0a5389e8b81efa99e932f5e9e2424b27ce1af095 max Sun May 17 14:53:57 2026 -0700 varFreqs: add GenomeIndia subtrack (9,768 WGS, 83 endogamous Indian populations, Bhattacharyya 2025) and wire into databases.tsv for the next varFreqsAll rebuild. TSV->VCF conversion synthesizes AC=round(AF*AN) with AN=19536 since the upstream release only ships AF, refs #36642 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> diff --git src/hg/makeDb/trackDb/human/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html index 8144f5d596f..5be886e2213 100644 --- src/hg/makeDb/trackDb/human/varFreqs.html +++ src/hg/makeDb/trackDb/human/varFreqs.html @@ -195,30 +195,39 @@ <td>1.2k</td> <td>WGS</td> <td>Elderly admixed individuals (São Paulo)</td> <td>—</td> <td>Yes</td> </tr> <tr> <td><a href="hgTrackUi?g=indigenomes">IndiGenomes</a></td> <td>India</td> <td>1k</td> <td>WGS</td> <td>Healthy individuals</td> <td>—</td> <td>Yes</td> </tr> +<tr> + <td><a href="hgTrackUi?g=genomeindia">GenomeIndia 9.7k</a></td> + <td>India</td> + <td>9.8k</td> + <td>WGS (≥23x)</td> + <td>83 anthropologically defined endogamous populations across India</td> + <td>—</td> + <td>Yes</td> +</tr> <tr> <td><a href="hgTrackUi?g=kova">KOVA Korea</a></td> <td>Korea</td> <td>5.3k</td> <td>1.9k WGS + 3.4k WES</td> <td>Normal tissue from cancer patients, healthy parents, volunteers</td> <td>—</td> <td>No</td> </tr> <tr> <td><a href="hgTrackUi?g=npm">NPM Singapore</a></td> <td>Singapore</td> <td>9.8k</td> <td>WGS</td> <td>Chinese, Indian, Malay ancestry</td> @@ -397,30 +406,39 @@ <h2>Credits</h2> <p>This track is only possible thanks to the data from millions of volunteers around the world, who donated blood, signed consent forms and provided health information about themselves and sometimes their families. Click on any of the tracks in the list above to see the specific credits for each project. Thanks to Alex Ioannidis, UCSC, for the motivation for this track and to Andreas Lahner, MGZ, for feedback.</p> <h2>References</h2> <p> All of Us Research Program Genomics Investigators. <a href="https://doi.org/10.1038/s41586-023-06957-x" target="_blank"> Genomic data in the All of Us Research Program</a>. <em>Nature</em>. 2024 Mar;627(8003):340-346. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/38374255" target="_blank">38374255</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10937371/" target="_blank">PMC10937371</a> </p> +<p> +Bhattacharyya C, Subramanian K, Uppili B, Biswas NK, Ramdas S, Tallapaka KB, Arvind P, Rupanagudi +KV, Maitra A, Nagabandi T <em>et al</em>. +<a href="https://doi.org/10.1038/s41588-025-02153-x" target="_blank"> +Mapping genetic diversity with the GenomeIndia project</a>. +<em>Nat Genet</em>. 2025 Apr;57(4):767-773. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40200122" target="_blank">40200122</a> +</p> + <p> Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, Viklund J, Kahari AK, Lundin P, Che H <em>et al</em>. <a href="https://doi.org/10.1038/ejhg.2017.130" target="_blank"> SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population</a>. <em>Eur J Hum Genet</em>. 2017 Nov;25(11):1253-1260. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28832569" target="_blank">28832569</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765326/" target="_blank">PMC5765326</a> </p> <p> Chirmade S, Wang Z, Mastromatteo S, Sanders E, Thiruvahindrapuram B, Nalpathamkalam T, Pellecchia G, Lin F, Keenan K, Patel RV <em>et al</em>. <a href="https://doi.org/10.1038/s41437-025-00809-2" target="_blank">