Genomic SNPettes - Neogen Genomics

ISSUE 2015-1
Genetics news from Neogen, a leader in food and animal safety and genomic solutions
Neogen introduces new genomic profiler for seedstock
Beef and dairy seedstock producers have a new option for DNA profiling that adds tens of thousands of gene markers to tests they use to
predict cattle performance.
detection of the male Y chromosome in female DNA. Recent findings
at the USDA Meat Animal Research Center have linked this condition
to cow infertility.
Neogen is introducing a new GeneSeek® Genomic Profiler™, the GGP
HD Bovine 150K. This tool screens cattle DNA for about 150,000
gene-marker variations linked to important traits in breeding stock for
increased genomic selection power. It also includes disease markers,
Igenity Profiles and other performance trait SNPs.
While female fertility is considered moderately heritable, open cows
are a large drag on ranch profit, so using genomics to achieve even
modest improvements are quite impactful, he said. In other situations,
breeders raise bulls with goals of improving daily gain or carcass com-
“Adding markers increases accuracy in predictive power, but adding the
right markers is just as important. How you design the product matters
a great deal,” said Dr. Stewart Bauck, general manager of Neogen’s
GeneSeek operations. “By working in collaboration with USDA experts
and independent researchers, GeneSeek has created the new GGP HD
Bovine 150K, which is the most powerful new profile for seedstock
selection on the market.”
Seedstock producers use genomic profiling to select, manage and
market cattle breeding stock. Profile data on bulls, and some elite
females, are used to calculate Genomic-Enhanced Expected Progeny Differences (GE-EPDs) or Genomic Predicted Transmitting Ability
(G-PTA). These rate how seedstock will pass along maternal, performance and carcass traits to their offspring.
“With GE-EPDs or G-PTAs, a seedstock provider can evaluate the future
value of a potential sire soon after it is born. They can get reliable
information that otherwise would take years to obtain. This helps them
focus their time, money and reputation on marketing seedstock of verified genomic merit,” Bauck said. “The insight also helps accentuate the
advantages and potential specialization of their bulls with customers.”
DNA testing is all about the value of time, Bauck explained. “If you wait
long enough, you can measure how a sire’s offspring perform. But
years may pass before you have progeny data on cow fertility. By then,
the bull has influenced four calf crops,” Bauck said. GE-EPDs give bull
buyers accurate information on these characteristics up front.
“We also have added new content for genetic conditions that are
emerging in the latest science,” he said. An example, he added, is
Genomics can aid in
breeding healthy, high
performing calves.
position, and genomic profiles help them deliver on these values.
The GGP HD Bovine 150K will be available through breed associations
including Angus Genetics Inc., where it will replace the GGP HD-80K.
It will also be used by other breed associations and researchers profiling elite seedstock and training populations. Associations are already
offering the GGP LD-30K, which has over 25,000 markers in use for
routine profiling of herd bulls. Neogen and GeneSeek also employ
state-of-the-art tools for data management and bioinformatics, ensuring easy access of data in the format that best fits your needs.
“The technology for cattle genomics continues to advance. The trend
is towards more powerful, and also more affordable, tests that have
increasing impact on future profits and performance,” Bauck said.
Neogen GeneSeek Operations
877-443-6489 (USA/Canada) • 402-435-0665
[email protected] • www.neogen.com
Microbiological testing with
16S Amplicon Sequencing
Neogen Corporation is a world leader in food safety and GeneSeek is harnessing its new
sequencing capability to assist in tool development. With the recent acquisition of the Illumina
MiSeq, GeneSeek and Neogen are greatly expanding their food safety tool kit. The MiSeq
system employs illumina sequencing by synthesis technology (SBS), the most widely used,
proven next-generation sequencing chemistry, making it an ideal platform for performing
rapid and cost-effective genetic analysis.
Scientist Jaehyoung Kim is involved in a 16S Amplicon Sequencing project using the MiSeq system. He describes his work below.
“16S ribosomal RNA (rRNA) sequencing is a common sequencing method used to identify and compare bacteria present within a given sample. 16S
rRNA gene sequencing is a well-established method for studying the microbial content, phylogeny and taxonomy of samples from complex microbiomes that are difficult or impossible to study via other biochemical methods.
“With the ability to combine many samples in a sequencing run, 16S rRNA sequencing now can serve as a cost-effective technique to identify bacterial strains that may not be found using other methods, something that is critical in protecting human safety in face of foodborne illness.
