Tag Archive for: Genomics

Wednesday, March 25, 2020 11:00 AM – 12:00 PM EDT

 

Summary

Even as sequencing costs decline, high-depth sequencing of the 7-17 Gbp wheat genome remains cost-prohibitive.  With the myBaits Expert Wheat Exome Panel, Daicel Arbor Biosciences provides the wheat research and breeding community a simple tool that reduces focused sequencing of the wheat high-confidence exome by more than an order of magnitude compared to whole genome sequencing. Based on the IWGSC RefSeq v1.0 reference genome, with a total target space of >200Mb, this is the most up-to-date panel currently available on the market for complete wheat exome sequencing.

In this webinar, Dr. Jacob Enk (R&D Manager for NGS at Daicel Arbor Biosciences) will present the latest performance developments of the Wheat Exome Panel, including its utility for hexaploid, tetraploid, and diploid cultivars of wheat, as well as upcoming complementary tools for targeted sequencing of exome-wide promoters and new exons as they are continually updated in RefSeq.

The myBaits Expert Wheat Exome Panel is available for immediate shipment from Daicel Arbor Biosciences, and can also be purchased as part of full-service NGS packages for library preparation, enrichment, sequencing and bioinformatics analysis. IWGSC members receive special discounted rates on all Wheat Exome kits and services.

Present by:

Dr. Jacob Enk
NGS R&D Manager
Daicel Arbor Biosciences

[ab_button text=”Register Here” link=”https://register.gotowebinar.com/register/1301270217479890445″]

LGC Biosearch Logo       

Ann Arbor, MI

Daicel Arbor Biosciences, a division of Chiral Technologies, Inc. and worldwide leader in next generation sequencing (NGS) target enrichment, today announced a partnership with Biosearch Technologies, the complete genomics portfolio of LGC Group. LGC Group was founded over 175 years ago, and today supplies products and services in the life sciences sector to improve human healthcare, agri-food technology, and the environment across the world. Together, the organizations will use their extensive resources for genetic testing and marker discovery to deliver custom sequencing solutions to the agrigenomics market.

Through the partnership, Biosearch Technologies will become the exclusive global provider of custom hybridization-based targeted sequencing oligonucleotide panels powered by myBaits technology to commercial agricultural organizations and seed breeding companies. Daicel Arbor Biosciences will maintain their strong presence in academic and government research laboratories by continuing to serve these researchers with catalog and custom panels. Overall, the partnership will allow Biosearch Technologies to leverage their established relationships with commercial organizations by delivering a complimentary technology necessary for marker discovery in crop sciences.

Alison Devault, Director of Genomics at Daicel Arbor Biosciences stated “Custom hybridization capture kits for targeted NGS have been our speciality for almost a decade, and perfectly complement LGC Biosearch’s robust expertise with genotyping assays for commercial ag-bio applications. We are truly excited for this partnership that will allow both parties to better serve key clients and provide innovative, complete NGS solutions for the entire ag-bio genomics market.”

Mark Dearden, VP of Strategy and Marketing at LGC, Biosearch Technologies commented “The addition of custom hybridization-based targeted sequencing panels to our portfolio adds a critical component to our NGS offering for the AgBio sector..  We are excited about taking this next step with Daicel Arbor Biosciences and will continue to invest to support our customer’s  mission critical applications.”

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About Daicel Arbor Biosciences

Daicel Arbor Biosciences, a division of Chiral Technologies, Inc. and a subsidiary of Daicel Corporation, is a development and manufacturing company founded by scientists to serve our peers in molecular biology applications. We are a passionate organization of scientists determined to deliver cost-effective, user-friendly products to researchers of genetics and synthetic biology. The team at Daicel Arbor Biosciences prides themselves on providing exceptional customer service and timely technical support to new or advanced users on our array of products. We routinely collaborate with our customers and research partners to develop innovative solutions to address their unique applications.

About LGC Biosearch Technologies

LGC is an international leader in the extended life sciences sector, including human healthcare, agri-food & the environment. LGC provides a comprehensive range of reference materials, proficiency testing schemes, and genomics reagents​, as well as research and measurement services. Its scientific tools and solutions enable organisations to advance research, develop new products and form an essential part of their quality and compliance procedures.

LGC’s 3,150 employees include internationally-recognised scientists who are experts in their field. Headquartered in London, it operates out of 19 countries worldwide and is extensively accredited to quality standards such as GMP, GLP, ISO 13485, ISO 17034, ISO 17043, ISO/IEC 17025 and ISO 9001.

LGC has been home to the UK Government Chemist for more than 100 years and is the UK National Measurement Laboratory and Designated Institute for chemical and bio measurement. LGC has been privately-owned since 1996 and has diversified through internal investment and acquisition to be an international leader in its chosen markets. LGC is now owned by funds affiliated with KKR.

