Update website content

browser/about/about.md

@@ -1,4 +1,4 @@
-The Genome Aggregation Database (gnomAD), originally launched in 2014 as the Exome Aggregation Consortium (ExAC), is the result of a coalition of investigators willing to share aggregate exome and genome sequencing data from a variety of large-scale sequencing projects, and make summary data available for the wider scientific community. The project is overseen by co-directors Heidi Rehm and Mark Daly, and steering committee members Samantha Baxter, Katherine Chao, Julia Goodrich, Konrad Karczewski, Daniel MacArthur, Benjamin Neale, Anne O'Donnell-Luria, Kaitlin Samocha, Matthew Solomonson, and Michael Talkowski. To learn more about the team that produces gnomAD please see our [team page](/team). A list of investigators and groups that have contributed data is available below.
+The Genome Aggregation Database (gnomAD™), originally launched in 2014 as the Exome Aggregation Consortium (ExAC), is the result of a coalition of investigators willing to share aggregate human exome and genome sequencing data from a variety of large-scale sequencing projects, and make summary data available for the wider scientific community. The project is overseen by co-directors Heidi Rehm and Mark Daly, and steering committee members Samantha Baxter, Katherine Chao, Julia Goodrich, Konrad Karczewski, Daniel MacArthur, Benjamin Neale, Anne O'Donnell-Luria, Kaitlin Samocha, Matthew Solomonson, and Michael Talkowski. To learn more about the team that produces gnomAD please see our [team page](/team). A list of investigators and groups that have contributed data is available below.
 
 The gnomAD database is composed of exome and genome sequences from around the world. We have removed cohorts that were recruited for pediatric disease, except for a small number of diverse cohorts where we have included unaffected relatives. As such, the gnomAD resource should serve as useful reference sets of allele frequencies for severe pediatric disease studies - however, note that some individuals with severe disease may still be included in the data sets such as biobanks, albeit likely at a frequency equivalent to or lower than that seen in the general population.
 

browser/about/contributors/alumni.md

@@ -7,6 +7,7 @@
 - Laurent Francioli (production and analysis)
 - Jeff Gentry (data generation)
 - Thibault Jeandet (data generation)
+- Steve Jahl (browser)
 - Diane Kaplan (data generation)
 - Monkol Lek (production and analysis)
 - Eric Minikel (analysis)

browser/about/federation/federation.md

@@ -0,0 +1 @@
+The gnomAD project has demonstrated the value of aggregating diverse allele frequency reference datasets that are processed consistently and represented in a single resource. However, this centralized approach is not feasible for all datasets, as some data cannot be exported from their local environments for security, policy or legal reasons. In order to incorporate these datasets into gnomAD, we have launched the Federated gnomAD project. This project includes participating sites from across the globe (site descriptions below). All sites involved in Federated gnomAD plan to process and quality control their data according to gnomAD best practices and freely share aggregate allele frequency data with the primary gnomAD database. All of the summary data will be aggregated with the primary gnomAD data in the gnomAD browser for ease of use by the wider scientific and clinical community.

browser/about/policies/policies.md

@@ -6,12 +6,6 @@ Data included in the gnomAD database has met our ethical requirements including
 
 While we hope gnomAD exists for decades to come, we recognize the importance of having a plan in place for preserving gnomAD datasets. Through our [collaboration](https://gnomad.broadinstitute.org/news/2020-10-open-access-to-gnomad-data-on-multiple-cloud-providers/) with Google Cloud Platform (GCP), Microsoft’s Azure, and Amazon Web Services (AWS), we have ensured that the public would continue to have access to any past gnomAD datasets as long as at least one of those public dataset hosting entities remains in business. Additionally we will do everything possible to sustain the existing browser for as long as financial/staffing commitments allow.
 
