c3fee0a7bfcd442f7e2b148b594c8829a3ac0094 jnavarr5 Tue Nov 11 15:34:37 2025 -0800 Bolding the names of the tracks on the track description page. Mentioning which tracks are only available for which assemblies. refs #36642 diff --git src/hg/makeDb/trackDb/human/varFreqs.html src/hg/makeDb/trackDb/human/varFreqs.html index 6bbcbbc81c1..fffbc9b59ca 100644 --- src/hg/makeDb/trackDb/human/varFreqs.html +++ src/hg/makeDb/trackDb/human/varFreqs.html @@ -1,54 +1,59 @@ <h2>Description</h2> <p> This container track contains annotation tracks with individual level genotypes, usually phased, and tracks where only the variant frequencies, aka allele frequencies, are shown. The tracks were collected from the following projects. Only the projects 1000 Genomes (its own track), HGDP, SGDP, HGDP+1k and MXB provide individual-level genotypes. All others provide only allele frequencies, their genotypes require signing a data access agreement. </p> +<p> +<b>Available on hg19 and hg38:</b></p> <ul> <li> <b><a href="https://www.mxbiobank.org/" target="_blank">Mexico Biobank (MXB)</a></b>: This track displays phased alleles from the Mexico Biobank Project (MXB), based on array genotyping of 6,011 individuals sampled across all 32 states of Mexico during the 2000 National Health Survey (ENSA 2000) conducted by the National Institute of Public Health (INSP). Frequencies can be plotted onto a map on <a href="https://morenolab.shinyapps.io/mexvar/" target="_blank">MexVar</a>. The hg38 track was lifted from hg19. (Publication?) </li> <li> <b><a href="https://www.simonsfoundation.org/simons-genome-diversity-project/" target="_blank">Simons Genome Diversity Project (SGDP)</a></b>: Funded by the Simons Foundation, the Simons Genome Diversity Project is a large-scale effort that sequenced high-coverage genomes from 300 individuals (279 in this track) representing 142 diverse and often indigenous populations worldwide. Its goal was to capture the full range of human genetic diversity to better understand population history, migration, and adaptation. It is sampling populations in a way that represents as much anthropological, linguistic and cultural diversity as possible, and thus includes many deeply divergent human populations that are not well represented in other datasets. SGDP emphasizes breadth of global representation and population history, whereas HGDP emphasizes continuity and comparability across major population groups. Not all iits data is public, so this track contains only 279 genomes. For details, see (Mallick et al, Nature 2016). The hg38 track was lifted from hg19. </li> - +</ul> +<p> +<b>Available only on hg38:</b></p> +<ul> <li> <b><a href="https://pmc.ncbi.nlm.nih.gov/articles/PMC7115999/" target="_blank"></a>Human Genome Diversity Project (HGDP)</b>: 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. The Human Genome Diversity Project (HGDP) was launched in the early 1990s to study the genetic variation and evolutionary history of modern humans across global populations. Its goal was to document the full spectrum of human genetic diversity, particularly in indigenous and geographically isolated groups, to better understand population structure, migration, adaptation, and disease susceptibility.The project collected samples from ~1,000 individuals representing over 50 populations worldwide, including groups from Africa, Europe, Asia, Oceania, and the Americas. These data have become a foundational reference for population genetics and human evolution studies. @@ -168,143 +173,145 @@ TSV data can be requested on the <a href="https://www.kobic.re.kr/kova/downloads" target="_blank">KOVA Downloads</a> website. Coverage 100x for WES, 30x for WGS. For details see (Lee et al, Exp Mol Med 2022). </li> </ul> <h2>Display Conventions</h2> <p>Most tracks only show the variant and allele frequencies on mouseover or clicks. When zoomed in, tracks display alleles with base-specific coloring. Homozygote data are shown as one letter, while heterozygotes will be displayed with both letters. </p> <p> -Full haplotype display - only for the MXB and HGDP tracks: In "pack" mode, this track -sorts the haplotypes. This can be +Full haplotype display - only for the <b>MXB</b> and <b>HGDP</b> tracks: +In "pack" mode, this track sorts the haplotypes. This can be useful for determining the similarity between the samples and inferring inheritance at a particular locus. -For a full description of how the display works, please see our -<a href="../goldenpath/help/hgVcfTrackHelp.html">Haplotype Display help page</a>. -Briefly, each sample's phased and/or homozygous genotypes are split into haplotypes, +Each sample's phased and/or homozygous genotypes are split into haplotypes, clustered by similarity around a central variant (in pink), and sorted for display by their position in the clustering tree. Click a variant to center on it. The tree (as space allows) is drawn in the label area next to the track image. Leaf clusters, in which all haplotypes are identical (at least for the variants used in clustering), are colored purple. </p> +<p> +For a full description of how the display works, please see our +<a href="../goldenpath/help/hgVcfTrackHelp.html">Haplotype Display help page</a>. <p> -For NCBI ALFA: This track has no single VCF with INFO fields, but uses multiple subtracks instead, -one per ancestry. +For <b>NCBI ALFA:</b> This track has no single VCF with INFO fields, but uses multiple subtracks +instead, one per ancestry. </p> <h2>Data Access</h2> <p>Most of the data in these tracks are not available for download from UCSC. Only individual variants can be browsed on our website. But the data can be downloaded for free from the original projects. Accessing the data usually requires a click-through license