This Entrez help document provides guidelines for searching "Cancer Chromosomes" in Entrez.
It includes search examples and provides additional details about the search system and the other Entrez databases.

For a quick start guide, go directly to the sample queries.

1. Overview
• Scope
• Main Features
2. Search for Cytogenetic, Clinical and/or Reference Information
• Search Examples
• Entrez Query Box (Free Text Search)
• Quick Search (Fielded Search)
• Advanced Search (Fielded Search)
• Advanced Search Examples
3. Search Fields for Quick and Advanced Search Forms
• Cytogenetic Section
• Clinical Section
• Reference Section
• Field Qualifiers (examples)
4. Search Results
• Display Menu
• Summary Report
• Detailed Report
• Similarity Report
• Linked Items

Overview

Scope

Three databases, the NCI/NCBI SKY (Spectral Karyotyping)/M-FISH (Multiplex-FISH) and CGH (Comparative Genomic Hybridization) Database, the NCI Mitelman Database of Chromosome Aberrations in Cancer, and the NCI Recurrent Chromosome Aberrations in Cancer are now integrated into NCBI's Entrez system as the "Cancer Chromosomes" database.Queries are performed using the same approach as the other Entrez databases such as PubMed and GenBank. Features of Entrez such as History, Clipboard, and Preview/Index, function as they do for all Entrez databases.

Search for results obtained using the following techniques: chromosome banding (karyotype), spectral karyotyping (SKY), multiplex-FISH (M-FISH), fluorescent in situ hybridization (FISH), and comparative genomic hybridization (CGH).

Main Features

1. Seamless searching of multiple forms of aberration data. Karyotypic, SKY/M-FISH, and CGH data can be searched based on the underlying cytogenetic features of the aberrations they demonstrate. In other words, the textual genetic data, both the short and long form karyotype data, and CGH data can be searched in an integrated fashion. Seamless searching is a process in which all data are searched simultaneously for any particular aberration(s). This process employs the use of "pseudo documents" and is described in more detail here.)
2. The ability to find similar cases based on textual content (data in word form, such as clinical data and cytogenetic comments).
3. The ability to display common elements in a list of cases or clones/cells, based either on textual content or common cytogenetic features.
4. Context sensitive display.

Searches based on case information, such as diagnosis and site, result in a case-based report (i.e., a list of all cases displaying the searched element), while searches based on underlying cytogenetic features are displayed as a clone/cell report (i.e., each clone or cell is searched separately and will be listed separately in the report; in a case with several clones, the report will only list those clones which contain the searched element).

Search for Cytogenetic, Clinical, and/or Reference Information

Queries are performed using the same approach as the other Entrez databases such as PubMed and Nucleotide. Search using any of three methods:

• Entrez Query Box Search
• Quick Search
• Advanced Search

The fielded searches (i.e., searches using a form with "fields" or windows to be completed, as described below) can also be accomplished as a free text search in the Entrez query box by using bracketed terms (Field Qualifiers) corresponding to each field.

Search Examples

All terms shown below can be entered using any of the three search methods listed above.
Note: Diagnostic terms differ: the SKY/M-FISH database uses ICD-3-O terms, whereas the Mitelman and Recurrent databases use a different system. The menus include all ICD-O-3 entered into the database to date and all terms used in the Mitelman and Recurrent databases. To search for a diagnosis in all databases simultaneously, select both terms from the menu [use the shift key (Mac) or control key (PC and Unix) to select more than one term]. For example: search for "Carcinoma, undifferentiated, NOS OR Undifferentiated Carcinoma" to obtain all cases with this diagnosis (the first terms is from ICD-O-3 and the latter term is from Mitelman). Improvements are planned to deal with this complexity.

1. Which cases have breakpoint at 9q34?
   
     9q34
   
   
2. Which cases have a gain of 8p23?
   
     +8p23
   
   
3. Which cases have a breakpoint at 9q34 and 22q11?
   
     9q34 22q11
   
   
4. Which cases have a junction between breakpoints 9q34 and 22q11?
   
     9q34J22q11
   
   
5. Which cases have a loss of part of or the entire 'p' arm in chromosome 7?
   
     -7p
   
   
6. Which cases have loss of the complete chromosome region 4q2 (4q21 to 4q28) ?
   
     -4q2*
   
   
7. Which cases have a loss somewhere within chromosome 10 ?
   
     -10q OR -10p
   
   
8. Which cases have a whole chromosome gain of 19 ?
   
     +19
   
   
9. Which cases have breakpoints at 9q34 and 22q11 and also an isochromosome of 17q [i(17)(q)]?
   
     9q34 22q11 17qJ17q
   
   
10. Which cases have breakpoints at 9q34 and 22q11 and also an isochromosome of 17q [i(17)(q)] but not an additional chromosome 8?
    
