PAG XXVI - Town and Country Hotel, San Diego, CA

13 - 17 January 2018

Join us for the 2018 Plant and Animal Genome (PAG) XXVI Conference in San Diego, California! We are once again hosting an exciting workshop where we will highlight how Allegro Targeted Genotyping is being used to answer emerging questions in agricultural research. Come meet our team and learn how Allegro provides high sample mulitplexing, the ability to interrogate over 100,000 SNPs in a single assay, and incredibly flexible design possibilities for targeting new markers.

Stop by our booth (#107) to learn about recent advances in genotyping, RNA-Seq and other NGS applications and of course collect some great PAG swag!

Check out our poster (#) "NuGEN’s Allegro Targeted Genotyping: A sensitive and cost-effective sequencing workflow for any genome." Presented by Michael Lovci, PhD Bioinformatics Scientist.

Join us for a workshop on Genotyping by NGS

Location: Royal Palm 5,6
When: 16 January 2018 - 1:30PM

1:30PM
Luke Sherlin

Director of Product Management

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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Luke Sherlin

Director of Product Management

Dr. Sherlin has been with NuGEN since 2010, and currently acts as the Director of Product Management. Prior to joining NuGEN, Luke was a Support and Technical Marketing manager at Phalanx Bio. He earned his Ph.D. at the University of California, Santa Barbara, in Biological Chemistry and performed post-doctoral research at Northwestern University prior to working in industry.

1:50PM
Samantha Beeson - Development of a predictive algorithm for recurrent exertional rhabdomyolysis in Thoroughbred and Standardbred racehorses

University of Minnesota, McCue Lab

Exertional rhabdomyolysis (ER) is a painful condition characterized by rapid-onset muscle cell necrosis and subsequent leakage of intracellular contents into the systemic circulation in response to exercise. Approximately 5-10% of Thoroughbred (TB) and 6% of Standardbred (STDB) racehorses suffer from recurrent exertional rhabdomyolysis (RER). Heritability for RER ranges from 0.34-0.42% in TBs and 0.39-0.45% in STDBs. Genome-wide association studies (GWAS) have identified nine genomic regions of interest (ROIs) significantly associated with RER in TB (n=491) and STDB (n=476) horses: two in TBs, six in STDBs, and one shared locus. In addition to 297 positional candidate genes located in GWAS ROIs, 2,115 biologic candidate genes for ER were identified by literature search, keyword-based gene prioritization, and use of publicly available differential gene expression data (36-gene overlap). Variants were identified from whole genome sequences (WGS) from 10 RER cases and 10 controls in each breed and imputed from low-density equine SNP array data in the entire GWAS cohort. Random forest (RF) feature importance scores for WGS variants were used to select potentially predictive variants in stages using window sizes of 50kb, 1Mb, chromosome, and genome. Based on allelic differences between cases and controls, location relative to positional and biologic candidate genes, predicted functional effect, and RF importance scores, 32,781 variants were selected for NuGEN Allegro targeted genotyping. Results from this analysis will be used to assess WGS imputation accuracy from low-density equine arrays and validate putative functional and predictive variants for RER susceptibility in TB and STDB racehorses.

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Samantha Beeson - Development of a predictive algorithm for recurrent exertional rhabdomyolysis in Thoroughbred and Standardbred racehorses

University of Minnesota, McCue Lab

Samantha Beeson is a dual DVM/PhD degree student at the University of Minnesota College of Veterinary Medicine. Her thesis work is focused on determining the genetic basis of recurrent exertional rhabdomyolysis (RER) in Thoroughbred and Standardbred racehorses. Additional projects she has been involved in include investigation of genetic determinants of gait in Standardbred horses, creation of a fine-scale recombination map for the domestic horse, and assessment of genotype imputation performance between low- and high-density equine SNP arrays. Outside of research, Sam has a passion for comedy and theater and spends much of her free time involved with improv and sketch comedy shows, both as a performer and behind-the-scenes. If Sam isn't busy analyzing genomes or stage managing a late night talk show, she's probably running, biking, or skiing. 

2:30PM
Jean-Philippe Pichon - Targeted Sequencing for Custom Genotyping

Research Coordinator, Plant Engineering Platform of Biogemma

High-throughput genotyping is a key tool for both research and breeding projects. For most species, especially for field crops, commercial arrays are now available. Although they surpass other technologies in terms of throughput and cost per plant, these arrays might be poorly adapted to specific material and dedicated development is unlikely to be gainful. In fact, more flexible formats permitting to address various ranges of SNPs and more appropriate sets of SNPs are highly desirable for some projects. Here we report the development or the implementation of high-throughput genotyping technologies based on targeted sequencing. We have first leveraged the Sequence Capture (SeqCap) to reduce the complexity of NGS libraries and to focus the sequencing effort on selected markers. Apart from reliability and robustness, the cost per plant remains the main driver for HT genotyping. To overcome SeqCap-based method limitations in this respect, we have assessed several generations of the Single Primer Enrichment Technology (SPET from NuGEN). Both SeqCap-based and PCR-based methods took advantage of the availability of reference genome, essential for probe and primer design, respectively.

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Jean-Philippe Pichon - Targeted Sequencing for Custom Genotyping

Research Coordinator, Plant Engineering Platform of Biogemma

<p>Jean-Philippe Pichon is the coordinator of the Plant Engineering Platform of Biogemma. Prior to the current position, he was project/team leader of the molecular biology core lab of the Upstream Genomic Group of Biogemma where he managed both the molecular characterizations of cereal transformants and the wet-lab genomic activities. As such, he contributed initially to the development of microarray-based transcriptomic studies and more recently to the NGS-based researches encompassing transcriptomics, genomics and epigenetics. He began to work in technology development and implementation as R&amp;D engineer in French start-ups (Nucleica and Apibio) involved in IVD. His career in genomics started at the Ecole Normale Supérieure de Lyon (UMR 2714 CNRS-bioMérieux) where he got is PhD working on the transcriptional activity of Human Endogenous Retroviruses in model system and cancer. In Biogemma, he has been involved in partnerships with private companies, for instance for the adaptation of the Sequence Capture to polyploïd species. He has been also involved in several national and European collaborative projects.</p>