-## gnomAD Open Science Policy
-
-The gnomAD team has a firm commitment to open science. This includes, but is not limited to, making our data and code open-source, posting pre-prints, and prioritizing publishing in journals that support open access.
-
-We request that developers integrating gnomAD data in their tools include a statement acknowledging the inclusion of gnomAD data (e.g., "This tool is powered by the gnomAD v4.1 release data."). However, to avoid confusion and misattribution, we ask that you refrain from incorporating "gnomAD"/"Genome Aggregation Database" into the name of your tool and from using the gnomAD logo without permission.
-
 ## Data Generation
 
 A full description of the methods used to aggregate and call variants across the exomes and genomes in this project will be provided shortly. In brief: we pulled raw data together from as many exomes and genomes as we could get our hands on, aligned and processed each of these data types through unified processing pipelines based on Picard, and performed variant calling with the GATK HaplotypeCaller following GATK best practices. Processing and variant calling at this enormous scale was only possible thanks to the hard work of the Broad Institute's Data Sciences Platform, and the Intel GenomicsDB team. Downstream analysis relied heavily on the [Hail](https://hail.is/) toolkit.

browser/about/policies/terms.md

@@ -1,4 +1,4 @@
-## Terms of use
+## gnomAD™ Terms of use
 
 All data here are released openly and publicly for the benefit of the wider biomedical community. You can freely download and search the data, and we encourage the use and publication of results generated from these data. **There are absolutely no restrictions or embargoes on the publication of results derived from gnomAD data**. However, we encourage you to [contact the consortium](mailto:[email protected]) before embarking on large-scale analyses to check if your proposed analysis overlaps with work currently underway by the gnomAD consortium. All users of gnomAD data agree to not attempt to reidentify participants.
 
@@ -10,6 +10,12 @@ Screenshots of the website may also be used without restriction. As with any use
 
 Some annotations may have restrictions on usage. For instance, SpliceAI annotations have been computed by Illumina and are provided with permission under a CC BY NC 4.0 license for academic and non-commercial use [SpliceAI](https://github.com/Illumina/SpliceAI). It is the responsibility of users to abide by all relevant licensing requirements.
 
+## gnomAD™ Open Science Policy
+
+The gnomAD team has a firm commitment to open science. This includes, but is not limited to, making our data and code open-source, posting pre-prints, and prioritizing publishing in journals that support open access.
+
+We request that developers integrating gnomAD data in their tools include a statement acknowledging the inclusion of gnomAD data (e.g., "This tool includes data from the gnomAD v4.1 release."). However, to avoid confusion and misattribution, we ask that you refrain from incorporating "gnomAD" or "Genome Aggregation Database'' into the name of your tool and from using the gnomAD logo without permission. gnomAD™ is a trademark owned by The Broad Institute, Inc.
+
 ## Citation in publications
 
 We request that any use of data obtained from the gnomAD browser cite [the gnomAD flagship paper](https://broad.io/gnomad_lof) and any online resources that include the data set provide a link to the browser. For use of the SV data, we request cite [this paper](https://broad.io/gnomad_sv) for use of the SV data.

browser/help/faq/general/do-you-have-videos-on-how-to-use-gnomad.md

@@ -0,0 +1,9 @@
+---
+question: 'Do you have videos on how to use gnomAD?'
+---
+
+Yes, we have a few different videos that cover how gnomAD is created as well as guidance on how to use it.
+
+- [Using gnomAD - tips and tricks](https://www.broadinstitute.org/videos/mpg-primer-using-gnomad-tips-and-tricks)
+- [gnomAD: Using large genomic data sets to interpret human genetic variation](https://www.broadinstitute.org/videos/gnomad-using-large-genomic-data-sets-interpret-human-genetic-variation)
+- [gnomAD v4: Behind the scenes (2023)](https://www.youtube.com/watch?v=my98du_c_7U&list=PLEEE2A91B09B77B4A&index=28)

browser/help/helpPageTableOfContents.ts

@@ -30,6 +30,7 @@ const helpPageTableOfContents: { topics: string[]; faq: FaqTopic[] } = {
       topics: [
         'whats-the-difference-between-the-different-versions-of-gnomad',
         'what-features-are-not-yet-in-v4-and-where-can-i-find-them',
+        'do-you-have-videos-on-how-to-use-gnomad',
         'what-are-the-restrictions-on-data-usage',
         'i-have-identified-a-rare-variant-what-phenotype-data-are-available',
         'can-i-get-access-to-individual-level-genotype-data-from-gnomad',

browser/src/DataPage/GnomadV2Downloads.tsx

@@ -291,7 +291,7 @@ const GnomadV2Downloads = () => {
 
         <p>
           For more information about these files, see our{' '}
-          <Link to="https://gnomad.broadinstitute.org/new/2024-08-release-gnomad-browser-tables">
+          <Link to="https://gnomad.broadinstitute.org/news/2024-08-release-gnomad-browser-tables">
             changelog entry
           </Link>{' '}
           on the browser tables, and the <Link to="/help/v4-browser-hts">help text</Link>.

