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To determine whether structural inference could also be used to annotate somatic MCPH1 variants, we identified 18 variants documented in COSMIC or TCGA and compared them with known BRCA1 functional variants (Supplementary Table S10).
While proton-pumping activity was disrupted in many of the spectrally shifted variants, we identified single tuning mutations that incurred blue and red shifts of 42 nm and 22 nm, respectively, that did not disrupt proton pumping.
Hence, it is reasonable to conclude that some of the rare TLR6 variants we identified in the TB patients have altered function.
Similar to the minor splice variants we identified in YAC transgenic brain, many PBL-derived variants are strong candidates for NMD [37], [38].
Of the 10 rare missense variants we identified, five are FMF-related mutations (E148Q, A289V, I591T, K695R, A744S; INFEVERS Database: http://fmf.igh.cnrs.fr/ISSAID/infevers/.) E148Q is one of the most common mutations in FMF patients.
Because all brain-derived 5' ATXN3 splice variants we identified were also seen in PBLs [13] and lymphocyte-rich splenic tissues, which are unaffected in human disease, they are unlikely to explain the selective neuronal toxicity observed in SCA3.
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The variants we identify correspond to 163 distinct genes, of which 93 are also reported by Hysi et al. Conversely, they report 137 significantly associated lead variants, 23 of which we did not analyse because they did not pass our quality control.
To mechanistically characterize these variants, we identify novel molecular events involved in the STX1 regulation of DAT.
Currently, 17% of clinically significant variants we identify in HCM patients are novel even after we have tested over 2,000 probands across 6 years.
In addition to structural variants, we identify 9 million base pairs of novel sequences (>100 bp), on average, per individual that are not present in the human genome reference sequence, as shown in the AsmVar demo plot (Fig. 4).
From a total of 14 MS autopsy cases from our brain bank, homozygous for the risk or the protective variant, we identified 10 cases that contained chronic active white matter lesions, in which we examined the variant impact on astrocytic phenotypes.
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