      9q34 22q11 17qJ17q NOT +8
    
    
11. Which cases have a junction between 8q24 and 14q32, and a gain of 8q24. ?
    
      8q24J14q32 +8q24
    
    
12. Which cases have a junction between 8q24 and 14q32, and a gain of 1q32, and a diagnosis of Burkitt's lymphoma ?
    
      8q24J14q32 +1q32 Burkitt[DIAGNOSIS]
    
    

Entrez Query Box Search (Free Text Search)

Enter one or more terms in the Entrez query box at the top of the page and press "Go." As with all other Entrez databases, the examples shown above may be combined using "qualifiers" and Boolean expressions. The qualifiers for this database are described below. The Boolean expression use is documented in the Entrez Help document. Note: There is no space between the term searched for and its qualifier; the Boolean operators, AND, OR, and NOT must be entered in UPPERCASE.

This search format is a free text search which uses bracketed terms (called qualifiers) which correspond to each field (topic). These terms are added automatically and can be viewed by clicking on the Details link after the search has been performed. This tells you exactly how Entrez executed your search. Within the Details window, you can modify and resubmit your search strategy. (See the general Entrez Help Document for more information on the Details Link.) To help the user understand these free text searches, we point out that they are accomplished by searching what we refer to as a "pseudo document," which contains both the textual information and the genetic information, the latter transformed to pseudo words.

For advanced queries, use either the same syntax, as guided by the Preview/Index link above, or use the Advanced Search.

Note: Diagnostic terms differ: the SKY/M-FISH & CGH database uses ICD-O-3 terms (NCI Metathesaurus), while the Mitelman and Recurrent databases use a different system (see Mitelman search forms). To search for a diagnosis in all databases simultaneously, enter both types of terms, separated by "OR."

Quick Search (Fielded Search)

For each field, enter a single or multiple entries, separated by a space (not a comma). Use the Boolean operators AND, OR, NOT for multiple subjects in the same field, following the format given in the examples for each field, and press "Go."

Morphology (diagnosis) and Topography (organ site): Select the desired terms from the pull-down menus.
Note: Diagnostic terms differ: the SKY/M-FISH database uses ICD-3-O terms, whereas the Mitelman and Recurrent databases use a different system. The menus include all ICD-O-3 entered into the database to date and all terms used in the Mitelman and Recurrent databases. To search for a diagnosis in all databases simultaneously, select both terms from the menu [ use the shift key (Mac) or control key (PC and Unix) to select more than one term]. For example: search for "Carcinoma, undifferentiated, NOS OR Undifferentiated Carcinoma" to obtain all cases with this diagnosis (the first terms is from ICD-O-3 and the latter term is from Mitelman). Improvements are planned to deal with this complexity.

For a detailed explanation of each search field see "Search Fields for the Quick Search and Advanced Search Forms" below.

Advanced Search (Fielded Search)

There are three available search sections: Cytogenetic, Clinical and Reference. Click on the headings to advance from one section to the other. When searching using more than one section, press the "Submit" button after completing all sections.

For each field, enter a single or multiple entries, separated by a space (not a comma). Use the Boolean operators AND, OR, NOT for multiple subjects in the same field or use the AND/OR/NOT radio buttons provided for certain categories.

For a detailed explanation of each search field see "Search Fields for the Quick Search and Advanced Search Forms" below.

Advanced Search Examples

1. Which cases have breakpoint at 9q34?
   
    
   
   
   
2. Which cases have breakpoints at 9q34 and 22q11 with a junction between them and an isochromosome of 7p [i(7)(p10)]?
   
    
   
   
   
3. Which cases have breakpoints at 9q34 and 22q11 with a junction between them and an isochromosome of 7p [i(7)(p10)], but not an additional chromosome 8?
   
    
   
   
   
4. Which cases have a junction between 8q24 and 14q32, and a gain of band 8q24. ?
   
    
   
   
   
5. Which cases have a junction between 8q24 and 14q32, and a gain of band 1q32 with a diagnosis of Burkitt's lymphoma ?
   
    
   

Search Fields for the Quick Search and Advanced Search Forms

This section contains a detailed explanation of the search fields used in the Advanced Search Forms and a table demonstrating the Field Qualifiers.

