Open Access Research article

Allelotypes of lung adenocarcinomas featuring ALK fusion demonstrate fewer onco- and suppressor gene changes

Hironori Ninomiya1, Motohiro Kato45, Masashi Sanada4, Kengo Takeuchi12, Kentaro Inamura1, Noriko Motoi1, Hiroko Nagano1, Kimie Nomura1, Yukinori Sakao3, Sakae Okumura3, Hiroyuki Mano67, Seishi Ogawa4 and Yuichi Ishikawa1*

Author Affiliations

1 Division of Pathology, The Cancer Institute, Ariake 3-8-31, Koutou-ku, 135-8550, Tokyo, Japan

2 Pathology Project for Molecular Targets, The Cancer Institute, Ariake 3-8-31, Koutou-ku, 135-8550, Tokyo, Japan

3 Thoracic Oncology Center, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Ariake 3-8-31, Koutou-ku, 135-8550, Tokyo, Japan

4 Cancer Genomics Project, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, 113-8656, Tokyo, Japan

5 Department of Pediatrics, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, 113-8656, Tokyo, Japan

6 Department of Medical Genomics, Graduate School of Medicine, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, 113-8656, Tokyo, Japan

7 Division of Functional Genomics, Jichi Medical University, 329-0498, Tochigi, Japan

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BMC Cancer 2013, 13:8  doi:10.1186/1471-2407-13-8

Published: 5 January 2013

Additional files

Additional file 1: Table S1.:

Frequencies of fusion variants of ALK rearrangements. Table S2. Cases with TP53 mutations and their smoking status. Table S3. Chromosomal arms and number of cases with gain with or without ALK fusion. Table S4. Chromosomal arms and number of cases with loss with or without ALK fusion. Table S5. P-values for comparisons of the frequencies of chromosome aberrations in all chromosome arms between tumours with or without ALK fusion. Table S6. Number of cases with copy number gain or loss at selected loci with or without ALK fusion. Table S7. Significance of the differences in frequencies of copy number changes (gains and losses) between tumours with or without ALK fusion.

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Addtional file 2: Figure S1.:

Mutation rates for EGFR, TP53 and KRAS according to cumulative smoking are shown. EGFR and KRAS mutations were only detected among ALK fusion negative cases, so ALK fusion positive cases were not included in the analysis. Note the gradually decrease in EGFR mutation rate with increase in cumulative smoking. KRAS mutations were detected only among smokers.

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Additional file 3: Figure S2:

Comparisons of copy number alteration rates at selected loci with or without ALK fusion. Note that 5p15.33 including TERT shows the highest gain both in ALK fusion positive and negative tumours, the frequencies being identical.

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