SNP and Variation

1
SNP and Variation

• Ka-Lok Ng
• Asia University

2
References

• http//www.mun.ca/biology/scarr/4241rm_chapter31.h
  tml
• http//www.bioinfo.rpi.edu/bystrc/courses/biol454
  0/lecture21/lec21.pdf

3
Introduction

• Having sequenced the genomics ? then studies the
  nature and distribution of variation between
  individuals
• Variation at DNA level nucleotide insertions,
  deletions, and Single Nucleotide Polymorphism
  (SNP) or small nucleotide polymorphisms
•     SNP refers to any site where two or more
  different nucleotides are segregating in
  population.    Cluster of linked SNPs
  haplotype    SNPs and haplotypes are
  increasingly important component in biological
  studies which range from ecology and evolution to
  biomedical (disease association study)  
   These variations apply to characterization of
  population structure and history or functional
  study of genes.    They are indispensable for
  recombination mapping purposes (linkage
  analysis) or used as positional markers for
  physical mapping
• SNPs are the most common genetic variations occur
  once every 100 to 300 bases.

4
The Nature of Single Nucleotide Polymorphisms

• Classification of SNPs
• Most common changing from one base to another
• This could either be transversions or transitions
• Could also be insertions and deletions, also
  termed indels
• Some geneticists see two-nucleotide changes and
  small insertions/deletions of a few nucleotides
  as SNPs, therefore simple-nucleotide
  polymorphism may be a better description
• Microsatellites, longer sequence repeats, and any
  other molecular polymorphism (transposable
  element insertions, deletions, chromosome
  inversions and translocations, and aneuploidy)
  are not regarded as SNPs
• Aneuploidy is an error in cell division that
  results in the "daughter" cells having the wrong
  number of chromosomes. In some cases there is a
  missing chromosome, while in others an extra.

5
Classification of SNPs

• SNPs classified on nature of affected nucleotide
• Noncoding SNP 5 or 3 nontranscribed region
  (NTR), 5 or 3 untranslated region (UTR),
  intron, or intergenic

6
3.1 (Part 1) Human promoter SNPs that affect
gene expression

• Coding SNP replacement polymorphisms (change
  the amino acid encoded for) or synonymous
  polymorphisms (change the codon but not the amino
  acid)
• Nonreplacement polymorphisms include both
  synonymous and noncoding polymorphisms, but,
  could still affect gene function by having an
  effect on transcriptional or translational
  regulation, splicing, or RNA stability.
• This type of polymorphism is important in
  increased genetic variation (Fig 3.1).
• Fig. 3.1 a collection of over 140 human
  promoter SNPs that have been associated with an
  effect on gene expression or TF binding, and in
  many cases, a clinical outcome

Fig. 3.1. Human promoter SNPs that affect gene
expression. These are loci for which a SNP has
been implicated in modulation of transcript
levels, either by statistical association or
using a biochemical assay in cell lines that are
dispersed throughout the human genome. The figure
shows where some of these nonreplacement
polymorphisms lie and affect gene expression.
7
3.1 (Part 2) Human promoter SNPs that affect
gene expression

• Fig. 3.1. Human promoter SNPs that affect gene
  expression.

8

• SNPs can also be classified as transitions or
  transversions
• Transitions change purine to a purine (A ?? G)
  or a pyrimidine to a pyrimidine (C ?? T)
•    Transversions change purine to pyrimidine
  and vice versa (A or G ? C or T and vice versa)
• Transitions tend to occur just as frequently as
  transversions and are actually more prevalent
  (???), despite transversions having twice as many
  possible changes
• This holds broadly true for both coding and
  noncoding SNPs
• In part a result of difference in ab initio
  (protein prediction) mechanisms where certain
  types of mutations arise and are repaired
• Due to the nature of the genetic code,
  transitions are less likely to affect amino acids
  than transversions.
• This means transitions are thought to have a
  higher probability of retaining the proper coding
  regions

number of transitions/number of transversions gt 1
in coding region
9

• Synonymous
• TGT ? TGC results in Cys ? Cys
• Nonsynonymous replacement
• TGT ? TGG results in Cys ? Trp
• can be conservative or nonconservative
• Nonsynonymous nonsense mutation, introduction of
  a stop codon
• TGT ? TGA results in Cys ? stop
• Nonsynonymous read through mutation
• TAA ? TTA results in stop ? Ile

