e461209cf1fd3758d63641915cd91ca9c8ab3020 lrnassar Thu Sep 24 17:00:10 2026 -0700 Remove tool output accidentally left in the mei description page, per CR. refs #37524 getTrackReferences writes its diagnostics to stdout rather than stderr, so six "Failed to fetch complete links from NCBI" lines ended up in the References section of mei.html and rendered as visible text on the track description page. NCBI is still not answering, so rather than rerun the tool the references are now assembled from the citation blocks already present on the six subtrack pages. That also restores the publisher links for every paper, which the failed lookups had degraded to bare PubMed URLs. Also make the INFO SEQ guard in meiHgsvc3CsvToBed.py require a usable string, so an empty SEQ= value would fall back to the ALT-derived sequence instead of silently producing an empty one. No record in either callset carries an empty SEQ today and the rebuilt output is byte-identical. diff --git src/hg/makeDb/trackDb/human/mei.html src/hg/makeDb/trackDb/human/mei.html index ee66fe4ea7e..170960355d6 100644 --- src/hg/makeDb/trackDb/human/mei.html +++ src/hg/makeDb/trackDb/human/mei.html @@ -1,178 +1,172 @@ <h2>Description</h2> <p> This track collection shows <b>Mobile Element Insertions (MEIs)</b> in the human genome. Mobile elements are stretches of DNA that have copied themselves into new genomic locations during evolution, and a few families remain active enough to keep producing new insertions in the human population today. The three element classes responsible for almost all MEIs in humans are <b>Alu</b> (~300 bp SINE retrotransposons), <b>L1/LINE-1</b> (typically 6 kb autonomous retrotransposons) and <b>SVA</b> (composite elements of ~700-3000 bp). Polymorphic MEIs - sites where some individuals carry the inserted element while others do not - are an important source of structural variation, can disrupt or alter gene expression, and have been implicated in a number of human diseases. </p> <p> Tracks in this collection report MEI calls from several sources: long-read genome assemblies, short-read whole-genome sequencing, and curated aggregations of published insertion calls. Items are colored by element class. Because the callsets differ in cohort, sequencing technology and caller, the same insertion site may be present in one subtrack and absent from another. </p> <h3>Available subtracks</h3> <ul> <li><a href="hgTrackUi?db=hg38&g=meiHgsvc3">HGSVC3 65 MEIs</a> - mobile element insertions identified in 65 diverse long-read assembled samples relative to the reference assembly (HGSVC3, Logsdon et al. 2025, <em>Nature</em>). Available on both GRCh38/hg38 (12,642 MEIs) and T2T-CHM13/hs1 (12,919 MEIs).</li> <li><a href="hgTrackUi?db=hg38&g=meiDeepmei1kg">DeepMEI 1000G MEIs</a> - 91,617 mobile element insertions called by the DeepMEI convolutional neural network on the 3,202 high-coverage 1000 Genomes samples (Xu et al. 2023, bioRxiv). hg38 only.</li> <li><a href="hgTrackUi?db=hg38&g=meiHmeid">HMEID 5675 MEIs</a> - 36,699 mobile element insertions called by MELT on 5,675 samples from the NyuWa Chinese cohort and the 1000 Genomes Project, with per-cohort and per-super-population allele frequencies (Niu et al. 2022, <em>Nucleic Acids Res</em>). hg38 only.</li> <li><a href="hgTrackUi?db=hg38&g=meiSwegen">SweGen 1000 MEIs</a> - 18,090 mobile element insertions called by MELT v2.0.2 on the 1,000 SweGen Swedish whole-genome samples (Ameur et al. 2017, <em>Eur J Hum Genet</em>), lifted from GRCh37 to hg38. The short-variant frequencies for the same cohort are in the <a href="hgTrackUi?db=hg38&g=swefreq">SweGen</a> subtrack of <a href="hgTrackUi?db=hg38&g=varFreqs">SNV Frequencies</a>.</li> <li><a href="hgTrackUi?db=hg38&g=meiEul1db">euL1db Insertions</a> - curated L1-HS insertion polymorphisms aggregated from 32 published studies covering 943 samples (euL1db, Mir et al. 2015, <em>Nucleic Acids Res</em>), lifted from hg19. Available on hg19 and hg38.</li> <li><a href="hgTrackUi?db=hg38&g=meiEul1dbRef">euL1db Ref L1HS</a> - the L1-HS copies already present in the reference genome, as catalogued by euL1db from the RepeatMasker annotation. The companion to the euL1db Insertions track. Available on hg19 and hg38.</li> </ul> <p> Related: <a href="hgTrackUi?db=hg38&g=longReadVariants">Long-read Structural Variants</a> contains the parent SV callsets from which several of these MEI tracks are derived. <a href="hgTrackUi?db=hg38&g=rmsk">RepeatMasker</a> shows all annotated mobile elements in the reference genome (regardless of whether they are polymorphic). </p> <h2>Display Conventions and Configuration</h2> <p> In the four insertion callsets (HGSVC3, DeepMEI, HMEID and SweGen) each MEI is shown as a 1-bp anchor block at the position where the insertion attaches to the reference, colored by element class: </p> <ul> <li><span style="display:inline-block;background-color:#0072B2;width:18px;height:12px;vertical-align:middle;"></span> <b>Alu</b> — SINE (Short INterspersed Element)</li> <li><span style="display:inline-block;background-color:#D55E00;width:18px;height:12px;vertical-align:middle;"></span> <b>L1</b> — LINE-1 (Long INterspersed Element-1)</li> <li><span