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Molecular Genetics. The Human Genome: Biology and Medicine. Introduction Basic Genetic Mechanisms Eukaryotic Gene Regulation The Human Genome Project Test 1 Genome I - Genes Genome II – Repetitive DNA Genome III - Variation Test 2 Monogenic and Complex Diseases Finding ‘Disease’ Genes - PowerPoint PPT Presentation
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• 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