browser/src/DataPage/GnomadV4Downloads.tsx

@@ -270,8 +270,9 @@ const GnomadV4Downloads = () => {
 
         <p>
           For more information about these files, see our{' '}
-          <Link to="https://gnomad.broadinstitute.org/new/2024-08-release-gnomad-browser-tables">
-            changelog entry
+          <Link to="https://gnomad.broadinstitute.org/news/2024-08-release-gnomad-browser-tables">
+            https://gnomad.broadinstitute.org/news/2024-08-release-gnomad-browser-tables/ changelog
+            entry
           </Link>{' '}
           on the browser tables, and the <Link to="/help/v4-browser-hts">help text</Link>.
         </p>

browser/src/DataPage/__snapshots__/DataPage.spec.tsx.snap

@@ -7433,10 +7433,10 @@ exports[`Data Page has no unexpected changes 1`] = `
 
         <a
           className="-Link c13"
-          href="https://gnomad.broadinstitute.org/new/2024-08-release-gnomad-browser-tables"
+          href="https://gnomad.broadinstitute.org/news/2024-08-release-gnomad-browser-tables"
           onClick={[Function]}
         >
-          changelog entry
+          https://gnomad.broadinstitute.org/news/2024-08-release-gnomad-browser-tables/ changelog entry
         </a>
 
         on the browser tables, and the 
@@ -24914,7 +24914,7 @@ exports[`Data Page has no unexpected changes 1`] = `
 
         <a
           className="-Link c13"
-          href="https://gnomad.broadinstitute.org/new/2024-08-release-gnomad-browser-tables"
+          href="https://gnomad.broadinstitute.org/news/2024-08-release-gnomad-browser-tables"
           onClick={[Function]}
         >
           changelog entry

browser/src/FederationPage.spec.tsx

@@ -0,0 +1,18 @@
+import { expect, test } from '@jest/globals'
+import 'jest-styled-components'
+
+import React from 'react'
+import renderer from 'react-test-renderer'
+
+import FederationPage from './FederationPage'
+
+import { BrowserRouter } from 'react-router-dom'
+
+test('Federation Page has no unexpected changes', () => {
+  const tree = renderer.create(
+    <BrowserRouter>
+      <FederationPage />
+    </BrowserRouter>
+  )
+  expect(tree).toMatchSnapshot()
+})

