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Association for Molecular Pathology (AMP) Annual Meeting & Expo
Precision medicine starts here
The Association for Molecular Pathology (AMP) is the leading organization in the field of molecular and genomic laboratory medicine, and their annual meeting and expo is an important gathering of the international molecular diagnostics community.
We're looking forward to seeing you at the 2020 AMP annual meeting. In the meantime, we invite you to review the materials we presented at past AMP meetings and reach out to us with any questions or requests via the "speak with us" link below.
AMP 2019: workshops and posters
Tumor analysis using spatial transcriptomics and high-throughput qPCR (presented by bioSyntagma)
Spatial analysis of immune response reveals patient stratification independent of molecular subtype and PD-L1 expression
Breast cancer consists of numerous intrinsic molecular subtypes, providing the basis for clinical treatment decisions. Lately, it is becoming increasingly recognized that factors other than intrinsic cancer characteristics, such as immune components' activity in the tumor microenvironment, have important effects on treatment choices and efficacy. The PD-1/PD-L1 pathway represents a popular target for assessing efficacy of immunotherapy due to its involvement in tumor immunosuppression. However, making treatment decisions based on patient stratification using molecular subtypes or overall PD-L1 expression has proven to be minimally effective. bioSyntagma has developed a method, the Molecular Fingerprint (mPrint), that enables multiplexed analysis of spatially defined regions in formalin-fixed, paraffin-embedded (FFPE) tumor samples allowing for analysis of the gene signatures unique to the tumor microenvironment. The method developed in this study utilizes the SmartChip Real-Time PCR System to analyze a panel of 248 cancer relevant genes with high throughout qPCR.
ThuPLEX HV: a simplified system for preparation of molecular-tagged NGS libraries from FFPE and cell-free DNA
Creating next-generation sequencing (NGS) libraries from FFPE and cell-free DNA is critical to developing clinical assays. The systems used for generating the libraries must have simple, streamlined workflows that can accommodate clinical samples while not compromising accuracy. To satisfy these requirements, we have developed a complete, fast, and modular NGS library prep system that enables accurate, reproducible sequencing readouts from challenging sample types. For ease of use and automatability, the ThruPLEX HV system features optional tunable fragmentation of intact genomic samples from blood, tissue, or other sources. The fragmentation approach does not require additional enzymatic steps and results in highly reproducible fragment sizes optimized for Illumina platforms.
Since accurate measurement of low-frequency mutations is critical when looking for rare alleles in heterogeneous samples (e.g., tissue biopsies or plasma), the ThruPLEX HV system includes optional molecular tags to ensure the most accurate data possible. These distinct molecular tags are well-balanced to ensure optimal representation and accuracy, which are critical considerations when looking for rare alleles in these sample types. By combining the included molecular tags with deeper sequencing, this system can provide a greater degree of accuracy than is otherwise attainable. Additionally, ThruPLEX HV was designed to accommodate a large input volume, which improves mutation detection by increasing the complexity of the input and eliminates the need to concentrate precious DNA samples prior to library preparation. A final important consideration for low-frequency mutations is achieving even coverage throughout the genome in order to ensure optimal read depth at all relevant loci. To facilitate the necessary even coverage, our system has been optimized across a broad range of GC contents.
Here, we illustrate the robust performance of the system with cell lines, severely degraded FFPE DNA, and cell-free DNA samples.
AMP 2018: workshops and poster
From raw sample to sequence-ready library: fully integrated and automated nucleic acid extraction and NGS library prep system
Next-generation sequencing (NGS) library preparation remains a manual or semiautomated process, requiring intensive manual labor and/or multiple instruments to perform nucleic acid extraction, library prep, and quantitation. In this workshop, attendees learned how industry experts from Rheonix, Inc. used the fully integrated and automated Encompass Optimum workstation to obtain high-quality sequencing results directly from raw samples including FFPE, blood, buccal swabs, and bacteria while reducing technician time, turnaround time, and cost.
Obtaining clinically relevant sequencing readout from single cells and cell-free DNA
In this workshop, we presented data using novel library-preparation workflows that enable NGS from single cells, trophoblasts, cell-free DNA, FFPE, fine needle aspirates, and other challenging sample types. These methods allow researchers and clinicians to obtain clinically relevant information from their sequencing data such as CNVs, SNVs, indels, and other genomic aberrations. We also described the incorporation of unique molecular tags to enhance sensitivity.
These simple, single-tube workflows are easily portable to a wide array of automation platforms for high-throughput sample processing. A broad range of indexes, including unique dual indexes, can also be used to increase read assignment confidence.
SMARTer PicoPLEX Gold: A new generation of single cell NGS library high reproducibility, and greatly improved coverage and fidelity for precision medicine
Accurate, reproducible detection of mutations and copy number variations (CNV) from small amounts of DNA, including single cells and fixed tissue, is key for genetic analysis of clinical samples to assist in identifying the best treatment regimen and molecular diagnoses of diseases such as cancer. Increasing demand for genetic analysis from limited samples, including single cells, has created an increasingly unmet need for technologies that allow for economical and accurate analysis of those samples.
A primary application for single-cell analysis is Preimplantation Genetic Testing (PGT). PGT has grown dramatically in the last ten years, enabled by improvements in the array and sequencing platforms, as well as by the patented SMARTer PicoPLEX WGA (PicoPLEX) quasi-random priming technology—the international gold standard for whole genome amplification (WGA) for subsequent detection of CNV in fixed or unfixed single cells. Initially, PicoPLEX chemistry was optimized to allow for reproducible detection of aneuploidies and CNVs in embryo biopsies. The original versions of the technology are not optimized for other applications such as genetic analysis in cancer screening, diagnosis of disease, or therapeutic drug monitoring due to the frequency of false-positive mutation rates.
To address the need for accurate detection of single nucleotide variants (SNVs), we enhanced the PicoPLEX chemistry using optimized enzymes, primers, and protocols that improve sequencing coverage, uniformity, and accuracy while increasing the resolution for CNV detection and retaining reproducibility. This enhanced chemistry named SMARTer PicoPLEX Gold Single Cell DNA-Seq Kit (PicoPLEX Gold) is a single-cell library-prep kit with a simple, four-step protocol to convert fixed or unfixed single cells into NGS libraries in under three hours with minimum hands-on-time.
Libraries prepared from single GM12878 cells using the PicoPLEX Gold kit were sequenced on an Illumina NextSeq® platform to a depth of ~35 million read pairs (2 x 150 cycles), generating >50% genome coverage. This coverage represents a 2-fold improvement over the original PicoPLEX kit, along with a 4X reduction in duplication rates. The PicoPLEX Gold kit detected 3.5X more SNVs compared to Multiple Displacement Amplification (MDA) with the same number of reads. Our proprietary high-fidelity polymerases used in the PicoPLEX Gold kit produced up to 50% lower allele drop-in (false-positive) rates than MDA. The increased coverage and low bias of the PicoPLEX Gold kit translated to extremely low allele-dropout rates (ADO), ~5X lower than MDA. Therefore, a single PicoPLEX Gold kit library enables reliable, high-resolution CNV analysis with shallow sequencing, and an accurate and reproducible SNV and CNV analysis with deeper sequencing.
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