A basic review of genetics A basic review of genetics

Dr. Danny ChanAssociate Professor

Assistant Dean (Faculty of Medicine)

Department of Biochemistry Department of Biochemistry The University of Hong KongThe University of Hong Kong

Cells and genesCells and genes

50,000,000,000,000 cells

Nucleus (99.9% of the genes)

Cells and genesCells and genes

Mitochondria (few more genes)

~20, 0000 genes

Genes are on DNAGenes are on DNA

Cytosine

Thymine

Guanine

Adenine

OCH2OO P

O

O-

N

N

O

CH3

OCH2OO P

O

O-

N

N

O

NH2

OCH2OO P

O

O-

H

O

N

N

O

NH2

N

N

OCH2OO P

O

O-

N

N

N

N

NH2

3’

5’

DNA sequence genetic code genes

DDeoxyriboseNNucleicAAcids

Genes determine why we are the way we are!Genes determine why we are the way we are!

Genes are passed on from one Genes are passed on from one generation to the nextgeneration to the next

Genetic traitsGenetic traits

You have inherited genes from your father that make proteins

instructing your hair cells or eye cells to produce hairs and eyes that are the same colours

and shape as your father.

Genetic traits can also be a behavior, feelings, or responses to a given environment

DNA are super-coiled into chromosomesDNA are super-coiled into chromosomes

chromosome

22 pairs of autosomes and 1 pair of sex chromosomes

Human GenomeHuman Genome

Autosomes Sex chromosomes

24 pairs of chromosomes

Other primate chromosome numbersOther primate chromosome numbers

21 pairs of chromosomes

Other speciesOther species

30 pairs of chromosomes

39 pairs of chromosomes

4 pairs of chromosomes

The genome projectsThe genome projects

How similar are we to other species?How similar are we to other species?

~98.5%~93%

How about with other humans?How about with other humans?

~99.5%

What makes us different

from one another?

Variations in DNA sequence or Variations in DNA sequence or PolymorphismsPolymorphisms

• Variable number tandem repeats (VNTRs)

• Microsatellites

• Single nucleotide polymorphisms (SNPs)

• Small insertions and deletions (Indels)

• Copy number variations (CNVs)

Variations in DNA sequence or Variations in DNA sequence or PolymorphismsPolymorphisms

• Variable number tandem repeats (VNTRs)

• Microsatellites

• Single nucleotide polymorphisms (SNPs)

• Small insertions and deletions (Indels)

• Copy number variations (CNVs)

Repeat units of nucleotides 1-6bp in length

The most widely used are the (CA)n microsatellites

CACACACACACACACACACACACA

CACACACACACACACACACACACACACACACA

6 (CA) allele6 (CA) allele

8 (CA) allele8 (CA) allele

MicrosatellitesMicrosatellites

are substitutions, insertions or deletions of a single base

TCGAGAGGCTAGGCTAGGA

TCGAGAGGCCAGGCTAGGASubstitutionSubstitution

T-alleleT-allele

C-alleleC-allele

TCGAGAGGCTTAGGCTAGGA

TCGAGAGGCAGGCTAGGA

InsertionInsertion (+) allele(+) allele

(-) allele(-) allele

Single nucleotide polymorphisms (SNPs)Single nucleotide polymorphisms (SNPs)

deletiondeletion

SNPs arise during DNA replicationSNPs arise during DNA replication

Opportunities for errors

Single base errors/changes create

3 x 109 bases

SNPs SNPs

101077 SNPs SNPs

Genetic differences and similarities Genetic differences and similarities between peoplebetween people

You

Rest of the world

Genetic signature

Some SNPs affect the way we lookSome SNPs affect the way we look

Some affect our susceptibility to diseasesSome affect our susceptibility to diseases

Others affect our response to drugs/painOthers affect our response to drugs/pain

or .. no differences!or .. no differences!

