Sentence examples for matched normal genomes from inspiring English sources

We thought we could map the tumor and matched normal genomes back to the reference to start figuring out what was different.

We generated consensus sequences for the promoters and exons of genes in the tumors and their matched normal genomes using SAMtools [ 58].

We identified genes with tandem repeats in the exons and promoters of 18,439 genes in 35 colorectal tumors and their matched normal genomes (see Methods and Additional file 1: Table S1 and S2).

For those genes where both the tumor and matched normal genomes contain a repeat, we next asked how many repeats are unstable, that is, varying in the copy number of their repeat unit.

This observation is in line with the previous observation [ 13] that this pathway is the least divergent pathway between colorectal tumors and their matched normal genomes in terms of gene copy number variation and gene expression.

Most work on repeat instability in colorectal cancer focuses on variation between tumor and matched normal genomes in merely five marker repeats [ 23], a tiny fraction of the more than 3 million human microsatellite loci [ 24, 25].

Second, putative somatic breakpoints in each of the three cancer genomes were generated by subtracting those that were also detected in the matched normal genome.

These are repeats with the same repeat unit that occur in the promoter or exon of the same (homologous) genes in a tumor and its matched normal genome.

The expected coverage median for the diploid matched normal genome was determined to be 38 using Gaussian kernel density estimation (Fig. 4A).

Transduction by non-reference L1s is more difficult to identify because it requires a list of all active polymorphic L1s or a search of the matched normal genome for L1s.

To find out whether a tumor genome shows a significant difference in repeat incidence or variability to a normal genome, it is necessary to compare (i) the incidence or variability of repeats in a tumor genome relative to its matched normal genome to (ii) the incidence or variability of repeats between two normal genomes.