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The pairwise statistics allow aggregation from several causal variants located proximally (e.g., within the same gene), which can add power.
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In chickens, the availability of 600 K Affymetrix Chicken SNP array could contribute to narrowing down candidate genomic segments and pinpointing several dominating causal variants.
To boost the power to identify functional or causal variants, several strategies have been implemented: directly increasing sample size and transethnic approaches.
An attraction of this method of analysis is that it allows several markers to be entered into the regression simultaneously in analyses whose aim is to narrow down potential causal variants when several markers in linkage disequilibrium with one another are all related to phenotype.
Target capture of custom designed regions and exome sequencing has allowed identification of causal variants in several Mendelian disorders [ 7], variants associated with complex diseases [ 8], and recurrently mutated cancer genes [ 9].
There are several causal mechanisms by which a genetic variant may be associated with multiple risk factors (11).
Together, these data identified several candidate genes for additional studies to identify causal variants predisposing to increased risk for developing melanoma.
Our aims in this study were to comprehensively identify ALL predisposition variants in ETV6 and to determine the extent to which they contributed to the overall risk of childhood ALL.Whole-exome sequencing of an index family with several cases of ALL was done to identify causal variants for ALL predisposition.
Several approaches, such as fGWAS (16), use functional annotations as priors for potential causal variants.
Our functional annotation of the statistically most promising correlated candidate causal variants also provides provisional evidence to implicate a contribution by several new potential candidate genes in PrCa risk.
However, existence of multiple causal variants in tight linkage is plausible, for instance if any of several mutations within a single gene, or combinations of those mutations, alter disease susceptibility.
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