PolITiGenomics

Politics, Information Technology, and Genomics

SNP vs. SNP

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July 17th, 2009

Spy vs. Spy

At the NHGRI Sequencing Advisory Panel meeting last week, there was some confusion about how we use SNP array data and dbSNP in the DNA sequencing world. SNP arrays are, when you boil it down, a quick and cheap way to sequence, i.e., determine the nucleotide at, specific DNA positions in the genome. For each sample to be sequenced at The Genome Center, we use SNP array data from that sample to measure breadth of sequence coverage we have achieved. In short, at certain points in the sequencing of a sample, variation calling is done, generating, among other things, single nucleotide variants (SNVs, single nucleotides that differ from the standard human reference sequence). Once our variant detection pipeline is able to find 99% or more of the SNPs found on the SNP array of that sample, we are confident that we have good coverage of the genome.

dbSNP, a catalog of common SNPs, is used in a different way. Any individual is expected to have somewhere around 75-85% of his or her SNVs in common with those in dbSNP. Thus, we expect that when calling SNVs, about 80% of them should appear in dbSNP, i.e., not be private mutations. Thus, dbSNP concordance (the percentage of SNVs found in dbSNP) is used to measure an approximate false positive rate of the detection algorithm. If the rate of dbSNP concordance is much lower than 80%, your results likely have a lot of false positives.

So SNP arrays from the samples are used to measure breadth of coverage and dbSNP is used to measure the accuracy of variant detection. What is the difference between a SNP and a SNV? A SNV is a private mutation while a SNP is a mutation that is shared amongst a population.

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9 Responses to “SNP vs. SNP”

  1. Great bit. Thanks for keeping me up-to-date now that I’m no longer working at NIH.

  2. Thank you!
    Could not find a definition of SNV anywhere!

  3. No problem, glad I could help.

  4. [...] SNP (single nucleotide polymorphism) vs. SNV (single nucleotide variant) As their name suggests, both are concerned with aberrations at a single nucleotide. However, a SNP is when an aberration is expected at the position for any member in the species – for example, a well characterized allele. A SNV on the other hand is when there is a variation at a position that hasn’t been well characterized – for example, when it is only seen in one individual. It is really all a question of frequency of occurrence. PolITiGenomics: SNP vs. SNP [...]

  5. I think caution ought to be considered when describing polymorphisms—especially in lay discussions—as aberrations or even defects.

    I’ve had discussions with medical personnel either using or condoning expressions like “THEIR DEFECTS” and “genetically deviant” when discussing children with idiopathic autism who were caused the clinical condition by vaccines. They even reference supposed genetic studies, which they seem to not realize are merely epidemiological and thus statistical studies a la the preferred applied science of medicine, to boost their characterizations.

    They seem to not realize that research in basic science is showing that children with idiopathic autism evidently have functional polymorphisms—not defective genes—that are distributed throughout the population. They seem to have just more copies (copy number variants).

  6. [...] polymorphisms (because sometimes they are more than a single base of the DNA). And I have also seen SNV becoming more widely used as more individuals are sequenced (single nucleotide [...]

  7. [...] [1]:A SNV is a private mutation while a SNP is a mutation that is shared amongst a population[1] http://www.politigenomics.com/20…This answer .Please specify the necessary improvements. Edit Link Text Show answer summary [...]

  8. Thank you very much for this article.. Finally a good and simple explanation… Have been confused on how to use dbSNP and SNParray all this while… Just wondering, do you use any reference for the percentage of dbSNP concordance used (80%) in order to deduce false positives? Or is it based on experience?

    Thank you.

  9. Thank you for your good explaination.. :)
    I have been confused all these while on how/when to use SNParray and dbSNP.

    If you don’t mind, I would like to ask some questions regarding the percentage mentioned in your post.

    You did mention that “Any individual is expected to have somewhere around 75-85% of his or her SNVs in common with those in dbSNP” and
    ” If the rate of dbSNP concordance is much lower than 80%, your results likely have a lot of false positives”.

    May I know if those percentage are taken from a book/paper? If yes, I would be very grateful if you can suggest me any. Or does the percentage are based on your personal expert experience?

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