For more information, please visit www.lgcgroup.com

Contact for Daicel Arbor Biosciences:
Michele Gentile
Daicel Arbor Biosciences

Contact for LGC, Biosearch Technologies:
Julian Quigley
LGC
Julian.quigley@lgcgroup.com
+44 20 8943 8491

Curio Logo

San Diego, California

Arbor Bioscience and Curio Genomics announced an exciting expansion of their existing partnership today at the 28th International Plant and Animal Genome conference in San Diego. The enhanced partnership promises to deliver a host of additional first-in-class products and solutions to the plant research and development community in commercial, as well as, non-profit foundations, consortia, and academic institutions.

With a potential deal value exceeding $1 million, the multiyear partnership leverages the core expertise and experience of each company to deliver cutting-edge, robust and comprehensive products for customers. Daicel Arbor Biosciences brings decades of combined expertise in NGS with novel advanced synthesis chemistry and expert scientific consulting to develop both catalog and custom targeted sequencing panels. Curio Genomics brings decades of experience in big-data commercial software platforms designed from the beginning for limitless scalability and extensibility, essential for genomic research with larger data sets, new types, and greater demand to integrative analyses each year.

“This is a transformative partnership for Curio,” said David Brabec, Curio’s Chief Business Officer. “We know that researchers, both commercial and academic, want and need solutions that are continuously cutting-edge, if we are going to continue feeding a growing world in a time when our climate is rapidly changing. Daicel Arbor Biosciences’ decades of combined scientific expertise in NGS and their track record of delighted customers was a key for us choosing them as our first major partner.”

“Curio is the perfect partner as we continue to expand Arbor’s solutions to enhance and simplify research for our customers,” said Arbor Bioscience’s Director of Genomics, Alison Devault. “The plant genomics space is an incredibly exciting business opportunity, but also a truly meaningful research space for translational and social impact. We are proud to be making such a visible commitment to this important and adapting market.”

Product Roadmap

The companies’ announcement included immediate plans to expand their existing and acclaimed wheat exome and complete genome analysis solution by fully integrating their current offerings by mid-2020 with new capabilities for wheat researchers, such assupport for RNA-Seq and methylation analysis, to be released later in 2020, and over the course of the multiyear partnership. The companies also announced immediate plans to co-develop products for additional species beyond wheat and will disclose these product plans at a later date.

“With Arbor’s decades of combined experience in NGS, we will leverage the power of the Curio® platform to provide whole genomic research teams a collaborative and endlessly extensible environment for real-time processing, analysis and interpretation of plant genomic data,” said Curio’s co-founder and CTO, Shawn Quinn. “We are excited to provide complete solutions for researchers from question to sample to insight and back again.”

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About Daicel Arbor Biosciences, Inc.

Daicel Arbor Biosciences, a division of Chiral Technologies, Inc. and a subsidiary of Daicel Corporation, is a development and manufacturing company founded by scientists to serve our peers in molecular biology applications. We are a passionate organization of scientists determined to deliver cost-effective, user-friendly products to researchers of genetics and synthetic biology. The team at Daicel Arbor Biosciences prides themselves on providing exceptional customer service and timely technical support to new or advanced users on our array of products. We routinely collaborate with our customers and research partners to develop innovative solutions to address their unique applications.

About Curio Genomics

Curio Genomics leverages its decades of big data commercial software development experience to provide the robust, rapidly extensible bioinformatics platform called Curio™. The guiding principle of Curio Genomics is that software should facilitate genomic research, not consume it. Through fully integrated partnerships with Next-Gen Sequencing leaders, Curio provides powerful, first-in-class product solutions that empower researchers from sample-to-insight. For information about Curio Genomics unique bioinformatics software platform, visit www.curiogenomics.com

Contact for Daicel Arbor Biosciences:

Michele Gentile
mgentile@arbor.daicel.com

Contact for Curio Genomics:

David Brabec
Curio Genomics
dbrabec@moxiegenomics.com
+1 734 726 7581

PAG XXVIII Website

Booth #308

San Diego, CA

Summary of Industry Workshops

Advances in Visualizing Genome Organization – from Haplotypes to Chromosomal Barcoding


James A. Birchler – University of Missouri
Whole chromosome paints have previously been developed for each chromosome of maize that rely on thousands of unique oligonucleotide probes along the length of each chromosome. This set is genotype independent and will label the respective chromosome across all tested maize lines. With the availability of genomic sequences for both B73 and Mo17 inbred lines, the ability to generate probe collections specific to those genotypes is available. Toward this end, Presence/Absence Variation (PAV) and SNPs were used for predicted oligos from one inbred sequence that were absent in the other and vice versa for chromosome 10 from the respective inbreds. The developed oligopaints were effective at distinguishing the two homologues of 10 in a B73/Mo17 hybrid. These haplotype specific probe sets were used to visualize recombination events from progeny of a B73/Mo17 hybrid and in Recombinant Inbred Line populations that fix recombination events from the two parental lines. Ongoing studies are examining the behavior of homologues in meiosis.