browser/src/FederationPage.tsx

@@ -0,0 +1,243 @@
+import React from 'react'
+import styled from 'styled-components'
+import { Link, PageHeading } from '@gnomad/ui'
+
+// @ts-ignore - TS2307 Cannot fine module ... or its corresponding type declarations.
+import FederatedGnomadMap from '../about/federation/FederatedGnomadMap.png'
+// @ts-ignore - TS2307 Cannot fine module ... or its corresponding type declarations.
+import AustralianGeneticDiversityDatabaseLogo from '../about/federation/AustralianGeneticDiversityDatabaseLogo.png'
+// @ts-ignore - TS2307 Cannot fine module ... or its corresponding type declarations.
+import CanadaGnomadLogo from '../about/federation/CanadaGnomadLogo.png'
+// @ts-ignore - TS2307 Cannot fine module ... or its corresponding type declarations.
+import ChinaGnomadLogo from '../about/federation/ChinaGnomadLogo.png'
+// @ts-ignore - TS2307 Cannot fine module ... or its corresponding type declarations.
+import EuropeanGenomePhenomeArchiveLogo from '../about/federation/EuropeanGenomePhenomeArchiveLogo.png'
+// @ts-ignore - TS2307 Cannot fine module ... or its corresponding type declarations.
+import InstituteForGenomicsStatisticsAndBioinformaticsLogo from '../about/federation/InsituteForGenomicsStatisticsAndBioinformaticsLogo.png'
+// @ts-ignore - TS2307 Cannot fine module ... or its corresponding type declarations.
+import PrecisionHealthResearchSingaporeLogo from '../about/federation/PrecisionHealthResearchSingaporeLogo.png'
+// @ts-ignore - TS2307 Cannot fine module ... or its corresponding type declarations.
+import QatarGenomeLogo from '../about/federation/QatarGenomeLogo.png'
+
+// @ts-expect-error
+import federationContent from '../about/federation/federation.md'
+
+import DocumentTitle from './DocumentTitle'
+import InfoPage from './InfoPage'
+import MarkdownContent from './MarkdownContent'
+import {
+  StatsTable,
+  StatsTableHeaderRow,
+  StatsTableBody,
+} from '../src/StatsPage/StatsPageTables/TableStyles'
+
+const CenteredContainer = styled.div`
+  display: flex;
+  justify-content: space-around;
+`
+
+const LogoContainer = styled.div`
+  display: flex;
+  align-items: center;
+  gap: 2rem;
+  margin: 2rem 0;
+`
+
+const SingleLogo = styled.img`
+  width: 200px;
+  height: auto;
+`
+
+const DoubleLogo = styled(SingleLogo)`
+  width: 400px;
+`
+
+type Dataset = {
+  country: string
+  samples: string
+  source: string
+  lead: string
+  link?: string
+}
+
+const datasets: Dataset[] = [
+  {
+    country: 'Africa',
+    samples: 'TBD',
+    source: 'African Genome Variation Database',
+    lead: 'Nicky Mulder',
+  },
+  {
+    country: 'Australia',
+    samples: '10,000',
+    source: 'Our DNA',
+    link: 'https://populationgenomics.org.au/',
+    lead: 'Daniel MacArthur',
+  },
+  {
+    country: 'Brazil',
+    samples: '21,000',
+    source: 'Genomas SUS',
+    lead: 'Leandro Colli',
+  },
+  {
+    country: 'Canada',
+    samples: '60,000',
+    source: 'Canadian Genomic Data Commons',
+    lead: 'Jordan Lerner-Ellis',
+  },
+  {
+    country: 'China',
+    samples: '10,000',
+    source: 'China Kadoorie Biobank (>500K)',
+    link: 'https://gnomad.org.cn',
+    lead: 'Xiao Li',
+  },
+  {
+    country: 'Europe',
+    samples: 'TBD',
+    source: 'European Genome Phenome Archive',
+    link: 'https://ega-archive.org/',
+    lead: 'Abeer Fadda',
+  },
+  {
+    country: 'Europe',
+    samples: '30,000',
+    source: 'European Reference Network for Rare Neurological Diseases',
+    link: 'https://www.ern-rnd.eu/',
+    lead: 'Holm Graessner',
+  },
+  {
+    country: 'Germany',
+    samples: '10,000',
+    source: 'Clinical sequencing',
+    link: 'https://www.igsb.uni-bonn.de/en',
+    lead: 'Peter Krawitz',
+  },
+  {
+    country: 'Germany',
+    samples: 'TBD',
+    source: 'The German Human Genome-Phenome Archive (GHGA)',
+    lead: 'Drew Behrens',
+  },
+  {
+    country: 'Japan',
+    samples: '100,000',
+    source: 'Tomoku Medical Megabank Organization',
+    link: 'https://www.megabank.tohoku.ac.jp/english/',
+    lead: 'Soichi Ogishima',
+  },
+  {
+    country: 'Qatar',
+    samples: '25,000',
+    source: 'Qatar Biobank',
+    link: 'https://www.qphi.org.qa/',
+    lead: 'Chadi Saad',
