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This different approach also revealed very high mutational frequencies in both B-cell populations.
The second patient (patient B) was analysed for mutational frequencies in the Ig-VH repertoire.
The mutational frequencies in the most commonly altered codons of KRAS, BRAF, and PIK3CA genes were in accordance to those previously described in the literature.
Datasets kept on the cBioPortal server were used for computing mutational frequencies in primary tumors, utilizing the CGDS-R package in R (http://www.R-project.org) [ 17, 18].
We analysed the mutational frequencies in 75 VH4 rearrangements before treatment and 5 months and 6 months later, when B cells were again detectable in the periphery (Fig. 4b).
IDH1/ IDH2 mutational frequencies in the particular study were 27% for post-MDS AML, 25% for therapy-related MDS/AML, 15% for de novo MDS, 13% for de novo AML and 3% for MPN.
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Both the frequency of mutated Ig sequences and the mutational frequency in the IgD+CD27- subset was significantly (P < 0.05) lower when compared with the IgD+CD27+ subset.
Compared to mucinous lesions, serous malignancies exhibited a relatively high mutational frequency in borderline tumors (35%) and fewer mutations in carcinoma (9%) (Tables 2 and 3).
Consequently, the mutational frequency in common regions was 1.79 and 0.89 mutations per megabase for MPNST-NF1-001 MPNST-NF1-001 MPNST-NF1-001vely, and MPNST-NF1-002 MPNST-NF1-002 MPNST-NF1-002respectively01 and MPNST-SP-002, respectively.
Numerous hypotheses could account for the observed data, broadly falling into two categories – active mechanism(s) resulting in the decrease of mutational frequency in UCRs, or negative pressure consistent with evolutionary selection against such mutations.
Once out of the shadow of KRAS, BRAF and NRAS (n = 209), a list of 15 top-ranked, potentially new RAS pathway activation-associated genes was identified, in which ADAMTSL3, ITGB4, APC2, GNAS, PTPRS, ATG2B showed >5% mutational frequency in the 209 remaining tumors, while TGFBR2, SLC2A4, INSRR, NLRP3, MAP3K9, MAPT, MN1, MCM3AP and PTK2B had 2.5 4.9% frequencies (see Supplementary Table 1).
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