ASHG 2016: New Products Address Long-Range Sequencing

The 66th annual American Society for Human Genetics conference was held October 18–22 in Vancouver, Canada. Attendance totaled 7,998, up 2.9% compared to last year, when the show was held in Baltimore, Maryland (see IBO 10/15/16). The exhibition hall was at maximum exhibitor capacity with 250 vendors.

The conference featured 3,439 abstracts as well as 17 invited sessions. As Committee Chair Tony Antonellis, PhD, told IBO, one change he noticed from last year was the number of presentations reporting results involving large data sets. For example, one paper presented results of a genomic analysis of over 110,000 samples that led to the identification of 200 genetic loci associated with multiple sclerosis. The effort was led by the International Multiple Sclerosis Genetics Consortium.

As Dr. Antonellis noted in the conference brochure, the programmers made a particular effort to stress clinical content. Presentations highlighting diagnostic applications were featured on an invited session on Wednesday on diagnostic functional genetics. A talk by F. W. Verheijen, PhD, of Erasmus University Medical Center listed the requirements for diagnostic functional genetics: material availability, a relatively fast assay, a simple read out (biochemical, structural, mechanistic), reproducibility, multiplexing, economical use and the availability of SOPs.

The use of long reads and long-range sequencing was an area of interest, as both 10X Genomics and Pacific Biosciences had a notable presence at the conference, with new products and workshops. 10x Genomics launched a dedicated instrument for single-cell RNA sequencing, the Chromium Single Cell Controller, with an introductory price of $50,000. The system is the same as the company’s Chromium Controller but without the genomics workflow. Both instruments partition cells or High Molecular Weight (HMW) DNA molecules and apply barcodes, allowing for the reconstruction of long stretches of short-read DNA, or so-called linked reads, post sequencing using bioinformatics. The Single Cell Controller enables a seven-hour library preparation workflow and works with all Illumina sequencers.

10X also highlighted its recently introduced Chromium De Novo Assembly Solution and the Supernova Assembly for lower-cost diploid de novo assemblies. It is designed for the Illumina HiSeq 2500 or X. The Solution also is designed with a simple workflow that can be completed in less than two weeks, according to the company.

Pacific Biosciences, whose RSII and Sequel systems provide long-read data, addressed the strengths of its technology compared to 10x Genomics and another so-called synthetic long-read approaches, including Illumina’s Moleculo technology, in a Thursday exhibitor workshop. “[S]ynthetic linked reads, such as those generated by 10X Genomics using Illumina short-read sequencing data, require amplification both in the linked-read library prep (emulsion PCR) as well as during the bridge amplification step for sequencing-by-synthesis (SBS). This results in coverage drop-out in high- and low-GC regions of the human genome due to PCR-amplification bias. The resulting linked-read sequencing data has non-uniform coverage across a whole human genome, resulting in coverage ‘holes,’” explained Luke Hickey, senior director, Human BioMedical Sciences, at Pacific Biosciences. “In addition to genome-wide coverage holes, the linked reads are also non-contiguous, and are missing data between linked-read mapping sites. The missing sequence data often includes structural variants, such as insertion sequence, resulting in a high false-negative rate, and lack of sensitivity for this variant type. The non-contiguous coverage also causes issues for identifying deleted sequences due to the inability to distinguish between sequence drop-out due to PCR bias from the sequencing method (i.e., high-/low-GC regions) vs. actual differences in the underlying genome.” 

Also addressing longer reads was a new product by Sage Science, maker of the Pippin electrophoresis system for targeted DNA size selection. At the show, the company previewed the SageHLS (HMW Library System) for purification of DNA from cell suspensions. It addresses long-range and optical mapping applications. It is designed to purify 50 Kb to 2 Mb DNA from blood samples, cell lines or bacterial cultures.

Thermo Fisher Scientific launched two products at the show. The PharmacoScan Solution genotyping microarray is designed for pre-emptive screening of pharmacogenomic content related to ADME pathways of commonly prescribed drugs. Specifically designed for clinical trials and population screening, the array contains 6,627 markers in 1,191 genes. The single assay interrogates SNPs, indels and CNVs. Eighty-eight samples are processed on 24-format array plates. The list price is $150, and volume discounts are available.

Thermo Fisher also introduced the Clariom D Pico and Clariom S Pico assays for transcriptome profiling. The Clariom D Pico, priced at $300, is designed for discovery coding and noncoding genes, exons and splicing events. The Clariom S Pico, priced at $200, is designed for identification of expression changes. According to the company, they provide a more affordable solution than RNA-Seq.

Agilent Technologies officially launched its SureGuide CRISPR guide libraries, based on the company’s SurePrint oligo platform, for pooled functional screening. Agilent highlighted library quality, particularly the uniform distribution of guides, as a product differentiator. Available in three formats to address researchers’ needs at multiple stages of the workflow, the libraries are available as catalog or custom content. The three formats are Ready-to-Package genome-wide knock-out libraries for all exons for human and mouse; Read-to-Clone libraries of linear DNA for the user who wants to design their own guide sequences for mammalian cells; and Ready-to-Amplify for fully customized design.

QIAGEN debuted its QIAseq cf (cell-free DNA) All-in-One kit, a single solution for DNA extraction and library preparation for liquid biopsy analysis using Illumina or Ion Torrent NGS systems. It supports input cfDNA inputs of 1–100 ng. It includes QIAamp Mini Columns for isolation of cfDNA from up to 5 mL of plasma. For Illumina sequencers, PCR-free amplification for 10 ng of isolated cfDNA reduces potential amplification bias. Ion Torrent users can employ the HiFi PCR master mix. Later this year, QIAGEN will begin shipping the QIAscout for single-cell isolation. For use with an inverted microscope, the system utilizes a 12,000 microraft array, a release device magnetic wand and a magnetic collection plate.

NanoString Technologies launched the nCounter Vantage 3D DNA (SNV) Solid Tumor Panel and nCounter Vantage 3D Protein Solid Tumor Signaling Pathway Panel for FFPE tumor samples. Describing the product at an exhibitor workshop, NanoString discussed the new probe design for SNV detection in DNA and RNA. The 3D Protein Solid Tumor Signaling Pathway Panel assay measures total proteins and phosphorylated proteins.

< | >