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We examined this on the breast most cancers cell line MCF7 for which sequence data from each input materials as well as a number of ChIPseq experiments for a variety of DNA-associated proteins (ER, EGR1, GATA3, CTCF, MAX, and EP300) are available 34 Utilizing downstream segmentation evaluation with CBS, we noticed that CopywriteR accurately and reproducibly detected copy quantity adjustments (Figure 5 B; left panel and Additional file 2 : Determine S8).
We analyzed melanoma PDX pattern T99 using CopywriteR and onTarget methods, each with and with no matching reference (‘relative' and ‘absolute', respectively). Thus, these analyses show that CopywriteR is exclusive in its potential to extract accurate copy number info from targeted sequencing data with out a reference. We in contrast the performances of CopywriteR and onTarget on WES knowledge obtained from DNA of an FFPE melanoma biopsy.
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The lower deflection of copy quantity profiles obtained from Nimblegen arrays as compared with other DNA copy number platforms has been described before 27 , 28 In sum, CopywriteR accurately detects CNAs and performs just like the dedicated DNA copy quantity method arrayCGH. To extend our evaluation of the potential of CopywriteR, we next analyzed the entire sequence dataset of nine mouse mammary tumors, and measured the performance of CopywriteR and onTarget approaches based mostly on downstream segmentation evaluation.