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From: Harold Vannoy <>
Subject: [DNA] Need Help In Understanding and Using the Term "SNP"
Date: Sun, 28 Mar 2010 06:11:18 -0400


Being fairly new to all of this, I am continuing to struggle with
understanding and using correct nomenclature. One term that I believe
that I may have been misusing is SNP (Single Nucleotide
Polymorphism). I thought that I understood that FTDNA tested Y-DNA
using "STRs" and that they tested mtDNA using "SNPs." I also thought
that 23andMe did all of their testing using "SNPs." However, when I
refer to the "SMGF Glossary" for their definition of "SNP," I find
the following:

"(Single Nucleotide Polymorphism) A change or mutation in a single
base pair in a DNA sequence. ..."

Also when I check the ISOGG "Glossary of Genetic Terms - 2010" I find:

"Single Nucleotide Polymorphism (SNP which is pronounced 'snip')
Variation in the nucleotide allele at a certain nucleotide position
in the human genome. ..."

So, does this mean that I should more correctly be understanding that
FTDNA does their mtDNA testing (and 23andME does all of their
testing) of the "genetic sequence" by testing each "nucleotide" (or
"base pair") and then comparing the resulting measurements (or
"alleles") to a "reference" (such as the "rCRS" for mtDNA) to
determinie if there are differences in the two values? Would these
"differences" then be referred to as the "SNPs" (or
"mutations")? Can someone please help me here?

If what I have just proposed is true, then I have some problem with
the "preamble" from the download of my mtDNA test results from
23andMe which says:

"# This data file generated by 23andMe at: Sun Nov 15 02:22:31
2009
#
# Below is a text version of your data. Fields are
TAB-separated
'# Each line corresponds to a single SNP. For each SNP, we provide
its identifier '
'# (an rsid or an internal id), its location on the reference human
genome, and the '
# genotype call oriented with respect to the plus strand on the human
reference
# sequence. We are using reference human assembly build 36. ..."

Should it, more correctly, say that each line corresponds to a
"nucleotide" (or "base pair")?

Also, shouldn't each result be better referred to as an "allele"
instead of a "genotype" (wouldn't the "genotype" be made up of all of
the individual "allele" values that were determined)?

Can someone please help me with this??

Also can anyone recommend a good "reference" that I can refer to in
order to better understand "nomenclature" issues such as this?

Thank you in advance.

Harold Vannoy


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