10

• SNP and disease
• Sickle-cell anaemia a disease caused by a
  specific SNP an A?T mutation (GTGAG ? GTGTG) in
  the b-globin gene changes a Glu ? Val, creating a
  sticky surface on the haemoglobin molecule that
  leads to polymerization of the deoxy form
• SNP and blood groups A, B and O alleles
• A and B alleles differ by four SNP substitutions
• They code for related enzymes that add different
  saccharide (sugar, general formula (CH2O)n) units
  to an antigen on the surface of red blood cells
  (rbc)
• Allele Sequence
  Saccharide
• A .gctggtgacccctt
  N-acetylgalactosamine
• B .gctcgtcaccgcta
  galacotse
• O .cgtggt-acccctt
  --
• The O allelle has undergone a mutation causing
• a phase shift, and produce no enzyme. The rbc of
  type O
• contain neither the A nor the B antigen, This is
  why people with
• type O blood are universal donors in bolld
  transfusions.
• The loss of activity of the protein does not
  seem to carry
• any adverse consequences.

The ABO antigens are terminal sugars found at the
end of long sugar chains (oligosaccharides) that
are attached to lipids on the red cell membrane.
The A and B antigens are the last sugar added to
the chain.  The "O" antigen is the lack of A or B
antigens but it does have the most amount of next
to last terminal sugar that is called H antigen.
http//matcmadison.edu/is/hhps/mlt/mljensen/BloodB
ank/lectures/abo_blood_group_system.htm
11

• In classical population genetic theory, genetic
  loci are only regarded as polymorphic if the
  frequency of the most common allele is lt 95 ?
  that is a 5 changes
• Most SNP are first detected in a sample of fewer
  than 10 individuals, so the frequency criterion
  is not applied all single nucleotide changes are
  described initially as candidate SNPs.
• NCBI dbSNP http//www.ncbi.nlm.nih.gov/SNP/index
  .html
• Seattle SNP http//pga.mbt.washington.edu

12

• From Fig. 3.1 ? chromosome 1 FY, and do a NCBI
  search
• NCBI ? SNP ? keyword ? FY AND homo ? refSNP ID
  rs17851571

13

• Comment - polymorphisms ? mutations
• Confusion arises over the distinction between
  polymorphisms and mutations, largely due to dual
  usage of the term mutation.
• All SNPs arise as mutations, in the sense that
  the conversion of one nucleotide into another is
  a mutational event. But by the time a seq.
  variant is observed in a population, the event
  that created it is usually long past, so the
  observed SNP is no longer a mutation it is just
  a rare seq. variant or a polymorphism.
• Since the distinction only applies to a small
  fraction of all SNPs, then the term polymorphism
  is more general.

14
Distribution of SNPs

• Distribution of SNP's lies within the domain of
  population genetics
• Study of relationship between SNP's and
  phenotypic variation lies in the domain of
  Quantitative Genetics
• Application of SNP ? Quantitative trait loci
  (QTL), which are loci that contribute to
  polygenic phenotypic variation
• Neutral theory of molecular evolution
• Balance between mutation and genetic drift
• Rate of mutations introduced into a population
  rate at which polymorphisms are lost
• Most mutations whether deleterious, advantageous
  or neutral in effect, are lost within a few
  generations
• The effect of selection acts to reduce the
  frequency of slightly deleterious alleles, but on
  occasion tends to favor a new allele (positive
  selection) or maintain two or more polymorphisms
  (balancing selection) at some loci

15

• Three key concepts are important in
  characterizing SNP variation
• Allele frequency distribution
• Linkage disequilibrium
• Population stratification (??)
• Aspects of frequency distribution
• Population structure - example SNP can be more
  frequent in one population than another. As
  migration is a potent (???) source of diversity,
  isolation affects the rate at which variation is
  lost (i.e. no variation) due to drift.
• Nucleotide Diversity - the average fraction of
  nucleotides that differ between a pair of alleles
  chosen at random from a population
• Hs lower nucleotide diversity, with an average
  of one SNP every kbp between the chromosomes of
  any individuals
• Fly and maize an order of magnitude greater
  polymorphism, with one SNP every 50-100 bp
• Linkage Disequilibrium and Haplotype Maps
• Linkage Disequilibrium (LD) Non-random
  association of alleles
• LD allows mapping of disease loci in large
  population
• In humans - LD is commonly observed for several
  tens, and in many cases, 100 kbps of either side
  of SNP
• LD has an effect on haplotypes which display
  clustered distribution
• Broad approximation - Genome tens of thousands
  of blocks
•     Each block   up to 100,000 bases
•                         3 5 common
  haplotypes
•     Each haplotype tens or hundreds of SNPs in
  LD

16
3.2 (Part 1) Nucleotide diversity in natural
populations

• Fig. 3.2 Nucleotide diversity in natural
  population. (A) Observed and expected of SNP
  frequencies for 874 SNP's from 75 candidate human
  hypertension loci. Rare alleles are the most
  frequent, and the number of SNPs in each
  frequency class declines as the more rare allele
  becomes more common.

