Neogen offers a range of genomic solutions for research and development utilizing both catalog and custom genotyping/sequencing technologies. GeneSeek has more than 18 years of genomic research experience utilizing populations from mice, production animals, and companion animals through many plant species.

Cattle

Neogen's GeneSeek operations is on the forefront of cattle genomics and cattle genomic testing. GeneSeek is the exclusive provider of DNA testing solutions for AI sire dairy bull studs and a majority of the registered purebred cattle breeding associations.

GeneSeek Genomic Profilers (GGP) are the international gold standard for dairy performance testing due to their custom content and innovative design.

GGP Bovine 50K

The GGP Bovine 50K leverages Neogen's leading SNP selection process to precisely choose the best 50,000 SNP markers to deliver a more accurate evaluation of genetic merit, genome wide selection, comparative genetic studies, and higher density imputation.

GGP Bovine 150K

The GGP Bovine 150K features more than 150,000 SNPs for the most accurate prediction of elite breeding animals available on the market today.

GGP Bovine F-250

The newest offering for Bovine discovery is the GeneSeek Genomic Profiler F-250 (GGP F-250). The array was developed in conjunction with the University of Missouri and other collaborators, the GGP F-250 genotyping chip makes use of Illumina Infinium chemistry and features nearly 200,000 SNPs for accurate evaluation of functional variants such as non-synonymous, frameshift, and premature stop mutations. An additional 35,000 strategically selected SNP assays are included that allows researchers the ability to investigate genetic merit, apply genome -wide selection, and the ability to accurately impute to higher density arrays.

Companion Animals

CanineHD BeadChip

Neogen's GeneSeek laboratory is a leader in providing testing with Illumina BeadChip technology. The CanineHD BeadChip array is an ideal test for use by researchers investigating the canine genome. Data collected from this research can be used to provide information about canine health, as well as providing insight into the inheritance of important human diseases.

The CanineHD BeadChip offers highly polymorphic SNP content which provides uniform genomic coverage ideal for genome-wide association studies (GWAS), determination of genetic merit, identification of quantitative trait loci (QTL), and comparative genetic studies in any breed. This BeadChip was created through a collaborative effort by the LUPA Consortium, an initiative dedicated to using the canine genome to unravel complex disorders in both humans and dogs. The CanineHD BeadChip, which is powered by Illumina Infinium chemistry, currently contains more than 170,000 markers with an average of greater than 70 markers per megabase (Mb). The BeadChip is in the process of being updated and will soon include nearly 225,000 SNP's.

DNA Parentage Test

The Canine DNA Parentage Test is used to confirm familial relationships between parents and offspring. Breeders and owners of dogs use this test to ensure accuracy of breeding records, confirm and guarantee pedigrees, and protect breed integrity. More info can be found here.

Feline 63K Array

The Illumina Infinium iSelect 63K Cat DNA Array was released for use in February 2011 by the Morris Animal Foundation for use by researchers conducting GWAS and array-based studies. Pending approval of research projects by the Morris Animal Foundation, Neogen's GeneSeek laboratory is capable of processing samples on this platform.

Custom Panels and Arrays

Neogen's GeneSeek operations lab has developed custom panels for research and commercial use that have been very successful globally. We specialize in high through put, rapid turn-around genotyping and our experts would be happy to help you select the appropriate testing platform to fit you needs. If standard genotyping chip options are not appropriate for your particular goals, GeneSeek laboratories also offer custom Illumina Infinium BeadChips and Affymetrix Axiom arrays, as well as custom low density marker assisted selection panels. Assays can be tailored to many specific needs for targeted region genotyping including validation studies, association studies or marker assisted breeding programs. We also offer bioinformatics, electronic reporting and a knowledgeable customer service team to translate the data collected into practical, useful information.

