ~60kb

In a Nigerian African population, LD In a Nigerian African population, LD extends for ~5kb, a much shorter extends for ~5kb, a much shorter distancedistance

What do we conclude from these What do we conclude from these findings? findings?

Resources for genetic mappingResources for genetic mapping

CEPH- (Centre d’Etude du CEPH- (Centre d’Etude du Polymorphisme Humaine) Large Polymorphisme Humaine) Large database of pedigrees/nuclear database of pedigrees/nuclear familiesfamilies

dbSNP- database of SNPs found in the dbSNP- database of SNPs found in the human genomehuman genome

Successfully mapped: Type I diabetes, Successfully mapped: Type I diabetes, cystic fibrosis, Breast cancer (BRCAI cystic fibrosis, Breast cancer (BRCAI and II), Crohn’s disease, etc.and II), Crohn’s disease, etc.

Haplotype mappingHaplotype mapping A A haplotype haplotype is a pattern of SNPs in a is a pattern of SNPs in a

contiguous stretch of DNAcontiguous stretch of DNA Due to linkage disequilibrium, SNPs are Due to linkage disequilibrium, SNPs are

typically inherited in discrete haplotype typically inherited in discrete haplotype blocks spanning 10-100kbblocks spanning 10-100kb

Greatly simplifies LD analysis, because Greatly simplifies LD analysis, because rather than screen all SNPs in a region, we rather than screen all SNPs in a region, we just need to screen a few and the rest can just need to screen a few and the rest can be inferredbe inferred

A complete human haplotype map is still A complete human haplotype map is still underwayunderway

Example haplotype mapExample haplotype map

Figure 12.4 from Primrose and Twyman

SNPs and PharmacogenomicsSNPs and Pharmacogenomics Refers to the complete list of genes that determine Refers to the complete list of genes that determine

the overall efficacy and toxicity of a drugthe overall efficacy and toxicity of a drug Tries to account for all genes that influence:Tries to account for all genes that influence:

– Drug metabolismDrug metabolism

– Drug transport/exportDrug transport/export

– ReceptorsReceptors

– Signaling pathways, etc.Signaling pathways, etc.

Your genotype would allow a physician to Your genotype would allow a physician to determine the optimal dose and medication for determine the optimal dose and medication for optimal therapyoptimal therapy

Pharmas are spending a lot of money to discover Pharmas are spending a lot of money to discover clinically relevant SNPsclinically relevant SNPs

Population Genetics 101:Population Genetics 101:Measuring Genetic VariationMeasuring Genetic Variation

Observed vs. expected heterozygosityObserved vs. expected heterozygosity

HHoo = Observed fraction of heterozygous individuals = Observed fraction of heterozygous individuals

HHee = Expected fraction based on allele frequencies = Expected fraction based on allele frequencies

The frequency f(X) of allele X is the fraction of times The frequency f(X) of allele X is the fraction of times it occurs over all loci (2 per individual)it occurs over all loci (2 per individual)

HHee = 1 – the probability of homozygosity = 1 – the probability of homozygosity

= 1 – [f= 1 – [f22(X) + f(X) + f22(Y) + … ] for all alleles (X,Y,…)(Y) + … ] for all alleles (X,Y,…)

Example: 10 Unique GenotypesExample: 10 Unique Genotypes(in bp lengths of microsatellite)(in bp lengths of microsatellite)

Allele AAllele A Allele BAllele B # # individualsindividuals

243243 243243 11

255255 259259 11

257257 257257 11

257257 259259 11

259259 259259 11

261261 261261 99

261261 263263 33

261261 267267 11

263263 263263 44

263263 271271 11

Ho ≈ 0.30

He ≈ 0.69

H = 1: high diversity

H = 0: asexual mitoticreproduction

Ho << He indicates selective pressure or non-random mating

Sib-pair analysis in nuclear familiesSib-pair analysis in nuclear families

Conventional linkage analysis is usually the “first line of Conventional linkage analysis is usually the “first line of attack” but seldom works for complex diseases (why?)attack” but seldom works for complex diseases (why?)

For a slightly more powerful test, analysis can be restricted For a slightly more powerful test, analysis can be restricted to to nuclear families nuclear families in which ≥2 children have the disease.in which ≥2 children have the disease.

Figure 12.1 from Primrose and Twyman