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What Is Deep SNP Testing in DNA?

written by: Ollie Hicks•edited by: Paul Arnold•updated: 11/26/2009

Genetic testing is a fascinating area of study. Deep SNP testing takes advantage of the characteristics of single nucleotide polymorphisms - or SNP/'snip' - to chronologically and genetically isolate a test subject to a particular branch or 'clade' in terms of genetic lineage.

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    What is a Single Nucleotide Polymorphism?

    Prior to addressing the question of ‘What is deep SNP testing?’, let us address the question, ‘What is an SNP?’ An SNP – or ‘snip’, as it is pronounced - is a single nucleotide polymorphism. It is a subtle single nucleotide change in a DNA sequence.

    The DNA molecule consists of four different types of nucleotide, each one contains one of the four different bases – adenine, thymine, guanine or cytosine. Genes – the codes for constructing proteins – are made up out these four bases, much as words are made up out of letters. So for example, the code for a short peptide sequence might read, AACGGGTG.

    How would a single nucleotide polymorphism affect this code? It would mean a mutation would bring about a change in just one letter of the code, so that it now reads AACCGGTG - the guanine in position 4 has been replaced by a cytosine. If this SNP was in an exon – i.e. the part of the gene that actually codes for a protein – then it might affect the function of the protein, for good or ill. Many SNPs are found in the introns, however – the non-coding parts of the genes.

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    The Y-chromosome And Genetic Testing

    4759E38DBB29A28245EE23BA4DBFE862C41783F0 large Geneticists and genealogists can now use the existence of SNPs to theoretically map out an individual’s genetic family tree back to the last known common ancestor. Since mutations in the germ-line cells are passed on to descendants, organisms sharing an SNP are likely to share a common ancestor. However due to the sharing of genetic information between X-chromosomes at meiosis, the Y-chromosome3 (with its significant non-recombining area) constitutes the only way to reliably trace a consistent patrilineal lineage of a group sharing a common mutation.1

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    How Is Deep SNP Testing Different?

    Testing for only a single SNP, however, is to paint with a very broad brush. Deep SNP testing,2 instead, tests for a wide range of known polymorphisms, in order to pin an individual down to a particular ‘sub-clade’ or branch of his genealogical tree, perhaps going back many thousands of years. It utilises the idea that all members of a group sharing an SNP mutation, including the originator, can be traced back to that originating event – and sub-groups with subsequent mutations assist in estimating the time period involved. Knowledge of the measurable rate of mutation in the sex chromosomes assists population geneticists in coming up with figures for dating the time of a mutation – although these may be subject to dispute.

    This is a complex approach: a simpler shortcut may be to test for short tandem repeats, or STRs. These are repeated sequences of DNA which vary in number of repeats according to genetic inheritance. The ‘haplotypes’ arrived at through STR testing correspond roughly with the ‘haplogroups’ identified through deep SNP testing.

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    1 Schlecht J, Kaplan ME, Barnard K, Karafet T, Hammer MF, et al. 2008 Machine-Learning Approaches for Classifying Haplogroup from Y Chromosome STR Data. PLoS Comput Biol 4(6): e1000093. doi:10.1371/journal.pcbi.1000093

    2 Bettinger, Blaine. 'What do the results of a Deep SNP test mean?' 20/06/2009. (25/09/2009). <>

    3 Jobling Mark A., Tyler-Smith, Chris. 'The human Y chromosome: An evolutionary marker comes of age'. Nature reviews. Genetics ISSN 1471-0056. Nature Publishing Group, London, (2000). 2003, vol. 4, #8, pp. 598-612

    4 'Understanding Your Y-chromosome DNA Test Results'. (25/09/2009). <>

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