.. in health, personalities or responses to the environment

SNPs affecting gene functionSNPs affecting gene function

mRNA

Gene

t-RNA

Newly synthesized

protein

ProteinAlteredProtein

Protein function and phenotypeProtein function and phenotype

ProteinAlteredProtein

Alteredproteinfunction

AlteredPhenotyp

e

Mum Dad

Hair color Hair color

Height Height

Longevity Longevity

Body fat Body fat

Intelligence Intelligence

Eye color Eye color

A pair of homologous chromosomesA pair of homologous chromosomes

2 sets1 set

1 set

oocyte

SpermSomatic cell

Meiosis I Meiosis II

Diploid cell

Fourhaploid cells

DNAreplication

Homologouschromosome

pairing

Meiosis (making sperm or oocytes)Meiosis (making sperm or oocytes)

Genetic recombination in meiosisGenetic recombination in meiosis

Doubling Cross-over and exchange DNA

Genes get shuffled during recombination

Phenotypes Phenotypes

Observable or measurable traits

Genes + environment

Begins in the womb and continues throughout life

Phenotypes Phenotypes

Differences in some phenotype are determined mostly by genes

Height

How genes influence personality, behavior and perception is less well understood

We can now interrogate SNPs across our genome all at once

Understand how some SNPs are affecting our phenotype

… … from our genomefrom our genome

Genotype-phenotype relationship

Learning more about our phenotypes Learning more about our phenotypes

Correlating genetic variations and diseasesCorrelating genetic variations and diseasesphenotypesphenotypes

• Family linkage analysis

• Case-control association study

Need a large pedigree!Need a large pedigree!

Correlating genetic variations and diseasesCorrelating genetic variations and diseasesphenotypesphenotypes

• Case-control association study

Need a large cohort!Need a large cohort!

• Rare genetic diseases

• Common diseases

Rare genetic diseases Rare genetic diseases

Single gene

Monogenic disorder

Early-onset

Rare

(Osteogenesis imperfecta)

(1:30,000 – 1:70,000)

(prenatal)

An autosomal dominant

disease for which the gene resides on this chromosome

6 (CA) allele CACACACACACA

8 (CA) allele CACACACACACACACA

7 (CA) allele CACACACACACACA

1 (CA) allele CA

2 (CA) allele CACA

3 (CA) allele CACACA…

…

5 65 6 4 74 7 2 32 3

Marker studiedMarker studied

2 32 3 1 51 5 4 44 4

Marker studiedMarker studied

1 51 5 3 53 5 6 76 7

Marker studiedMarker studied

2 42 4 2 52 5 2 72 7

Marker studiedMarker studied

1 31 3 1 21 2 4 54 5

Marker studiedMarker studied

22 4 4 22 5 5 22 7 7

Marker studiedMarker studied

((24)4) ((25)5) ((27))(33)(33) (14)(14)

((23)3)

((26)6) (1(12)) ((26)6)

((24)4)

(16)(16)

(14)(14)

(46)(46)

(34)(34) (13)(13) (58)(58)

(18)(18)

(13)(13) (78)(78)

(18)(18)

(47)(47)

(46)(46) (67)(67)

Genotype other family membersGenotype other family members

The key is to identify a genetic marker that is always inherited by family members with the disease but not

by those who do not have the disease

Disease geneDisease geneGene resides hereGene resides here

Fine mappingFine mapping

Define the region of maximal linkageDefine the region of maximal linkage

Causative mutation!

• The logarithm (in base 10) of the odds of linkage

– the ratio of the likelihood that loci are linked to the likelihood that they are not linked

• A LOD of 3.0 = odds of 1000/1 in favour of linkage

– Equivalent to a 5% chance of error

Logarithm of odds (LOD) scoreLogarithm of odds (LOD) score

Degree of linkageDegree of linkage

• Advantages:– Localization of areas associated with increase

disease risk across the genome

– Can study multiple markers simultaneously

• Disadvantages– Multi-generational cases difficult to recruit with

high mortality conditions

– Difficult to study late-onset diseases/traits

– Difficult to study complex traits

Family linkage studiesFamily linkage studies

Genetics

Many genes may be involved

Environment

Interactions between environment and genes

2 4

1

3

Interaction between genes

(common)

(Risk factors)

Diabetes

Osteoporosis

Osteoarthritis

Alzheimer

Cancer

Complex traitsComplex traits

• Linkage deals with a specific genetic relationship between loci on a chromosome

• Association describes a statistical relationship between genes or genetic variants and the disease/trait of interest

Association study for complex traitsAssociation study for complex traits

Case Control

Large Cohort required

Good phenotype definition

Case-Control Association StudiesCase-Control Association Studies

Allele 1(T)

Allele 2 (A)

Gene A

An example for one SNP in a geneAn example for one SNP in a gene

Case Control

Allele 2 is a possible risk allele

Uneven distribution of the SNP variants indicates an association

Control case association studyControl case association study

Case Control

• Identifies disease susceptibility gene variants by comparing genetic variants between people with and without the disease of interest.

