1. SNPs and CNPs
By: David Wendel

2. What are SNPs? (“snips”)
Single Nucleotide Polymorphisms or (SNV)
Occurs when one nucleotide is altered in a genome
Four versions- one for each
nucleotide
Similar to mutations
Two or more versions of a
sequence must each be present
in at least one percent of the general
population

3. What are SNPs? (cont.) Many have no effect on cell function
Do not directly cause disease
Most found outside of protein sequences
Likely to alter protein functions if inside
Help pinpoint disease on human genome map
Evolutionarily stable

4. What are CNPs (“cnips”)
Copy Number Polymorphisms or (CNV)
Alterations in DNA
Affect sections of DNA
Different number of copies of
sections
Thousands to millions
Occurs in over 1% of
population - polymorphism
Considered normal variations

5. SNPs and CNPs in Humans Human DNA is very similar
99.6% of human DNA is identical to all other humans
Other 0.4% is made up of CNPs and SNPs
SNPs- 80% of the 0.4%
Small scale variant
CNPs- 20% of the 0.4%
Large scale variant

6. How do we find SNPs? Genomic Approaches Functional Approaches
Two main ways scientists identify, categorize, and catalog SNPs
Genomic Approaches
Functional Approaches
Primer Extension is also used

7. Genomic Approaches Scientists who want to see the big picture
Hundreds of scientists involved
Genomes of numerous individuals are compared
Computer-powered data analysis
Results available to anyone on internet

8. Functional Approaches
Scientists interested in particular diseases or drug responses
Select genes known in a process
Examine the genes in people with and without a disease
Identify SNPs that correspond with particular response

9. Primer Extension
Less expensive
Alternative method

10. Haplotypes A set of single nucleotide polymorphisms
Set is on a single chromosome of a chromosome pair that is statistically associated
Associations can identify other polymorphic sites in the region
SNPs close together on the chromosome
Valuable for investigating genetics behind diseases

11. HAPMAP (Haplotype Map)

12. HAPMAP (Haplotype Map) cont.
Hapmap- a catalog of common genetic variants that occur in human beings
What the variants are
Where the variants occur in our DNA
How they are distributed among populations
Able to see how SNPs are organized on chromosomes
Construction of Hapmap occurs in three steps:
Single Nucleotide Polymorphisms
Adjacent SNPs inherited together compiled into haplotypes
“Tag” SNPs in haplotypes identified that uniquely identify those haplotypes.

13. Hapmap I 2005 This was the first phase of the project
The project was launched in October 2002
Original goal to be finished was September 2005
Finished first draft in February 2005
Contained 1,000,000 most common SNPs

14. Hapmap II 2006 Results from Phase II were released in August 2006
These results were published in February 2007
10,000,000 SNPs were included in this Hapmap

15. Hapmap III 2010 The third phase was published in 2010
Data from 1,184 individuals
11 global populations
1,410,616 SNPs were released for detailed studies
Ten 100-kilobase ENCODE regions were sequenced in 692 of these individuals
Allowed integration of SNPs and CNPs

16. Average Person and SNPs
Density of SNPs per base pair varies with every person
SNPs occur about one in every base pairs
About 3,750,000 total