ISSUE 2016-3

Genetics news from Neogen, a leader in food and animal safety and genomic solutions

Neogen GeneSeek Operations877-443-6489 (USA/Canada) • 402-435-0665 geneseekinfo@neogen.com • www.neogen.com

GeneSeek has been providing parentage profile services to canine kennel clubs and registries, both large and small, for a number of years. Traditionally, canine parentage testing has been based off microsatellite (STR) markers as is the case in many other species and identification profiles for parentage analysis based on STR markers consist of 13–22 different markers.

Although STR markers have been used for many years in both agricultural species and human databases, the technology presents inherent challenges. Analysis of the markers is very “hands-on” and is not well suited for automation due to the difficulty in allele size calling. This can introduce inconsistencies and possible errors, resulting in overall poor reproducibility.

STR markers also present challenges because there are relatively few markers included in a panel. In some situations, the STR panel does not include enough markers to discern parentage in cases with closely related sires and in addition, the panel may not be well suited for parentage determination in breeds with less genetic diversity.

In addition to parentage, dog breeders and owners are showing an increased interest in genetic health predictions that can be derived from genomic data. The introduction of an identification profile based on single nucleotide polymorphisms (SNPs), would provide a set of markers more suitable to automation and increase consistency and reliability of results, for better parentage analysis across breeds.

SNP testing technology platforms also provide the opportunity to gain more knowledge from a single sample submission and tests that could be used to increase health awareness and produce desirable traits with well-planned breeding strategies.

GeneSeek has analyzed a selected set of SNP markers from over 6,000 canine samples genotyped on the Illumina Infinium® CanineHD BeadChip1. The minor allele frequencies of these markers were determined across the 112 breeds represented and nearly 180 trios2

were examined using the SNP markers. Based on this analysis, 200 of the most informative markers across breeds were chosen to be presented at the 2016 International Society of Animal Genetics (ISAG) Meeting in Salt Lake City, Utah.

The sequences of these markers will be made available to labs interested in performing testing for a comparison study and results will be presented at the 2017 ISAG meeting in Dublin, Ireland. GeneSeek will be facilitating the transition from STR-based parentage testing to SNP-based testing for the American Kennel Club early this fall, paving the way for the introduction of this new profile on a larger scale.

If you are interested in learning more about the SNP parentage profile or obtaining sequence information, contact Lindsey Kock, DVM at LKock@neogen.com.

1. D. Bannasch, University of California Davis, Davis, CA, USA. A. Boyko, Cornell University, Ithaca, NY, USA.

2. J. Donner, Genoscoper Laboratories, Helsinki, Finland. C. Cole, S. Davison, Mars Veterinary, Portland, OR, USA. M. Dunn, American Kennel Club, Raleigh, NC, USA.

Canine SNP Parentage Profile

GeneSeek was a sponsor of the recent Nebraska Cattlemen’s Ball, a fundraiser for University of Nebraska Medical Center cancer research. GeneSeek donated DNA testing kits for the live auction, which were won by Bill and Barb Rishel of Rishel Angus (pictured above right with GeneSeek’s Dr. Stewart Bauck). The ball was held on a ranch south of Lincoln and about 4,000 visitors attended to hear music and contribute to cancer research. The volunteering effort has raised millions of dollars for UNMC cancer studies over the years.

When it comes to genomic services, it’s easy to focus on the technology rather than the people behind the results. At Neogen’s GeneSeek® subsidiary there are many different departments and specially trained employees that help to fulfill the mission of the company and provide customers with accurate and timely information each and every day.

One area at GeneSeek that rarely receives the credit they deserve, is the customer support team. Day in and day out, these individuals work hard to manage customer inquiries received by phone, email and on occasion, in person. Due to the nature of their duties, they are required to understand the entire cycle of a sample, from the initial sample collection, to submission and processing, to finishing the sample and delivering the results report to the customer.

“Customer support has the benefit of working with all the departments within GeneSeek, so we are able to assist customers with the variety of questions about genetic testing,” Stephanie Schuler, customer support team member said. “Having a team dedicated to this is somewhat rare in the industry and really sets GeneSeek apart from others.”