In a sample of several hundred alleles, the
most common class of SNPs are singletons (which
appear only once in the sample), followed by
doubletons, tripletons, and so on. Only between
1/3 and ½ of all SNPs are common in the sense
that the more rare allele is present in more than
5 of the individuals.
17
3.2 (Part 2) Nucleotide diversity in natural
populations

• (B) LD (D) decays with time (number of
  generations) in proportion to the recombination
  rate r.
• (C) The level of nucleotide diversity is a
  function of recombination rate, and hence
  chromosomal position, as in this example for
  fruit-fly.

(B) As number of generations ?, frequency of SNP
segregate ? (no more clustering) ? LD ? (C)
as r ?, nucleotide diversity ?
18

• NCBI dbSNP http//www.ncbi.nlm.nih.gov/SNP/inde
  x.html

dbSNP accepts submissions for SNP, microsatellite
repeats, and small-scale deletion and insertion
polymorphisms
dbSNP summary for various species
19

• dbSNP

• Submitted data
• The submitter HANDLE is a short tag that uniquely
  defines each submitting laboratory in the
  database
• A unique ssSNP identifier SNP order record, such
  as ss4923558, HANDLE YUSUKE
• Keyword ss4923558 AND homo
• Keyword ss4923558 will return multiple records !
  More than 11 rsSNP records
• More than one submitter ? more than one ssSNP ?
  these ssSNP are clustered into reference SNP
  identifier ? rsSNP

20

• dbSNP

Alleles A/G Ancestral Allele G Handle YUSUKE,
EGP_SNPS, PERLEGEN, ABI Fasta seq.
gtgnldbSNPrs3737559allelePos301totalLen601t
axid9606snpclass1alleles'A/G'molGenomicbui
ld126
21

• Gene View of SNP

22

• Go to the bottom of the page
• JBIC sample size 1270, Allele frequency of A
  and G
• Other populations have a smaller sample size

23

• Click NCBI Assay ID ? ss4923558 ?
• Japanese Millennium Genome Project
• Measured in a group of East Asian DNA samples
• There is no individual genotype data for ss4923558

• Click HandleSubmitter ID
• YUSUKEIMS-JST082810 ?
• Allele frequency
• G 0.8929
• A 0.1071
• Sample Size 1270 (number of chromosomes)

24

• Entrez SNP search terms
• http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbS
  np

25

• SNP integration in Genome Browsers
• Ensembl http//www.ensembl.org/index.html
• rs3737559

• SNP rs3737559 is located in the following
  transcripts
• Genotype and Allele frequencies per population

BioMart
26

• The local DNA seq. within 100 kb on either side
  of the SNP is shown.

27
The different types of SNPs are color coded as to
type (e.g. coding, intronic, flanking or other).
Deletion and insertion polymorphisms are
indicated with a triangle. The letters (K, M, R,
S, W, Y) inside the SNP squares indicate the type
of SNP using IUPAC ambiguity codes.
28

• UCSC Genome browser http//genome.ucsc.edu/cgi-bin
  /hgGateway
• BRCA1 gene

29

• NCBI Entrez Gene
• Gene BRAC1
• http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbg
  enecmdsearchtermbrca1

SNP GeneView
The coding SNPs in the BRCA1 gene. Those that do
not change the aa are colored in green, those
that result in a different aa are colored in red.
30
SNP association studies

• Association studies
• A case group of people vs. a control group of
  people
• The case group - are diagnosed with some disease
  (e.g. cystic fibrosis), react to some type of
  medicine, or are even specially healthy (e.g.
  more than 100 years old)
• The control group are people that do not exhibit
  the feature selected for the case group.
• For case-control studies, a selection of SNPs is
  genotyped in both the case and control groups
• alleles (case group) gt alleles (control group) ?
  potential markers for the observed phenotype

31
SNP and disease

• Functional variation a SNP may be assoicated
  with a nonsynonymous substitution in a coding
  region