A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

BackgroundOncopanel genomic testing, which identifies important somatic variants, is increasingly common in medical practice and especially in clinical trials. Currently, there is a paucity of reliable genomic reference samples having a suitably large number of pre-identified variants for properly assessing oncopanel assay analytical quality and performance. The FDA-led Sequencing and Quality Control Phase 2 (SEQC2) consortium analyze ten diverse cancer cell lines individually and their pool, termed Sample A, to develop a reference sample with suitably large numbers of coding positions with known (variant) positives and negatives for properly evaluating oncopanel analytical performance.ResultsIn reference Sample A, we identify more than 40,000 variants down to 1% allele frequency with more than 25,000 variants having less than 20% allele frequency with 1653 variants in COSMIC-related genes. This is 5-100x more than existing commercially available samples. We also identify an unprecedented number of negative positions in coding regions, allowing statistical rigor in assessing limit-of-detection, sensitivity, and precision. Over 300 loci are randomly selected and independently verified via droplet digital PCR with 100% concordance. Agilent normal reference Sample B can be admixed with Sample A to create new samples with a similar number of known variants at much lower allele frequency than what exists in Sample A natively, including known variants having allele frequency of 0.02%, a range suitable for assessing liquid biopsy panels.ConclusionThese new reference samples and their admixtures provide superior capability for performing oncopanel quality control, analytical accuracy, and validation for small to large oncopanels and liquid biopsy assays.Peer reviewe

Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions

BackgroundTargeted sequencing using oncopanels requires comprehensive assessments of accuracy and detection sensitivity to ensure analytical validity. By employing reference materials characterized by the U.S. Food and Drug Administration-led SEquence Quality Control project phase2 (SEQC2) effort, we perform a cross-platform multi-lab evaluation of eight Pan-Cancer panels to assess best practices for oncopanel sequencing.ResultsAll panels demonstrate high sensitivity across targeted high-confidence coding regions and variant types for the variants previously verified to have variant allele frequency (VAF) in the 5-20% range. Sensitivity is reduced by utilizing VAF thresholds due to inherent variability in VAF measurements. Enforcing a VAF threshold for reporting has a positive impact on reducing false positive calls. Importantly, the false positive rate is found to be significantly higher outside the high-confidence coding regions, resulting in lower reproducibility. Thus, region restriction and VAF thresholds lead to low relative technical variability in estimating promising biomarkers and tumor mutational burden.ConclusionThis comprehensive study provides actionable guidelines for oncopanel sequencing and clear evidence that supports a simplified approach to assess the analytical performance of oncopanels. It will facilitate the rapid implementation, validation, and quality control of oncopanels in clinical use.Peer reviewe

Commissioning Status of the 3 MeV RFQ for the Compact Pulsed Hadron Source (CPHS) at Tsinghua University

The 3 MeV Radio Frequency Quadrupole (RFQ) accelerator for the Compact Pulsed Hadron Source (CPHS) is in its initial stage for the commissioning at Tsinghua University. Braze of the flanges was completed in January, 2012. The RFQ cavity has been delivered to Tsinghua University after the final field tuning. In 2012 the 3-meter-long RFQ is expected to deliver 3 MeV protons to the downstream High Energy Beam Transport (HEBT) with the peak current of 50 mA, pulse length of 0.5 ms and beam duty factor of 2.5%. The initial commissioning is now underway

Dendritic cells-mediated CTLs targeting hepatocellular carcinoma stem cells

Immunotherapy, especially using dendritic cells (DCs)-based vaccine, appears promising in the treatment of hepatocellular carcinoma (HCC) following surgery. However, the therapeutic efficacy of current DC vaccines loaded with HCC antigen is limited in clinical practice. One important reason might be that the DC vaccines for the treatment of HCC were not aimed at targeting the hepatocellular carcinoma cancer stem cells (HCCCSCs). Therefore, establishing an immunotherapy to kill HCC stem cells could be a novel therapeutic strategy. In this study, we have developed an immunotherapy to target CD133 + HCC cells in the treatment of HCC. This study had three main findings; (1) CD133 +HCC cells RNA loaded DCs could induce special CD8 + cytotoxic T lymphocytes (CD133 +Huh7-CTLs) response against CD133 + Huh7 cells in vitro. (2) Huh7 cells-induced tumor growth in vivo was effectively inhibited by CD133 +Huh7-CTLs. (3) the great inhibition potential of CD133 +Huh7-CTLs to Huh7-induced tumor growth might not be only associated with anti-tumor cytokines such as IFNγ, but also to CD133 +Huh7-DCs induced specific CTLs. This study shows an experimental proof that CD133 +HCC cells RNA loaded DC vaccine has potential in treating HCC and may provide a new therapy for clinical post operative adjuvant therapy in future. © 2010 Landes Bioscience.link_to_OA_fulltex

The Compact Pulsed Hadron Source: A Design Perspective

During the past. decades, large-scale national neutron sources have been developed in Asia, Europe, and North America. Complementing such efforts, compact hadron beam complexes and neutron sources intended to serve primarily universities and industrial institutes have been proposed, and some have recently been established. Responding to the demand in China for pulsed neutron/proton-beam platforms that are dedicated to fundamental and applied research for users in multiple disciplines from materials characterization to hadron therapy and radiography to accelerator-driven sub-critical reactor systems (ADS) for nuclear waste transmutation, we have initiated the construction of a compact, yet expandable, accelerator complex-the Compact Pulsed Hadron Source (CPHS). It consists of an accelerator front-end (a high-intensity ion source, a 3-MeV radio-frequency quadrupole linac (RFQ), and a 13-MeV drift-tube linac (DTL)), a neutron target station (a beryllium target with solid methane and room-temperature water moderators/reflector), and experimental stations for neutron imaging/radiography, small-angle scattering, and proton irradiation. In the future, the CPHS may also serve as an injector to a ring for proton therapy and radiography or as the front end to an ADS test facility. In this paper, we describe the design of the CPHS technical systems and its intended operation