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Exact(40)
WES was performed on DNA extracted from formalin-fixed paraffin-embedded tumor biopsy samples and matched blood samples.
WES was performed for 38 tumor samples from 18 patients and matched blood samples using the SureSelect Human All Exon Kit Agilent Technologiess) according to the manufacturer's protocols, as previously described (Supplementary Table S1 31,34,35.
Exome sequencing and verification were performed for nine pairs of ESCC and the matched blood samples, followed by validation with additional samples using Sanger sequencing.
To dissect the genetic alterations associated with intrinsic and acquired resistance, we performed WES on 49 longitudinal tumor (and matched blood) samples from 17 patients with metastatic melanoma, 10 of whom initially responded to CPB, with 5 having durable responses and 5 who eventually progressed (Supplementary Data 1 and Supplementary Fig. 1).
All these mutations were not detected in matched blood samples.
No matched blood samples from those patients were available.
Similar(20)
Wherever matched blood sample is not available, the blood sample with similar coverage was used.
Whenever possible we used a patient matched blood sample as a control.
Observed loss of KIT allele in the corresponding case primarily represented neoplastic event since the matched blood sample was found to have 2 copies of KIT.
The variant was observed along with the normal allelic nucleotide in the electropherograms of tumor tissue and matched blood sample of the corresponding patient.
Fragment analysis was performed with Gene Mapper software (Life Technologies, USA) and data was analyzed using Coffalyser software (MRC, Holland) where DNA copy number ratios of tumor samples were computed using the matched blood sample.
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