1. Fatchiyah, PhD Dept Biology UB Fatchiyah.lecture.ub.ac.id

2. Why do we care about genetic variations?
1. Genetic variations underlie phenotypic differences among different individuals
2. Genetic variations determine our predisposition to complex diseases and responses to drugs and environmental factors
3. Genetic variations reveal clues of ancestral human migration history

3. Main Types of Genetic Variations
A. Single nucleotide mutation
Resulting in single nucleotide polymorphisms (SNPs)
Accounts for up to 90% of human genetic variations
Majority of SNPs do NOT directly or significantly contribute to any phenotypes
B. Insertion or deletion of one or more nucleotide(s)
1. Tandem repeat polymorphisms
Tandem repeats are genomic regions consisting of variable length of sequence motifs repeating in tandem with variable copy number.
Used as genetic markers for DNA finger printing (forensic, parentage testing)
Many cause genetic diseases
Microsatelites (Short Tandem Repeats): repeat unit 1-6 bases long
Minisatelites: repeat unit bases long
2. Insertion/Deletion (INDEL or DIPS) polymorphisms
Often resulted from localized rearrangements between homologous tandem repeats.
C. Gross chromosomal aberration
Deletions, inversions, or translocation of large DNA fragments
Rare but often causing serious genetic diseases

4. How many variations are present in human genome?
SNPs appear once per kb interval or on average 1 per 300 bp. Considering the size of entire human genome (3.2 x109 bp), the total number of SNPs is well above 11 million. The high density and relatively easier assay make SNPs the ideal genomic markers.
In sillico estimation of potentially polymorphic variable number tandem repeats (VNTR) are over 100,000 across the human genome
The short insertion/deletions are very difficult to quantify and the number is likely to fall in between SNPs and VNTR.

5. Types of Single Base Substitutions
Transitions
Change of one purine (A,G) for another purine, or a pyrimidine (C,T) for another pyrimidine
Transversions
Change of a purine (A,G) for a pyrimidine (C,T), or vice versa.
The cytosine to thymine (C>T) transition accounts for approximately 2 out of every 3 SNPs in human genome.

6. SNP or Mutation? Call it a SNP IF Call it a mutation IF
the single base change occurs in a population at a frequency of 1% or higher.
Call it a mutation IF
the single base change occurs in less than 1% of a population.
A SNP is a polymorphic position where the point mutation has been fixed in the population.

7. From a Mutation to a SNP

8. SNPs Classification Intergenic region Gene region
SNPs can occur anywhere on a genome, they are classified based on their locations.
Intergenic region
Gene region
can be further classified as promoter region, and coding region (intronic, exonic, promoter region, UTR, etc.)

9. Coding Region SNPs Synonymous Non-Synonymous
Missense – amino acid change
Nonsense – changes amino acid to stop codon.
Geospiza Green Arrow™ tutorial by Sandra Porter, Ph.D.

10. The Consequences of SNPs
The phenotypic consequence of a SNP is significantly affected by the location where it occurs, as well as the nature of the mutation.
No consequence
Affect gene transcription quantitatively or qualitatively.
Affect gene translation quantitatively or qualitatively.
Change protein structure and functions.
Change gene regulation at different steps.

11. Simple/Complex Genetic Diseases and SNPs
Simple genetic diseases (Mendelian diseases) are often caused by mutations in a single gene.
-- e.g. Huntington’s, Cystic fibrosis, PKU, etc.
Many complex diseases are the result of mutations in multiple genes, the interactions among them as well as between the environmental factors.
-- e.g. cancers, heart diseases, Alzheimer's, diabetes, asthmas, etc.
Majority of SNPS may not directly cause any diseases.
SNPs are ideal genomic markers (dense and easy to assay) for locating disease loci in association studies.

13. Main Genetic Variation Resources
NCBI dbSNP
NCBI Online Mendelian Inheritance in Man (OMIM)
International HapMap Project
Perlegen
Genome Variation Server (Seattle SNPs)

14. Where to Find Bioinformatics Resources for Genetic Variation Studies?
OBRC: Online Bioinformatics Resources Collection (Univ. of Pittsburgh)
The most comprehensive annotated bioinformatics databases and software tools collection on the Web, with over 200 resources relevant to genetic variation studies.
HUGO Mutation Database Initiative

15. NCBI dbSNP Database: Overview
URL:
The NCBI’s Single Nucleotide Polymorphism database (dbSNP) is the largest and primary public-domain archive for simple genetic variation data.
The polymorphisms data in dbSNP includes:
Single-base nucleotide substitutions (SNPs)
Small-scale multi-base deletions or insertions variations (also called deletion insertion polymorphisms or DIPs or INDELs)
Microsatellite tandem repeat variations (also called short tandem repeats or STRs).

16. dbSNP Data Stats (build 128, Oct, 2007)

17. dbSNP Data Types The dbSNP contains two classes of records:
Submitted record
The original observations of sequence variation; submitted SNPs (SS) records started with ss (ss )
Computationally annotated record
Generated during the dbSNP "build" cycle by computation based the original submitted data, Reference SNP Clusters (ref SNP) start with rs (rs )

18. dbSNP Submitted Record
Provides information on the SNP and conditions under which it was collected.
Provides links to collection methods (assay technique), submitter information (contact data, individual submitter), and variation data (frequencies, genotypes). ss

19. SNPs records submitted
From Submitted Record to Reference SNP Cluster
SNP position mapped
to the reference genomic contigs
SNPs records submitted
by researchers
If the SNP position not unique, it will be assigned to the existing RefSNP cluster
If the SNP position is unique, a new RS# is assigned

20. Different Ways to Search SNPs in dbSNP
dbSNP Web site
Direct search of SS record; batch search; allow SNP record submission; NO search limits
Entrez SNP
Search limits options allows precise retrieval
Entrez Gene Record’s SNP Links Out Feature
Direct links to corresponding SNP records; access to genotype and linkage disequilibrium data
NCBI’s MapViewer
Visualize SNPs in the genomic context along with other types of genetic data.

21. Search SNPs from dbSNP Web Page
dbSNP Web site

22. Search SNPs from Entrez SNP Web Page
The dbSNP is a part of the Entrez integrated information retrieval system and may be searched using either qualifiers (aliases) or a combination search limits from 14 different categories.

23. Entrez SNP Search Limits
Organisms
Chromosome (including W and Z for non-mammals)
Chromosome Ranges
Map Weight (how many times in genome)
Function Class (coding non-synonymous; intron; etc.)
SNP Class (types of variations)
Method Class (methods for determining the variations)
Validation Status (if and how the data is validated)
Variation Alleles (using IUPAC- codes)
Annotation (Records with links to other NCBI database)
Heterozygosity (% of heterozygous genotype)
Success Rate (likelihood that the SNP is real)
Created Build ID
Updated Build ID

24. Assessing Polymorphisms: Linkage Disequilibrium, Haplotype Block, and Tag SNPs
Adapted from Nature 426, 6968: (2003)
Linkage Disequilibrium (LD): If two alleles tend to be inherited together more often than would be predicted, then the alleles are in linkage disequilibrium.
If most SNPs have highly significant correlation to one or more of neighbors, these correlations can be used to generate haplotypes, which represent excellent proxies for individual SNP.
Because haplotypes may be identified by a much small number of SNPs (tag SNPs), assessing polymorphisms via haplotypes dramatically reduces genotyping work.