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European Society for Human Genetics (ESHG)

Confidence is the currency of science.

IDT will be participating in European Society for Human Genetics (ESHG) 2020 virtually this year. Learn why top sequencing companies choose IDT and why IDT scores high in customer service—especially for our NGS products.

Poster presentation

  • Enabling variant calling in challenging FFPE samples by coupling a novel library preparation chemistry with exome sequencing
    Poster 2020-A-1645-ESHG

    This study demonstrates that the xGenTM Exome Research Panel v2, when combined with xGen Prism DNA library preparation, provides researchers with a complete human exome FFPE-sequencing solution with robust performance across FFPE samples of varying quality.

Corporate satellite: on-demand session

Though targeted next generation sequencing (NGS) is widely applied in genetic diagnostics and research, achieving high sensitivity presents challenges, such as detecting low levels of mutant sequences or target RNA molecules due to a low fraction of aberrant cells.

Our first presentation reviews two studies: 1) the detection of gene-doping using a DNA-based NGS panel and 2) the measurement of minimal residual disease (MRD), the persistence of leukemic cells after treatment, and using an RNA-based NGS panel. Our second presentation highlights a sequencing protocol for SARS-CoV-2 based on the established amplicon sequencing approach known as the ‘ARTIC method’.

  • Detection of low levels of mutant sequences with NGS
    Presented by: Eddy de Boer
    University of Groningen, University Medical Center Groningen, Department of Genetics

    Targeted NGS effectiveness is challenged when high sensitivity is required—for example, in the detection of low levels of mutant sequences or when the presence of the target RNA molecule is low due to a low fraction of aberrant cells. Here are two studies aimed at overcoming such challenges: 1) detection of gene doping [1] using a DNA-based NGS panel and 2) measuring minimal residual disease (MRD) [2], the persistence of leukemic cells after treatment, using an RNA-based NGS panel.

    1) Existing PCR-based methods for gene doping detection in athletes target exon-exon junctions in the intron-less transgene, but evasion is possible by tampering with cDNA sequences. We designed tamper-resistant xGen Lockdown Probes directed at all exon-exon junctions of 5 potential doping genes. All junctions were detectable with a sensitivity of 1296 cDNA copies in 1000 ng of genomic DNA and plasmid-derived sequences were observable; optimizations are possible.

    2) Measuring MRD is important for monitoring leukemia recurrence; current monitoring uses flow cytometry and digital droplet PCR (ddPCR). NGS advantages include the ability to analyze different genetic aberrations and patients in 1 experiment. We designed a) xGen Lockdown Probes targeting the breakpoints of 13 fusion transcripts; b) non-labeled probes blocking wild-type transcripts; and c) xGen Lockdown Probes fully tiling housekeeping genes for quantification. Our NGS method reached a maximum sensitivity of 1 aberrant cell per 10,000 and was mostly within a factor 10 compared to ddPCR. Further optimizations are easy and will likely boost sensitivity.
  • A rapid, scalable, cost-effective amplicon sequencing method for genomic surveillance of SARS-CoV-2
    Presented by: Dr. Joshua Quick
    UKRI Future Leader Fellow, Institute of Microbiology and Infection, University of Birmingham

    A sequencing protocol for SARS-CoV-2 based on the established amplicon sequencing approach known as the ‘ARTIC method’ was posted to protocols.io on Jan. 23, 2020, only five days after the genome was deposited. The protocol was rapidly adopted and used to generate thousands of genomes from more than 10 countries, including many of the first genomes produced by those countries.
     
    The approach uses a multiplex PCR to produce amplicons that tile across the viral genome, then native barcoding to multiplex up to 24 amplicon pools, equivalent to >2300 individual amplicons per library. Since the method relies on PCR amplification, the vast majority of reads generated are on-target with 10,000 to 100,000 reads, enough reads to cover the whole viral genome with the 20x coverage required for analysis. The MinION portable sequencer provides ample capacity to sequence a 24-barcode library to high depth, and can be nuclease-treated and reused to save costs. The baseline cost per sample is £35 using a MinION flowcell, but with volume reduction and flowcell reuse, this cost can fall to under £20 per sample. This portability and cost-effectiveness make it suitable for working in the field or in a laboratory setting in LMICs. We have strived to continuously develop the method to increase genome completeness and accuracy and reduce cost. To improve the multiplex PCR 11, regions of weaker amplification were identified and alternate primer pairs were added to the pools. This release, known as V3, increased the coverage for all the targeted regions, improving genome completeness. Further changes made to the nanopore library preparation protocol reduce hands-on time and increase the barcode assignment rate to 64.5%, with a misassignment rate of only 0.001%, which is crucially important when analyzing amplicon data.

Explore some of our NGS solutions

Overview
Virus research
ARTIC
xGen Prism DNA Library Prep Kit
xGen Exome Research Panel v2
NGS Discovery Pools
xGen Lockdown Probe Pools
xGen Lockdown Panels
xGen Blocking Oligos
Custom NGS Adapters

Event information

Date:

June 6-June 10, 2020

Location:

Virtual