Kai Wang – Fujian Agriculture and Forestry University

Sugarcane (Saccharum spp., Poaceae) is a leading crop for sugar production providing 80% of the world’s sugar. However, the genetic and genomic complexities of this crop such as its high polyploidy level and highly variable chromosome numbers have significantly hindered the studies in deciphering the genomic structure and evolution of sugarcane. Here, oligo-FISH technology was optimized and a suitable system for sugarcane was established. The creation of oligo-FISH remarkably improves our ability to conduct cytological research on sugarcane, and bring us deep insights into the genomic structure and evolution of sugarcane.

Takayoshi Ishii – Arid Land Research Center, Tottori university

Andreas Houben – Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

We developed a tool to visualize defined genomic sequences in fixed nuclei and chromosomes based on a two-part guide RNA with the recombinant Cas9 endonucleasecomplex. In contrast to classical in situhybridization, RGEN-ISL (RNA-guided endonuclease – in situ labelling) does not require DNA denaturation and therefore permits a better structural chromatin preservation. The application of differentially labelled tracrRNAs allows the multiplexing of RGEN-ISL. We established a combination of RGEN-ISL, immuno-staining and EdU labelling to visualize in situ specific repeats, histone marks and DNA replication sites, respectively. The broad range of adaptability of RGEN-ISL to different temperatures and combinations of methods has the potential to advance the field of chromosome biology.

Complete Wheat Exome Analysis – From DNA to Variant Calling

Burkhard Steuernagel – The Sainsbury Laboratory and John Innes Centre

Disease resistance in plants is often conferred by members of a gene family that encode for intracellular receptors. These receptors have a nucleotide binding domain and leucine rich repeats (NLR). Resistance-gene Enrichment Sequencing (RenSeq) targets NLR genes and enables several cost-effective methods to identify such genes. We have designed RenSeq bait libraries for wheat and used them in combination with two complementary approaches. MutRenSeq deploys mutational genomics to target specific resistance genes. AgRenSeq is used for association genetics in a natural diversity panel. Both techniques have been used to identify several novel genes.

Shawn Quinn – Curio Genomics

As part of a collaboration with Daicel Arbor Biosciences the extensible Curio Genomics platform serves as the foundation that enables interpretive and real time analysis of NGS data generated from libraries that are enriched to focus on the high-confidence exon-annotated genome in hexaploid wheat.

In this talk we will demonstrate specific examples of how the platform scales to allow research partners to efficiently ask compound and complex bioinformatic questions of the massive genome of Chinese Spring Wheat samples. We’ll also show how the platform’s unique approach to the storage and processing of wheat genome data empowers researchers to conveniently collaborate with others, perform analyses, compare between samples, change analytical settings, apply different filters, and visualize results – all in real time.

Ute Baumann – The University of Adelaide

Posters Presentations from Daicel Arbor Biosciences & Collaborators

Multi-Cultivar Wheat Tetraploid and Hexaploid Exome Capture with a Single Enrichment Kit

Cannabis sativa Genotyping and Exon Sequencing Using a New Jamaican Lion-Derived Hybridization Capture Panel

SMRT-RenSeq for NLR Resistance Gene Characterization in Arachis, Glycine and Musa Species

Meiotic Crossovers Characterized by Haplotype- Specific Chromosome Painting in Maize

myTags® Synthetic FISH Probes Design Schemes for Plant and Animal Molecular Cytogenetics – Recombination, Translocation, Ploidy and Karyotyping Applications

Palaeochip: A Capture Enrichment Approach to Ancient Environmental DNA

Related Products & Services

myTagsmyTags Custom Fish Probes

myReadsmyReads NGS Services

myBaits myBaits Expert Wheat Exome Panel

myBaitsmyBaits Custom Panels

Ann Arbor, MI

Daicel Arbor Biosciences, a division of Chiral Technologies, Inc and worldwide leader in next generation sequencing (NGS) target enrichment, announces a partnership with Curio Genomics for bioinformatics analysis of the wheat genome. Arbor has an ongoing collaboration with the International Wheat Genome Sequencing Consortium (IWGSC), an international organization dedicated to developing a gold-standard reference genome for bread wheat cv. Chinese Spring, to provide IWGSC members with a standardized exome panel for research and development. Adding the Curio Genomics strategic partnership allows Daicel Arbor Biosciences to harness the power of the Curio Genomics platform in an end-to-end solution, from DNA to variant analysis, for wheat exome sequencing through their myReads® NGS services division.

