| euL1db |
| The European database of L1-HS retrotransposon insertions in humans |
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| euL1db is the European database of L1-HS retrotransposon insertion polymorphisms (RIP) in humans. More information about euL1db data structure is provided in the [Help] section. |
| L1-HS is a retrotransposon subfamily, which belongs to the LINEs (Long Interspersed Nuclear Elements). This subfamily is only found in humans (the « HS » stands for « human-specific »). The position of L1-HS copies is highly polymorphic among individuals. More information about L1-HS is provided in the [Background] section. |
| "Mir AA, Philippe C, Cristofari G. euL1db: the European database of L1HS retrotransposon insertions in humans. Nucleic Acids Res. 2015 Jan 28;43(Database issue):D43-7. doi: 10.1093/nar/gku1043. PubMed PMID: 25352549 ". Be sure to mention the release date / version of the database used in your work to faciliate the examination of your data by reviewers and the readers. |
| euL1db only accepts human-specific L1 retrotransposon insertions (L1-HS). |
| There are many ways to interrogate euL1db. You could start with these [examples] of euL1db use, or by reading the [Help] or [FAQ] sections. If you are eager to try euL1db, why not to start by finding if your favorite gene contains known L1 insertion polymorphisms, by clicking [here]? |
| Please check out the [Submission] tab in the navigation top panel and get in [contact] with us by simply e-mailing us. |
| No, euL1db accepts entries obtained with a broad range of techniques, both genome-wide or more targeted. |
| No, euL1db is focused on human data. |
| Yes, euL1db can hold clinical data since it is organized in a sample-wise manner. By submitting to euL1db you are responsible to ensure that patients involved have consented to participate to the study. Data in euL1db are anonymous. |
| Unless the participants in a given study have explicitly consented to have their genetic and personal information published in an online public database, we cannot accept any information that can be used to trace back to an individual. |
| As long as your submission does not contain personally identifiable information, we encourage the inclusion of clinical information in euL1db submissions. Usually this takes the form of established clinical vocabularies like HPO or MeSH. In addition, we encourage the reporting of clinical significance associated with a particular variant, when known. |
| No, but they are definitely much more organized and annotated than the original publication. |
| Yes, euL1db clearly marks any insertion as Somatic or Germline and also provides the validation status. |
| Yes, euL1db will provide a unique accession number, which will correspond to a Study ID. Please note that we currently have not implemented an embargo system that would allow users to enter data and to only release them upon publication. Thus submitted data will be freely accessible to everyone as soon as they have passed the curation process. |
| SRIP (sample retrotransposon insertion polymorphism) is a real insertion detected in a given sample. Several samples from different individuals might possess an SRIP at the same genomic location. A private L1-HS insertion will correspond to an SRIP only found in samples of the same individual. Inversely, an L1-HS insertion which is fixed in the human population will appear as an SRIP at the same location in all the genome-wide samples of euL1db. Thus SRIP are highly redundant. In contrast, MRIP (meta retrotransposon insertion polymorphisms) are virtual insertions obtained by merging overlapping or close SRIP, which are likely to correspond to the same retrotransposition event. Thus MRIP are non-redundant. More information about SRIP and MRIP is provided in the [Help] section. |
| SRIP are redundant and MRIP are non-redundant (see [Question 14]). |
| Yes, it is possible to download all euL1db data from the [Download] tab. |
| euL1db is an archive. We report insertions as they are submitted to us, usually in association with a peer-reviewed publication. The veracity of the data is the responsibility of the submitting investigators. When available, euL1db stores the methods used in a given study to confirm insertion calls and the deduced validation status. These validation data are presented as an integral part of the study data. Another possibility is to look whether this particular insertion was found in multiple independent studies. If you have concerns regarding a particular variant or data set, we recommend you to contact the submitter for additional supporting information. |
| In the [Search] tab, type the genomic coordinates or the gene name in the provided text box. The result is a table of MRIP found. It can be exported in a tabular text format by clicking on the Export Button on the top left of the page. |
| euL1db displays data using coordinates in the hg19 reference genome (hg19, GRCh37 NCBI assembly). However data can be submitted with coordinates in any reference genome version, and we will convert the submitted coordinates to hg19 coordinates. This information is stored in the Study table. |
| In contrast to dbRIP, euL1db stores data in a sample-wise manner and contains the most recent datasets obtained by high-throuhput sequencing, including the 1000 Genome Project. In contrast to euL1db, dbRIP contains non-autonomous human retrotransposons such as Alu or SVA sequences and not only L1-HS insertions. |
| The data structure logics in dbVar/DGVa and euL1db are comparable (sample-wise variants and merged variants). euL1db is specialized for L1-HS insertions, while dbVar/DGVa can include any type of structural variants, including mobile element insertions. However, the set of informations for L1-HS insertions provided by euL1db is much more exhaustive, and most of the studies stored in euL1db have not been deposited in dbVar/DGVa. |