Information
Terminology
SNP
A SNP (Single-Nucleotide Polymorphism - pronounced snip) is a variation of a single nucleotide (A, G, C or T) at some location in your genome. The presense of particular variants, or groups thereof, can tell you a lot about yourself (hair color, height, muscle type, allergies, response to disease, response to pharmaceuticals, heritage, etc.).
Personal genome vendors will typically produce an analysis that covers some of these attributes - but will also provide you with 'raw' data, should you wish to investigate further.Your 'raw' data from any vendor will be a list of several hundred thousand SNPs, located across the autosomes (chromosomes 1-22), the sex chromosomes (X and Y), and possibly the mitochondrial chromosome. Given that your genome contains two copies of each autosome, and either XX (female) or XY (male), the data contains a 'genotype' composed of the two variants at each location.
Vendors, Name, Supported, Price, Sample, Autosomal SNPs, Y SNPs, X SNPs, MT SNPs, Raw Data, ------, -----------, -------, --------, ----------------, --------, --------, ---------, ----------, 23andMe, Yes, 199/99 USD, Saliva, 967,000, 3,089, 26,087, 2,737, Yes, ancestryDNA, Yes, 99 USD, Saliva, 682,549, 885, 17,604, Yes, FamilyTree, Yes, 99 USD, Cheek Swab, 708,092, 18,091, Yes, 23andMe picing is 199 USD domestically and 99 USD abroad.
CLI Usage
Use this if you just want to convert your data to the correct format so you can start querying your genome.
$ npm install dna2json -g
$ dna2json
Usage: dna2json <input file> <output file>
$ dna2json dna.txt dna.json
This will take a while...
Module Usage
var dna = require('dna2json');
var fs = require('fs');
var txt = fs.readFileSync('dna.txt');
dna.parse(txt, function(err, snps){
// snps = the object with your mutations
});
SNP-JSON
Every vendor has their own format for your DNA. I decided to make a standard format called SNP-JSON. This library will convert custom formats to this standard.
SNP-JSON looks like this
{
"rs4477212": {
"chromosome": 1,
"genotype": "AA"
},
"rs3094315": {
"chromosome": 1,
"genotype": "AA"
},
"rs3131972": {
"chromosome": 1,
"genotype": "GG"
},
"rs12124819": {
"chromosome": 1,
"genotype": "AA"
},
"rs11240777": {
"chromosome": 1,
"genotype": "GG"
},
"rs6681049": {
"chromosome": 1,
"genotype": "CC"
},
...
}
Explanation:
- The key is the RSID or vendor ID.
- Chromosome is which chromosome the data came from (1-22, X, Y, or MT).
- Genotype is the value for the RSID.
Differences between formats
SNP-JSON, SNPedia and vendor formats use different notations to indicate indels and no-calls., Format, Insertion, Deletion, No Call, Reference, ---------------, ----------------------, ----------, ---------, -------------, 23AndMe, I, D, -, https://customercare.23andme.com/hc/en-us/articles/212196888-What-does-not-determined-or-not-genotyped-mean-, AncestryDNA, I, D, 0, https://www.ancestry.com/dna/en/legal/us/faq#raw-6, FamilyTreeDNA, I, D, -, https://www.familytreedna.com/learn/autosomal-ancestry/universal-dna-matching/read-family-finder-raw-data-file/, SNP-JSON, I, -, ?, SNPedia, (the actual letters), -, N/A, https://www.snpedia.com/index.php/Talk:Rs5030655, ## Using your SNP-JSON
Just Write Code™
In this example we will determine if you are immune to norovirus:
var dna = require('./dna.json');
if (dna.rs601338.genotype == 'AA') {
// congrats you are immune!
}
Genosets
Once you have your data in the right format you can use the library of genosets by genomejs.
You can view a list of these by searching npm for genoset
You can also publish your own tools that analyze your DNA! Here is a tool that we recommend to get you started GQL
LICENSE
(MIT License)
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