About dbCRID

  • dbCRID (Database of Chromosomal Rearrangements In Diseases) is the largest database of curated database of human Chromosome rearrangements and associated diseases.
  • Current release: v 0.9 (06/30/2010).
  • Please direct questions and comments to dbCRID@biolead.org.
  • Related Databases

  • AtlasGeneticsOncology, Atlas of Genetics and Cytogenetics in Oncology and Haematology
  • ChimerDB 2.0, A knowledgebase for fusion genes updated
  • CytoD 1.0, A database of cytogenetic abnormalities.
  • DACRO, A disease-Associated Chromosomal Rearrangements Online.
  • Decipher, , A Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources
  • HYBRIDdb,A database of hybrid genes in the human genome.
  • Mitelman, A database of Chromosome Aberrations and Gene Fusions in Cancer.
  • SKY/M-FISH &CGH, A public platform for investigators to share and compare their molecular cytogenetic data.
  • TICdb, A database of Translocation breakpoints In Cancer.
  • References

  • Kong F, Zhu J, Wu J, Peng J, Wang Y, Wang Q, Fu S, Yuan L and Li T: dbCRID: a database of chromosomal rearrangements in human diseases. Nucleic Acids Res. [PubMed] [Full-text]
  • Glossary

        Breakpoint Gene: The genes on which the breakpoints located.

        Case ID: A case is the CRs related to the same chromosome (“chromosomes” for Translocation) in an occurance of a disease. An occurance of a disease may have aberrations on several chromosomes and so includes several cases. The case ID is numbered with the recording order.

        Deletions: Loss of a gene or chromosome segment from a chromosome.

        DOID: The disease name given by the literature was systematized according to the Disease Ontology (format-version: 1.2) and the DOID for the disease was recorded.

        Duplications: The duplicating or repeating of a chromosome segment resulting in extra segment copies in a chromosome.

        Event ID: An event is one of the CRs of the same case. One case can involve several events with different CRs. The event ID is generated sequentially in different CR types.

        First breakpoint; Second breakpoint; Third breakpoint; Fourth breakpoint; Insertion breakpoint: For a translocation event, there should be four breakpoints: when two different chromosomes are involved, there are two breakpoints on the first chromosome (the 5’ end breakpoint designated as First breakpoint and the 3’ end breakpoint as Second breakpoint), and two breakpoints on the second chromosome (the 5’ end breakpoint designated as Third breakpoint and the 3’ end breakpoint as Fourth breakpoint). When only one chromosome involved, the four breakpoints are named sequentially from the 5’ end to the 3’ end. For other types of chromosome rearrangements, breakpoints are on the same chromosome, and named sequentially from 5’ to 3’. For duplications, the extra copies of chromosome segments were inserted into the same chromosome at breakpoints named Insertion breakpoint.

        Junction Sequence Category: Junction sequences are sequences around the breakpoint and rejoined the broken DNA ends. If the junction sequences are provide by the literature, we recorded the junctions and classified as "reported". If the breakpoints are given at nucleotide level (A level), we downloaded 100bp long sequences around the breakpoints inferring from the breakpoint location using human genome sequence (NCBI build 37), and classified as "inferred". If both the junction sequences and breakpoints position (A level) provided and the inferred sequences are coincident with the reported, we marked the junctions as "confirmed". If the breakpoints are not precisely positioned, the junctions can not be inferred either, and classified as "unavailable".

        Insertions: A chromosome segment is removed from one chromosome and inserted into another nonhomologous chromosome. It is a nonreciprocal type of translocation.

        Inversions: A chromosome segment breaks off from the chromosome and re-inserted into the chromosome at the same breakage sites but in the reverse direction.

        Involved Gene: Genes located at the chromosome segments but not the breakpoints. So these genes were designated as Involved gene to be distinguished from Breakpoint Gene.

        Karyotype: The karyotype of the cases were extracted or inferred from the literature, and described according to standard cytogenetics nomenclature: the International System for Human Cytogenetics Nomenclature (ISCN 2009).

        Precision: The accuracy of the positioning of chromosome rearrangements divided into 3 levels: chromosome (C), gene (B), and nucleotide (A) level.

        Reciprocal Translocations: A type of translocation involving the exchange of chromosome segments between two chromosomes instead of the same chromosome.

        Ring Chromosomes: The two ends of a chromosome have been broken and re-joined together forming a circular chromosome structure.

        Translocations: A chromosome segment is moved from one location to another within the same chromosome, or a segment of one chromosome is transferred to another nonhomologous one. In dbCRID, cases of non-reciprocal translocation were included in this group.