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This was not surprising as the normal sample, acquired one month after diagnosis, was known to contain 10 15% blasts.
To estimate allelic copy number, germline heterozygous sites in the normal sample were called via GATK Haplotype Caller21,27.
To account for tumor-in-normal contamination (e.g. case SJHGG003_A), we required tumor MAF > 0.05 if mutant reads were observed in the normal sample for "Somatic" calls.
Sixteen cancer samples clustered together, while five cancer samples formed a separate cluster within the normal sample cluster.
As expected, TH phospholipid synthesis was >4-fold higher in the MPNST respect to the normal sample (Fig. 6C).
If both the normal sample and the tumor sample from a patient showed the same pattern for all markers, the tumor was regarded microsatellite stable (MSS).
In this case, the signal intensity of each SNP in the target sample is expressed as a ratio over that of the normal sample or reference pool.
There are serious implications in this assumption as identification of germline and rare somatic variants depend on the normal sample being the matched pair.
A total of 1.92×107 and 2.36×107 qualified reads were obtained from the NPC tissue (T10) and the normal sample (N10), respectively (Table 1).
It is more difficult to identify the informative SNPs in a tumor-only analysis when the genotype of the normal sample is unknown.
No proteins were probed by the antibody or the lectins in the normal sample, as opposed to the TSE affected sample, in which the lectins recognized di- and monoglycosylated PrPSc (Fig S2C).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com