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On the contrary, nD variants had no impact on melanoma susceptibility (P = 1).
The repartition of R, r, D, and nD variants in each protein domain indicated in Table 4 showed that 63% of D variants were located in four domains (intracellular 2 and transmembrane 2, 5, and 7) whereas only 18% of nD variants were located in these domains (P < 0.0001).
Finally, in order to investigate the respective role of MC1R protein domains in melanoma, the number of D and nD variants in different domains was compared between patients and controls.
Rare variants, which were defined by an allele frequency <1% and predicted to be damaging by at least 1 of 3 prediction tools, were predicted to be damaging (D) variants, while variants without any damaging effect were regarded as nondamaging (nD) variants.
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Finally, a patient carrying the unreported ABCC8/A355T c.1063G>AA; nd-NA/2) variant inherited the mutation from his mother, who was diagnosed with gestational diabetes at the age of 26 years.
Next we explored the effect of increasing the number of disease-causal variants (ND) while holding PAR constant in order to model the impact of allelic heterogeneity on the performance of the different algorithms.
This variant of ND is now called ND in SC style.
As can be seen, as ND increases, each variant's risk contribution decreases, along with power.
Third, the association of variants in CRHR1 with ND that we detected is relatively weak; if we applied Bonferroni correction to our thresholds for P values, all detected associations became nonsignificant.
In order to study the impact of MC1R protein domains on melanoma predisposition, the different classes of MC1R variants (R, r, D, and nD) were positioned on the different protein domains.
For example, we recently detected a significant interaction between variants of CHRNA4 and CHRNB2 in affecting ND, such that CHRNB2 contributes significantly to the etiology of ND together with CHRNA4 through gene-gene interaction [34].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com