Genetics of Complex TraitsGenetics of Complex Traits and Diseases and Diseases

张咸宁zhangxianning@zju.edu.cn

Tel ： 13105819271; 88208367 Office: A705, Research Building

2012/09

Genetic Susceptibility易感性• An inherited predisposition to a

disease or disorder which is not due to a single-gene cause and is usually the result of a complex interaction of the effects of multiple different genes, i.e. polygenic inheritance.

Any disease is the result of the combined action of genes and environment

Classification of genetic disorders:1. Chromosome disorders:2. Single-gene disorders:3. Complex (multifactorial,

polygenic) disorders:4. Somatic cell genetic disorders:5. Mitochondrial genetic disorders:

• ABO blood group depends (with rare exceptions) on the genotype at just one locus, the ABO locus at chromosome 9q34. Rhesus hemolytic disease of the newborn depends on the genotypes of mother and baby at the RHD locus at chromosome 1p36, but also on mother and baby's being ABO compatible. Hirschsprung disease depends on the interaction of several genetic loci. Adult stature is determined by the cumulative small effects of many loci. Environmental factors are also important in the etiology of Rhesus hemolytic disease, Hirschsprung disease, and adult height.

Why study the genetics of common diseases?

• Understanding the underlying genetics will lead to understanding the causes, which may lead to better and more specific therapies

• Identification of the responsible genes helps to identify those who are at risk in families and in the population, allowing individualized health assessment and targeted prevention

How to Determine the Genetic Components of Complex Diseases?

• Family, twin and adoption studies• Segregation analysis• Linkage analysis• Association studies and linkage

disequilibrium• Identification of DNA sequence

variants conferring susceptibility

• Trait: Any detectable phenotypic property or character.

• Qualitative trait: A genetic disease trait that either present or absent. The pattern of inheritance for a qualitative trait is typically monogenetic, which means that the trait is only influenced by a single gene.

• Quantitative trait: are measurable characteristics such as height, blood pressure, serum cholesterol, and body mass index. A quantitative trait shows continued variation under the influence of many different genes.

Quantitative trait:Normal distribution• Height• Weight• Shape• Color• Blood pressure• metabolic activity• reproductive rate Polygenes: small-but-equal effect QTL (quantitative trait loci)

Successive Approximations to a Gaussian Distribution: QTL

Liability易患性• A concept used in disorders which

are multifactorially determined to take into account all possible causative factors.

Familial aggregation: Affected individuals tend to cluster in families.

prevalence of the disease in a relative “r”

of an affected person

r= ---------------------------------------------------

population prevalence of the disease

• • The higher the familial aggregation, the larger The higher the familial aggregation, the larger the the rr..

• • If If rr = 1, then the relative is at no greater risk = 1, then the relative is at no greater risk

than anyone in the general population.than anyone in the general population.

Twin studies suffer from many limitations

• Monozygotic (MZ) twins are genetically identical clones and should always be concordant (both the same) for any genetically determined character.

• Dizygotic (DZ) twins share half their genes on average, the same as any pair of sibs.

Genetic Differences between Identical Twins

• All individuals, even monozygotic twins, differ in:

– their repertoire of antibodies and T-cell receptors (because of epigenetic rearrangements and somatic cell mutations);

– somatic mutations in general

– the numbers of mitochondrial DNA molecules (epigenetic partitioning);

– the pattern of X inactivation, if female.

Genetic analysis of quantitative traits

• Correlation:

• Heritability:

Correlation is a statistical measure of the degree of association of variable phenomena (a measure

of the degree of resemblance or relationship between 2 parameters).

Coefficient of correlation (r)

• Positive correlation: r>1

• No correlation: r=0

• Negative correlation: r<1

Heritability (Heritability (hh2))遗传率遗传率 : : The proportion of the total variation of a character attributable to genetic as opposed to environment factors.

