If active, the above deletion mechanism through repeat-mediated recombination represents a novel route for the variation of sequence recognition by Type I RM systems.
Such a pharmacogenetically favorable set of circumstances is rare and may explain why, to our knowledge, COMT provides the clearest demonstration to date of a qualitative pharmacogenetic effect in which not just the magnitude but the direction of the behavioral effect of a drug is determined by variation in sequence of its target gene.
While 40% of the variation in hybridization ratio was accounted for by variation in sequence identity of the heterologous sample to the platform sample, other characteristics of the DNA sequence, such as GC content and alignment characteristics, also contributed to variation in hybridization ratio [ 40].
While ~40% of the variation in hybridization ratio can be accounted for by variation in sequence identity of the heterologous sample relative to D. melanogaster, other individual characteristics of the DNA sequences, such as GC content, also contribute to variation in hybridization ratio, as does technical variation.
By examining the sequence variation of fully sequenced members of each phylum, we could show that even phyla with very low levels of nucleotide content variation were often highly variable in their sequences.
Although the breadth of neutralization by b12 is somewhat limited either by variations in sequence of the CD4 binding loop or by distal mutations that seem to affect accessibility to its epitope on the native Env trimer [ 44].
Nevertheless, the obvious differences in cluster patterns between different SNPs can be explained by variations in sequence context, affecting hybridization of extension primers to the target molecules and to the spotted signature tags.
One drawback of assaying variation by using sequence capture and mapping of short reads to the reference genome is that we are unable to comprehensively assay copy number variation caused by insertion of sequence not present in the reference.
Two well defined phylogenetic (sister) groups of R. solani AG-3 that cause diseases associated with potato and tobacco have been identified recently by analysis of sequence variation in ribosomal DNA (rDNA) [ 6- 8] and beta-tubulin genes [ 9]: the AG-3 PT and TB.
In the 1000 genome project [ 12] sample identity was verified by comparison of sequence variation to the Hap Map database information for the corresponding sample and bioinformatics tools were written to assess levels of cross-contamination (e.g. ContEST [ 13] and subsequently VerifyBAM [ 7]).
