SNP: Single Nucleotide
Polymorphism
Definition: DNA sequences where a single nucleotide in the
genome differs between individuals (or between species etc.)
Some SNP terminology...
allele: refers to the variant:
- AAGCCTA to AAGCTTA
- the alleles are C and T.
Almost all SNPs are biallelic (only have
two alleles)
- do not see AAGCATA and AAGCGTA
Coding SNPs
Coding SNP: a
SNP that falls in
the coding
region of a gene.
Because of
redundancy in
the genetic
code, not all
SNPs cause a
change in the
protein.
Coding SNPS do not necessarily change
the protein sequence. These are called
silent or synonymous SNPs.
CCATACAGT
P
T
S (Proline-Tyrosine-Serine)
CCATATAGT
P
T
S (Proline-Tyrosine-Serine)
SNPS that change the coding sequence are called
nonsynonymous SNPS
Non-Synonymous SNPs:
Missense and Nonsense SNPs
A SNP that changes the amino acid is
called a missense SNP.
CCATACAGT (Proline-Tyrosine-Serine)
P
T
S
CCATCCAGT
P
S
S
(Proline-Serine-Serine)
- SNPs that insert a premature stop codon are
called nonsense SNPs
CCATACAGT
P
T
S (Proline-Tyrosine-Serine)
CCATAAAGT
P
(Proline-Stop)
SNPS in non-coding regions of DNA
• Can occur in non-coding region of genes
(intron and promoter)
• Are found in intergenic regions of genes
How many SNPs are there?
• ~3.1 million genotyped SNPS in humans
(about 1 every 1000 bp)
• Each SNP has an allele frequency: the
frequency of the alleles in a population
may differ:
90% of population CCATACAGT
10% of population CCATATAGT
Minor allele
What can SNPs tell us
• Traits
• Disease risk
• Ancestry Tracking/ Population Info
Traits partially determined by SNPs
height
hair color
bitter taste
SNPs and disease risk
Example: BRCA1 protein is directly
involved in repair of damaged DNA.
- hundreds of SNPs have been found in BRCA1.
- women with certain BRCA1 SNPs have up to 85% risk of
developing breast cancer
SNPs have been associated with:
-Alzheimer's
-Crohn’s disease
-and many many more
SNPs and drug sensitivity
Warfarin: the most widely prescribed anticoagulant drug
in North america (2 million americans a year).
Dosage is done by trial and error:
too little: lead to clots resulting in heart attack or stroke
too much: uncontrolled bleeding
2 SNPs in the CYP2C9 gene affects the body’s ability to
process warfarin- If you have the “sensitivity” alleles your
body can tolerate much less warfarin than those without
the alleles.
Historically isolated populations may have different
allele frequencies than others:
• allele for blue eyes is
more common in
populations of
Northern Euopean
decent
• alleles for Tay Sachs disease are more common in
Ashkenazi Jewish populations
• allele for sickle cell anemia is more common in
populations of African decent
• allele for Warfarin sensitivity is a more common in
asian populations
Do you want to know your own
SNPs?
There are now companies that will analyze your SNPs
for you:
Do you want to know?
Pros:
• Can start preventing diseases early (coronary
heart disease, breast cancer)
• May be interested in genetic risks in pregnancy
• May want to know about your ancestry
Cons:
• Many tests on the market are not regulated as
diagnostics- may be inaccurate
• Ignorance is bliss
• You may let the genetic information negatively
affect you life (and ignore the environmental
component)
Your SNP LAB
With permission you can genotype two of your own
SNPs
We can test for: Muscle Type
ACTN3 is a protein that is only turned on in fast-twitch muscle
fibers (the kind of muscles use in power sports like sprinting
and weightlifting)
C allele- functional protein (CC & CT are power athletes)
T allele- nonsense SNP. People with two T alleles have no
functional alpha-actin-3 (TT are endurance athletes)
A study of olympic weightlifters
everyone of them has at least
one copy of C
Would you change your behavior if you knew your genotype?
We can test Lactose intolerance
The enzyme lactase is responsible in the
body for breaking down the sugar in milk
called lactose.
Everyone makes lactase as a baby. As you grow older, the
about of lactase produced generally decreases- making it harder
to digest milk
There is a SNP in the region that turns off the lactase gene:
G allele: lactase shut off adulthood (GG is lactose intolerant)
A allele : lactase produced into adulthood (AA & AG are lactose tolerant)
Population breakdown:
Prevalence of lactose tolerance varies widely. The A allele is
rarely seen in Asian or African populations (i.e. tend to be
lactose intolerant)
Neandertals
Svante Paabo
Neandertals
Neanderthal cranial capacity is thought to
have been as large as babies or larger as
adults than Homo sapiens
Neandertals were heavily built with robust
bone structure.
They were much stronger than Homo
sapiens, having particularly strong arms
and hands
Neandertals
First appear in the European fossil record about 400,000
years ago
Lived in Europe and Western Asia as far east as Southern
Siberia and as far south as the Middle East
came into contact with modern humans from at least 80,000
years ago
About 1-4% of DNA is derived from Neandertal.
We will look at one site (rs16845098), and see if your
sequence is from the ancestral human (T) or Neandertal
(C).
Photic sneeze
How will you test your genotype?
PCR based method for SNP detection: tetraprimer ARMS PCR
Has 4 primers:
-2 inner primers that are specific to a different
allele
-2 outer primers
Allele 1 specific primer
After PCR primers specific to the G allele will make 2
products:
- Amplify non specific segment between two outer
primers
- Amplify product from the G specific primer to the
opposing outer primer
Allele 2 specific primer
After PCR primers specific to the A allele will make 2
products:
- Amplify non specific segment between two outer
primers
- Amplify product from the A specific primer to the
opposing outer primer
Tetra-primer ARMS primer overview
G allele:
A allele:
In both cases you get non specific bands from the outer primers!
Real example of Tetra-primer ARMS
PCR
We can test for Earwax
Type:
-
wet type: Some people have
moist, honey-brown to dark brown
earwax
dry type: Others have dry grey
and flakey earwax
type depends on a SNP in a single
gene: ABCC11 (wet allele is
dominant)
Population breakdown:
wet type more common in Africans and Europeans
dry type more common in Native Americans and Asians
We can test for eye color
Eye color is determined by
the amount and type of
pigments in the eyes iris
SNPs in at least 3 genes are
responsible for eye color
HERC2:
• AA allele: 85% chance of brown, 14% chance of green,
1% chance of blue
• AG allele: 56% chance of brown, 37% chance of green,
or 7% chance of blue
• GG allele- 72% chance blue, 27% chance of green, 1%
chance of brown
We can test for Bitter taste receptor
PTC (phenythiocarbamide): a
chemical found in broccoli and
brussel sprouts that binds to the
bitter taste receptor encoded in
the TAS2R38 gene.
A SNP in TAS2R38 affects how
well the receptor works:
G allele: functional receptor
(for GG & GC PTC tastes bitter)
C allele: broken receptor
(for CC PTC tastes bitter)