CMZ -- CDZ

• h2 = ----------------------- 100 -- CDZ

• • If If ccMZ MZ >> >> ccDZDZ then then hh2 is high (approaches 1) is high (approaches 1)

• • If If ccMZMZ = = ccDZ DZ then then hh2 is low (approaches 0) is low (approaches 0)

[c = concordance][c = concordance]

Concordance RateTrait or Disease MZ twins DZ twins Heritability

Alcoholism 0.6 0.3 0.6Autism 0.92 0.0 >1Cleft lip/palate 0.38 0.08 0.6Diabetes, type 1 0.35-0.5 0.05-0.1 0.6-0.8Diabetes, type 2 0.7-0.9 0.25-0.4 0.9-1.0Measles 0.95 0.87 0.16Schizophrenia 0.47 0.12 0.7

Heritability (h2) for Various Diseases

Common Disease Mendelian Subtype Involved Gene 

Atherosclerosis Familial hypercholesterolemia LDL receptor (LDLR)Breast cancer Familial breast/ovarian cancer BRCA1, BRCA2Amyotrophic lateral Familial ALS Superoxide dismutase (SOD1) Sclerosis

Parkinson disease Familial Parkinson disease -synucleinAlzheimer disease Familial AD PS1, PS2, APPHypertension Liddle syndrome Renal sodium channel (SCNN1B)

Mendelian Forms of Common Complex Diseases

Spectrum of Complexity for Common Spectrum of Complexity for Common Diseases: From “Simple” to ComplexDiseases: From “Simple” to Complex

Alzheimer disease (AD) Alzheimer disease (AD)

• Complex genetic contributions to AD Complex genetic contributions to AD may come from:may come from:– One or more incompletely penetrant genes One or more incompletely penetrant genes

that act independently;that act independently;– Multiple interacting genes; orMultiple interacting genes; or– Combination of genetic and environmental Combination of genetic and environmental

factorsfactors

Spectrum of Complexity for Common Spectrum of Complexity for Common Diseases: From “Simple” to ComplexDiseases: From “Simple” to Complex

Alzheimer disease (AD) Alzheimer disease (AD)

• Familial ADFamilial AD– Approximately 10% of patients have a Approximately 10% of patients have a

monogenic form of AD with highly monogenic form of AD with highly penetrant, age-related, autosomal dominant penetrant, age-related, autosomal dominant inheritanceinheritance

– Presents earlier than typical AD: as early as Presents earlier than typical AD: as early as 33rdrd decade (20s) compared with 7 decade (20s) compared with 7thth-9-9thth decades for typical AD decades for typical AD

– Three genes: Three genes: PS1PS1, , PS2PS2, , APPAPP

Even “Sporadic” AD May Have a Even “Sporadic” AD May Have a Genetic ComponentGenetic Component

• Apolipoprotein E (Apolipoprotein E (APOEAPOE))– Protein component of LDL particleProtein component of LDL particle– Constituent of amyloid plaques in ADConstituent of amyloid plaques in AD– Three alleles: Three alleles: 22, , 33, , 44

44//4: >90% show AD by age 804: >90% show AD by age 8022//3: <10% show AD by age 803: <10% show AD by age 8044/- /- : 25-50% show AD by age 80: 25-50% show AD by age 80• Environmental factors also involvedEnvironmental factors also involved

– Association between presence of Association between presence of 4 allele and AD 4 allele and AD following head trauma is seen in professional boxersfollowing head trauma is seen in professional boxers

Genetic Testing for Genetic Testing for APOE APOE GenotypesGenotypes

• Testing asymptomatic individuals for Testing asymptomatic individuals for 4 4 remains controversialremains controversial– Poor predictive valuePoor predictive value– No effective therapeutic intervention No effective therapeutic intervention

available to prevent onsetavailable to prevent onset

• Available through direct-to-consumer Available through direct-to-consumer marketingmarketing

CNVs are common in all genomes surveyed …

• Blue = pathogenic• Red = deletion• Green = duplication

And sequence variants are even more common…

Sequence Variants of Uncertain Clinical Significance:

Lessons from BRCA1/BRCA2

• Complete sequencing of both genes in over 150,000 people

• >10,000 deleterious mutations and variants identified

• Each week, 10-20 new ones detected

B. Ward (Myriad Genetics), personal communication with Prof. Grody WW,UCLA

Genetic mapping of complex traits

• Linkage analysis

• Association studies

Genetic mapping of complex traits

Linkage analysis: genome scan which analyzes the disease pedigrees using hundreds of polymorphic markers (STR) throughout the entire genome.

