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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, genes TBC1D3F (ENSG00000189309, protein coding TBC1 domain family member 3B) and TBC1D3C (ENSgained205019) gained in the IMR fibroblast sample are copied not only in the hiPSCs derived from IMR but also in hiPSCs derived from other fibroblasts, and are further having a significant association between the gained copy number and a high expression value in hiPSC samples.
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Chr3 transfer increased the FER copy number by 2 after chr3 transfer in both cell lines changing this region status from "loss" (copy number less than ploidy level) to "gain" (copy number higher than ploidy level).
In practice, we compute the posterior probabilities of a clone belonging to either one of the three defined genomic states (loss, modal/unaltered and gain copy state) from a spatial mixture model framework.
This is not surprising since null hypotheses for detecting marginally amplification or deletion are highly dependent on the definition of the "complementary" state (e.g. for deletion the "complementary" state corresponds to modal or gain copy).
Volatile genes have the ability to evolve by losing or gaining copies without drastic selective consequences, providing new functions or pruning old ones.
2. P. aerophilum after its divergence, gained a copy of LysRS2, and lost its copy of LysRS1.
Similarly, after its divergence S. solfataricus gained a copy of LysRS2, and lost its copy of LysRS1 (two gains and two losses).
One progeny with the HB3 allelic background gained a copy of this locus.
In particular, MUTED has fewer copies while HELLS and OSTM1 gained more copies in all domestic goats than in wild goats (Additional file 1: Table S21).
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