The annual Association for Biomolecular Resource Facilities (ABRF) conference was held March 25–28 in San Diego, California. The conference hosted a total of 740 participants, consisting of 519 attendees and 221 exhibitors. Conference technology tracks were centered on genomics, imaging and proteomics/MS. The ABRF represents 340 labs and administrative offices. Members include the largest academic core laboratory facilities in the US.

IBO attended day three of the conference. Exhibits and talks at the show were heavily focused on NGS and single-cell analysis. In her Genomics plenary presentation, Barbara Wold, PhD, Bren Professor of Molecular Biology at the California Institute of Technology, discussed new approaches to single-cell RNA profiling to cost effectively characterize single cells. Although RNA-Seq provides long transcripts and is affordable, it does not adequately capture cellular heterogeneity. Examples of alternative options to single cell analysis she discussed included laser capture of small pools of cells, as small cell pools can give a strong representation of cell-type; use of a part of the cell to provide information about the whole cell, highlighting research looking at myofiber nuclei to determine cell type; and regulating cell identity by engineering changes.

In the Genomics track, two presentations focused on NGS for research and diagnostics, exploring the progress at two academic sequencing labs. Each presenter highlighted the diagnoses made using NGS, as well as the institutional collaborations in which they are involved. Yaping Yang, PhD, Associate Professor, Molecular and Human Genetics, at Baylor College of Medicine, discussed Baylor Genetics’ use of clinical exome sequencing for diagnostics and discovery. For exome interpretation, she recommended genome-wide searchers, integration with other genomics data and in silico reanalysis. In the future, she noted that whole-genome sequencing and multi-omics should replace exome sequencing if cost allows.

In his talk on WGS, Shawn Levy, PhD, director of the Genomics Services Lab at the HudsonAlpha Institute of Biotechnology, examined his lab’s use of WGS, recommending 40x coverage for clinical genomics. He described many of the labs’ projects, highlighting the usefulness of hyper-variable and hyper-conserved regions of the human genome. Like Dr. Yang, he noted the use of reanalysis to find new diagnoses based on the discovery of new disease genes.

In the afternoon presentations, Molly He, senior director of Scientific Research provided a look behind the scenes of the company’s development of the latest version of its SBS chemistry, designed to improve speed and reducing phasing (a sequencing-by-synthesis consequence in which repeated amplification results in the de-synchronizing of signals leading to higher noise to signal). The company’s efforts included protein engineering and the develop of a high-throughput solution assay to determine the intrinsic properties of polymerases.

ABRF’s Genomics Research Group reported on the results of a study on the current state of single-cell RNA-Seq technologies. The experimental study evaluated five platforms (WaferGen’s iCell8, Illumina/Bio-Rad Laboratories’ ddSEQ, Fluidigm’s 96-cell IFT and HT-IFC, and 10x Genomics’ Chromium). The ddSEQ and Chromium platforms were the only ones utilizing UMIs (Unique Molecular Identifiers). Results for all of the platforms were correlated to bulk RNAseq. Because of the recent release, data for the ddSEQ was oversampled, which may have influenced results. The study found that for cumulative gene detection, about 100 cells or less of heterogeneous cell lines was the amount at which the experiments experienced point of diminishing returns for most technologies. For each platform, results were comparable for DMSO treated and TSA treated samples.

At the show, NanoString Technologies launched the nCounter PlexSet reagents, increasing the throughput of its nCounter digital gene expression system from 12 samples to up to 96 samples with 12-probe or 24-probe multiplexing. Time savings compared to qRT-PCR are realized through a protocol that requires only lysing, thus no nucleic acid purification, reverse transcription or amplification. Set-up time is 30 minutes. The minimum input amount is 50 ng of total purified RNA or 5,000 cells or 1 ng of RNA input with amplification. Future products will include 96 gene targets per sample.

BD Biosciences displayed its BD Resolve Single-Cell Analysis platform, which will be commercially released late summer. The system is designed to enable single-cell gene expression analysis of hundreds to more than ten thousand cells, using an innovative cartridge design and patented Molecular Indexing technology acquired through the 2015 purchase of Cellular Research (see IBO 8/31/15). The technology isolates single cells and labels individual mRNA molecules prior to NGS readout, after which highly accurate gene expression results can be obtained. The system is expected to compete with the Illumina/Bio-Rad Single-Cell Sequencing Solution and Fluidigm’s C1 platform, but for much higher numbers of cells. The company also displayed its BD Precise RNA quantification assays, launched last year. Designed for both targeted and whole transcriptome analysis, they also utilize Molecular Indexing and are used with BD’s FACS systems for rapid, selective single cell isolation in standard SBS plates. After isolation, multiple samples can be pooled and NGS ready libraries prepared in a single tube to save costs. Currently available are WTA kits, targeted kits and predesigned panels.  Custom panel development of gene-specific panels is also available.

Bionano Genomics showed its new Saphyr optical mapping solution for discovery of large-scale structural variants, which for the most part cannot be identified with NGS. The system identifies structural variants from 1,000 bp to megabased pairs by labeling, stretching, and imaging megabase-size molecules that are then reassembled to create a physical map. The third-generation system has 10x higher throughput for one genome per day (followed by 24 hours of analysis time), lowering the cost per sample and enabling a broader set of applications, such as population studies and clinical research. Only one capillary electrophoresis­–based NanoChannel array chip has to be run now, compared to multiple chips with the previous system (the Irys). The system is priced at $350,000.

At its booth, Menarini Silicon Biosystems highlighted the recently launched DEPArray _NxT, the third version of its system for identification and isolation of rare single cells. Microfluidic channels sort cells based on dielectrophoretic force, and bright field imaging enables cell identification. Cells are recovered in collection tubes. It allows recovery at 100% purity, according to the company. New features include a benchtop configuration, faster operation time and automated cell selection for FFPE samples. FFPE sample throughput is approximately 90 minutes. The system is run with dedicated kits.

At the show, Advaita showed its recently released iVariant Guide NGS variant analysis solution. The solutions’ database contains over 210,400 genes and more than 920 pathways. A clean and intuitive interface facilitates use and features a cloud-based search portal, and visual displays.

ABRF 2018 will be held in April 22–25 in Myrtle Beach, South Carolina.