Employment of the popLowess strategy enriches copy number populations of data as observed in the contour plot.
5. Susceptible regions are enriched for copy number variants Copy number variants (CNVs) are regions (1 Kb to 1 Mb) of the human genome whose copy number is polymorphic in the population.
To analyze single nucleotide polymorphism (SNP) in HPV genome, RCA was applied to enrich copy number of an episomal HPV58 genome from each of three cervical lesion samples.
Moreover, large scale projects that aim at sequencing of full-length cDNA use normalization procedures to enrich low copy transcripts, and these procedures seem to increase the fraction of underspliced transcripts that retain one or several introns [ 26, 27].
As expected, we found that RCA enriched HPV58 genome copy number in the sample 13 from 1154 copies to 7317908 copies (more than 6300-fold enrichment) while displaying no enrichment activity to host GAPDH linear DNA.
We examined whether tumors harboring PI3K-pathway alteration were enriched for MYC copy-number gain (single-copy or greater) and found a positive association (P = 0.0002, Fisher's two-tailed exact test; Figs. 1, S2A).
Repetitive contigs are slightly shorter than contigs enriched in low copy probes (average 38.32 CB units versus 44.35 CB units).
Similarly, among the 370 contigs that showed microsynteny to AT chromosomes, 166 were enriched in low copy probes, and only 17 are repeat-enriched.
Both breakpoints were found to be enriched for low copy repeats, which, according to the Segmental Duplication Database (http://humanparalogy.gs.washington.edu/), share a 49.9 kb segment with 95% sequence similarity (no.9417), and the proximal breakpoint coincided with published DNA copy number variants.
Whole genome DNA sequencing uncovered multiple TE-enriched, copy number variant regions bearing a significant fraction of hypomethylated and expressed TEs, almost exclusively in free-living mycelium propagated in vitro.
