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ISSUE 2015-4
Genetics news from Neogen, a leader in food and animal safety and genomic solutions
Neogen GeneSeek Operations877-443-6489 (USA/Canada) • 402-435-0665 [email protected] • www.neogen.com
Neogen readies to introduce GGP-F250In collaboration with researchers at the University of Missouri, GeneSeek will soon bring a new solution to the cattle genomics community through the development of a functional variant genotyping chip known as the GGP-F250. This research-based chip was first developed to meet the needs of four United States Department of Agriculture (USDA) and National Institute of Food Agriculture (NIFA) projects that researcher Dr. Jerry Taylor and his team were working on. However, after discussing the chip with GeneSeek, they decided they would develop the project as a commercial product.
“GeneSeek has a very different business model compared to other genomic companies and still has the entrepreneurial spirit that it had as a small start-up,” Dr. Taylor said. “They saw the opportunity to deliver a product to the research community based on the development of our assay and it has been great working with a smart technical team and supportive, flexible business management team.”
Simply stated, GGP-F250 is composed of SNPs that researchers predict to have functional effects on proteins but they do not fully know what physical or disease trait(s) they may correspond to. The information gained from this chip will come from the data being correlated to the physical and disease traits of the animals on which it is run and will allow researchers to better understand which functional variants in a specific cow’s overall DNA cause differences in her fertility, feed efficiency and disease susceptibility.
“We are in the interesting position that we know where most of the common variants are in the bovine genome because researchers have sequenced the genomes of over 3,000 animals. However, other than the mutations that are within
genes, we have no idea as to which of the non-coding variants have regulatory functions. This will change
as the work to elucidate these regions is performed,” Dr. Taylor said. “I can see
these assays evolving from the current design which is very gene-centric, to include regulatory variants as they are discovered and the community will have access to a genotyping product that will enable research to identify which of these variants causes trait variation,” he added.
This work is important because the USDA and NIFA have invested a good
deal of funds over the last five years to elucidate the mechanisms underlying
reproductive loss, disease resistance and feed efficiency in beef and dairy cattle. Dr. Taylor explained
that these traits have been very difficult to improve through conventional breeding programs due to the cost or difficulty in obtaining phenotypes. However, if researchers can identify variants that directly cause variation in these traits they can be placed on low-cost genotyping platforms and used to facilitate genetic improvement of these traits in all animals regardless of their breed.
“I think this chip will be very useful for researchers worldwide and hope the community will form a consortium to generate future designs based on the functional annotation of the bovine genome that will occur in the next year,” Dr. Taylor said.
Partnership brings Ion Torrent technology to agriculture industryThrough GeneSeek’s partnership with Thermo Fisher, Ion Torrent technology is now more accessible to farmers and the agriculture industry than ever before. This state-of-the-art, DNA sequencing technology is used in other industries and will allow farmers the opportunity to greatly improve their livestock populations through innovative breeding programs that are based on hundreds to thousands of genetic traits.
“The old saying that ‘information is king’ really holds true for the adoption of GBS (genotyping-by-sequencing) for all applications including livestock breeding,” Dr. Christopher Adams, senior product manager at Thermo Fisher, said. “The benefit of technology improvement in general is the ability to make valuable decisions more quickly and easily, and implement beneficial changes more readily. In the case of agriculture, this is important because it will produce better animal populations faster, leading to higher food yields, more desirable products and more broadly accessible products.”
Because Thermo Fisher is a company focused on new technology development and commercialization, partnerships with companies like GeneSeek allow them to branch out into applied markets and use their technology to assist in real problems of high priority, Dr. Adams added. GeneSeek takes away the technical issues a customer would experience if they internally adopted and implemented this type of technology, creating a very multi-beneficial partnership.
In addition, the partnership allows Thermo Fisher to have readily available access to “real world” samples for testing and validation purposes, while GeneSeek is able to provide new data to their customers—ensuring the best solutions for
the agriculture industry as a whole.
“GeneSeek is pioneering the use of NGS (next-generation sequencing) for genotyping animals for improved breeding purposes and thus should be considered an industry leader and technology expert,” Dr. Adams said. “Adopting any new technology is a challenge especially one that is considered highly complex like NGS. GeneSeek’s willingness to stay on the cutting edge of science is a testament to their desire to stay one step ahead of their competitors.”
Greatly improve livestock populations through innovative breeding programs from GeneSeek.
GeneSeek earns Industry Partner Award from Red Angus
Red Angus breeders were pioneers in utilizing per-formance data and EPDs to make long-lasting and positive genetic improvement in their cattle. Now that genomics and DNA testing have exploded on the scene, the Red angus breed is moving forward with even more confidence in its ability to provide the right genetics at the right time.
