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SNPs and CNPs

SNPs and CNPs. By: David Wendel. What are SNPs? (“snips”). S ingle N ucleotide P olymorphisms or (SNV) Occurs when one nucleotide is altered in a genome Four versions- one for each nucleotide Similar to mutations

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SNPs and CNPs

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  1. SNPs and CNPs By: David Wendel

  2. What are SNPs? (“snips”) • SingleNucleotidePolymorphisms 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? • 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 500- 1000 base pairs • About 3,750,000 total

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