Genomic Characterization and Comparison of Multi-Regional and Pooled Tumor Biopsy Specimens

<div><p>A single tumor biopsy specimen is typically used in cancer genome studies. However, it may represent incompletely the underlying mutational and transcriptional profiles of tumor biology. Multi-regional biopsies have the advantage of increased sensitivity for genomic profiling, but they are not cost-effective. The concept of an alternative method such as the pooling of multiple biopsies is a challenge. In order to determine if the pooling of distinct regions is representative at the genomic and transcriptome level, we performed sequencing of four regional samples and pooled samples for four cancer types including colon, stomach, kidney and liver cancer. Subsequently, a comparative analysis was conducted to explore differences in mutations and gene expression profiles between multiple regional biopsies and pooled biopsy for each tumor. Our analysis revealed a marginal level of regional difference in detected variants, but in those with low allele frequency, considerable discrepancies were observed. In conclusion, sequencing pooled samples has the benefit of detecting many variants with moderate allele frequency that occur in partial regions, but it is not applicable for detecting low-frequency mutations that require deep sequencing.</p></div

Schematic overview of the comparison of mutation and expression patterns from multiregion sequencing of whole-exome and whole-transcriptome.

<p>Regional samples of each cancer were closely grouped over 2-D space based on principal component analysis (PCA). The differences in genomic variants and in gene expression between sequencing are shown.</p

Pairwise correlations and scatter plots of expression profiles from whole transcriptome sequencing data.

<p>Pearson’s correlation coefficients included all coding genes.</p

Percent of differentially expressed genes in multiregional samples (blue) and between the pooled sample and regional samples (orange).

<p>Each bar represents the distribution of the fraction of genes showing fold change difference in expression ((A) > 2-fold, (B) > 3-fold, and (C) > 4-fold) between each pair of samples. For every possible comparison between the four regional samples (a total of six comparisons) and between the four regional samples and the pooled sample (four comparisons) in each tumor case, genes showing a difference in fold change were selected for fraction calculation.</p

Profile of variants listed on the COSMIC DB and labeled as the same tissue type.

<p>The fraction of each circle indicates tumor variant allele frequency.</p

The characteristics of common, shared and private variants from regional samples.

<p>(A) Fractions of common, shared, and private variants identified among different regions. (B) Fractions of common, shared, and private variants identified from pooled- or mixed-samples. (C) Variant allele frequency (VAF) distribution of common, shared, and private variants identified among different regions.</p

Additional file 2: Table S2. of Predicting multi-class responses to preoperative chemoradiotherapy in rectal cancer patients

List of TO and MI genes used as the features for the prediction model. (XLSX 20.9 kb