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SNPs 2
SNPs 2
-Insertion/Deletion Polymorphisms
SINGLE NUCLEOTIDE POLYMORPHISMS
Minisatellites
repeat unit: 14-100
example:
Spinocerebellar ataxia Type10 (SCA10) (OMIM:+603516) is caused by largest tandem repeat
seen in human genome. Normal population has 10-22 mer pentanucleotide ATTCT repeat in
intron 9 of SCA10 gene; where as SCA10 patients have 800-4500 repeat units, which causes
the disease allele up to 22.5 kb larger than the normal one.
INSERTION/DELETION POLYMORPHISMS
example:
Association between coronary heart disease and a 287 bp Indel Polymorphism
located in intron 16 of the angiotensin converting enzyme (ACE) have been reported
(OMIM 106180). This Indel, known as ACE/ID is responsible for 50% of the inter
individual variability of plasma ACE concentration.
ESTIMATED NUMBERS
Mutation
If the
variation is
present
less than 1
percent of
the time
(<= 1%)
SINGLE NUCLEOTIDE POLYMORPHISMS
(SNPs)
Transitions
change of one purine (A,G) for a purine,
or a pyrimidine (C,T) for a pyrimidine
A G G A C T T C
Transversions
change of a purine (A,G) for a pyrimidine (C,T),
or vice versa
A C A T G C G T C A C G T A T G
TRANSITIONS AND TRANSVERSIONS
Non-coding SNPs:
5’ and 3’ UTRs
Introns
Intergenic Spaces
rare mutations
that cause
medelian
diseases with
allele frequency
below 1%.
SNPs DISTRIBUTION
1 SNP per 1 kb sequence, or nucleotide
diversity of 10 x 10-4 in the human genome
Highest (%)
of SNPs The number of SNPs seems to be correlated
with the length of the chromosomes
• DISEASE MAPPING
Direct / Indirect Association Studies
• PHARMACOGENOMICS
• POPULATION GENETICS
DISEASE MAPPING
• Linkage Analysis
– Within-family associations between marker
and putative trait loci
• Linkage disequilibrium: 0 1
( = probability of allelic association)
Linkage equilibrium: = 0
Complete linkage disequilibrium: = 1
Linkage versus Linkage-Disequilibrium
Both linkage and linkage-disequilibrium (LD) measures a
correlation, or co-segregation, or association, between a
genetic marker and the disease affection status
SNP
SNP
Phenotype
Black eye
1 2 3 4 5 6
GATATTCGTACGGA-T
Brown eye Haplotypes
GATGTTCGTACTGAAT
Black eye GATATTCGTACGGA-T AG- 2/6
Blue eye GATATTCGTACGGAAT GTA 3/6
Brown eye GATGTTCGTACTGAAT AGA 1/6
Brown eye GATGTTCGTACTGAAT
DNA Sequence
The term genotype can refer to the SNP alleles that a person
has at a particular SNP, or for many SNPs across the genome
INTERNATIONAL HAP MAP PROJECT
The HapMap Home Page URL: http://www.hapmap.org/index.html.en
The HapMap will be a tool that will allow researchers to find genes and
genetic variations that affect health and disease
PHARMACOGENOMICS
Pharmacogenomics is a science that examines the inherited variations in
genes that dictate drug response and explores the ways these variations
can be used to predict whether a patient will have a good response to a
drug, a bad response to a drug, or no response at all
PHARMACOGENOMICS
SNPs in genes encoding drug targets or drug metabolism pathways can
determine the therapeutic utility of pharmacologic agents