Genetic Classifications of Alzheimer's subtypes

[J11]

An even more powerful method has emerged to unravel the different features of Alzheimer's.
The below article subdivides Alzheimer's into the domains of memory, language, executive function and visuospatial.
The creation of these so called coherent subgroups should allow for identifying SNPs with smaller GWAS sample sizes.

What is your genetic AD domain?
https://www.ncbi.nlm.nih.gov/pmc/articl ... 510324.pdf

An R program that could look up SNP lists would be very convenient.
We should collectively look into this idea of an R program for genotype lookup!
All of us have used the slow and inefficient direct lookup approach for individual SNPs and it is very tiresome.
A software approach would make this much much easier.

The software itself should be super easy to write, though it would be of significant help to many of those on forum
if we could simply find R software that has already been written perhaps with add on features.

Basically, what we want is to input SNPs and a genochip/exome/whole genome file into R and then retrieve
gentoypes. We all know that this can be a very tedious task when this must be done one by one.

We could post to this thread SNP lists that others could then easily run through R.
This would be of substantial value.
We could have polygenic SNP lists for AD, IQ etc..
Perhaps addings in gene lists and then asking for the corresponding SNPs within these genes would also be helpful.
The programming would not be overly difficult if we had to make our own R package.

[J11]

The SNP genotyper R package will provide substantial rewards with little effort.

As an illustration, below is a list of all SNPs listed on NCBI clinvar's for variants considered pathogenic for Alzheimer's Disease.
https://www.ncbi.nlm.nih.gov/clinvar

An R package could provide us with an immediate analysis of this list.
This would not be overly helpful in this instance as nearly all of the variants below are PSEN1/2, though there are now many
polygenic studies involving hundreds and hundreds of variants which also could be analyzed as easily (e.g., intelligence).


rs63749884
rs63750666
rs121909715
rs34637584
rs756751089
rs63749824
rs63750599
rs63750815
rs63751141
rs63750450
rs63751272
rs63751278
rs63751037
rs1566630910
rs63750004
rs63750306
rs63750306
rs63750391
rs63749885
rs63750590
rs63750265
rs63750577
rs63751144
rs63751068
rs63750082
rs63750053
rs267606983
rs63751287
rs63750526
rs63751163
rs63751320
rs121917807
rs63750900
rs63750886
rs63749891
rs63749891
rs63750231
rs63750231
rs63751235
rs1566650594
rs63750687
rs63750218
rs661
rs63750083
rs281875357
rs121917808
rs774676466
rs63751294
rs63751011
rs63750424
rs193922906
rs74315402
rs80356710
rs80356711
rs74315405
rs63749964
rs63750264
rs63750264
rs63750264
rs63750399
rs63750973
rs63750643
rs63749810
rs63751039
rs63750671
rs193922916
rs281865161
rs387906496


These are the SNPs considered to be likely pathogenic for AD
(Sorry for posting them row wise, though it would be easier to then copy and paste these into a spread sheet program.) :

rs63749851
rs1553268799
rs1561901881
rs1561905293
rs866101707
rs371900329
rs63751399
rs1566630791
rs63751278
rs63750418
rs1566638673
rs1555355250
rs63750009
rs63749836
rs63751287
rs63751229
rs63750219
rs63750687
rs1566656702
rs63751223
rs1566657804
rs1567885728
rs1568339995
rs429358
rs63750734