The team’s duties begin from the moment a sample is received. Oftentimes, they receive samples that do not have any information regarding how they are to be processed, Stephanie explained. “To keep turnaround time at a minimum, we aim to reach out to the customer in a timely manner in an attempt to gather the necessary information required to begin processing their samples. This can often be a challenge, as in most cases we only have a return address to go off, if we’re lucky.”

Another important role of the customer support team is requesting the proper permissions from customers on behalf of other customers for chain of custody. Commercial cattle producers often provide new owners of their cattle with a copy of the Igenity or GeneSeek result report they obtained for the animal. Later, the new owner may decide to run additional testing on the animal they purchased. When they reach out to GeneSeek, the customer support team confirms with the original owner that the new owner did in fact purchase the animal and that they have permission to use the sample they

initially submitted. This provides each customer extra security knowing their data is being utilized by only those who have their explicit permission.

“The service that we provide our customers is always appreciated. New customers especially enjoy receiving the required information to begin submitting samples for genetic testing, and are always excited to see what their GeneSeek or Igenity results revealed about their breeding program,” Stephanie said. “It is astonishing to watch the exponential growth of the genomic industry from the heart of it all here at Neogen, and the commitment of service that we are able to provide gives us the upper hand when

compared against our competitors.”

For example, last February during winter storm Kayla, the team was up and operating, turning out data, with some customers coming by to pick up sampling supplies when other businesses were closed.

“We understand the results we provide can change the path of a customer’s operation and it’s important to communicate this information efficiently,” Stephanie said. “It’s going to take more than a little winter storm to affect the dedication we have to our customers.”

GeneSeek provides industry leading customer support team

Visit GeneSeek at the 4th Plant Genomics Congress USA, September 12–13, 2016 in Philadelphia, Pennsylvania.

Data Analyst I

The GeneSeek Data Group is currently seeking candidates for a Data Analyst 1 position. The ideal candidate will possess a science based degree with a gen-eral understanding of animal science and genomics. Candidates must have the ability to learn and integrate unique software programs with common labora-tory protocols. The selected candidate will be responsible for quality control, report generation and customer support from an international customer base. The position is ideal for those who thrive in a fast paced environment. Complete training will be provided.

Education and/or Experience: Bachelor’s degree from four-year college or university in genetics, molecular biology, biology, bioinformatics or related field.

Apply at careers.neogen.com

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 TechniciansGeneSeek 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 proficient in a variety of molecular biological techniques, and reliably follow established SOPs accu-rately 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 careers.neogen.com

Barley Illumina iSelect 50k SNPchip coming soonA new Illumina barley 50K SNP chip has been developed by researchers at the James Hutton Institute (Dundee, Scotland) and their collaborators in the international barley research community. Following generation of a new barley genome reference and screening of large exome capture datasets, it has been possible to significantly improve variant representation and increase the SNP content of the established 9K SNP chip.

Neogen’s GeneSeek has worked with the James Hutton Institute and Illumina on the design of the chip and will be running samples on behalf of Hutton researchers over the coming months for their ongoing research project needs. GeneSeek would also be pleased to run this chip on behalf of any other groups within the barley consortium who may have an interest in this area.

Overall, Barley is the world’s fourth most important cereal crop, both in terms of area of cultivation and in quantity of grain produced. In addition to whiskey and beer, barley is also a major component of the animal feed that underpins the meat and dairy industries.

Barley straw is a source of nutrition for ruminants, used for animal bedding in the winter, and used for frost protection in horticulture.

In 2012, an international consortium of scientists published a high resolution draft of the barley genome which has helped produce new and better barley varieties that are vital for the industries mentioned above.

The breakthrough was a critical step towards barley varieties able to cope with the demands of climate change and the fight against cereal crop diseases that cause millions of pounds of losses annually.

The barley genome is almost twice the size of that of humans and determining the sequence of its DNA has presented a major challenge. This is largely because its genome contains a large proportion of closely related sequences that are difficult to piece together into a true linear order.

For more information on extensive options for plant genotyping, visit genomics.neogen.com/en/plant.