The Curio Genomics platform streamlines bioinformatics analysis by moving beyond the typical pipeline approach of serial processes through parallel processing sequencing data. Curio’s ability to bring together both analytical processing and data visualization into a common toolset allows researchers to experiment and ask questions of the data in a very fluid fashion. Curio’s unique incremental and parallel approach to processing wheat exome samples allows users to compare, change analytical settings and, apply different filters all in real time with the results immediately at their fingertips.

“We are excited to partner with Daicel Arbor Biosciences and expand our genomics portfolio to include wheat and other agricultural crops.” stated David Brabec, Partner at Moxie Genomics (the company behind the Curio Genomics platform). “Our on-premise system is designed for large scale breeding organizations while our cloud-based solution delivers immediate access to wheat researchers across the globe”

Sequencing and analysis of the entire bread wheat genome is incredibly difficult and costly due to its enormous size, complex sub-genomes, and more than 85% of the genome being composed of repetitive elements. Daicel Arbor Biosciences initially reduced sequencing costs of each sample with the myBaits® Expert Wheat Exome capture panel the high-confidence exon-annotated genome in hexaploid wheat the resulting data with Curio’s platform.

“The IWGSC is committed to ensuring that the wheat breeders have state-of-the-art genomic resources. In this partnership, our members as well as the scientific community will benefit from having access to a unified analysis platform which streamlines data sharing and can facilitate comparative analyses across the consortium,” said Kellye Eversole, Executive Director of the IWGSC.

Daicel Arbor Biosciences is launching the full-service offering this month which includes the myBaitsÒ Expert Wheat Exome capture panel and Curio Genomics bioinformatics analysis through the myReads NGS services or as stand-alone products. The bioinformatics service provides whole genome alignment as well as variant calling from Chinese Spring or other cultivars of hexaploid wheat. Daicel Arbor Biosciences’ partnership with the IWGSC and Curio Genomics will continue as Arbor plans to develop new iterations of the exome panel and data analysis pipeline as further understanding of the wheat genome grows. Additionally, Daicel Arbor Biosciences is developing panels specific to disease and drought resistance for wheat researchers.

“The Curio platform delivers rapid processing of data in a user-friendly interface for our clients.” explained Jacob Enk, PhD, Senior Scientist at Daicel Arbor Biosciences. “We are proud to add this high-performance solution for IWGSC members and the wheat research community.”

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About Daicel Arbor Biosciences

Daicel Arbor Biosciences, a division of Chiral Technologies, Inc. and a subsidiary of Daicel Corporation, is a development and manufacturing company founded by scientists to serve our peers in molecular biology applications. We are a passionate organization of scientists determined to deliver cost-effective, user-friendly products to researchers of genetics and synthetic biology. The team at Daicel Arbor Biosciences prides themselves on providing exceptional customer service and timely technical support to new or advanced users on our array of products. We routinely collaborate with our customers and research partners to develop innovative solutions to address their unique applications.

About Curio Genomics

Curio Genomics’ proprietary parallelized bioinformatics platform enables unprecedented data processing speed. Intuitive and easy to use interfaces allow researchers to ask simple and complex questions simultaneously as the data is being processed providing extensive analytic versatility and power. This unique approach also allows complex questions to be asked across multiple samples and data sets, making it possible to share, query, annotate and comment on data in real time, empowering collaboration and distributed research. For information about Curio Genomics bioinformatics tools, visit www.curiogenomics.com

About the International Wheat Genome Sequencing Consortium

The IWGSC, with 2,400 members in 68 countries, is an international, collaborative consortium, established in 2005 by a group of wheat growers, plant scientists, and public and private breeders. The goal of the IWGSC is to make a high-quality genome sequence of bread wheat publicly available, in order to lay a foundation for basic research that will enable breeders to develop improved varieties. The IWGSC is a U.S. 501(c)(3) non-profit organization. www.wheatgenome.org

Contact for Daicel Arbor Biosciences:

Michele Gentile – Updated 1.18.21

mgentile@arbor.daicel.com

Contact for the IWGSC:page2image173303536

Isabelle Caugantpage2image173306032

IWGSC Communications Directorpage2image173309872

communications@wheatgenome.orgpage2image173313744

+1 916 840 8801

Twitter: @wheatgenome

Contact for Curio Genomics:

David Brabec

Moxie Genomics, Inc.
+1 734 726 7581

dbrabec@moxiegenomics.com