PAG XXV | Flexible and Cost-Effective Genotyping By Targeted Sequencing

Joe Don Heath,

Next-generation sequencing (NGS) technology is increasingly being adopted as an essential research and development tool in plant and animal genomics. As accessibility and affordability continue to improve, NGS is being used for marker-assisted selection (MAS) to accelerate plant breeding and selection, as well as in transcriptomics, plant or animal-pathogen interactions and epigenetics. We will present a highly multiplexed novel targeted sequencing genotyping solution that is cost-effective, flexible and features a simple workflow.

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PAG XXV | Targeted Genotyping-By-Sequencing with Single Primer Enrichment Technology (SPET): A Case Study in Black Poplar

Davide Scaglione, IGA Technology Services, Udine, Italy

Genotyping-by-sequencing has now become a widely adopted strategy to generate massive genotypic information to a fraction of the cost used in array technologies. Sequencing-based genotyping carries several advantages such as greater scalability, given the current sequencing platforms, and being an “open system”, allowing for the scoring of polymorphisms that were not necessarily a prior knowledge. However, one major limitation of widely adopted genotyping-by-sequencing methods, driven by restriction enzymes or oligomers, is its random access to the genome. On the other side, enrichment methodologies based on hybridization come with some limitation in cost, hand-on time, enrichment efficiency and dilution of the sequencing coverage on valuable sites. Here we propose the NuGEN Ovation Target Enrichment - a method originally developed for exon-centric enrichment - as a unique tool for large-scale targeted genotyping. Slight modification to the original sequencing protocol allowed to generate RAD-like stacks of reads on 90,000 pre-selected SNPs over 540 black poplar genotypes, maximizing efficiency. Moreover, the sequencing of extra bases, from both paired reads, allowed the discovery of hundreds of thousands novel SNPs, sampling rarer variants not originally included in the panel. The system showed its powerful combination of array-like target SNP paradigm along with the random sampling of variants of traditional genotyping-by-sequencing solutions, circumventing ascertainment bias. Data showed complete usability for the discovery of trait-associated polymorphisms within the 7th Framework Programme EU-funded project WATBIO.

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PAG XXV | RNA-Seq Simplified. Solutions for Every Sample.

Denise Stephens, Field Application Scientist

RNA-Seq solutions for Agrigenomics presented by Denise Stephens, Field Application Scientist at NuGEN Technologies. In this presentation, we discuss NuGEN’s RNA-Seq solutions for a broad range of sample inputs and quality. In addition, an overview of our technology (AnyDeplete and SPIA) used in the RNA-Seq portfolio is described.

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Target Enrichment for NGS Analysis of SNPs, CNVs, Gene Fusions and More

Dr.Steven Kain and Dr. Jonathan Scolnick, NuGEN Technologies

NuGEN scientists describe the novel Single Primer Enrichment Technology (SPET) and its utility in identification of gene fusion events in RNA samples, targeted gene expression, variant detection and copy number variation in DNA samples.

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Get Rid of the Noise

Dr.Ashesh Saraiya and Dr.Maureen Peterson, NuGEN Technologies

NuGEN scientists describe the use of Insert Dependant Adaptor Cleavage (AnyDeplete) technology in effectively depleting unwanted transcripts and its utility in reducing sequencing costs, improving dynamic range for usable reads and improving overall efficiency of seqeuncing.

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A Novel Approach to Epigenetic Methylation Analysis

Dr. Ben Schroeder, NuGEN Technologies

Scientist, Ben Schroeder, describes the Ovation RRBS Methyl-Seq System, a novel solution for RRBS Methyl-Seq studies. Learn how this system enables PhiX-free Illumina sequencing and the ability to identify unique molecules in a simple, one day workflow.

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Genotyping-By-Sequencing Using Single Primer Enrichment Technology (SPET)

Dr. Davide Scaglione, IGA Technologies

IGA Technology describes how they use Single Primer Enrichment Technology as a scalable and cost-effective method for genotyping-by-sequencing.

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A comprehensive target enrichment panel for fusion detection

Ashesh A. Saraiya1, Brandon Young2, Tobias Meißner2, Brian L. Jones2, Stephanie C. Huelga1, Marie Edie1, and Doug A. Amorese1

Harnessing the Power of SPIA Amplification for Viral Detection From Limited and Degraded Samples

Ashesh A. Saraiya1, I-Ching Wang1, Maureen Peterson1, Stephanie Huelga1, Bin Li1, Kurt S. Schwalm2, Darrel L. Dinwiddle2,3, and Doug Amorese1

Customized Depletion of Unwanted Transcripts from mRNA-Seq Libraries

Benjamin Schroeder, Zulfiqar Gulzar, Piotr Mieczkowski, Stephanie Marie DeYoung, Neeta Vora, I-Ching Wang, Lin Pham, Doug Amorese

A Simple Method for RNA-Seq From Mixed Microbe/Host Samples

Maureen Peterson, I-Ching Wang, Stephanie Huelga, Bin Li, Kurt S. Schwalm, Darrell L. Dinwiddie, Doug Amorese, and Ben Schroeder

Customized Depletion of Unwanted poly-A transcript from mRNA-Seq Libraries

Zulfiqar Gulzar, I-Ching Wang, Stephanie C. Huelga, Lin Pham, Douglas A. Amorese

Flexible Method for Targeted Transcript Depletion from RNA-Seq Libraries - Mouse, Rat, Drosophila and Arabidopsis

Steve Kain, Lin Pham, I-Ching Wang, Marie Eide, Dana Burow and Doug Amorese

Genetic Diveristy of the BNYVV Virus by Whole Genome Sequencing - Some New Insights

E. De Bruyne, G.Willems, L. Broos, Y. Galein and J.Hermes

Single Primer Enrichment Technology (SPET) for Targeted RNA Sequencing

Svenja Debey-Pascher, Jonathan Scolnick, I-Ching Wang, Stephanie Huelga and Doug Amorese

A Novel rRNA Depletion Method to Enable Whole Transcriptome Analysis of Single Cells with RNA-Seq

Lin Pham, Bin Li, Maureen Peterson, I-Ching Wang and Doug Amorese

Improved Method for Reduced Representation Bisulfite Sequencing (RRBS)

Ben Schroeder, Mike Phelan, Lin Pham, Steve Kain and Doug Amorese