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 | 0 | Yes | | FamilyTree | Yes | 99 USD | Cheek Swab | 708,092 | 0 | 18,091 | 0 | 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)

Copyright (c) 2013-2016 Fractal [email protected]

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.