+Long Interspersed Nuclear Element-1 (LINE-1, L1) is the only retrotransposon family +in modern humans that still autonomously generates new copies by an RNA-mediated +copy-and-paste mechanism. The L1-HS subfamily (HS for "human-specific") is +responsible for ongoing retrotransposition activity and contributes to inter-individual +genetic diversity: on average, two human genomes differ at hundreds of sites with +respect to L1 insertion presence or absence. New L1-HS insertions are a recognised +source of germline mutation and somatic mosaicism, and have been observed in many +cancers and brain tissues. +
++This track shows the curated set of L1-HS insertion polymorphisms catalogued in +euL1db, the European database +of L1HS retrotransposon insertions in humans (Mir et al. 2015). Each feature is +a Meta Retrotransposon Insertion Polymorphism (MRIP) — a non-redundant +genomic site obtained by merging close Sample Retrotransposon Insertion Polymorphisms +(SRIPs) reported across 32 published studies covering more than 900 samples. +
+ ++Each item is a single MRIP. The score is the euL1db pseudo-allele frequency +(field pseudoAlleleFreq) scaled to 0–1000. Items are coloured by the +lineage of contributing SRIPs: +
+
+
+germline — all contributing SRIPs are germline insertions
+
+somatic — all contributing SRIPs are somatic insertions
+
+mixed — both germline and somatic SRIPs at this site
+
+unknown — lineage not reported
+
+Clicking an item opens a detail page that lists the studies and PubMed IDs +reporting the insertion, the detection methods used, the tissues, clinical +conditions and populations represented, and a table of the contributing samples +(truncated to 200 rows for very large aggregations — see +euL1db for the full sample +breakdown). Filters are available for pseudo-allele frequency, SRIP and study +counts, lineage, PCR validation, and whether the MRIP is annotated as already +present in the reference genome. +
+ ++euL1db integrates published L1-HS insertion calls from a wide range of +detection assays. Most studies used enrichment-based protocols +(RC-seq, L1-seq, Ewing PCR, TIP-seq), high-throughput whole-genome +sequencing analysed with TranspoSeq, MELT or similar pipelines, or +fosmid-based long-read approaches. For each accepted study the original +authors' sample-level calls (SRIPs) were curated and re-mapped to hg19 +where needed. SRIPs that are within 200 bp of each other on the same strand +and are germline are merged into a single non-redundant MRIP. Somatic events +are not merged, reflecting the unique nature of independent retrotransposition +events. See Mir et al. 2015 for full curation details. +
++Track files were generated from the euL1db v1.00 release (data dump downloaded +March 2018, last updated 14 October 2014) using the script +meiEul1dbToBed.py, which joins the MRIP, SRIP, Sample, +Individual, Study and Methods tables and emits a BED9+ file. For details of +the build process see the makeDoc text file +hg19/mei.txt, and the scripts directory +src/hg/makeDb/scripts/mei. +The Helman2014 study used numeric chromosome names (23 = X, 24 = Y); these +were renamed in the build script. The hg19 BED was lifted to hg38 with +liftOver using the standard hg19ToHg38.over.chain.gz chain. +Of 8,991 hg19 MRIPs, 8,988 lifted successfully; the 3 unlifted MRIPs are +listed in the build directory. +
+ ++The data can be explored interactively in table format with the +Table Browser or the +Data Integrator and exported from there +to spreadsheet or tab-separated tables. From scripts, the data can be accessed +through our REST API, +track=meiEul1db. +
++For automated download and analysis, the annotation is stored in a bigBed +file that can be downloaded from +our download +server. The file for this track is called eul1db.bb. Individual regions +or the whole genome annotation can be obtained using our tool bigBedToBed, +which can be compiled from the source code or downloaded as a precompiled binary +for your system. Instructions for downloading source code and binaries can be +found here. +The tool can also be used to obtain features within a given range, e.g. +bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/mei/eul1db.bb -chrom=chr21 -start=0 -end=100000000 stdout +
++The original annotation source data can be downloaded from +eul1db.unice.fr via the +Download tab. +
+ ++Thanks to Gaël Cristofari and colleagues at IRCAN (Nice, France) for +making the euL1db data freely available, and to the original study authors +whose data are aggregated. Track built at UCSC by the Genome Browser group. +
+ ++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 +
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