An Integrated Next-Generation Sequencing System for Analyzing DNA Mutations, Gene Fusions, and RNA Expression in Lung Cancer

We developed and characterized a next-generation sequencing (NGS) technology for streamlined analysis of DNA and RNA using low-input, low-quality cancer specimens. A single-workflow, targeted NGS panel for non-small cell lung cancer (NSCLC) was designed covering 135 RNA and 55 DNA disease-relevant targets. This multiomic panel was used to assess 219 formalin-fixed paraffin-embedded NSCLC surgical resections and core needle biopsies. Mutations and expression phenotypes were identified consistent with previous large-scale genomic studies, including mutually exclusive DNA and RNA oncogenic driver events. Evaluation of a second cohort of low cell count fine-needle aspirate smears from the BATTLE-2 trial yielded 97% agreement with an independent, validated NGS panel that was used with matched surgical specimens. Collectively, our data indicate that broad, clinically actionable insights that previously required independent assays, workflows, and analyses to assess both DNA and RNA can be conjoined in a first-tier, highly multiplexed NGS test, thereby providing faster, simpler, and more economical results.

Abstract 1389: A unified and streamlined targeted sequencing system for the quantification of DNA mutations and RNA expression markers in lung cancer

Introduction: The promise of precision medicine relies on the identification of DNA and RNA markers that can individualize patient management. Methods such as next-generation sequencing (NGS) can deduce DNA or RNA sequences, but both types of nucleic acid have not been efficiently and effectively combined into a single NGS workflow. We describe a comprehensive methodology for targeted clinical NGS that reports DNA and RNA variants, provides a streamlined workflow, and accommodates low-input total nucleic acid (TNA) from challenging clinical specimens.

Methods: Sample QC was performed using a novel qPCR assay that quantifies discrete populations of amplifiable DNA and RNA from TNA material. PCR-based target enrichment was performed using QuantideX® NGS reagents (Asuragen) and sequenced on the MiSeq® System (Illumina). Bioinformatic analyses were conducted using QuantideX® Reporter (Asuragen), a software suite that directly incorporates pre-analytical QC information into the variant calling.

Results: Targeted DNA- and RNA-seq panels were developed that query 54 lung cancer DNA targets and 135 RNA targets, including >100 gene fusions and mRNA expression markers associated with clinical actionability. Gene-specific primers were formulated as multiplex PCR or RT-PCR reactions to independently interrogate DNA or RNA variants, respectively, from TNA or combined into a 189-plex RT-PCR to report multi-categorical nucleic acid variants. Integration of the bioinformatics pipeline and variant caller with wet-lab QC results enhanced mutation call sensitivity at <10% abundance, improved PPV for low-input specimens, and achieved absolute quantification of RNA.

The NGS panels were assessed with cell-line and synthetic controls and a residual clinical cohort of 97 NSCLC FFPE specimens. Mutations were accurately detected from as few as 5-10 DNA templates and down to <5% abundance, and RNA translocations could be observed in sub-nanogram quantities of fusion-positive FFPE TNA. The unified DNA/RNA panel identified clinically-relevant DNA and RNA variants and maintained similar coverage uniformity to the separate DNA and RNA panels. Analysis of 61 lung adenocarcinoma and 36 squamous cell carcinoma specimens revealed mutation distributions in driver genes and RNA fusions consistent with the known spectrum of variants from each tumor type as previously reported by TCGA and other groups.

Conclusions: QuantideX targeted NGS chemistries can unify the analysis of DNA and RNA markers associated with lung cancer and report SNVs, indels, fusions, and aberrantly expressed mRNA transcripts from a single NGS run. This novel technology offers reliable, accurate and comprehensive molecular characterizations of challenging tumor specimens by integrating wet-bench and dry-bench methods and improving the efficacy of routine laboratory testing.

Citation Format: Gary J. Latham, Julie Krosting, Michael Dodge, Robert Zeigler, Liangjing Chen, Jason Plyler, Shobha Gokul, Junya Fujimoto, Vassiliki Papadimitrakopoulou, Ignacio Wistuba, Richard Blidner, Brian Haynes. A unified and streamlined targeted sequencing system for the quantification of DNA mutations and RNA expression markers in lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1389.

