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In 10 out of 53 patients (18.9%) where multiple samples were analysed results were discordant with respect to mutation findings with wild-type and mutated tumours in the same patient.
Whether BRAF inhibitors have the same effectiveness in patients with concordant and discordant BRAF mutation findings has to be evaluated.
This study characterises for the first time intraindividual heterogeneity of BRAF mutation findings in a larger melanoma patient population with up to 13 analysed tumours per patient.
This directly updates the mutation findings presented on the right-hand side, as well as the section on mutated genes or mutated cell lines respectively (see Additional file 1).
However, heterogeneity in BRAF mutation findings has been documented between primary tumour and metastases (Houben et al, 2004) and between different metastases (Lin et al, 2011; Yancovitz et al, 2012).
A cut off phred quality score of 20 was used to reduce false positives due to sequencing errors, ensuring that only high quality bases with an error rate of ≤ 1% were eligible for mutation findings.
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Eighty-nine weren were further excluded from analysis as they had BRRSO before mutation finding (Table 1).
Others have confirmed this observation 18– 20; for example, Woodage et al. 18 have confirmed the relatively high frequency of this mutation, finding 7.2% of over 5,000 Ashkenazi Jews to be carriers.
This shows how the state of the art progresses by sharing code (even without publications) - the authors did not have to write their own mutation finding tool, they could run existing programs on a new corpus.
This type of analysis has not been provided by other quality-control softwares, however, it would be particularly useful for careful examination of mutation finding from a high coverage data, to improve analyses of, e.g., somatic mutations, cancer cells, or mitochondrial heteroplasmy.
Indeed, such a pipeline appears to be an essential component to the Genome Commons that some have envisaged (Brenner, 2007; Field et al., 2009), as well as a valuable addition to the process of mutation finding through text mining (Horn et al., 2004; Kuipers et al., 2010).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com