• Any particular association between a genetic variant and a disease does not mean that the variant is important in causation.

Association studiesAssociation studies

“a huge assistance in high throughput mapping of polygenic

diseases and a minor pest”

Linkage disequilibrium (LD)Linkage disequilibrium (LD)

LD relates to recombination eventsLD relates to recombination events

The nonrandom association between alleles in a

population due to their tendency to be co-inherited

because of reduced recombination between them

Hot spots

Cold spots

Gro

up o

f ext

ant

Gro

up o

f ext

ant

chro

mos

omes

chro

mos

omes

Ancestral segmentAncestral segmentNew segment introduced by recombinationNew segment introduced by recombination

MutationMutation

Ancestral Ancestral chromosomechromosome

Gro

up o

f ext

ant

Gro

up o

f ext

ant

chro

mos

omes

chro

mos

omes

Ancestral segmentAncestral segmentNew segment introduced by recombinationNew segment introduced by recombination

MutationMutationSNPsSNPs

Ancestral Ancestral chromosomechromosome

Ancestral segmentAncestral segmentNew segment introduced by recombinationNew segment introduced by recombination

MutationMutation

Ancestral Ancestral chromosomechromosome

Gro

up o

f ext

ant

Gro

up o

f ext

ant

chro

mos

omes

chro

mos

omes

Ancestral Ancestral chromosomechromosome

Polymorphisms within regions Polymorphisms within regions of reduced recombination will of reduced recombination will

mark the same associationmark the same association

Haplotype blockHaplotype block

polymorphic segment of DNA marking an ancestral variantpolymorphic segment of DNA marking an ancestral variant

LD MapLD Map

To identify all common DNA polymorphisms

The International HapMap ProjectThe International HapMap Project

Started October 2002 Define the LD pattern for

different populations

Microsatellites SNPsSNPs

~ 107 to choose from

Using high density of SNPs for disease huntingUsing high density of SNPs for disease hunting

Enhancing mappingAccuracy and speed

Genome wide association scan (GWAS)Genome wide association scan (GWAS)

Now able to assess ~2.5M SNPs in a genome all at once

Various platforms are available for mostly common SNPs (>5 % in the general population)

NHGRI GWA Catalogwww.genome.gov/GWAStudies

Published Genome-Wide Associations through 12/2010, 1212 published GWA at p<5x10-8 for 210 traits

Missing heritabilityMissing heritability

Rare SNPs with strong effect not yet identified?Rare SNPs with strong effect not yet identified?

Next generation sequencingNext generation sequencing

1000 genomes project1000 genomes project

http://www.1000genomes.org

Goal of the 1000 genomes projectGoal of the 1000 genomes project

Rare genetic Rare genetic variantsvariants

Common genetic Common genetic variantsvariants

Diabetes

Osteoporosis

Osteoarthritis

Alzheimer

Cancer

Cystic fibrosis

Huntington disease

Osteogenesis imperfecta

Achondroplasia

Knowledge gap?

discover >95 % ofdiscover >95 % of

SNPs, CNVs, indelsSNPs, CNVs, indels~1% across the genome,0.1-0.5% in gene regions

?

• Small insertions and deletions (indels)

• Copy number variations (CNVs)

• miRNA

• Epigenetic controls

Other variations for considerationOther variations for consideration

Mega load of genetic data will be available .. Mega load of genetic data will be available .. Are we ready with the phenotype information? Are we ready with the phenotype information?

PhenotypePhenotype

PhenotypePhenotype

PhenotypePhenotype

PhenotypePhenotype

$$

$$$$

$$$$$$

$$$$$$$$$$

GenotypeGenotype

GenotypeGenotype

GenotypeGenotype

GenotypeGenotype