L (θ)

• Lods (log odds score): Z(θ) = log[------------ ]

L (1/2)

Lod score (z)

• A measure of the likelihood of genetic linkage between loci.The log (base 10) of the odds that the loci are linked (with recombination θ) rather than unlinked.

• For mendelian characters a lod score greater than +3 is evidence of linkage;one that is less than –2 is evidence against linkage.

Identity by State (IBS) and Identity by Descent (IBD)

• Both sib pairs share allele A1. The first sib pair have two independent copies of A1 (IBS but not IBD); the second sib pair share copies of the same paternal A1 allele (IBD). The difference is only apparent if the parental genotypes are known.

Sib Pair Analysis

(A)By random segregation sib pairs share 0, 1 or 2 parental haplotypes 1/4, 1/2 and 1/4 of the time, respectively.

(B) Pairs of sibs who are both affected by a dominant condition share one or two parental haplotypes for the relevant chromosomal segment.

(C) Pairs of sibs who are both affected by a recessive condition share both parental haplotypes for the relevant chromosomal segment.

Affected sibling-pair analysis

Suggested Criteria for Reporting Linkage

Category of linkage

Expected No. of occurrences by chances in a whole genome scan

Range of approximate p value

Range of approximate lod scores

Suggestive 1 7 x 10-4 – 3 x 10-5 2.2 - 3.5

Significant 0.05 2 x 10-5 – 4 x 10-7 3.6 - 5.3

Highly significant

0.001 <3 x 10-7 >5.4

Confirmed 0.01 in a search of a candidate region that gave significant linkage in a previous independent study

Lod score: 3.6 for IBD testing of affected sib pairs, 4.0 for IBS

•Given that the loci are truly linked, with recombination fraction q, the likelihood of a meiosis being nonrecombinant is 1 - θ and the likelihood of it being recombinant is θ. •If the loci are in fact unlinked, the likelihood of a meiosis being either recombinant or nonrecombinant is 1/2. Family AThere are five recombinants and one nonrecombinant.The overall likelihood, given linkage, is (1 - θ)5. θThe likelihood given no linkage is (1/2)6

The likelihood ratio is (1 - θ)5. θ / (1/2)6

The lod score, Z, is the logarithm of the likelihood ratio.Family BII1 is phase-unknown.

If she inherited A1 with the disease, there are five nonrecombinants and one

recombinant.If she inherited A2 with the disease, there are five recombinants and one

nonrecombinant.The overall likelihood is 1/2 [(1 - θ)5. θ / (1/2)6] + 1/2 [(1 - θ). θ 5 / (1/2)6]. This allows

for either possible phase, with equal prior probability.The lod score, Z, is the logarithm of the likelihood ratio.Family CAt this point nonmasochists turn to the computer.

Genome-wide scanning: autozygosity mapping

Positional cloningPositional cloning

• Disease mapping - chromosome deletion mutation

- linkage analysis

• Fine mapping

• Candidate genes- pathogenic mutation

screening- functional assay

Another method combines genome scanning and the use of animal models

Population Associations• The low success rate of linkage studies for cx traits

in the 1990s suggested that many of the susceptibility factors must be relatively weak, highly heterogeneous, or both.

• Rather than studying affected relatives, association studies seek populationwide associations between a particular condition and a particular allele or haplotype somewhere in the genome.

Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science. 1996; 273:1516.

Population Associations• Association is simply a statistical statement about the co-

occurrence of alleles or phenotypes.

HLA-DR4, 36% UK / 78%, rheumatoid arthritis• A population association can have many possible causes,

not all of which are genetic.

Direct causation:

An epistatic effect:

Population stratification: HLA*A1 and

Type I error: false positives

Linkage disequilibrium (LD):

Association is quite different from linkage, except where the family and the population

merge• Linkage is a specific genetic relationship

between loci (physical sites on the cs)

• Association is a relation between specific alleles and/or phenotypes.

