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PTK6 copy number gain (copy number greater than or equal to 3.0) was observed in 15 of 93 breast tumors (15%) in SNP analysis.
This analysis produced a list of regions per sample that was then filtered for those regions that showed gain (copy number ratio >2.5) or loss (copy number ratio <1.5) across ≥40% (n≥29) of all samples.
Copy number gain, copy number loss.
Copy neutral, copy gain, copy loss and CNLOH are in gray, pink, blue and green, respectively.
Five (15%) of the 34 tumors showed a copy-number gain (copy number of 3).
This was the only autosomal region that retained the same "no gain" copy number in all 98 cases.
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Other PTPR genes that gain copies in cancer include PTPRF and PTPRH.
We performed FISH analysis on six GC tissues and found two samples with gained copy number of OCT1 gene (figure 1F).
By analyzing the CRC cohort in The Cancer Genome Atlas (TCGA), we found that the Elf3 gene (located in 1q32.1) is recurrently amplified in CRC, and gained copy number variation significantly associates with increased mRNA expression level.
In addition, tumors were classified according to the number of gene copies as normal (≤4 copies), low gain (4 6 copies) or high gain (>6 copies) tumors.
That is why, for example, DC appears farthest to the left in this graph of 2011 to 2013 NAEP Grade 4 Reading Gains copied from Baker's article.
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