“We are targeting the variable V3 and V4 regions of the 16S rRNA gene. Custom-designed sample barcode allows us to multiplex hundreds of
samples in a single MiSeq run and has allowed us to sequence hundreds of food samples and environmental samples simultaneously.”
Dr. Ronald Green joins Neogen’s Board of Directors
Neogen Corporation announced recently
that Dr. Ronald Green has been named to
Neogen’s Board of Directors.
Dr. Green is vice president of Agriculture
and Natural Resources of the University
of Nebraska system, and vice chancellor
of the Institute of Agriculture and Natural
Resources at the University of NebraskaLincoln. In the positions, he leads all programs in agriculture and natural resources in the University of Nebraska’s system
of five campuses, including oversight of
a $206 million budget and 1,957 employees in teaching, research and
extension programs.
“Since our founding in 1982, a strength of Neogen has been the quality
of individuals on our Board of Directors, and the addition of Dr. Green
certainly continues that tradition,” said James Herbert, Neogen’s chief
executive officer and chairman. “Our Board provides valuable oversight,
advice and support to senior management based on relevant experience
gained in their personal careers.”
Prior to joining the University of Nebraska in July 2010, Dr. Green served
as the senior director of Pfizer Animal Health overseeing global technical
services for Animal Genetics.
Dr. Green has served on the animal science faculties of Texas Tech
University (1989–1994) and Colorado State University (1994–2000),
reaching the rank of full professor in 1997. He has been recognized
with a number of distinguished local, regional and national teaching
and research awards for the work he led with 25 Ph.D. and M.S.
students and colleagues in beef cattle breeding and genetics in those
positions.
From 2003–2008, Dr. Green served as the national program leader
for animal production research for the USDA’s Agricultural Research
Service and as the executive secretary of the White House’s interagency working group on animal genomics within the National Science and Technology Council. In this role he directed a $45 million
annual research portfolio and was one of the principal leaders in the
international bovine, porcine, and ovine genome projects.
Neogen Corporation develops and markets products dedicated to
food and animal safety. The company’s Food Safety Division markets
dehydrated culture media and diagnostic test kits to detect foodborne
bacteria, natural toxins, food allergens, drug residues, plant diseases
and sanitation concerns. Neogen’s Animal Safety Division is a leader
in the development of animal genomics along with the manufacturing
and distribution of a variety of animal healthcare products, including diagnostics, pharmaceuticals, veterinary instruments, wound care
and disinfectants.
In today’s cattle business, demand is growing for accurate DNA profiling. Our stateof-the-art genomics lab is designed to deliver this advantage. GeneSeek processes
over one million DNA samples per year, making us the world’s largest genotyping
agribusiness. We are owned by Neogen Corporation, which is investing significantly
in technology that makes DNA testing affordable and easy for you. Our door is open
for visitors, so if you are curious to see what we do, we invite you to stop by.
Porcine Epidemic Diarrhea Virus (PEDV) and
Porcine Deltacoronavirus (PDCoV)
After PEDV was officially confirmed to have entered the U.S. in May of 2013, it
spread very rapidly. With the mortality rate approaching 100% in the very young
piglets it infected, and continues to infect, significant losses to the swine industry
have been experienced. The Veterinary Diagnostics group at GeneSeek already
provided rapid screening tests for various porcine diseases and with the announcement of PEDV, they immediately sprang into action.
The main route of PEDV transmission is fecal-oral which is greatly facilitated by
contaminated trucks, trailers, fomites, and people tracking the virus. Additionally, it
has been shown that PEDV can become airborne and that the virus particles can
remain infectious in the air long enough to consider airborne PEDV as potential
transmission route.
Hypertrophic cardiomyopathy
in cats
As of February 2015, there were 33 states with at least one confirmed positive
case of PEDV. Other than supportive care, there is no effective treatment available
and there are very few vaccines currently on the market.
Some cats suffer from an inherited heart disease
known as hypertrophic cardiomyopathy. The cause
of the disease is unknown, but hereditary factors are
thought to play a role in its development.
Humans also suffer from this disease, which causes
the heart muscle to thicken and as a result, blood
flow is interrupted. This causes other organs in the
body to work much harder, and can lead to a number of problems including blood clots, or thrombosis,
and congestive heart failure.
Hypertrophic cardiomyopathy can occur very early in
the cat’s life, and is sometimes seen even in kittens.
While the disease is often fatal, some cats are able
to live comfortably on medication.