style="display:inline-block;background-color:#009E73;width:18px;height:12px;vertical-align:middle;"></span> <b>SVA</b> (SINE-VNTR-Alu) — composite retrotransposon</li> <li><span style="display:inline-block;background-color:#CC79A7;width:18px;height:12px;vertical-align:middle;"></span> <b>HERVK</b> (Human Endogenous Retrovirus K) — endogenous retrovirus</li> <li><span style="display:inline-block;background-color:#000000;width:18px;height:12px;vertical-align:middle;"></span> <b>snRNA</b> — small nuclear RNA</li> </ul> <p> The two euL1db subtracks differ. Their items span real genomic intervals rather than a 1-bp anchor, and they are colored on a different basis: euL1db Insertions by the lineage of the contributing insertion calls (germline, somatic, both, or unknown) and euL1db Ref L1HS by L1HS sub-group. Each of those pages describes its own color scheme. </p> <p> Filters available on the subtrack configuration page allow restricting the displayed items by element class, insertion length, allele frequency, number of carrier samples, the number of MEI callers that supported the call, validation by L1ME-AID or PALMER, and overlap with reference segmental duplications and tandem repeats. </p> <h2>Data Access</h2> <p> Each subtrack has its own description page with details on file location, the autoSql schema, citation and download instructions. </p> <h2>References</h2> -Failed to fetch complete links from NCBI after 10 tries. Try again later or just use the PubMed paper link. -Failed to fetch complete links from NCBI after 10 tries. Try again later or just use the PubMed paper link. -Failed to fetch complete links from NCBI after 10 tries. Try again later or just use the PubMed paper link. -Failed to fetch complete links from NCBI after 10 tries. Try again later or just use the PubMed paper link. -Failed to fetch complete links from NCBI after 10 tries. Try again later or just use the PubMed paper link. -Failed to fetch complete links from NCBI after 10 tries. Try again later or just use the PubMed paper link. - <p> Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, Viklund J, Kähäri AK, Lundin P, Che H <em>et al</em>. -<a href="https://www.ncbi.nlm.nih.gov/pubmed/28832569" target="_blank"> +<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> Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K <em>et al</em>. -<a href="https://www.ncbi.nlm.nih.gov/pubmed/36055201" target="_blank"> +<a href="https://linkinghub.elsevier.com/retrieve/pii/S0092-8674(22)00991-6" target="_blank"> High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios</a>. <em>Cell</em>. 2022 Sep 1;185(18):3426-3440.e19. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/36055201" target="_blank">36055201</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9439720/" target="_blank">PMC9439720</a> </p> <p> Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, 1000 Genomes Project Consortium, Devine SE. -<a href="https://www.ncbi.nlm.nih.gov/pubmed/28855259" target="_blank"> +<a href="http://genome.cshlp.org/lookup/pmidlookup?view=long&pmid=28855259" target="_blank"> The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology</a>. <em>Genome Res</em>. 2017 Nov;27(11):1916-1929. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/28855259" target="_blank">28855259</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668948/" target="_blank">PMC5668948</a> </p> <p> Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D <em>et al</em>. -<a href="https://www.ncbi.nlm.nih.gov/pubmed/40702183" target="_blank"> +<a href="https://doi.org/10.1038/s41586-025-09140-6" target="_blank"> Complex genetic variation in nearly complete human genomes</a>. <em>Nature</em>. 2025 Aug;644(8076):430-441. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/40702183" target="_blank">40702183</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12350169/" target="_blank">PMC12350169</a> </p> <p> Mir AA, Philippe C, Cristofari G. -<a href="https://www.ncbi.nlm.nih.gov/pubmed/25352549" target="_blank"> +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gku1043" target="_blank"> euL1db: the European database of L1HS retrotransposon insertions in humans</a>. <em>Nucleic Acids Res</em>. 2015 Jan;43(Database issue):D43-7. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/25352549" target="_blank">25352549</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383891/" target="_blank">PMC4383891</a> </p> <p> Niu Y, Teng X, Zhou H, Shi Y, Li Y, Tang Y, Zhang P, Luo H, Kang Q, Xu T <em>et al</em>. -<a href="https://www.ncbi.nlm.nih.gov/pubmed/35212372" target="_blank"> +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkac128" target="_blank"> Characterizing mobile element insertions in 5675 genomes</a>. <em>Nucleic Acids Res</em>. 2022 Mar 21;50(5):2493-2508. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/35212372" target="_blank">35212372</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8934628/" target="_blank">PMC8934628</a> </p> + <p> Xu X, Huang Y, Wang X, Cheng J, Yuan H, Bu F. <a href="https://doi.org/10.1101/2023.03.07.531451" target="_blank"> Identification of mobile element insertion from whole genome sequencing data using deep neural network model</a>. <em>bioRxiv</em>. 2023 March 8. doi:10.1101/2023.03.07.531451. </p>