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NU carried out genotyping and mutation screening, data collection, data analysis, and drafted the manuscript.
This framework also established the confidence for conclusions derived from likelihood ratios based statistical tests for mutation screening data.
Re-analysis of our ATM, BRCA1, and BRCA2 mutation screening data revealed that these genes do not harbor pathogenic alleles (other than modest-risk SNPs) with minor allele frequencies >0.1% in Caucasian Americans, African Americans, or East Asians.
With the availability of 1000G and EVS mutation screening data, it is now possible to use external data to bin rare sequence variants into allele frequency categories and then, using independent observational data, estimate odds ratio as a function of frequency.
In the mutation screening data reported here, rare key functional domain missense substitutions in the MRN genes were more frequent (24 vs. 12 observations) than truncating variants and conferred a slightly higher OR (3.07 vs. 2.61) with a lower P value (0.029 vs. 0.14).
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For the functionally relevant obesity MC4R mutations, we used the previously published mutation screen data (525 trios) [21].
We proposed the model on the basis of clinical BRCA1 and BRCA2 mutation-screening data and then demonstrated its effectiveness by an analysis of ATM case-control mutation-screening data [ 7, 45].
The logistic regression test for trends that we used also provides a simple approach to combining evidence from rare missense substitutions with evidence from protein-truncating sequence variants to build a more complete and statistically powerful approach to assessing case-control mutation-screening data than would be afforded by either method alone.
SMC contributed to the mutation screening and data analysis and helped to refine the laboratory platform.
NF contributed to the mutation screening and data analysis and helped to refine the laboratory platform.
FD contributed to the mutation screening and data analysis and helped to refine the laboratory platform.
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