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Identifying Chromosomal Abnormalities

  Sample User Question
Analysis/Comments
Flow Chart
Step By Step Guide
Additional Notes 		 

Sample User Question back to top

You have been asked to identify chromosomal abnormalities in people with carcinoma of the kidney. Specifically you would like to know if there is any involvement of 9q13.

Analysis/Comments back to top

Two databases that contain chromosomal abnormality data for cancers are SKY/M-FISH & CGH and Mitelman Database of Chromosomal Aberrations. Both allow searching by cancer site, type of cancer and chromosomal breakpoints. Mitelman is drawn entirely from the literature, while SKY/M-FISH & CGH consists of submissions which may or may not have been published. Both of these databases can also be searched using the Cancer Chromosomes resource.

Flow Chart back to top

  1. Spectral Karyotyping/Multiplex Fluorescence In Situ Hybridization and Comparative Genomic Hybridization (SKY/M-FISH and CGH) Database
  2. Mitelman Database of Chromosome Aberrations in Cancer
  3. Entrez Cancer Chromosomes [searches both of the above]

Step By Step Guide back to top

Spectral Karyotyping/Multiplex Fluorescence In Situ Hybridization and Comparative Genomic Hybridization (SKY/CGH) Database
  • Search for kidney carcinoma 9q13 with SKY/M-FISH or CGH (an OR search) in the pull-down menu. Do not use Boolean connectors.
  • Look at SKY component of records.
    • Select SKY Image button.
    • Select Table View button.
  • Look at CGH component of records.
    • Select CGH button.
    • Select CGH Table View button.
    • Look at Details of Chromosome 9. There is a loss which starts at pter and goes to q22.
  • You can also use the CGH Case Comparison Tool to search on 9q13.
Mitelman Database of Chromosome Aberrations in Cancer

  • Go to the Quick Searcher.
  • Select "kidney" from the Topography menu.
  • Select multiple entries containing "carcinoma" from the Morphology menu.
Entrez Cancer Chromosomes
  • Enter kidney[site] AND carcinoma AND 9q13 in the search box
  • Three entries from SKY/M-FISH and CGH and three entries from Mitelman are matched.

Additional Notes back to top

Range searching across these two resources does not seem to be standardized. Exact searches do not show 9q13 as a breakpoint. Examination of the SKY and CGH data tables do show some changes in ranges that include 9q13.


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