chore(gnomad): bump version to 4.1.1

client/src/app/components/pages/human-result/human-result.component.html

@@ -206,17 +206,19 @@ <h3 class="mb-0">gnomAD</h3>
           <!-- gnomAD variant -->
           <div class="col-12 mt-3" *ngIf="variant" [@toggle]>
             <h4 class="mt-0 mb-3 d-inline-block align-middle">
-              Population Allele Frequencies of {{ variantString }} from gnomAD
+              Population Allele Frequencies of
+              Chr{{ hg38Variant.chr }}:{{ hg38Variant.pos }}&nbsp;{{ hg38Variant.ref }}&gt;{{ hg38Variant.alt }}
+              from gnomAD
             </h4>
             <a class="mb-3 d-inline-block ml-3 align-middle"
-              href="https://gnomad.broadinstitute.org/variant/{{ variant.chr }}-{{ variant.pos }}-{{ variant.ref }}-{{ variant.alt }}?dataset=gnomad_r2_1"
+              href="https://gnomad.broadinstitute.org/variant/{{ hg38Variant.chr }}-{{ hg38Variant.pos }}-{{ hg38Variant.ref }}-{{ hg38Variant.alt }}?dataset=gnomad_r4"
               target="_blank">
               <button mat-button color="primary">
                 <mat-icon class="mr-1 icon-18px">open_in_new</mat-icon>
                 More on gnomAD
               </button>
             </a>
-            <app-gnom-ad [variant]="variant"></app-gnom-ad>
+            <app-gnom-ad [variant]="hg38Variant"></app-gnom-ad>
           </div>
 
           <!-- gnomAD gene -->

client/src/app/services/api.service.ts

@@ -108,7 +108,7 @@ export class ApiService {
   }
 
   getGnomADVaraint(variant: Variant): Observable<any> {
-    const url = `${environment.apiHost}/data/gnomAD/variant/${variant.chr}:${variant.pos}${variant.ref}>${variant.alt}`;
+    const url = `${environment.apiHost}/data/gnomAD/variant/${variant.chr}:${variant.pos}${variant.ref}>${variant.alt}?build=${variant.build || 'hg19'}`;
     return new Observable(observer => {
       this.http.get(url).subscribe((res: any) => {
         res = res || {};

server/app.js

@@ -66,6 +66,8 @@ console.log(`Running @ ${config.env}`);
 console.log(`DECIPHER control data using collection ${config.decipher.control.name}`);
 console.log(`DECIPEHR disease data using collection ${config.decipher.disease.name}`);
 console.log(`DECIPHER disease access is restricted to ${config.decipher.disease.allowedReferer}`);
+console.log(`gnomAD data using version ${config.gnomad.version} ` +
+  `(collections: ${config.gnomad.variant.name}, ${config.gnomad.gene.name})`);
 
 const httpServer = http.createServer(app);
 // Mongoose

server/config/index.js

@@ -21,6 +21,9 @@ const config = {
         version: process.env.DECIPHER_DISEASE_VERSION,
         name: `DECIPHERDisease${process.env.DECIPHER_DISEASE_VERSION ? `.${process.env.DECIPHER_DISEASE_VERSION}` : ''}`
       }
+    },
+    gnomad: {
+      version: process.env.GNOMAD_VERSION || '2.1.1',
     }
   },
 
@@ -41,6 +44,9 @@ const config = {
         version: process.env.DECIPHER_DISEASE_VERSION,
         name: `DECIPHERDisease${process.env.DECIPHER_DISEASE_VERSION ? `.${process.env.DECIPHER_DISEASE_VERSION}` : ''}`
       }
+    },
+    gnomad: {
+      version: process.env.GNOMAD_VERSION || '2.1.1',
     }
   },
 
