User Guide


Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer

Abnormality

Check "Yes" in the "Sole Abnormality" field in the Cases Cytogenetics Searcher to find cases that contain this chosen abnormality and no other. Enter a single or multiple entries, separated by a comma. Click the "And" radio button to get results with all of the multiple entries or the "Or" radio button to get results with any of the multiple entries. Use standard wildcard characters, i.e., "*" matches a string of any length and "_" matches a single character. All abnormality searches are automatically wildcarded on the right, but not on the left. Thus, a wildcard must be used to obtain the derivative chromosomes containing the chosen abnormality, e.g., "*t(2;10)(p21;q22)" will present all the "der" chromosomes with this translocation. Use "not" to exclude an entry from results, e.g., "+7, not +2".

Age

Enter simple integers, e.g., '4' or '25' or ranges, e.g., '4-8' or '>10'. Use 0 to denote less than 12 months.

Authors

Enter a single author or multiple authors, separated by a comma. Results will contain references with all authors specified. Use standard name format without periods after initials, e.g., 'Johnson H' Entering 'Mendel' will match any author whose last name is 'Mendel', regardless of initials. Entering 'Mendel G' will match only an author whose last name is 'Mendel' and whose only initial is 'G'. Use standard wildcard characters, i.e., '*' matches a string of any length and '_' matches a single character. Entering 'Mendel *', with an internal space, is equivalent to entering 'Mendel'. Entering 'Mendel*', with no internal space, will match any author whose last name begins with 'Mendel', including, for example, 'Mendelsohn H'. Use the single-character wildcard ('_') to represent the following non-English characters in a name ( ö, å, é, ä, ü, Ö, Å, É ).

Breakpoint

Check "Yes" in the "Sole Abnormality" field in the Cases Cytogenetics Searcher to find cases that contain this chosen abnormality and no other. Enter a single or multiple entries, separated by a comma. Click the "And" radio button to get results with all of the multiple entries or the "Or" radio button to get results with any of the multiple entries. Use standard wildcard characters, i.e., '*' matches a string of any length and '_' matches a single character. Breakpoints have an implicit wildcard for band numbers, e.g., '1p' will match any breakpoint on 1p, and '14q3' will match breakpoints on 14q31 or 14q32. Use "not" to exclude an entry from results, e.g., '2q21, not 2p13'.

Clones

Enter simple integers, e.g., '4' or '25' or ranges, e.g., '4-8' or '>10'.

Chromosomes

Enter simple integers, e.g., '46' or '50' or ranges, e.g., '46-50' or '>62'.

Genes

Enter gene designation to find rearranged gene, e.g., "BCR". Enter gene designations separated by slash "/" to find gene fusions only, e.g., "BCR/ABL1". Wildcard(s) may be used, e.g. "BCR/*" or "*/ABL1". Use plus "+" before gene designation to retrieve amplifications associated with homogeneously staining regions, giant marker chromosomes, ring chromosomes, and double minutes, e.g., "+MYCN".

Journal

Use valid MEDLINE abbreviations (see List of Journal Abbreviations).

Morphology

Use morphology designation followed by '(all subtypes)' to get all subclassified cases within entry (i.e. 'Acute myeloid leukemia (all subtypes)' will present AML NOS and FAB types M0-M7)

Special Hereditary Disorder

Enter a special hereditary disorder from the List of Special Hereditary Disorders.

Special Morphology

Enter a special morphology from the List of Special Morphologies.

Year

Enter simple integers, e.g., '1995' or range, e.g., '1992-1997' or '>1996'.

Abnormality

Abnormal element of a karyoptype, e.g., 't(1;6)(p21;q12)'.

  • The nomenclature for chromosomal abnormalities follows the recommendations proposed by ISCN . See ISCN Abbreviated Terms and Symbols for a brief summary and explanation of terms and symbols. The short ISCN system for designating structural chromosome abnormalities is used. Therefore, the transcription of some complex rearrangements originally described in the detailed system may give rise to some ambiguities. However, the bands involved in an aberration are always specified. Otherwise, no attempts have been made to "interpret" karyotypic changes; e.g., inferred breakpoints were not cataloged. Nor have obvious mistakes been corrected: Breakpoints localized to non-existing bands are listed as given in the original report.
  • Only clonal aberrations are recorded in the database.
  • Chronic myeloid leukemias with t(9;22) as the sole abnormality are not registered.

