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Regions of LD contain multiple DNA variants, all of which may be strangely associated with a disease, due to being on the same conserved haplotype.
This is attributed to the nature of the haplotype-based methods, which can better detect functional haplotypes such as cis-interactions among multiple DNA variants in a haplotype block region [ 52, 53], which is an advantage of haplotype analysis compared to the SNP analysis.
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The relative plasticity of C/EBPβ homodimer in accommodating multiple DNA sequence variants is borne out in vivo, as the top motif associated with the cellular C/EBPβ cistrome shows considerable degeneracy at the −1 and −2 positions.
Instead of searching for a single locus, multiple independent DNA variants are being selected to identify those responsible for the occurrence of a disease [ 2].
This correlates with the observations made in patients proband EII2 carrying the p.Val1106Ala variant has no detectable mtDNA lesions, in spite of polyneuropathy symptoms, whereas in the muscle tissue of proband CII1 carrying the p.Gln968Glu variant, multiple DNA deletions are evident, but the phenotype is still relatively mild (PEO).
Hence, it appears to be a suitable candidate for detecting differences in allele frequencies in multiple DNA pools and thereby identify sequence variants.
Improvements in the interpretation of phenotypes are likely to come from causal DNA variants showing significant and multiple associations with different omics data [ 11].
Known but relatively uncharted effects on epigenetic marks at multiple sites include age, sex, the environment and DNA variants such as Single Nucleotide Polymorphisms (SNPs).
For calling variants, we utilized a statistical method, CRISP, that is designed for variant detection using sequence data from multiple DNA pools[15].
In Section 2, we introduce our method vipR that makes use of data from multiple DNA pools for achieving a higher sensitivity in detecting variants in large DNA pools.
We have developed a novel statistical approach that is able to identify rare variants by comparing the distribution of allele counts across multiple DNA pools using contingency tables.
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