on the respectice websites: </p> <p> -MXB: Allele frequencies by geographical state and ancestry are available via +<b>MXB:</b> Allele frequencies by geographical state and ancestry are available via the <a target="_blank" href="https://morenolab.shinyapps.io/mexvar/">MexVar platform</a>. Raw genotype data are available under controlled access at the EGA (Study: EGAS00001005797; Dataset: EGAD00010002361). For the VCFs, email andres.moreno@cinvestav.mx. </p> <p> -MCPS: VCFs with summarized allele frequencies are available from +<b>MCPS:</b> VCFs with summarized allele frequencies are available from the <a target="_blank" href="https://rgc-mcps.regeneron.com/">MCPS website</a>. </p> <p> -Regeneron one million exomes: VCFs with summarized allele frequencies are available from +<b>Regeneron one million exomes:</b> VCFs with summarized allele frequencies are available from the <a target="_blank" href="https://rgc-research.regeneron.com/me/resources">RGC ME website</a>. </p> <p> -TOPMED: VCFs with summarized allele frequencies are available from +<b>TOPMED:</b> VCFs with summarized allele frequencies are available from the <a target="_blank" href="https://bravo.sph.umich.edu/">TOPMED BRAVO website</a>. They require a login. </p> <p> -GenomeAsia Pilot: VCFs are available from UCSC and also from the +<b>GenomeAsia Pilot:</b> VCFs are available from UCSC and also from the the <a target="_blank" href="https://browser.genomeasia100k.org/#tid=download">GenomeAsia 100K website</a>. No license nor login. </p> <h2>Methods</h2> <p> -MXB: Genotyping was performed with the Illumina Multi-Ethnic Global Array +<b>MXB:</b> Genotyping was performed with the Illumina Multi-Ethnic Global Array (MEGA, ~1.8M SNPs), optimized for admixed populations and enriched for ancestry-informative and medically relevant variants. Only autosomal, biallelic SNPs passing quality control are included. Samples were selected from 898 recruitment sites, with prioritization of indigenous language speakers. Data processing included GenomeStudio → PLINK conversion, strand alignment, removal of duplicates, update of map positions using dbSNP Build 151 and low-quality variants/individuals, and relatedness filtering. </p> <p> -SGDP: The version used was +<b>SGDP:</b> The version used was <a target="_blank" href="https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/" >https://sharehost.hms.harvard.edu/genetics/reich_lab/sgdp/vcf_variants/</a>, merged with bcftools and lifted to hg38 with CrossMap. </p> <p> -KOVA: V7 of the TSV.gz was obtained from the KOVA staff and converted to VCF. If it not available -for download from our site but can be requested from the KOVA website. +<b>KOVA:</b> V7 of the TSV.gz was obtained from the KOVA staff and converted to VCF. If it not +available for download from our site but can be requested from the KOVA website. </p> <h2>Credits</h2> <p> -MXB: We thank the Center for Research and Advanced Studies (Cinvestav) of Mexico for +<b>MXB:</b> We thank the Center for Research and Advanced Studies (Cinvestav) of Mexico for generating and providing the frequency data, the National Institute of Medical Sciences and Nutrition (INCMNSZ) for DNA extraction, and the Ministry of Health together with the National Institute of Public Health (INSP) for the design and implementation of the National Health Survey 2000 (ENSA 2000). We also thank the ENSA-Genomics Consortium for their contributions to sample collection and data processing that made possible the construction of the MXB genomic resource. </p> <p> -MCPS: Data produced by Regeneron RGC and collaborators, which are the +<b>MCPS:</b> Data produced by Regeneron RGC and collaborators, which are the University of Oxford, Universidad Nacional Autónoma de México (UNAM) and National Institute of Genomic Medicine in Mexico. The Regeneron Genetics Center, University of Oxford, Universidad Nacional Autónoma de México (UNAM), National Institute of Genomic Medicine in Mexico, Abbvie Inc. and AstraZeneca UK Limited (collectively, the "Collaborators") bear no responsibility for the analyses or interpretations of the data presented here. Any opinions, insights, or conclusions presented herein are those of the authors and not of the Collaborators. </p> </p> <p> -Regeneron Million Exomes: The Regeneron Genetics Center, and its collaborators +<b>Regeneron Million Exomes:</b> The Regeneron Genetics Center, and its collaborators (collectively, the "Collaborators") bear no responsibility for the analyses or interpretations of the data presented here. Any opinions, insights, or conclusions presented herein are those of the authors and not of the Collaborators. This research has been conducted using the UK Biobank Resource under application number 26041. </p> <p> -SGDP: This project was funded by the Simons Foundation. Thanks to David Reich and Swapan +<b>SGDP:</b> This project was funded by the Simons Foundation. Thanks to David Reich and Swapan Mallick for help with importing the data. </p> <p> -KOVA: Thanks to Insu Jang and the KOVA director for providing variant frequencies in TSV format. +<b>KOVA:</b> Thanks to Insu Jang and the KOVA director for providing variant frequencies in TSV +format. </p> <p>Thanks to Alex Ioannidis, UCSC, and Andreas Lahner, MGZ, for feedback on this track.</p> <h2>References</h2> <p> Barberena-Jonas, C. et al. (2025). MexVar database: Clinical genetic variation beyond the Hispanic label in the Mexican Biobank. <em>Nature Medicine (in press)</em>. </p> <p> Sohail M, Moreno-Estrada A. <a href="https://journals.biologists.com/dmm/article-lookup/doi/10.1242/dmm.050522" target="_blank"> The Mexican Biobank Project promotes genetic discovery, inclusive science and local capacity building</a>. <em>Dis Model Mech</em>. 2024 Jan 1;17(1).