To that end, the Red Angus Association of America (RAAA) recognized GeneSeek, Inc. as an important industry partner in the breed’s genetic improve-ment efforts. GeneSeek was presented with the Red Angus Industry Service award during the 2015 Red Angus Association of America National
Convention. Halla Pfeiff, RAAA DNA and breed im-provement projects coordinator, made the presen-tation to Jill Ginn, GeneSeek territory manager.
“Not only has this groundbreaking company taken immense genomic steps in the beef industry, they have defined the concept of customer service,” said Pfeiff. “Many hours have been spent working with the GeneSeek staff. They have assisted with problem solving different parentage scenarios, re-evaluation of samples and aided the development and implementation of genomic merit tests. Gen-eSeek is constantly increasing the number of tools available to their customers to help with any por-
tion of the DNA process. We are pleased to present them with this Industry Service Award.”
The Red Angus Association of America serves the beef industry by enhancing and promoting the competitive advantages of Red Angus and Red Angus-influenced cattle. RAAA provides commer-cial producers with the most objectively described cattle in the industry by seeking and implementing new technologies based on sound scientific prin-ciples that measure traits of economic importance.
For more information, visit redangus.org.
For the latest food safety, animal safety and life science news, Neogen announcements and useful information, check out the Neogen blog at www.neogen.com/blog
Genomics Sales Representative
Reporting to the Director of Sales, the successful candidate will help grow the sales of existing genomic products in assigned market segments and should have experience in agriculture/animal production and a background in mo-lecular biology. Working independently and as part of a team, they should also have a strong drive to collaborate with customers to find solutions to their genomics needs, focused on the GeneSeek mission of high quality and afford-able genotyping. The ideal candidate is comfortable working with the technical staff in agri-businesses to develop and implement comprehensive solutions for genomics, as well as interfacing with researchers and their projects.
Responsibilities include positioning Neogen as a serious participant in the suc-cessful sales and marketing of genomic-based services and diagnostics to the agricultural biotechnology industry as well as preparing comprehensive plans for business development in target sectors. The position is also responsible for coordinating technical support and customer service issues with the techni-cal service department and will work with the marketing department to keep management up todate on market conditions.
Education and/or Experience: Bachelor’s degree in biological sciences from an accredited four-year college or university; knowledge of genomic (genotyp-ing, next generation sequencing technologies) market segments. Business-to-business sales experience and business/marketing management experience is desired as well as experience/exposure to animal breeding/genetics, diagnos-tic testing, or genomic analysis.
Contact Jeremy Walker at [email protected] or 402-435-0665, or visit www.neogen.com for more information.
Career opportunities at Neogen’s GeneSeek OperationsNeogen Corporation continues to grow as a global leader in food safety and animal safety technologies with more than 1,000 employees. We are always looking for talented individuals and appreciate your interest in contributing to our success.
Laboratory Technicians
GeneSeek has a number of openings for lab techs. If you are currently finishing up your educational program, working in a lab, or you have students looking for work, we welcome applications at neogen.com. As part of the GeneSeek team you will perform laboratory tests and services to support customer data generation through sample processing and DNA extraction. The range of duties include sample and reagent preparation, DNA extraction and isolation, quality analysis prior to genotyping, analysis of reagents for performance, and other related tasks.
As part of the team, the ideal candidate should be are proficient in a variety of molecular biological techniques, and reliably follow established SOPs ac-curately to support ISO and GLP processes. They should also have the ability to maintain laboratory notebooks, sample archives and sample or specimen repository. In addition to sample processing, the candidate will contribute to maintaining the laboratory including ordering supplies and equipment, cali-brating instruments, performing preventive maintenance and assuring a clean and safe environment. In our team, we emphasize assistance in training new staff to better manage laboratory workload and provide suggestions that will maximize laboratory efficiency.
Education and/or Experience: Associate’s degree (A.A. or A.S.) in science or lab related field; or 1–2 years related experience and/or training; or equivalent combination of education and experience. Bachelor’s degree (B.S. or B.A.) or other advanced degree (M.S. or Ph.D.) is preferred.
Apply at www.neogen.com.
Get social: Neogen is also on Facebook, Twitter, YouTube, LinkedIn and Instagram. #geneseek
Neogen Canada opens to assist Canadian GeneSeek customersThe increasing popularity of GeneSeek’s agrigenomic services in Canada, including the GeneSeek® Genomic Profiler and Igenity® Profile for Beef and Dairy Cattle, has led to the opening of Neogen Canada. Neogen’s new location will focus initially on further enhancing the access to GeneSeek’s genomic services for Canadian customers.
“It became increasingly obvious that we needed to expand our presence in Canada to provide our Canadian customers with the same easy access to advanced genomic services as our customers in the U.S.,” said Dr. Stewart Bauck, general manager of Neogen’s GeneSeek operations. “Our new location will provide our Canadian custom-ers the same access to the technology, and also offer all the benefits of dealing directly with a Canadian location—including avoiding the requirements of shipping biological samples internationally, as well as invoicing in Canadian dollars.”