• Linkage does not of itself produce any association in the general population. Linkage creates association within families, but not between unrelated people.

Genome-Wide Association Studies (GWAS)

Association studies depend on linkage disequilibrium (LD)

• The occurrence together of 2 or more alleles at closely linked loci more frequently than would be expected by chance. → allelic association

• EMLD (http://request.mdacc.tmc.edu/qhuang/ Software/pub.htm)

• D’:0 （ no LD ） ~±1 (complete association)

SNP: A change in which a single base in the DNA differs from the usual base at that position.

Millions of SNP's have been cataloged in the human genome. Some SNPs such that which causes sickle cell are responsible for disease. Other SNPs are normal variations in the genome.

Haplotype

• A group of alleles in coupling at closely linked loci, usually inherited as a unit.

Haplotype

Tag SNPs• A select, minimal subset of all the SNPs

in a genomic region, chosen because they are in linkage disequilibrium with one another in the population. Tag SNPs are useful because they form a minimum set of SNPs whose alleles constitute haplotypes capable of representing all the common haplotypes in that region.

HapMap: A set of haplotypes, defined by tag SNPs, distributed throughout the genome, used

for association studies.

Measures of LD• If 2 loci have alleles A, a and B, b with

frequencies pA, pa, pB and pb → 4 possible haplotype: AB, Ab, aB and ab; pAB, pAb, paB and pab.

• If no LD, pAB= pApB and so on. The degree of departure, D = pABpab – pAbpaB.

• D’=(pAB - pApB )/Dmax (the maximum value of pAB - pApB possible with the given allele ∣ ∣frequencies)

• △2=(pAB - pApB)2/(pApapBpb)

Nature, Feb 11,2007

A new generation of genomewide association studies (GWAS) has finnaly broken the logjam in cx dis

research??

Linkage and Association: Complementary Techniques

• Linkage operates over a long chromosomal range, scan the entire genome in a few hundred tests– 250 ASP, 300 markers = 1.5-3 x 105 tests– candidate regions impracticably large for

positional cloning• LD short range phenomenon

– TDT, 300 trios, 25 kb LD = 108 tests– Need to focus on predetermined candidate

regions by animal models, known gene, or linkage studies

Difficulties in Identification of DNA Sequence Variants Conferring Susceptibility to Cx diseases

• No single gene mutation is necessary or sufficient to cause the disease– even a true susceptibility allele will be found in some

controls and be absent from some patients.– The main determinants of susceptibility may be

different in different populations• No genetic way to identify true determinant among a set

of alleles in a strong LD• The genetic variants causing susceptibility to common

diseases may not be obvious mutations– May be SNPs in noncoding regions have small effect

on promoter activity, RNA splicing or mRNA stability.

How to Determine the Genetic Components of Complex Diseases?

• Family, twin and adoption studies• Segregation analysis• Linkage analysis• Association studies and linkage

disequilibrium• Identification of DNA sequence

variants conferring susceptibility

Characteristics of Inheritance of Complex Diseases

1. Diseases with complex inheritance are not single-gene disorders and do not demonstrate a simple Mendelian pattern of inheritance.

2. Diseases with complex inheritance demonstrate familial aggregation, because relatives of an affected individual are not likely to have disease-predisposing alleles in common with the affected person than are unrelated individuals.

3. Pairs of relatives who share disease-predisposing genotypes at relevant loci may still be discordant for phenotype(show lack of penetrance) because of the crucial role of nongenetic factors in disease causation. The most extreme examples of lack of penetrance despite identical genotypes are discordant MZ.

4. The disease is more common among the close relatives of the proband and becomes less common in relatives who are less closely related. Greater concordance for disease is expected among MZ verse DZ.

Acknowledge （ PPT特别鸣谢！）

• UCLA David Geffen School of Medicine

• www.medsch.ucla.edu/ANGEL/

• Prof. Grody WW (Divisions of Medical Prof. Grody WW (Divisions of Medical Genetics and Molecular Pathology), et al.Genetics and Molecular Pathology), et al.