Introduction Basic Genetic Mechanisms Eukaryotic Gene Regulation The Human Genome Project Test 1

• Introduction

• Basic Genetic Mechanisms

• Eukaryotic Gene Regulation

• Test 1

• The Human Genome Projects

• Genome I - Genes

• Genome II – Repetitive DNA

• Genome III - Variation

• Test 2

• Genes and Diseases

• Pharmacogenomics

• Test 3

• Your Presentations

• Your Presentations

• Happy New Year!

Molecular GeneticsThe Human Genome: Biology and Medicine

http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN

http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN

The Human Genome

The Human Genome

21 000

MUTATIONSMUTATIONS Rare variantsRare variants

PolymorphismsPolymorphisms

GENETIC VARIATIONS: alternatives of genomic DNA sequence (alleles) that are present in individual

(-s) or population (-s)

Minor allele frequency > 1%

Minor allele frequency < 1%

“Bad”: cause genetic

disease

Polymorphisms (common variation): majority – neutralThe rest: • slightly “bad” (predispose to disease)• slightly “good” (protect from disease)• both slightly bad and good (predispose to and protect from certain conditions)

Types of genetic variations

• Inversions• Duplications• Translocations• Transposon insertions

Variations exceeding 1000bp - STRUCTURAL VARIATIONS• less than 3 million bp - submicroscopic; larger– microscopic• InDels and duplications are called CNVs (copy number variations)

CCTAGTTGACTGATCGCGGGATTCACACACATGG

CCTGGTTGAC..ATCGCGGGATTCACACACACACATGG

Single (point) base changes• two alleles

SNPsSingle Nucleotide Polymorphisms; > 10, 000, 000

InDels(insertions/deletions)

• two alleles• > 1,000,000

SSR – short sequence repeats(VNTR - variable number tandem repeats)• many alleles • microsatellites (1-5)• minisatellites (6-100)• …> 1,000,000

Each person is unique

Molecular Biology of the Cell,4th Edition

At the same time, humans “are essentially identical twins”

10 000

7 000 000 000

< 3000 generations

RAO(R) – Recent African Origin (and Replacement)

Genetic diversity is highest in Africans

Population codes:AF, African- American; AS, Asian; CA, Caucasian; and HL, Hispanic- Latino.

Genetic diversity is highest in Africans

Use of common variations in genetic association studies

CD /CV (Common Disease/Common Variants) hypothesis:

Common diseases are underlied by a few common variants

CD/RV (Common Disease /Rare Variants) – diseases are driven by many rare alleles

SNP map Genes

SNPs• A map of human genome sequence variation...– The International SNP Map Working Group. Nature

(2001) 409, 928-933.

• Features of the map:– 1.42 million SNPs

– average density 1 SNP every 1.9 kilobases

– 60 000 SNPs fall within exons

– 85% of exons are within 5 kb of the nearest SNP

Good properties

• Many 90%

• Simple binary

• Even relatively

• Stable evolutionary

MARKERS

Properties of SNPs from a distinct point of view

Other SNP properties• ~ 0.1% affect protein function

- the same number might affect gene expression

• Distribution is non-uniform – genome-wide (0.1% - 10%)– between chromosomes (autosomes > X > Y)– more in non-coding than coding regions– in coding sequences silent substitutions>

missense– 2/3 are transitions (metC deamination in

CpGs)

• Cosmopolitan / Population-specific

Bad property - some SNPs (alleles) increase the risk of disease

Analysis of some SNPs can capture effects of other SNPs

MARKERS

This is possible owing to Linkage Disequilibrium (LD)

There are many haplotypes in the absence of LD

Gene SNPs

LDAA CC

AA AA

AA CC

AA AA

CC

CC

TT

TT

GG CC

GG AA

GG CC

GG AA

CC

CC

TT

TT

AA AATT

GG CCCCAA CCCC

GG AATT

There is a limited diversity of haplotypes if

LD is present

• LD - Linkage Disequilibrium – non-random association among alleles at two or more loci in POPULATION (or a measure of co-segregation of alleles in population)

• Haplotype – combination of alleles on a chromosome (usually used with respect to a small region)

• LD - Linkage Disequilibrium – non-random association among alleles at two or more loci in POPULATION (or a measure of co-segregation of alleles in population)

• Haplotype – combination of alleles on a chromosome (usually used with respect to a small region)

There is a limited diversity of haplotypes when LD exists

The strength of LD varies and can change

• PA and PB - allele frequencies

• PAB - haplotype frequencies

• D = PAB - PA x PB

• D’= D/DMax

AA

AA

CC

TT

GG

GG

CC

TT

50 %

50 %

0 %

0 %

AA

AA

CC

TT

GG

GG

CC

TT

40 %

40 %

10 %

10 %

AA

AA

CC

TT

GG

GG

CC

TT

25 %

25 %

25 %

25 %

TT

CC

All SNP alleles in this examplehave frequency = 50 %

AA

GG

D = 0.25D’= 1Complete LD

D = 0.15D’= 0.6Partial LD

D = 0D’= 0No LD

Aa

Bb

Processes shaping genetic variation and LD

GENETIC

• mutagenesis

• recombination

• gene conversion

DEMOGRAPHIC

• population age

• genetic drift

• population dynamics– migration– bottlenecks …NATURAL SELECTION

(i) Genetic processes: recombination

LD, recombination, and age of population

Recombinant DNA, 3rd Edition

N Engl J Med 2002;347:1512-1520. Genomic Medicine — A Primer.

Example of origin and decay of LD

(ii) Demographic processes: genetic drift and “founder” mutations

Recombinant DNA, 3rd Edition

(ii) Demographic processes: “bottleneck” effect

Raven & Johnson (2004) Biology. Fig. 21.6

(iii) Natural Selection: hitchhiking

LD islands or recombination deserts

Recombination rates vary by more than an order of magnitude across the genome

Human genome is made up of haplotype blocks

Human genome is made up of haplotype blocks

Haplotype map (HapMap) project – finished in 2005

‘tag’ SNPMARKERS

The practical aim of the HapMap project

If haplotypes are known, all common variation of a region can be determined through genotyping just a few tag SNPs

Structural variations (microscopic) in the human genome

INVERSION TRANSLOCATION

NATURE REVIEWS | GENETICS VOLUME 7 | FEBRUARY 2006 | 87

CNV

Structural variations (submicroscopic) in the human genome

Copy-number variations (CNV)

NATURE REVIEWS | GENETICS VOLUME 7 | FEBRUARY 2006 | 87

Possible influence of structural variants

Human Molecular Genetics, 2006, Vol. 15, Review Issue 1 R59

CNV map

NATURE| Vol 444|23 November 2006; pp 444-454

~1500 CNVs360Mb12% of genome

http://www.nature.com/nature/focus/1000genomes/

• Introduction

• Basic Genetic Mechanisms

• Eukaryotic Gene Regulation

• Test 1

• The Human Genome Projects

• Genome I - Genes

• Genome II – Repetitive DNA

• Genome III - Variation

• Test 2

• Genes and Diseases

• Pharmacogenomics

• Test 3

• Your Presentations

• Your Presentations

• Happy New Year!

Molecular GeneticsThe Human Genome: Biology and Medicine

http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN

http://priede.bf.lu.lv/ Studiju materiāli / MolekularasBioloģijas / MolGen / EN