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(American Journal of Pathology. 2000;157:689-690.)
© 2000 American Society for Investigative Pathology

Correspondence

Online Access to CGH Data of DNA Sequence Copy Number Changes

Haartman Institute and Helsinki University Hospital Helsinki, Finland

To the Editor-in-Chief:

We have combined and updated tables on DNA copy number amplifications and losses detected in human neoplasms by comparative genomic hybridization (CGH), reported in our recent reviews.^1,2 Listing of the chromosomal locations of recurrent DNA copy number changes in 73 tumor types from 283 reports available at the end of last year can be accessed online at http://www.helsinki.fi/~lgl_www/CMG.html.

When reviewing the CGH literature, we encountered several problems, mainly the following:

1. Different CGH systems (software applications) had been used.

2. There were no consensus criteria for thresholds of losses, gains, and amplifications. In our compilation, we chose to apply an intensity ratio of 1.5 or higher as the threshold value for amplifications.

3. The results, with some exceptions, had not been confirmed using other techniques.

Thus, one should be careful in comparing the original paper and our data file.

The online files include a figure constructed from the composite profiles of the listed recurrent DNA copy number sequence changes (Figure 1) . Major data updates of the files are scheduled for July and December 2000. In the meantime, occasional reports will be added to the compilation.

View larger version (49K): [in this window] [in a new window]   Figure 1. Recurrent DNA sequence copy number amplifications (above the chromosome) and losses (under the chromosome) among 73 human neoplasia subtypes. Each line represents a single tumor entity in which a particular amplicon or loss has been observed recurrently (for amplifications in 5% of cases and in at least three cases if numbered, <5% if not numbered; for losses in 30% of cases if numbered, in 10 but <30% if not numbered). The numbers have been assigned to the tumor entities in the tabulation available on our web site, http://www.helsinki.fi/~lgl_www/CMG.html. Areas in bold indicate recurrent changes seen in a great variety of tumor entities (the minimal overlapping area in different tumor entities).

References

1. Knuutila S, Bjorkqvist A-M, Autio K, Tarkkanen M, Wolf M, Monni O, Szymanska J, Larramendy ML, Tapper J, Pere H, El-Rifai W, Hemmer S, Wasenius V-M, Vidgren V, Zhu Y: DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies. Am J Pathol 1998, 152:1107-1123[Abstract]
2. Knuutila S, Aalto Y, Autio K, Bjorkqvist A-M, El-Rifai W, Hemmer S, Huhta T, Kettunen E, Kiuru-Kuhlefelt S, Larramendy ML, Lushnikova T, Monni O, Pere H, Tapper J, Tarkkanen M, Varis A, Wasenius V-M, Wolf M, Zhu Y: DNA copy number losses in human neoplasms. Am J Pathol 1999, 155:683-694[Abstract/Free Full Text]

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