Breakpoint

Cytogenetic band location of abnormality, e.g., '1p21', as defined by ISCN .

Case Number

Identification number used in database for each individual case within a reference. Multiple different tumors cytogenetically investigated in the same case are indicated by capital letters A, B, etc, following the Case Number.

Clinical Association

Provides information on associations between clinical parameters, most commonly outcome, and chromosomal changes and/or gene rearrangements resulting from chromosome aberrations. Information on "Abnormality", "Breakpoint" and/or "Gene" may not always be available.

Clone

Identical karyotype of one subset of cells from a sample. The operational definition of a clone follows the recommendation of ISCN : At least two cells with the same extra chromosome or structural aberration, or three cells with the same missing chromosome.

Country

Case origin when stated in publication; otherwise, in general the residence of corresponding author.

Gene

Provides information on rearranged genes located in breakpoints of acquired cytogenetic aberrations.

  • Molecular consequences of known neoplasia-associated chromosome changes are registered even if no cytogenetic investigation was performed.
  • References to articles on quantitative gene alterations as a result of unbalanced cytogeneticaberrations are not recorded except for amplifications in homogeneously staining regions (hsr), giant marker chromosomes, ring chromosomes (r), and double minutes (dmin).
  • Gene symbols are in accordance with the most recent Guidelines for Human Gene Nomenclature recommendations; hence there are no dashes, Roman numerals, or Greek letters within the gene designations.

Investigation Number

Number used in database for each consecutive investigation within a case or for a metastatic lesion at a different location.

  • Whenever a tumor was studied at different times, the karyotypes are presented chronologically.
  • From the second investigation onward, only the clones with new abnormalities are in general listed.
  • It should be noted that the relevant chromosome aberration may be present in only one of several karyotypes presented for the case.

Gene Fusions

Genes rearranged as a consequence of structural chromosome changes. References are provided to the first original publications in which the gene rearrangement was reported in a particular tumor type.

Morphology

Tumor histology.

  • The nomenclature of tumor histology is based on the International Classification of Diseases for Oncology (ICD-O), the Systematized Nomenclature of Medicine (SNOMED), the French-American-British (FAB) proposals for the classification of acute leukemias and myelodysplastic syndromes, and the WHO Classification of Tumours of Soft Tissue and Bone.
  • Tumors of the lymphoreticular system, as described according to the US National Cancer Institute Working Formulation (WF) and Kiel classification systems for non-Hodgkin's lymphomas (NHL), are converted to the REAL/WHO classification. All unspecified non-Hodgkin lymphomas are presented as 'Peripheral B-cell neoplasm, NOS'.
  • When chronic myeloproliferative disorders progress to acute myeoloid leukemia (AML), the following classification principle has been adopted: Patients with AML following, e.g. polycythemia vera, are entered under the latter diagnosis if they had not received genotoxic treatment, but as secondary AML if such treatment had been given. AML following a myelodysplastic phase is not registered as secondary.
  • Rare tumor types grouped under 'special type', e.g. 'Benign mesenchymal tumor, special type', are presented in 'Special Morphology'.

Previous Tumor

'Yes' indicates benign or malignant, treated or untreated neoplasm.

Recurrent aberration

Any aberration, structural or numerical, present in two or more cases of the same morphology or morphologic subentity, and, when applicable for solid tumors, topography. Hence, an identical aberration reported in two cases of AML M1 is recorded as recurrent whereas the same aberration when present in one case each of AML M1 and AML M2 will not appear as recurrent. Only well characterized abnormalities are presented, i.e., aberrations preceded by a '?' or separated by 'or' and abnormalities with breakpoints separated by '-' are excluded.

References

When a case has been reported in more than one publication, generally only the most recent reference is given. Therefore, a search for the original article may not yield any results. Data presented at congresses, conferences or workshops are not registered, even if abstracts were published in scientific journals.

Reference Number

Unique identification number used in database for each individual reference.

Series

A case is categorized as 'selected' when reported because of a specific/unusual karyotypic feature; otherwise, the case is classified as 'unselected'.

Special Hereditary Disorder

Constitutional chromosome abnormality or Mendelian disorder, specified in 'Special Hereditary Disorder'.

Tissue

Tissue used for cytogenetic investigation. Only neoplasms studied in direct preparations or after short-term in vitro culture are registered.

Topography

Tumor site, applicable for solid tumors, also grouped according to organ systems, e.g. 'Respiratory system (all sites)'.