+  },
+  {
+    country: 'Singapore',
+    samples: '10,000',
+    source: 'SG10K_Health data',
+    link: 'https://www.a-star.edu.sg/gis/our-science/precision-medicine-and-population-genomics/npm',
+    lead: 'Maxime Hebrard',
+  },
+  {
+    country: 'Taiwan',
+    samples: '1,500',
+    source: 'Taiwan Biobank',
+    link: 'https://genomes.tw/',
+    lead: 'Jacob Shujui Hsu',
+  },
+  {
+    country: 'UK',
+    samples: '50,000',
+    source:
+      'Avon Longitudinal Study of Parents and Children (ALSPC), Born in Bradford, Millennium Cohort Study (MCS), Fenland Study',
+    link: 'https://www.sanger.ac.uk/',
+    lead: 'Vivek Iyer',
+  },
+]
+
+export default () => (
+  <InfoPage>
+    <DocumentTitle title="Federated gnomAD" />
+    <PageHeading>Federated gnomAD</PageHeading>
+
+    <MarkdownContent dangerouslySetInnerHTML={{ __html: federationContent.html }} />
+
+    <br />
+
+    <CenteredContainer>
+      <img
+        src={FederatedGnomadMap}
+        alt="Locations of federated gnomAD data sources on a world map."
+        width="70%"
+      />
+    </CenteredContainer>
+
+    <br />
+
+    <CenteredContainer>
+      <StatsTable>
+        <thead>
+          <StatsTableHeaderRow>
+            <th>Country</th>
+            <th>Samples</th>
+            <th>Source</th>
+            <th>Lead</th>
+          </StatsTableHeaderRow>
+        </thead>
+        <StatsTableBody>
+          {datasets.map((dataset) => {
+            return (
+              <tr key={dataset.source}>
+                <td>{dataset.country}</td>
+                <td>{dataset.samples}</td>
+                <td>
+                  {dataset.link ? (
+                    // @ts-expect-error
+                    <Link href={dataset.link}>{dataset.source}</Link>
+                  ) : (
+                    dataset.source
+                  )}
+                </td>
+                <td>{dataset.lead}</td>
+              </tr>
+            )
+          })}
+        </StatsTableBody>
+      </StatsTable>
+    </CenteredContainer>
+
+    <br />
+    <br />
+
+    <CenteredContainer>
+      <LogoContainer>
+        <SingleLogo alt="gnomAD Canada logo" src={CanadaGnomadLogo} />
+        <SingleLogo alt="gnomAD China logo" src={ChinaGnomadLogo} />
+        <SingleLogo
+          alt="Australian Genetic Diversity Database logo"
+          src={AustralianGeneticDiversityDatabaseLogo}
+        />
+        <DoubleLogo
+          alt="Institute for Genomic Statics and Bioinformatics logo"
+          src={InstituteForGenomicsStatisticsAndBioinformaticsLogo}
+        />
+      </LogoContainer>
+    </CenteredContainer>
+    <CenteredContainer>
+      <LogoContainer>
+        <SingleLogo
+          alt="European Genome-Phenome Archive logo"
+          src={EuropeanGenomePhenomeArchiveLogo}
+        />
+        <SingleLogo
+          alt="Precision Health Research Singapore logo"
+          src={PrecisionHealthResearchSingaporeLogo}
+        />
+        <DoubleLogo alt="Qatar Genome logo" src={QatarGenomeLogo} />
+      </LogoContainer>
+    </CenteredContainer>
+  </InfoPage>
+)

browser/src/HomePage.tsx

@@ -275,9 +275,9 @@ export default () => (
       <Link preserveSelectedDataset={false} to="/about">
         Genome Aggregation Database
       </Link>{' '}
-      (gnomAD) is a resource developed by an international coalition of investigators, with the goal
-      of aggregating and harmonizing both exome and genome sequencing data from a wide variety of
-      large-scale sequencing projects, and making summary data available for the wider scientific
+      (gnomAD™) is a resource developed by an international coalition of investigators, with the
+      goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety
+      of large-scale sequencing projects, and making summary data available for the wider scientific
       community.
     </p>
     <p>

browser/src/NavBar.tsx

@@ -109,6 +109,11 @@ const NavBar = () => {
             Team
           </Link>
         </li>
+        <li>
+          <Link to="/federated" onClick={closeMenu}>
+            Federated
+          </Link>
+        </li>
         <li>
           <Link to="/stats" onClick={closeMenu}>
             Stats