GeneSeek's custom genotyping assays:

  • As few as 500 samples
  • Sample capacity to hundreds of thousands
  • Choose from 1-600,000 SNP assays
  • Multiple species on the same chip
  • Average genotyping success rates > 99%

Equine

GeneSeek Genomic Profiler (GGP) Equine SNP70 BeadChip

The GGP Equine SNP70 BeadChip is available from GeneSeek. The Equine SNP genotyping BeadChip is built on Illumina's Infinium platform and is one of the most comprehensive solutions available for genome-wide genotyping. This improved, second generation BeadChip features more than 65,000 evenly distributed SNPs derived from the EquCab2.0 SNP collection. The Equine BeadChip is a powerful tool to enable identification of genes and polymorphisms that contribute to traits of interest in all major horse breeds.

Affymetrix Equine HD array

The 670,000 SNP Affymetrix Equine HD array was designed after screening more than 2 million SNPs spanning the Equine genome. It provides optimal genomic coverage of known genetic diversity among domestic horse breeds, maximizing utility for research in equine genetics, including genome-wide association studies, high-resolution genetic mapping, Mendelian trait mapping, diversity analysis, and selection signature analysis.

SynchroGait®

SynchroGait® is a diagnostic DNA test based on a research project that identified a gene variant that has a major impact on the gait and coordination of horses. The SynchroGait® test enables you to identify one of the most important genetic factors that affects the performance of a trotting horse and that is permissive for alternative gaits, such as pacing in Icelandic horses. It is used to predict talent and trotting technique among horses used for harness racing and talent for different gaits among certain breeds of horses used for riding.

Equine Custom Panels and Arrays

Agena® MassARRAY® spectrometry based detection system for sensitive, accurate, and rapid genotyping

  • Easy-to-use multiplexed assay design and optimization software saves research time and helps maximize efficiency
  • Flexible SNP numbers allows for economical marker assisted selection
  • Parentage Testing

Mouse

The Giga Mouse Universal Genotyping Array (GigaMUGA) provides more than 143,000 SNP markers built on the Illumina Infinium platform. The GigaMUGA improves upon the 78,000 SNP MegaMUGA and includes nearly all of the predecessor's content. A majority of the SNP markers are distributed throughout the mouse genome and were selected to be informative in most mouse populations, including wild mice and multiple Mus species, but with a special emphasis for markers that are informative in the Collaborative Cross and Diversity Outbred population resources.

Plants

GeneSeek offers extensive options for plant genotyping. GeneSeek can do genotyping by sequencing, as well as SNP discovery for genotpying projects of all sizes and species of plant. With this sequencing information, GeneSeek can aid in developing custom genotyping tools tailored to your precise needs of genomic content from different plants. We offer services for every step of genomic improvement for a plant of interest.

Our services include:

  • Sequencing for SNP discovery
  • Bioinformatics to select the best SNPs for genome-wide association studies
  • Build high or medium density SNP arrays to create genomic models
  • Build low density arrays and panels for marker assisted selection
  • Use diagnostic tools to identify resistant of susceptible lines

Sequencing

Targeted Genotype by Sequencing

GeneSeek utilizes next-generation DNA sequencing (NGS) technologies to effectively genotype on specific targets, hundreds to thousands of genetic markers can be quickly and cost effectively identified or genotyped in large populations by using AmpliSeqTM GBS technology. GeneSeek's pipeline includes custom, focused sequencing assay design, multiplex enrichment PCR, sequencing, and variant calling.

Metagenomic sequencing

Discover the phylogenic diversity of microbiota. Next generation sequencing technology can be used to explore whole microbial communities without the need of culturing. Several variable regions of the 16S rRNA gene can be examined to allow for bacterial identification/classification.

Sheep & Goat

DNA testing in sheep can be used to verify parentage, help screen for undesirable mutations and assist in making the right breeding decisions for the herd. Genomic testing using chip based technologies can also be used to develop genomic predictions and genomically enhanced breeding values.

GeneSeek's genomic testing solutions for sheep include:

  • Genetic recessives and causative mutations
  • Genome-wide selection
  • Determination of genetic merit
  • Identification of quantitative trait loci (QTL)
  • Comparative genetic studies

OvineSNP50 Genotyping BeadChip

The OvineSNP50 BeadChip array features over 54,241 evenly spaced probes that target SNPs, offering more than sufficient SNP density for genome-wide association studies and other applications such as genome-wide selection, determination of genetic merit, identification of quantitative trait loci, and comparative genetic studies. The OvineSNP50 BeadChip provides uniform genome-wide coverage with a mean gap of 46kb.

