The number of IQ SNPs discovered continues to increase. It is expected that in the near term that many more will be found. How could a genoset be constructed on snpedia in order to create an IQ polygenic score?
What programming language does the genoset editor use?
- Please see our previous comments about polygenic risk scores. Especially with respect to IQ, they are neither robust nor interpretable in a manner that is useful to the public at this time, and they are highly prone to being both misleading and of little to no medical utility. It may well be an appropriate research topic, but that does not make it an appropriate genoset for SNPedia, and to be very specific about this, in the absence of any medical utility - and given the obvious misuse potential - we will prevent any such genoset from being promulgated in SNPedia. Greg (talk) 22:01, 18 March 2018 (UTC)
Thank you for your reply. I agree that reporting PGS would likely be premature at this time, though it is not clear how much longer this will remain true. Perhaps reporting a PGS for those at the 1% risk level will soon be justified. When snpedia does provide these PGS some time in the future they will be of great help to users to develop their big picture risk for diseases or expected phenotypes for traits.
"Moreover, splitting the PGS for SZ into two scores based on the sign concordance of SNPs with EA enables the prediction of disease symptoms and severity from genetic data for the first time to some extent" https://www.biorxiv.org/content/early/2018/01/31/114405.full.pdf+html J1 (talk)
- Thanks for your understanding. You might find this PRS-related article of interest: 10.1017/thg.2018.11, The Nature of Nurture: Using a Virtual-Parent Design to Test Parenting Effects on Children's Educational Attainment in Genotyped Families. Greg (talk) 03:51, 20 March 2018 (UTC)
Yes, this research was quite startling. Is everything genetic? The old nature nurture argument might turn out to have only nature. Anyone know how to extract phased genoytypes from ncbi? https://www.ncbi.nlm.nih.gov/variation/tools/1000genomes/ I was able to find phased genotypes for individuals this url, though it only gives you the genotypes for a single region. I would love to find a way to upload the 3,000 SNPs for the EA GWAS and find out the phased genotypes for a few people. This would then tell me how much variation there is between homologous chromosomes. Is there any other site that would have this information easily accessible? J1 (talk)
A million GWAS for Educational Attainment has been in the publication process for the last 8 months. The SNP results have finally been leaked and there are almost 3,000 significant SNPs. Reports suggest 0.80 correlation of measured IQ and the polygenic scores across human populations. These are the first 20 most p-value significant of the SNPs. Perhaps the time has been reached in which a PGS for IQ/EA should be considered for snpedia. At first perhaps only reporting results for those within the top 1% of scorers would be reasonable. Some prospective parents might also be interested to have an insight what the IQ of their possible children might be.
MarkerName CHR POS A1 A2 EAF Beta SE Pval rs9859556 3 49455986 T G 0.6905 0.029 0.001 3.98E-91 rs7623659 3 49414791 T C 0.3095 0.029 0.001 5.49E-91 rs11917431 3 49644012 T C 0.6973 0.029 0.001 6.86E-91 rs1873625 3 49666964 A C 0.6973 0.029 0.001 7.52E-91 rs11921590 3 49644193 T C 0.6973 -0.029 0.001 1.12E-90 rs2352974 3 49890613 T C 0.5 -0.026 0.001 4.55E-82 rs7029718 9 23358495 A G 0.5646 0.024 0.001 5.99E-72 rs7868984 9 23357826 T C 0.4388 -0.024 0.001 6.32E-72 rs11793831 9 23362311 T G 0.4354 0.024 0.001 9.40E-71 rs1334297 13 58335375 A G 0.784 0.026 0.002 1.05E-64 rs7325960 13 58314196 T G 0.216 0.026 0.002 1.54E-64 rs17262885 13 58313302 A G 0.216 -0.026 0.002 2.19E-64 rs9375188 6 98555272 T C 0.4966 0.021 0.001 1.98E-57 rs9401593 6 98549801 A C 0.5034 -0.021 0.001 2.50E-57 rs2526398 3 50187596 C G 0.3895 -0.022 0.001 6.28E-57 rs1487445 6 98565211 T C 0.4966 0.021 0.001 7.59E-57 rs1906252 6 98550289 A C 0.5034 0.021 0.001 8.86E-57 rs13018640 2 100821545 T C 0.5935 -0.021 0.001 3.12E-56 rs2309757 2 100807725 T C 0.4031 -0.021 0.001 1.82E-55 rs6709656 2 100806719 A G 0.5969 -0.021 0.001 2.03E-55 J1 (talk)
PGS are now approaching clinical utility. This Environmental-Genetic screening tool for colorectal cancer outperformed family history alone and is on the way. PMID: 29458155 Considering how financially efficient such technology likely could be and the current state of GWAS research, there probably could be a fair number of other PGS on the horizon. J1 (talk)