Visit GeneSeek at the World Dairy Expo, Booth EH 3613, from October 4–8, 2016 in Madison, Wisconsin.

© Neogen Corporation, 2016. 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 geneseekinfo@neogen.com • www.neogen.com

From the desk of Dr. Stewart BauckSometimes the smallest things can have big impacts.

At GeneSeek, we place a large emphasis on our core mission of providing high quality, ac-curate and cost-effective solutions for agricul-tural genotyping. While this consumes most of our daily time and attention, we also have to

focus on the business side, including our interaction with customers and their overall experience when it comes to working with GeneSeek.

As most of our customers know, the engine that drives the heart of our daily activity is the LIMS or Laboratory Information Management System. LIMS was developed to support and manage the samples we receive, in-cluding the overall work flow and processes, as well as the data reporting. LIMS is an integral part of how we manage our business and until recently, our LIMS system never communicated with our billing system, which is based on Solomon from Microsoft.

Although there were a variety of very good reasons for this, the conse-quence was that the billing process at the end of the month was compli-cated and resulted in errors requiring credits and re-billing.

To address the issue, GeneSeek’s operations team (led by Tim Mitchell), our finance team (led by Krista Potter) and our programming team (led by Adam McQuistan) set out in late fall of 2015 to create a new inter-face that would implement a real time data transfer between LIMS and Solomon. The goal was to track every sample and the associated tests, properly apply the correct product code or SKU, and implement the cost for our customers by the time it was finished processing.

The benefit to customers was focused on timely and accurate billing, im-proved transparency on the tests conducted and alignment to the orders submitted and tracked in LIMS. The new system went live in May and we are pleased to report it has been running smoothly. As expected with any change of this magnitude, some issues have invariably arisen, but have been dealt with promptly to apply permanent fixes.

As much as practically possible, we strive to ensure consistency to previ-ous reports. Detailed reports have been created in LIMS to assist custom-ers in reconciling between their batch submissions and the consolidated invoice, to help them in tracking their customer submissions. We encour-age our customers to contact us with feedback to let us know how we are meeting their needs.

It may seem like a small thing, and for most people focused on data de-livery, quality and turnaround time, discussions on billing and finance are probably not their favorite topic. But for our team this is an important new development and we are confident that it was worth every minute spent to get this project complete.

Originally beginning her Neogen career with our animal safety divi-sion in Lexington, Kentucky, Laurel Mastro came to Neogen in 2014 to manage the animal safety diag-nostics product line. While many of the 2,700 products in this area are ELISA test kits, she also worked frequently with Neogen’s animal genomics brand Igenity®.

One of the projects she began helping with was GeneSeek’s Igenity Dairy Heifer Program, which she said soon found to be consuming most of her time and quickly turned into a full-time job in itself.

“To me, genomics was always the most interesting technology that I worked with, so I never complained when it began taking over my job,” Laurel said. “It’s such exciting work because you can see the changes that occur on the commercial dairy from using genomics, and many commercial dairymen today are now seeing the value that genomics can have on their operations.”

Based on her work and passion for the job, in June of 2015 she was asked to join Neogen’s team in Lincoln and manage the dairy genomics segment full-time—to which she said she quickly accepted.

Now, just over a year later, Laurel said her position has continued to grow immensely and has required her to assist with all areas of dairy genomics including working with breed associations, AI studs and end users. Through her work she said it is this diverse client base she enjoys the most as well as traveling to industry events where she can showcase the work Neogen is doing in the field of animal genomics.

“The growth this industry has experienced in just the short time I have been a part of it is incredible,” Laurel said. “Genomics allows producers to select better cows, and leads to greater profitability on dairy farms. Ultimately, if we can select better cows we can cre-ate more dairy products for the world’s growing population. That’s a pretty cool industry to be a part of.”

In her free time you can find Laurel enjoying the outdoors, rock climbing or practicing yoga. She enjoys hanging out with her family and friends—along with her cat, Elizabeth, or Queen Elizabeth as she prefers to be called.

Featured employee: Laurel MastroGeneSeek Product Manager, Dairy Genomics