Sentence examples for matched normal sample from inspiring English sources

Normalization against a matched normal sample allows a better correction of confounding factors [ 13] and reduces the need for filters, but it is not always available [ 14], hence the relevance of optimal filtering and GC content bias correction.

If a matched normal sample is not available, normalization involves GC content bias correction, which removes a great part of the observed bias.

The fold change in somatic copy number was determined by dividing the normalized mean quantity of the target gene in the tumor sample by the normalized mean quantity of the target gene in the matched normal sample.

As the tumor model has been developed in several mouse backgrounds, there is no true matched normal sample, and the following strategy was employed to remove germline variants: (1) Removal of all known germline mouse variants using the current single-nucleotide polymorphism and indel calls provided by the Mouse Genomes Project63.

Briefly, a mismatched based was identified as a mutation after meeting the following criteria: (i) it was present in more than five distinct reads; (ii) the number of distinct reads containing the mismatched base was at least 10% of the total distinct reads; and (iii) it was present in <0.5% of the reads in the matched normal sample.

No matched normal sample was available for the 13 established cell lines included in the study.

Tumour and matched normal samples were included in this analysis to exclude germline variants.

Somatic variants were identified after deducting the normal/germline variants observed in the matched normal samples from those observed in the tumor samples.

To validate miR-21 ISH results we performed miR-21 qRT-PCR analysis in a series of 10 AVCs and their matched normal samples.

Sequencing of PIK3CA exons 9, 20 was done by PCR amplification and direct sequencing of both strands for all CRC cases and their matched normal samples as previously described (Saal et al., 2005; Abubaker et al., 2007).

The average number of reads per targeted base with WGS was 29.0 ± 5.3 for the six tumor specimens and 35.0 ± 4.6 for the matched normal samples, with over 93% of bases represented by at least 10 reads (Supplementary Table 3).