7e87cadb469b4e0eb4fb7f973154357cfe7fc345 lrnassar Mon Sep 21 15:56:18 2026 -0700 QA fixes for the mei (Mobile Insertions) track collection. refs #37524 Fix two data bugs found during QA and rebuild the affected bigBeds. meiEul1dbToBed.py looked up samples and individuals by name, but euL1db joins on 1-based row numbers, so neither join ever matched and the individual count, tissues, clinical conditions and populations were empty on all 8,991 insertions while the contributing-samples table printed row numbers. Both loaders now key on the row number, the table prints the sample name, and the adjacent population filter is case-insensitive so it actually drops "unknown". meiHgsvc3CsvToBed.py took alt[1:] on every record, which dropped the first base of the element on the 96 GRCh38 and 111 T2T-CHM13 records where PALMER2 is the only caller and ALT carries no anchor base; it now prefers INFO SEQ, which always matches SVLEN. Correct seven statements on the description pages against their sources: the HGSVC3 single-caller split was attributed to PALMER rather than L1ME-AID, its orthogonal concordance was 90.8% rather than 92.5%, euL1db was credited with aligning the L1HS consensus when the paper says it was processed from our RepeatMasker track, DeepMEI's network was described as a classifier rather than a genotyper and given the wrong training set, euL1db listed two detection methods absent from the data, and HMEID contradicted itself on the MELT ASSESS cutoff. Also: the SweGen bigDataUrl now points at _swegen.bb so the restricted callset is kept off the download server; the container page no longer claims the whole collection is long-read, lists the two euL1db subtracks, scopes its display conventions to the subtracks they describe, and cites all six papers; dead and wrong track links are repointed and pinned to a db; $db replaces hardcoded hg38 in paths on pages that serve three assemblies; the euL1db labels no longer carry hg38 counts and a lift note that made no sense on hg19; all six subtracks gain a dataVersion; the euL1db filter ranges match the data; and five autoSql field descriptions match what the files contain. Document the gbdb symlinks and the QA changes in doc/hg38/mei.txt, correct the HMEID bedToBigBed type there, and add an hg19.txt pointer since hg19 carries the two euL1db subtracks. diff --git src/hg/makeDb/trackDb/human/mei.html src/hg/makeDb/trackDb/human/mei.html index 0d9f2a04f42..ee66fe4ea7e 100644 --- src/hg/makeDb/trackDb/human/mei.html +++ src/hg/makeDb/trackDb/human/mei.html @@ -1,90 +1,178 @@

Description

This track collection shows Mobile Element Insertions (MEIs) 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 Alu (~300 bp SINE retrotransposons), L1/LINE-1 (typically 6 kb autonomous retrotransposons) and SVA (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.

-Tracks in this collection report MEI calls assembled from long-read -genome sequencing. Items are colored by element class. +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.

Available subtracks

-Related: Long-read Structural Variants +Related: Long-read Structural Variants contains the parent SV callsets from which several of these MEI tracks -are derived. RepeatMasker shows +are derived. RepeatMasker shows all annotated mobile elements in the reference genome (regardless of whether they are polymorphic).

Display Conventions and Configuration

-Each MEI is shown as a 1-bp anchor block at the position where the -insertion attaches to the reference. Items are colored by element class: +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:

+

+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. +

+

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.

Data Access

Each subtrack has its own description page with details on file location, the autoSql schema, citation and download instructions.

References

+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. + + +

+Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, Viklund J, Kähäri AK, Lundin P, Che H +et al. + +SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish +population. +Eur J Hum Genet. 2017 Nov;25(11):1253-1260. +PMID: 28832569; PMC: PMC5765326 +

+ +

+Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, +Nagulapalli K et al. + +High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 +trios. +Cell. 2022 Sep 1;185(18):3426-3440.e19. +PMID: 36055201; PMC: PMC9439720 +

+ +

+Gardner EJ, Lam VK, Harris DN, Chuang NT, Scott EC, Pittard WS, Mills RE, 1000 Genomes Project +Consortium, Devine SE. + +The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology. +Genome Res. 2017 Nov;27(11):1916-1929. +PMID: 28855259; PMC: PMC5668948 +

+

Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D et al. - + Complex genetic variation in nearly complete human genomes. Nature. 2025 Aug;644(8076):430-441. PMID: 40702183; PMC: PMC12350169

+ +

+Mir AA, Philippe C, Cristofari G. + +euL1db: the European database of L1HS retrotransposon insertions in humans. +Nucleic Acids Res. 2015 Jan;43(Database issue):D43-7. +PMID: 25352549; PMC: PMC4383891 +

+ +

+Niu Y, Teng X, Zhou H, Shi Y, Li Y, Tang Y, Zhang P, Luo H, Kang Q, Xu T et al. + +Characterizing mobile element insertions in 5675 genomes. +Nucleic Acids Res. 2022 Mar 21;50(5):2493-2508. +PMID: 35212372; PMC: PMC8934628 +

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+Xu X, Huang Y, Wang X, Cheng J, Yuan H, Bu F. + +Identification of mobile element insertion from whole genome sequencing +data using deep neural network model. +bioRxiv. 2023 March 8. doi:10.1101/2023.03.07.531451. +