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Talk:Gs156

From SNPedia

An anonymous user writes:

This comes up in promethease as overlapping with gs139, which is a bit confusing and contradictory.


The page NAT2 tells me that gs138, gs139 and gs140 using a 6 SNP algorithm and was introduced in 2009 and it uses these 6 snps

while genosets gs154 and gs156 are based on [PMID 21750470] was added in 2015 and is based on only 2 snps

So Promethease seems to be accurately reflecting the disagreement of 2 independent methods.

I've just done a manual test of Promethease, and have identified the following genotypes as also triggering both gs156 and gs139

['rs1041983(C;C)', 'rs1208(A;A)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(A;A)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(C;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(C;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(C;C)']
['rs1041983(C;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(T;T)']
['rs1041983(C;C)', 'rs1208(A;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(A;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(C;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(C;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(C;C)']
['rs1041983(C;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(T;T)']
['rs1041983(C;C)', 'rs1208(G;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(G;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(C;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(C;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(C;C)']
['rs1041983(C;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(C;T)']
['rs1041983(C;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;C)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(A;A)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(A;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(A;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(A;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;C)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(C;T)']
['rs1041983(T;C)', 'rs1208(G;G)', 'rs1799930(G;G)', 'rs1799931(G;G)', 'rs1801280(T;T)', 'rs1799929(T;T)']


the amino positions for these rs#s are

and with that you can go back to the original source http://nat2pred.rit.albany.edu/ and test the calls. That first one generates the following prediction

NAT2 sequence position Genotype
282 CC
341 TT
481 CT
590 GA
803 AA
857 GG
Results
P(Slow) = 0.1294
P(Intermediate) = 0.61225
P(Rapid) = 0.258351
Final Prediction : INTERMEDIATE (0.61225)

which doesn't suggest the sort of certainty I would have hoped for.

So do you trust an older method which uses more SNPs, or a newer one which uses less?

I can see at least 2 options.

  1. I can modify the text so that it's more clear that there are 2 different sources "according to source X you should be a"
  2. I can modify the genosets so that gs154 and gs156 aren't reported if and of gs138, gs139 or gs140 are called

This will allow us to give better(?) calls when more data is available, but still report something when only 2 snps are present.

--- cariaso 17:19, 2 April 2016 (UTC)

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