Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller

The supplementary materials include supplementary methods, supplementary figures, and supplementary tables. (PDF 706 kb

Additional file 1 of Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller

The spreadsheet lists all unique heterozygous NA12878 variants in the N0015 target region. (XLSX 1136 kb

GC-MS Based Plasma Metabolomics for Identification of Candidate Biomarkers for Hepatocellular Carcinoma in Egyptian Cohort.

This study evaluates changes in metabolite levels in hepatocellular carcinoma (HCC) cases vs. patients with liver cirrhosis by analysis of human blood plasma using gas chromatography coupled with mass spectrometry (GC-MS). Untargeted metabolomic analysis of plasma samples from participants recruited in Egypt was performed using two GC-MS platforms: a GC coupled to single quadruple mass spectrometer (GC-qMS) and a GC coupled to a time-of-flight mass spectrometer (GC-TOFMS). Analytes that showed statistically significant changes in ion intensities were selected using ANOVA models. These analytes and other candidates selected from related studies were further evaluated by targeted analysis in plasma samples from the same participants as in the untargeted metabolomic analysis. The targeted analysis was performed using the GC-qMS in selected ion monitoring (SIM) mode. The method confirmed significant changes in the levels of glutamic acid, citric acid, lactic acid, valine, isoleucine, leucine, alpha tocopherol, cholesterol, and sorbose in HCC cases vs. patients with liver cirrhosis. Specifically, our findings indicate up-regulation of metabolites involved in branched-chain amino acid (BCAA) metabolism. Although BCAAs are increasingly used as a treatment for cancer cachexia, others have shown that BCAA supplementation caused significant enhancement of tumor growth via activation of mTOR/AKT pathway, which is consistent with our results that BCAAs are up-regulated in HCC

Workflow of our GC-MS based untargeted metabolomic and targeted analyses for biomarker discovery.

<p>The number of candidate metabolites analyzed at specific steps is shown in parenthesis.</p

Example of a retrieved EIC for valine.

<p>The inset in the top left shows the expected ratios for the fragments based on the library to guide the visual inspection. The doted vertical lines show the expected and estimated elution time of the analyte. Although, the background signal of 73 from other compounds is reflected in the apex score, its impact on the AUC is diminished by baseline correction.</p

List of nine analytes confirmed by targeted analysis with their expected retention time and molecular weights for quantifier (M1) and qualifier fragments (M2-M3).

<p>* Number of TMS in Fiehn library</p><p>Fragment with a molecular weight of 73 was also monitored by default for all the analytes.</p

Characteristics of the study cohort.

<p>Characteristics of the study cohort.</p

Metabolites with significant changes in their levels in HCC vs. cirrhosis based on targeted analysis of plasma by GC-SIM-MS.

<p>The metabolites in the top two panels show increasing trend with the progression of HCC. The metabolites in the bottom panel are down-regulated in HCC vs. cirrhosis. While lactic acid and citric acid show decreasing trend with the progression of HCC, sorbose is down-regulated overall in HCC vs. cirrhosis.</p