fe0627da07b9f989bc642d824af381968163d9a8
lrnassar
  Wed Jul 8 13:40:04 2026 -0700
varFreqs: move ALFA to Global reference panels; add shared-sample bias caveat to description pages. refs #36642

Per Max's post-release feedback on the ticket: ALFA is not a European
cohort, it is an NCBI aggregator of dbGaP studies from many sources.
Moved from Europe to Global reference panels in the newsarch entry.

Also adds a shared-sample bias caveat to the Pooled allele frequency
section of both varFreqsAffected.html and varFreqsBackground.html. The
background page cites the concrete overlaps (1000 Genomes in both gnomAD
HGDP+1kG and HRC; HGDP/SGDP; AllOfUs/TOPMed; ALFA aggregating dbGaP
studies used elsewhere). The affected page cites the SPARK WGS cohort
being a subset of SPARK WES. Both explain that pooled AN is inflated and
pooled AF is skewed toward the frequency in the shared subset, and point
users to the per-cohort AC/AF/AN fields for unbiased single-cohort
numbers.

diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html
index 21b1e0272da..85b44b9edd4 100755
--- src/hg/htdocs/goldenPath/newsarch.html
+++ src/hg/htdocs/goldenPath/newsarch.html
@@ -200,35 +200,35 @@
 <p>
 The container track pulls together cohorts from across the world. A high-level
 summary of the regions and contributing projects is shown below; a
 complete table with per-cohort sample counts, data types, sub-populations
 and download status is on the
 <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varFreqs" target="_blank">container
 track description page</a>.
 </p>
 
 <table class="stdTbl">
   <tr><th>Region</th><th>Contributing cohorts</th></tr>
   <tr><td>East Asia</td><td>ToMMo, GenomeAsia, NPM, KOVA, WBBC, ChinaMAP, TPMI</td></tr>
   <tr><td>South Asia</td><td>IndiGen, GenomeIndia</td></tr>
   <tr><td>Africa</td><td>Tishkoff</td></tr>
   <tr><td>Americas</td><td>AllOfUs, TOPMed, ABraOM, Mexico Biobank</td></tr>
-  <tr><td>Europe</td><td>FinnGen, SweGen, GoNL, HRC, UK Biobank, ALFA</td></tr>
+  <tr><td>Europe</td><td>FinnGen, SweGen, GoNL, HRC, UK Biobank</td></tr>
   <tr><td>Middle East</td><td>Saudi</td></tr>
   <tr><td>Oceania</td><td>MGRB</td></tr>
   <tr><td>Disease cohorts</td><td>SFARI SPARK (WES + WGS), SCHEMA, GREGoR, GA4K</td></tr>
-  <tr><td>Global reference panels</td><td>SGDP, gnomAD HGDP+1kG</td></tr>
+  <tr><td>Global reference panels</td><td>SGDP, gnomAD HGDP+1kG, ALFA</td></tr>
   <tr><td>Long-read / linked-read</td><td>GA4K, CoLoRSdb, SVatalog</td></tr>
 </table>
 
 <p>
 License restrictions on some sources limit redistribution; see the
 container track description page for per-cohort details.
 </p>
 
 <p>
 We plan to continue updating this track as more population-scale
 allele-frequency datasets become available. If you are involved with a
 project that publishes variant frequencies and would like to contribute,
 please <a href="/contacts.html" target="_blank">reach out</a>.
 </p>