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

All next-generation sequencing (NGS) procedures include assays performed at the laboratory bench ("wet bench") and data analyses conducted using bioinformatics pipelines ("dry bench"). Both elements are essential to produce accurate and reliable results, which are particularly critical for clinical laboratories. Targeted NGS technologies have increasingly found favor in oncology applications to help advance precision medicine objectives, yet the methods often involve disconnected and variable wet and dry bench workflows and uncoordinated reagent sets. In this report, we describe a method for sequencing challenging cancer specimens with a 21-gene panel as an example of a comprehensive targeted NGS system. The system integrates functional DNA quantification and qualification, single-tube multiplexed PCR enrichment, and library purification and normalization using analytically-verified, single-source reagents with a standalone bioinformatics suite. As a result, accurate variant calls from low-quality and low-quantity formalin-fixed, paraffin-embedded (FFPE) and fine-needle aspiration (FNA) tumor biopsies can be achieved. The method can routinely assess cancer-associated variants from an input of 400 amplifiable DNA copies, and is modular in design to accommodate new gene content. Two different types of analytically-defined controls provide quality assurance and help safeguard call accuracy with clinically-relevant samples. A flexible "tag" PCR step embeds platform-specific adaptors and index codes to allow sample barcoding and compatibility with common benchtop NGS instruments. Importantly, the protocol is streamlined and can produce 24 sequence-ready libraries in a single day. Finally, the approach links wet and dry bench processes by incorporating pre-analytical sample quality control results directly into the variant calling algorithms to improve mutation detection accuracy and differentiate false-negative and indeterminate calls. This targeted NGS method uses advances in both wetware and software to achieve high-depth, multiplexed sequencing and sensitive analysis of heterogeneous cancer samples for diagnostic applications.

Functional DNA quantification guides accurate next-generation sequencing mutation detection in formalin-fixed, paraffin-embedded tumor biopsies

The formalin-fixed, paraffin-embedded (FFPE) biopsy is a challenging sample for molecular assays such as targeted next-generation sequencing (NGS). We compared three methods for FFPE DNA quantification, including a novel PCR assay (‘QFI-PCR’) that measures the absolute copy number of amplifiable DNA, across 165 residual clinical specimens. The results reveal the limitations of commonly used approaches, and demonstrate the value of an integrated workflow using QFI-PCR to improve the accuracy of NGS mutation detection and guide changes in input that can rescue low quality FFPE DNA. These findings address a growing need for improved quality measures in NGS-based patient testing.

Significance of the human immunodeficiency virus infection in patients submitted to cardiac surgery

BACKGROUND

To realize if cardiac surgery could interfere with the evolution of HIV infected patients to the acquired immunodeficiency syndrome (AIDS).

METHODS

The study group consisted of 30 HIV positive patients (0.21%) among 14,785 who underwent cardiac surgery at the Heart Institute of University of Sao Paulo Medical School (Incor-FMUSP) from November 1988 to December 1994. Patients were followed up until they were discharged from hospital and a new contact was kept at the end of the first semester of 1995.

RESULTS

All patients were asymptomatic at the time they were operated. Two patients progressed to death during hospitalization due to non-infectious complications and other three patients could not be traced. After all 25 patients had their progression evaluated. Six patients (24%) died within a period ranging from 1 to 46 months (average=17 months): 2 due to bacterial pneumonia and 04 due to AIDS-related complications. The average follow-up period for the 19 surviving patients was 33.6 months (ranging from 13 to 74 months), and only one of them (5.3%) saw the infection progress to AIDS. In summary, 5/25 (20%) saw HIV infection progress to AIDS within a maximum period of 74 months.

CONCLUSIONS

Data available up to now show no conclusive evidence of acceleration of HIV into AIDS associated with cardiac surgery.

Control of a remote microscope over the Internet

Globally connected research sites frequently find the need to share information on a timely basis. The sharing of data obtained from microscopy has historically required that the researcher take micrographs of the desired image and send the film to the other site or, more recently, scan the micrographs into a computer and send the micrographs through e-mail. The authors identified the need to control and view, in as close to real time as possible, images being viewed on a remote microscope. The goal was to develop a system that would be versatile, easy to learn and readily adapted from existing materials and that would allow several users to simultaneously view and control the microscope. The use of commercially available materials along with a simple, custom-designed slide holder allowed researchers at remote sites to view one of 15 slides and move the slide as needed. The penalty for use of the Internet vs. dedicated phone lines such as Integrated Services Digital Network (ISDN) is that only 1 frame/7 s can be viewed at video resolution. The advantages of cost and multiple, simultaneous use over a ubiquitous system outweigh the disadvantage for most users.