Cytogenetic Information Section

1. Chromosome Rearrangements in ISCN Short Form: includes deletions, derivative chromosomes, dicentrics, duplications, fission, homogenously staining regions (hsr), insertions, inversions, isochromosomes, rings, translocations, etc. Entries must conform to ISCN nomenclature [ISCN (1995)] An International System for Human Cytogenetic Nomenclature, Mitelman, F (ed); S. Karger, Basel, 1995;
2. Breakpoints: Enter one or more chromosome bands (chromosome number, arm, band; sub-bands can also be listed). Breakpoints have an implicit wildcard for band numbers: place an asterisk at the end of a term to search for all terms that begin with that word, e.g. "1q*" will match any breakpoint on 1q, and "1q2*" will match breakpoints from region 1q2 (1q21 to 1q25).
3. Junction: Enter two chromosomal bands with no space between them. In the free text search, type a 'J' between them. Please refer to Question #4 in the search examples for more details. This term represents breakage and union between two different chromosomes (e.g., a translocation); enter each junction to be searched in a separate window. Enter a single or multiple entries; click the "AND" radio button to get results with all of the multiple entries, the "OR" radio button to get results with any of the multiple entries, and the NOT button to exclude an entry from results.
4. Numerical Abnormalities: Gain or loss of whole chromosomes. Indicate gain by "+" and loss by "-" and use spaces to separate multiple entries. This field searches all techniques, including CGH. In the karyotyping results, "+" indicates additional chromosomes and "-" indicates loss of chromosomes in respect to ploidy. In the CGH results, "+" indicates gain of chromosomal material and "-" indicates loss of chromosomal material.
5. Bands Gained/Lost: chromosome bands gained or lost with respect to ploidy, evidenced either as duplications or deletions in karyotypes, or gain or loss in CGH studies. Whole chromosome or partial chromosome gain or loss can result in band gain or loss without being involved in a breakpoint.
6. Other Cytogenetics Comments: this can include search for terms such as dmin, hsr, FISH results (any probes or genes listed), etc.

Clinical Information Section

1. Morphology (diagnosis) and Topography (organ site): Select the desired terms from the pull-down menus. Note: Diagnostic terms differ: the SKY/M-FISH database uses ICD-3-O terms, whereas the Mitelman and Recurrent databases use a different system. The menus include all ICD-O-3 terms entered into the database to date and all terms used in the Mitelman and Recurrent databases. To search for a diagnosis in all databases simultaneously, select both terms from the menu [use the shift key (Mac) or control key (PC and Unix) to select more than one term]. For example: search for "Carcinoma, undifferentiated, NOS OR Undifferentiated Carcinoma" to obtain all cases with this diagnosis (the first terms is from ICD-O-3 and the latter term is from Mitelman). Improvements are planned to deal with this complexity.
2. Gender, Disease Status, Treatment, Hereditary Syndrome (Human and Mouse):select from the pull-down menus. For Specific Hereditary Syndrome, fill in any known disorder.
3. Other Clinical Information: Fill in any term which a submitter would have entered in the "Clinical Comments" field, including survival, previous tumors, metastatic information, specific drug treatment, etc.
4. Other Mouse Information: Fill in any term which a submitter would have entered in the Mouse Information field, including mouse strain, genotype, mouse model for a particular type of human cancer, etc.

Reference Information Section

1. Enter information to be searched.
2. For Journal, use valid MEDLINE abbreviations. Enter only one year since, at the present time, it is not possible to search for a range of years. To search multiple years, leave this field blank.

Field Qualifiers (Bracketed Terms)

Advanced Search Statements are accomplished by using Field qualifiers as discussed in the Entrez Help Document. The field qualifiers for the Cancer Chromosomes database are shown in the table below.

Search Results

Searches based on case information, such as diagnosis and site, result in a case-based report (i.e., a list of all cases displaying the searched element), while searches based on underlying cytogenetic features are displayed as a clone/cell report (i.e., each clone or cell is searched separately and will be listed separately in the report; in a case with several clones, the report will only list those clones which contain the searched element).

The number of cases or cells/clones found for each search is displayed at the top of the results page. The number of cases are separated into two groups: the number found from the SKY/M-FISH & CGH Database and the number found from the Mitelman databases, including the Recurrent Database.

The results obtained from the searches performed with this Cancer Chromosomes database can be manipulated to answer a number of questions, such as:

• How do I find cytogenetically related clones/cells?
• How do I find clinical similarities among cases that have a certain diagnosis?
• How do I find cytogenetic abnormalities between two or more clones/cells with the same or related diagnoses?

Use the Display menu and the Links at the right of each case to answer these and other questions.

Display Menu

Note: To have more documents analyzed than those shown on the first page of the report, increase the number of documents shown (in the Display bar).

Summary Report

This is the initial report from a search.