@@ -72,7 +78,19 @@ config[env].mongo.url = `mongodb://${config[env].mongo.username}:${config[env].m
 }/${config[env].mongo.database}`;
 
 config[env].omim = require(path.join(rootPath, 'config/omim', `${env}.json`));
-
+config[env].gnomad.variant = {
+  name:
+    config[env].gnomad.version === '2.1.1'
+      ? 'GnomAD'
+      : `Gnomad.${config[env].gnomad.version}`,
+  defaultBuild: config[env].gnomad.version === '2.1.1' ? 'hg19' : 'hg38',
+};
+config[env].gnomad.gene = {
+  name:
+    config[env].gnomad.version === '2.1.1'
+      ? 'GnomADGene'
+      : `GnomadGene.${config[env].gnomad.version}`,
+};
 config[env].liftover = {
   hg38Version: process.env.LIFTOVER_HG38_VERSION || 'hg38_201312',
   hg19Version: process.env.LIFTOVER_HG19_VERSION || 'hg19_200902',

server/controllers/gnomAD.controller.js

@@ -2,6 +2,7 @@ const GnomAD = require('../models/gnomAD.model');
 
 const utils = require('../utils');
 const db = require('../utils/db');
+const config = require('../config');
 
 // eslint-disable-next-line no-unused-vars
 const replace = (doc) => {
@@ -21,13 +22,18 @@ exports.findByVariant = (req, res) => {
     return res.status(404).send({ message: 'Invalid variant' });
   }
 
-  db.gnomAD.getByVariant(variant, null, build)
+  const majorVersion = config.gnomad.version.split('.')[0] || '2';
+  (majorVersion === '2'
+    ? db.gnomAD.getByVariant(variant, null, build)
+    : db.gnomAD.getByVariantV2(variant, null, build)
+  )
     .then((doc) => {
       return res.json(doc);
-    }).catch((err) => {
+    })
+    .catch((err) => {
       console.log(err);
       return res.status(500).send({
-        message: 'Server error occured'
+        message: 'Server error occured',
       });
     });
 };

server/models/gnomAD.model.js

@@ -1,4 +1,5 @@
 const mongoose = require('mongoose');
+const config = require('../config');
 
 const gnomADSchema = mongoose.Schema({
   chr: {
@@ -25,5 +26,5 @@ const gnomADSchema = mongoose.Schema({
     type: Number,
     select: false
   }
-}, { collection: 'GnomAD' });
+}, { collection: config.gnomad.variant.name });
 module.exports = mongoose.model('GnomAD', gnomADSchema);

server/models/gnomADGene.model.js

@@ -1,5 +1,6 @@
 const mongoose = require('mongoose');
 const ObjectId = mongoose.Schema.Types.ObjectId;
+const config = require('../config');
 
 const gnomADGeneSchema = mongoose.Schema({
   geneId: {
@@ -16,5 +17,5 @@ const gnomADGeneSchema = mongoose.Schema({
     type: Number,
     select: false
   }
-}, { collection: 'GnomADGene' });
+}, { collection: config.gnomad.gene.name });
 module.exports = mongoose.model('GnomADGene', gnomADGeneSchema);

server/utils/db/gnomAD.js

@@ -96,3 +96,32 @@ exports.getByVariant = (variant, projection, build) => {
   });
 };
 
+// Query by hg38 for newer version for gnomAD (v3+)
+exports.getByVariantV2 = async (variant, projection, build) => {
+  projection = projection || {};
+  projection['_id'] = 0;
+
+  if (build === 'hg19') {
+    // need to liftOver to hg38
+    try {
+      variant = await utils.liftover.liftOverVariant(variant, 'hg19', 'hg38');
+    } catch (err) {
+      console.error('Error while liftOver hg19 to hg38 for getByVariantV2', err);
+      return null;
+    }
+  }
+  if (!variant || !variant.ref || !variant.alt) {
+    console.error('Error: liftOver returned null variant for getByVariantV2');
+    return null;
+  }
+
+  return GnomAD.findOne(
+    {
+      hg38Chr: variant.chr,
+      hg38Pos: variant.pos,
+      ref: variant.ref,
+      alt: variant.alt,
+    },
+    projection
+  ).lean();
+};