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euL1db: the European database of L1HS retrotransposon insertions in humans.

Mir AA, Philippe C, Cristofari G - Nucleic Acids Res. (2014)

Bottom Line: They are mobile genetics elements-also known as jumping genes--but only the L1HS subfamily of Long Interspersed Nuclear Elements (LINEs) has retained the ability to jump autonomously in modern humans.The current version of euL1db centralizes results obtained in 32 studies.It contains >900 samples, >140,000 sample-wise insertions and almost 9000 distinct merged insertions. euL1db will help understanding the link between L1 retrotransposon insertion polymorphisms and phenotype or disease.

View Article: PubMed Central - PubMed

Affiliation: INSERM, U1081, Institute for Research on Cancer and Aging of Nice (IRCAN), F-06100 Nice, France CNRS, UMR 7284, Institute for Research on Cancer and Aging of Nice (IRCAN), F-06100 Nice, France Faculty of Medicine, Institute for Research on Cancer and Aging of Nice (IRCAN), University of Nice-Sophia-Antipolis, F-06100 Nice, France.

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Database organization, data model and content. (A) Relationship between euL1db objects. euL1db is organized by study. Each study contains one or more samples. A sample originates from a single individual. Individuals can be analyzed in multiple studies. An SRIP (sample retrotransposon insertion polymorphism) is a real insertion detected in a given sample and has a unique ID prefixed by srip. Several samples from different individuals might possess an SRIP at the same genomic location. A private L1HS insertion will correspond to an SRIP only found in samples of the same individual. Inversely, an L1HS 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. (B) Approach used in euL1db to define unique L1HS insertion events. Nearby SRIPs are merged into a single MRIP if they satisfy all the following requirements: (i) they are located within 200 bp of each other, (ii) they share the same strand orientation, and (iii) they are all germline. Somatic retrotransposition events are unique by nature, and are not merged with germline events, nor merged together. Therefore, somatic SRIPs give rise to MRIPs containing only a single SRIP. (C) Overlap between euL1db and dbRIP. Numbers correspond to MRIP records in euL1db and to L1HS records in dbRIP (transposable elements not belonging to the L1HS subfamily were not taken into account to draw this Venn diagram).
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Figure 1: Database organization, data model and content. (A) Relationship between euL1db objects. euL1db is organized by study. Each study contains one or more samples. A sample originates from a single individual. Individuals can be analyzed in multiple studies. An SRIP (sample retrotransposon insertion polymorphism) is a real insertion detected in a given sample and has a unique ID prefixed by srip. Several samples from different individuals might possess an SRIP at the same genomic location. A private L1HS insertion will correspond to an SRIP only found in samples of the same individual. Inversely, an L1HS 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. (B) Approach used in euL1db to define unique L1HS insertion events. Nearby SRIPs are merged into a single MRIP if they satisfy all the following requirements: (i) they are located within 200 bp of each other, (ii) they share the same strand orientation, and (iii) they are all germline. Somatic retrotransposition events are unique by nature, and are not merged with germline events, nor merged together. Therefore, somatic SRIPs give rise to MRIPs containing only a single SRIP. (C) Overlap between euL1db and dbRIP. Numbers correspond to MRIP records in euL1db and to L1HS records in dbRIP (transposable elements not belonging to the L1HS subfamily were not taken into account to draw this Venn diagram).

Mentions: The euL1db database is organized in several tables, which are interconnected in a dynamic way, through the MySQL relational database management system. A simplified view of the object relationships is depicted in Figure 1 and a more detailed view of the underlying database structure is shown in Supplementary Figure S1.


euL1db: the European database of L1HS retrotransposon insertions in humans.

Mir AA, Philippe C, Cristofari G - Nucleic Acids Res. (2014)

Database organization, data model and content. (A) Relationship between euL1db objects. euL1db is organized by study. Each study contains one or more samples. A sample originates from a single individual. Individuals can be analyzed in multiple studies. An SRIP (sample retrotransposon insertion polymorphism) is a real insertion detected in a given sample and has a unique ID prefixed by srip. Several samples from different individuals might possess an SRIP at the same genomic location. A private L1HS insertion will correspond to an SRIP only found in samples of the same individual. Inversely, an L1HS 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. (B) Approach used in euL1db to define unique L1HS insertion events. Nearby SRIPs are merged into a single MRIP if they satisfy all the following requirements: (i) they are located within 200 bp of each other, (ii) they share the same strand orientation, and (iii) they are all germline. Somatic retrotransposition events are unique by nature, and are not merged with germline events, nor merged together. Therefore, somatic SRIPs give rise to MRIPs containing only a single SRIP. (C) Overlap between euL1db and dbRIP. Numbers correspond to MRIP records in euL1db and to L1HS records in dbRIP (transposable elements not belonging to the L1HS subfamily were not taken into account to draw this Venn diagram).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4383891&req=5

Figure 1: Database organization, data model and content. (A) Relationship between euL1db objects. euL1db is organized by study. Each study contains one or more samples. A sample originates from a single individual. Individuals can be analyzed in multiple studies. An SRIP (sample retrotransposon insertion polymorphism) is a real insertion detected in a given sample and has a unique ID prefixed by srip. Several samples from different individuals might possess an SRIP at the same genomic location. A private L1HS insertion will correspond to an SRIP only found in samples of the same individual. Inversely, an L1HS 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. (B) Approach used in euL1db to define unique L1HS insertion events. Nearby SRIPs are merged into a single MRIP if they satisfy all the following requirements: (i) they are located within 200 bp of each other, (ii) they share the same strand orientation, and (iii) they are all germline. Somatic retrotransposition events are unique by nature, and are not merged with germline events, nor merged together. Therefore, somatic SRIPs give rise to MRIPs containing only a single SRIP. (C) Overlap between euL1db and dbRIP. Numbers correspond to MRIP records in euL1db and to L1HS records in dbRIP (transposable elements not belonging to the L1HS subfamily were not taken into account to draw this Venn diagram).
Mentions: The euL1db database is organized in several tables, which are interconnected in a dynamic way, through the MySQL relational database management system. A simplified view of the object relationships is depicted in Figure 1 and a more detailed view of the underlying database structure is shown in Supplementary Figure S1.

Bottom Line: They are mobile genetics elements-also known as jumping genes--but only the L1HS subfamily of Long Interspersed Nuclear Elements (LINEs) has retained the ability to jump autonomously in modern humans.The current version of euL1db centralizes results obtained in 32 studies.It contains >900 samples, >140,000 sample-wise insertions and almost 9000 distinct merged insertions. euL1db will help understanding the link between L1 retrotransposon insertion polymorphisms and phenotype or disease.

View Article: PubMed Central - PubMed

Affiliation: INSERM, U1081, Institute for Research on Cancer and Aging of Nice (IRCAN), F-06100 Nice, France CNRS, UMR 7284, Institute for Research on Cancer and Aging of Nice (IRCAN), F-06100 Nice, France Faculty of Medicine, Institute for Research on Cancer and Aging of Nice (IRCAN), University of Nice-Sophia-Antipolis, F-06100 Nice, France.

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Related in: MedlinePlus