Search results are listed by cases if only clinical or reference information is included in the search terms; they are listed as clones/cells whenever cytogenetic terms are searched. If a case contains several clones/cells, only one will be listed. If a case contains both SKY/M-FISH and CGH data, these data will be listed as separate clones/cells, which, due to weighing of the data, may not be displayed together if their cytogenetic data are dissimilar.

Detailed Report

Select the cases or clones/cells to be examined in detail, then select "Detailed Report" from the Display menu, and press "Display"

The resulting report is a human readable report of a "pseudo document," a conversion of numerical and textual data into one common set of terms for the purposes of statistical comparison.

Detailed Reports of cases provide the complete written karyotypes of all clones/cells, and links to the CGH Profiles, the clinical information, and the abstracts in PubMed.

For Mitelman and SKY/M-FISH clones/cells, detailed reports provide:

• Complete written karyotypes
• Breakpoints and junctions at different resolutions (chromosome band and chromosome arm). Each aberration is assigned a number to indicate the number of times the aberration is present in the karyotype/SKYGRAM.
• Numerical abnormalities: gain, loss, and frequency
• Structural abnormalities: number of aberrations for each chromosome

For CGH, detailed reports provide:

• Breakpoints at (chromosome band and chromosome arm) resolution.
• Neighboring Breakpoints. See discussion below on 'Neighbor breakpoints.'
• Whole chromosomes: gain and loss
• Chromosome bands: gain and loss, including those bands gained or lost with whole chromosome gain and loss

Similarity Report

Select the cases to be compared for their similarities, then select "Similarity Report" from the Display menu, and press "Display." Similarities can be shown at two levels of resolution: "high resolution" and "all resolutions." In the high resolution report, only those structural abnormalities that contain chromosome band information are displayed. In the "all resolutions report," all structural chromosomal abnormalities are displayed, including those with only chromosome or chromosome arm information.

The resulting report displays the similarities of diagnosis/site and cytogenetic abnormalities (including breakpoints, junctions, and bands gained or lost) among the selected cases or clones/cells at several levels: common to 100% of cases, common to 50%-90% of cases, and common to less than 50% of cases. The description of the pseudo document describes how the cytogenetic features can be derived from SKY, M-FISH, karyotypic, and CGH data. The common term or abnormality is shown in the left column and number of affected cases is shown in the right column; click on the latter number to see a list of all affected cases. Abbreviations used in the report are defined at the top of the report page.

If a case contains both SKY/M-FISH and CGH data, these data will be listed as separate clones/cells.

Gain and loss refer to both karyotypic and CGH patterns. If a whole chromosome is lost or gained, all the bands in that chromosome will be listed as lost or gained, respectively.

All chromosome bands under "Breakpoints" are linked to the NCBI MapViewer.

"Neighbor breakpoints" in CGH represent bands that are near to the actual breakpoints. Specifically they are within the distance corresponding to 5% of chromosome 1's standard ISCN height, calculated from the center of the given band.

These bands are used to find cytogenetically similar clones/cells. They are weighted as less important than the given band so that even if the given bands are not exactly correct, we will still find biological connections. Within the neighbor distance, bands that are closer to the actual breakpoint are weighted more than the farther bands.

Linked Items

Cases and Clones/Cells are linked to one another using a variety of criteria. There is a detailed discussion of these criteria in the Links section below, but for now, note that all of these linked items can be accessed in two different ways:

• By using the "Links" pull-down menu to the right of each summary report.
• By using the pull-down menu in the Display bar. The Display menu is used when you wish to examine a set of summary reports; the reports to be examined are selected with the checkboxes to the left of each summary report.

Related by Cytogenetics

Cytogenetic features from all forms of data are converted to pseudo documents. A pseudo document is comprised of words that are made for breakpoints, junctions, amplifications, deletions, abnormal terminals, and normal and abnormal chromosomes, in addition to the clinical textual content. By doing this we can reuse the statistical comparison used to detect textual documents. See the discussion Computation of Related Articles for how we detect related textual documents. Documents related by cytogenetics are those whose corresponding pseudo documents are statistically similar.

Related by Diagnosis/Site

For cases to be considered related by diagnosis/site, the statistical comparisons are limited to diagnosis and site terminology.

The three categories below use logic analogous to the two links described above:

Related by All Text

Related by Cytogenetics & Diagnosis/Site

Related by Cytogenetics & All Text

View Cases for Clones/Cells and View Clones/Cells for Cases

If the summary report lists cases, you can link to all Clones/Cells for the case(s); if the summary report lists Clones/Cells, you can link to the case(s) from which those Clones/Cells were obtained.

PubMed

Link to the Entrez PubMed summary document(s) cited in the Cancer Chromosome case. This link is available in the Display menu and from the summary report text itself.