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From SNPedia

See also wiki Basics.

First: remember the SNPedia guidelines - we aim to summarize the literature on variations that are reproducible, and, meaningful.

Then: A good way to find a suitable page to edit, is just to click on the Random page link along the left side. Hit that a few times till you find a SNP that seems suitably needy.

Helping a SNP[edit]

Pretend it sent you to Rs9939609

Across the top you will see the words 'Edit with form' and 'Edit'.

Click on 'Edit with form'. There are a few small 'fields' towards the top labeled 'SNP Summary' and 'Geno' then a larger area labeled 'Free text'.


In that box is a blob of slightly scary syntax. Here is what I currently see, except that my browser also does the 'word wrapping' so I don't have to scroll to the right.

{{ population diversity
| geno1=(A;A)
| geno2=(A;T)
| geno3=(T;T)
| CEU | 17.7 | 56.6 | 25.7
| HCB | 2.2 | 25.5 | 72.3
| JPT | 2.7 | 32.7 | 64.6
| YRI | 23.4 | 52.4 | 24.1
| ASW | 24.6 | 50.9 | 24.6
| CHB | 2.2 | 25.5 | 72.3
| CHD | 2.8 | 26.6 | 70.6
| GIH | 7.9 | 35.6 | 56.4
| LWK | 34.5 | 47.3 | 18.2
| MEX | 5.3 | 35.1 | 59.6
| MKK | 25.8 | 52.9 | 21.3
| TSI | 23.5 | 44.1 | 32.4
| HapMapRevision=28
}}

[[rs9939609]] is a [[SNP]] in the fat mass and obesity associated [[FTO]] gene, aka the "Fat Gene" [http://www.dailytimes.com.pk/default.asp?page=2007%5C04%5C16%5Cstory_16-4-2007_pg6_14]. The original paper describing it is here {{PMID|17434869}}.

[http://www.alzforum.org/new/detail.asp?id=1567] The researchers identified 10 different [[FTO]] SNPs in the first intron of the gene that associated with both BMI and [[type-2 diabetes]]. Because they all correlated with each other, they chose to examine one of the SNPs ([[rs9939609]]) in detail.

[[rs9939609]] has also been reported in a large study to be associated with [[type-2 diabetes]].
The risk allele (oriented to the dbSNP entry) is (A); the odds ratio associated with heterozygotes is 1.34 (CI 1.17-1.52), and for homozygotes, 1.55 (CI 1.3-1.84). {{PMID|17554300}}

Here's what that actually means


{{ population diversity
| geno1=(A;A)
| geno2=(A;T)
| geno3=(T;T)
| CEU | 17.7 | 56.6 | 25.7
...
| TSI | 23.5 | 44.1 | 32.4
| HapMapRevision=28
}}

this makes the brown/green/blue image appear. Changing the numbers, changes the graph. User:JlickBot mostly takes care of that so you can leave it alone.

? (A;A) (A;T) (T;T) 28



below that you will see

[[rs9939609]] is a [[SNP]] in the fat mass and obesity associated [[FTO]] gene, aka the "Fat Gene" [http://www.dailytimes.com.pk/default.asp?page=2007%5C04%5C16%5Cstory_16-4-2007_pg6_14]. The original paper describing it is here {{PMID|17434869}}.


[[ Any Page title ]]

means "link to a page in the wiki".


Notice the

[[rs9939609]] is a [[SNP]] in the fat mass and obesity associated [[FTO]] gene, aka the "Fat Gene" [http://www.dailytimes.com.pk/default.asp?page=2007%5C04%5C16%5Cstory_16-4-2007_pg6_14]. The original paper describing it is here {{PMID|17434869}}.

Magic is very often {{PMID|1234567}} which is the best and easiest way to point to a paper.


Before you click the save button, add a small summary telling us what you've changed or why. For more help see How to edit a page at wikipedia.

Some things bots will take care of for you[edit]

Overwrite[edit]

Rsnum

  • Chromosome
  • position

population diversity

ClinVar

Populate, but not alter[edit]

PMID Auto GWAS based on http://www.genome.gov/admin/gwascatalog.txt


Evaluating evidence[edit]

Separating actual genetic effect from noise has gained increasing interest as the frequency of genetic studies, often conflicting, increases [1]. While SNPedia content is currently driven primarily by interest - that is, that someone finds the topic interesting enough to update or list - it's useful to reflect on some emerging guidelines. Examples include PLOS ONE criteria for meta-analysis of GWAS studies and NHGRI GWAS catalog methods. One should also consider the strong bias against findings of no genetic association; a study may even end up interrupted if a predicted link doesn't pan out, or fail to get published. Most sources and databases tend to only include studies where an association was found. Typically a no-association is only reported if an alternate causal variant was found at the same time.


[PMID 24759409] Guidelines for investigating causality of sequence variants in human disease.

[PMID 24363797] Publication Bias in Recent Meta-Analyses.

[PMID 23785302] High Trans-ethnic Replicability of GWAS Results Implies Common Causal Variants.