OvineHD Array

The OvineHD array includes more than 600,000 genomic variants designed by the International Sheep Genomics Consortium (ISGC). The array includes nearly all the content from the original OvineSNP50 array. This higher density array will dramatically increase the power to identify key genes responsible for the desired measured traits.

OvineLD BeadChip

The OvineLD chip includes approximately 15,000 SNPs and is used to accurately impute up to the higher density Ovine arrays. In addition, the chip also contains many additional genetic recessive and causative SNP content.

GoatSNP50 BeadChip

The GoatSNP50 chip utilizes more than 50,000 SNP variants to provide uniform genomic covergage. The array was developed by the International Goat Genome Consortium who screened whole genome sequencing data in the following goat breeds: Alpine, Boer, Creole, Katjang, Saanen and Savanna. A total of 10 breeds were used to validate the 52k SNP content.

Other Sheep genetic tests available:

  • Ovine progressive pneumonia virus (OPPV) susceptibility
  • Scrapie susceptibility
  • Spider lamb
  • Myostatin
  • SNP parentage

Sheep & Goat Custom Panels and Arrays

Create assays tailored directly to your specific needs for targeted region genotyping, validation studies, association studies, or marker-assisted breeding programs. GeneSeek offers custom Illumina Infinium BeadChips and Affymetrix Axiom Arrays as well as less dense marker assisted selection panels.

Swine

GGP Porcine

Developed through collaborations between corporate and academic scientists, the GeneSeek Genomic Profiler (GGP) for Porcine includes the 34,000 SNPs that were most informative from the Porcine60K, it eliminates the 20,000 SNPs that did not have the best utility (low level of informativeness) in the major commercial breeds, it also includes an extra 17,000 SNPs to fill in the gaps of the chromosome and provide better coverage. It is important to note that the GGP chip also includes many more SNPs on the telomere regions of the chromosome to better account for recombination that may happen there. The GGP Porcine BeadChip also includes several genetic markers that may directly impact disease and performance traits.

PorcineSNP60 BeadChip

The PorcineSNP60 chip features 65,000 evenly spaced probes, offering more than sufficient SNP density for whole-genome association studies, determination of genetic merit, identification of quantitative trait loci, and comparative genetic studies.

Affymetrix Axiom® Porcine Genotyping Array

Axiom Porcine Genotyping Array is available in 96-array format and includes 658,692 markers discovered using whole-genome sequence data from 210 animals covering a broad range of commercial and non-commercial pig breeds that were selected for their relevance to world-wide breeding programs. This high-density array offers the power and resolution for a wide range of applications in pig breeding and genomics that include studying marker-trait association, evaluating pure lines, identifying multi-line reference populations, as well as research applications for genome-wide analysis and selective sweep analysis studies.

SeekGain GeneSeek's swine performance trait testing program

GeneSeek offers validated porcine performance trait DNA marker testing utilizing information from seven unique genes that impact:

  • Feed intake and conversion
  • Weight gain
  • Lean growth
  • Fat content
  • Meat quality
  • Litter size (estrogen receptor)
  • Litter size (erythropoietin)

Swine Custom Panels and Arrays

If standard genotyping chip offerings are not appropriate for your particular research goals, GeneSeek, offers custom Illumina Infinium BeadChips and Affymetrix Axiom Arrays. Create assays tailored directly to your specific needs for targeted region genotyping, validation studies, association studies or marker-assisted breeding programs.

GeneSeek's custom genotyping assays:

  • As few as 1,000 samples
  • Sample capacity to hundreds of thousands
  • Choose from 1,000–600,000 SNP assays
  • Multiple species on the same chip
  • Average genotyping success rates > 99%

Custom Panels & Arrays

Create assays tailored directly to your specific needs for targeted region genotyping, validation studies, association studies, or marker-assisted breeding programs. GeneSeek offers custom Illumina Infinium BeadChips and Affymetrix Axiom Arrays as well as less dense marker assisted selection panels.