We performed 454 whole exome pyrosequencing of tumor as well as adjacent not affected normal colonic tissue from microsatellite stable (MSS) and microsatellite instable (MSI) colon cancer patients and identified more than 50,000 small nucleotide variations for each tissue.
Filtering small nucleotide variations.
At an average read length of 499bp, this yielded a 38.8 fold average total coverage of the genome, and divided into 19.2X coverage for K6001 and 19.5X coverage for K6001-B7.Compared thethe S288c reference, we detected 7660 uniform small nucleotide variations.
The laboratory evolution strategy allowed inspection of a much wider genetic landscape, which was not limited to non-essential genes but also widely expanding the type of mutations (i.e. nucleotide variation, small insertion-deletion and duplication [ 35]) resulting in proteins with modified catalytic or structural activities.
Genetic alterations could be divided into several types, including large chromosomal amplification, translocation, deletion, small fraction loss, and single nucleotide variation.
These changes include single nucleotide variation (SNV), small insertion and deletion (INDEL), structural variation (SV) including deletion, duplication, inversion, translocation etc., and so on.
Genome-wide investigation of nucleotide variation at small RNA loci can determine the prevalence of functional variations in a species; this was first assessed in humans [ 15].
The large number of small nucleotide differences may have implications on phenotypic variation via the formation of new alleles.
IHHNV has been considered a slow-evolving, stable virus because shrimp populations in this region have recovered to pre-epizootic levels, and limited nucleotide variation has been found in a small number of IHHNV isolates studied from this region.
single nucleotide variation.