Effective immediately, GeneSeek’s Canadian customers can directly contact Neogen Canada on everything GeneSeek related, including the shipping of samples, billing, and technical support issues. Neogen Canada’s contact and shipping information:
Neogen Canada21 College Ave W • Guelph, ON N1G 1R7
Phone: 226-780-0267 • E-mail: [email protected]
For more information, visit www.neogen.com/genomics.
© Neogen Corporation, 2015. Neogen markets a complete line of food and animal safety solutions, and is a publicly-owned company listed on the Nasdaq Stock Market under the symbol NEOG.
Neogen GeneSeek Operations4131 N. 48th Street • Lincoln, NE 68504877-443-6489 (USA/Canada) • 402-435-0665 [email protected] • www.neogen.com
From the desk of Dr. Stewart BauckTechnology at GeneSeek
The past 17 years at GeneSeek has seen a major evolution in technology platforms as the science of genomics has changed rap-idly and technology providers have brought out ever more powerful tools. The early days featured heavy reliance on LiCor and ABI sequencers, particularly for micro-satellite
based parentage support for the breed associations. As time has moved on, and particularly following the development of the USDA bovine parent-age panel, the use of gel-based sequencing has declined significantly but remains a relevant part of our service portfolio, for its utility in the detection of large deletions associated with various genetic defect tests.
The first major genotyping platform for multiplexed SNP detection was the Sequenom (now Agena) Mass Array and up to the time period of launch of the Illumina arrays, the MALDI-TOF machines were the gold standard for routine SNP genotyping. With a focus on marker-assisted selection (MAS) or parentage panels for SNP numbers up to approximately 400 in a single product, this platform was—and still is—a major part of our daily workflow.
The significant revolution in animal genotyping came about in 2007 with the launch of the Illumina Bovine SNP 50 which ushered in the era of high density genotyping and quickly established Illumina as a major platform for our routine sample genotyping. Along with Illumina, GeneSeek also supports the Affymetrix Gene Titan giving us several options across the spectrum of arrays ranging from as small as 3,000 SNP, up to numbers approaching 800,000 SNP.
The latest additions to the solutions available to our customers was the intro-duction of next generation sequencers including the MiSeq, the Ion Torrent and the NextSeq, giving us capability for projects ranging from as little as 20 M reads, up to 400 M reads, suitable for whole genome sequencing. This technology represents a paradigm shift and, while in its early days, it offers the prospects of additional improvements in cost and quality for customers.
Finally, any discussion of technology at GeneSeek wouldn’t be complete without a nod to the changes in bio-informatics. This includes the installation of BC Platforms as a data management system for routine genotype storage and manipulation. (We do generate a large amount of data!) Coupled with that was the establishment of a server cluster tied together by the CONDOR network computing system, which allows us to provide analytics for custom-ers that want a more integrated solution for their data needs.
There is no shortage of fun things for our scientists to work with and we constantly strive to balance the need for a diversity of solutions to serve all of our customer’s needs, against the challenge of supporting all of the vari-ous platforms. So far, we believe we have the right balance, but one never knows what tomorrow will bring—there is one thing in our business that is a constant and that is change!
GeneSeek now certified to conduct Johne’s testingMycobacterium avium subspecies paratuberculosis (MAP) is a worrisome pathogen that causes a chronic, progressive granu-lomatous enteritis known as Johne’s disease or paratuberculo-sis in a diverse range of both ruminant and non-ruminant hosts.
The disease is endemic in many parts of the world and respon-sible for considerable losses to the livestock and associated in-dustries. Diagnosis and control are problematic, mostly due to the long incubation period of the disease. In addition, infected animals show no clinical signs making it difficult to detect. The organism also has the ability to survive and persist in the envi-ronment within soil and water.
When cattle become infected with MAP, Johne’s disease usually does not develop until years later. During this silent pre-disease period, cattle start shedding the bacteria within their feces, thereby progressively contaminating the environment. Then, once infection has progressed into disease, animals show non-responsive diarrhea and experience weight loss. Since there is no cure available, high culling rates and poor performance ac-cumulate to significant economic losses in herds that are posi-tive for MAP.
To combat this, early detection is key and the USDA/APHIS Na-tional Veterinary Services Laboratory (NVSL) offers a proficiency test for laboratories for the detection of the pathogen. Recently, GeneSeek has successfully completed the MAP PCR proficiency test, both for the individual animals and for pools of five.
Since the GeneSeek VDX lab has shown that the methods em-ployed meet the NVSL federal quality standard for proficiency, the lab is now certified to conduct Johne’s testing. GeneSeek is planning to make the testing service available to U.S. producers yet this year, so please stay tuned for more information to come.