In an effort to learn more about this disease, Kathryn
M. Meurs, DVM, PhD, associate dean of research
and graduate studies program at North Carolina
State College of Veterinary Medicine, has performed
whole genome sequencing on four affected cats
and on several unaffected cats as well. From her research she was able to identify thousands of variants,
which she is currently trying to sort through.
From this research, Kathryn is trying to identify the
causative variant, which will be done by evaluating
additional affected and unaffected cats with Sequenom assays at GeneSeek and looking at the highest
priority variants.
In the wake of the PEDV epidemic, another virus emerged known as Porcine
Deltacoronavirus (PDCoV). In order to distinguish between the two viruses, diagnostic testing is necessary, which GeneSeek offers for both PEDV and PDCoV.
Very similar to PEDV detection, any confirmed diagnosis of PDCoV is also reportable to USDA Veterinary Services and submissions for testing are required to have
the premise ID listed.
Fecal material, rectal swabs, environmental samples (Swiffer wipes or swabs),
and oral fluids are all sample types GeneSeek accepts for PEDV and PDCoV
testing. Test results can be received in the same day for for PEDV and the following day for PDCoV. If there are any questions regarding the acceptance of
different sample types, please contact Neogen.
Once complete, this research will help cats live longer, happier lives and provide more information on
hypertrophic cardiomyopathy in humans.
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
From the desk of
Dr. Stewart Bauck
It seems like only yesterday, but
it has been nearly a year since
GeneSeek moved from its offices in
the Technology Park of the University of Nebraska in Lincoln, to our current location at 4131 North 48th St.
Since its inception in 1998, GeneSeek had been a tenant of the Technology Park, an incubator space
that is designed for start-up companies. As we grew however, we
managed to take over the space and by the fall of 2013, we were
a bit like hobbits–each group occupying its own little space with
limited capability for efficient sample flow.
We needed to change and with the help of our corporate group in
Lansing, we began the search for a potential new home. Time was
pressing so the smart choice was to take possession of an existing
building and retrofit it to our needs—which is exactly what we did.
Featured employee: Jeremy Walker
Business development and marketing lead for the
GeneSeek business to business unit
Born and raised in Lincoln, Jeremy holds a bachelor’s of science degree in biology from Nebraska Wesleyan University and
a master’s of science in cell and molecular biology from the
University of Nebraska.
Jeremy has spent his entire professional career working in the
genomics sector, and prior to coming to GeneSeek in 2002,
was a Genotype Application Scientist at Li-Cor Biotechnology
in Lincoln and then at Sequenom in San Diego.
For the past 13 years Jeremy has excelled in his position at
GeneSeek and has been involved with several areas of the
business including lab processing, application/product development, application and product customer support, data informatics, business development, and marketing.
The GeneSeek team got a blank slate and designed a custom-built,
state-of-the-art genotyping lab, grounded on more than 15 years
of experience and with an eye to the future. Had you walked into
the new building this time last year, you would have seen teams
of workers simultaneously dismantling the interior of the building,
while others were in the process of constructing a whole new design
according to our specifications.
The challenge was large—design and build the new space while
maintaining production, and at some point, transition the entire operation without interruption so that customers experienced
no delays.
We huddled with our suppliers and crafted a plan to sequentially take
down, move, reinstall, and test equipment over a long weekend in
April 2014. Then, between Thursday night and Tuesday morning of
the following week, we managed to make it happen and everything
worked flawlessly.
This was a testament to the team led by Tim Mitchell, the operations
manager, and we couldn’t be more pleased. The design has allowed
us to accommodate a 30% increase in volume while actually reducing turn around time. Also, the new location was ready just in time
to host the Beef Improvement Federation meeting, which was a real
delight for us to show customers where their samples go each day.
If you happen to be coming through Lincoln and want to see what
a world class genotyping lab looks like, duck off I-80 and come see
us. The (new!) door is always open.
“I have enjoyed the ability to wear many hats in the growth
of GeneSeek and the opportunities I’ve had to be involved in
many aspects of the business operation,” Jeremy said.
“GeneSeek has been at the forefront of genomics and has
helped to revolutionize the application of genomics throughout
the animal breeding industry–I have enjoyed playing a key role
in this.”
In addition, Jeremy said he also enjoys traveling to various locations to interact with the key genomic scientists and thought
leaders from around the world. In his free time he is an avid
reader of classic literature and scientific journals, enjoys his
daily workout, and playing golf.
Neogen GeneSeek Operations
4131 N. 48th Street • Lincoln, NE 68504
877-443-6489 (USA/Canada) • 402-435-0665
[email protected] • www.neogen.com
© 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.