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Direct sequencing seems unable to provide satisfactory results for detection of EGFR mutations in samples containing a mixture of mutated and wild-type DNA.
However, all methods have shown to be able to detect mutations in samples with less than 10% mutated tumour cells (Heideman et al, 2012) and all samples used for extraction had in effect more than 30% of tumour cells.
If we assume the same background mutation rate across samples, the analysis will be biased toward falsely identifying as drivers those genes that have mutations in highly mutated samples and falsely missing those genes with a small number of mutations in samples with low mutation rates.
A direct sequencing method based on a nested PCR was established to detect mutations in samples with low viral load.
Compared with direct sequencing, in which mutant DNA needs to compose 25% or more of the total DNA to easily detect a mutation, the SNaPshot and sizing assays can detect mutations in samples in which mutant DNA composes 1.56% to 12.5% and 1.56% to 6.25% of the total DNA, respectively.
Assessment of a trend for more p16 mutations in samples from patients with more advanced histologic diagnoses was performed using the Cochran-Armitage trend test.
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The two somatic mutations in sample 1 were homozygous reference in both parents.
The FRET/MCA was used to detect the L1014S and L1014F kdr mutation in samples of the WHO bioassay (collected in 2004 2006).
Linkage analysis was used to determine the candidate region for the mutation in samples from 11 affected members and 14 unaffected members.
There are total 29,900 mutations in 498 samples after removing samples that do not fall into four subtypes.
Both assays have a sufficient analytical sensitivity to efficiently detect KRAS mutations even in samples with < 10% tumor cells.
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