Des i g n C o ntent | P rep are Li b rary | S eq uence | A nal yze Data®

TruSeq Genotype Ne Kit
A cost-effective, flexible solution for targeted genotyping by sequencing for any plant or
animal species.
HighlightslCustomizable Panel
Achieve consistent genotyping performance from content
designed by Illumina Concierge serviceslFlexible Solution
Identify novel variants and easily update your panel content
with new genotyping information

lIntegrated Workflow
Access streamlined library prep, reliable sequencing, anduser-friendly data analysis

Introduction
The TruSeq Genotype N e Kit is a flexible, cost-effective solution fortargeted genotyping by sequencing (GBS) for parentage, purity
studies, and breeding decisions for any plant and nonhuman animalspecies (Table 1). The TruSeq Genotype N e Kit is designed andoptimized to work with up to 5000 markers and is easily scalable fromhundreds to tens of thousands of samples.

All-Inclusive Solution
The integrated Illumina workflow for amplicon sequencing enableslabs to access a fully supported solution, from design through analysis(Figure 1). The TruSeq Genotype N eKit is designed and optimized foruse on the MiniSeq™, MiSeq®, and NextSeq® Series of Sequencing
Systems, without requiring additional instrumentation. A single sourceof technical and field specialists for design, library preparation,
sequencing, and data analysis, and the combined expertise of theIllumina support team, ensure rapid resolution and minimize potentiallaboratory downtime.

Confident Assay Design
The TruSeq Genotype N e Kit is a fully customizable sequencing assay.
Illumina Concierge Service offers design support for all oligonucleotide
probes for the TruSeq Genotype N e Kit to ensure consistentperformance. Illumina Concierge Service enables customers to:lInclude multiple marker types such as single nucleotide
polymorphisms (SNPs), insertions/deletions (indels), etc, in asingle panellUpdate existing panels without large sample commitmentlDesign panels even in the absence of a complete reference
sequence

Contact an Illumina representative for access to Illumina Concierge
Service.

Streamlined Workflow
A key element of Illumina NGS is high-quality library preparation.
Illumina library prep protocols can accommodate a range of throughput
needs, from lower-throughput protocols for small laboratories to fully
automated library preparation workstations for large laboratories or
genome centers. Different methods are employed to capture regions ofinterest from input DNA and prepare sequencing libraries.
The TruSeq Genotype N e assay uses an amplicon generation
approach. Amplicon generation employs a hybridization followed byextension-ligation approach, creating a single-stranded template froma double-stranded genomic DNA (gDNA) population that is later
amplified via PCR (Figure 2). The library preparation protocol can becompleted with less than 2.5 hours of hands-on time (Figure 3).

Figure 1: TruSeq Genotyping N e Workflow—The TruSeq Genotyping N e Kit provides a fully supported, comprehensive solution for genotyping by sequencing from probe
design with Illumina Concierge Service through library preparation, sequencing, and data analysis.

For Research Use Only. Not for use in diagnostic procedures.

Des i g n C o ntent | P rep are Li b rary | S eq uence | A nal yze Data

Figure 2: Amplicon Chemistry—The TruSeq Genotype N e Kit uses anextension/ligation-based method to prepare custom, sequencing-ready libraries.

Industry-Leading Data Quality
The TruSeq Genotype N e Kit is compatible with the MiniSeq, MiSeq,
and NextSeq Systems, which use proven Illumina sequencing bysynthesis (SBS) chemistry. More than 90% of the world's sequencing
data are generated by Illumina SBS chemistry.* Illumina systems
deliver the highest percentage of sequenced bases over Q30 in theindustry.1–5 With consistent high-quality results, researchers can beconfident in the accuracy of their data, even with challenging targets
of interest (eg, repetitive regions, GC-rich content).6

Simplified Data Analysis
Data can be seamlessly streamed from Illumina sequencing systems
to BaseSpace ® Sequence Hub, a user-friendly genomics cloudcomputing platform that offers simplified data management,
analytical sequencing tools, and data storage. The TruSeq Genotype
N e Kit uses the TruSeq Amplicon App to streamline analysis of custom
panels.

Figure 3: Library Prep Workflow—The TruSeq Genotype N e Kit enables simplified
library preparation with less than three hours of hands-on time.
* Data calculations on file. Illumina, Inc., 2015.

For Research Use Only. Not for use in diagnostic procedures.

Des i g n C o ntent | P rep are Li b rary | S eq uence | A nal yze Data

Table 1: TruSeq Genotype Ne Kit Specifications

Ordering Information

FeatureSpecification

SpeciesAny Nonhuman Species

ProductInput Requirement

50 ng Genomic DNA

Target Multiplexing

16–5000 in a single panel

TruSeq Genotype N e Kit(includes allnecessary reagents)

Sample Multiplexing

Up to 384

No. of Samples

CatalogNo.

96 samples, up to 384
20018978indexes

References
SummaryThe TruSeq Genotype N e Kit is a flexible, cost-effective solution fortargeted GBS for parentage, purity studies, and breeding
decisions. With content designed through Illumina Concierge
services, the TruSeq Genotype N e Kit provides a fully customizable
panel for GBS for any plant and nonhuman animal species. With an
integrated workflow that includes library preparation throughsequencing and data analysis, customers have a single source ofsupport.

Learn MoreTo learn more about the TruSeq Genotype N e Kit and other plant andanimal sequencing and genotyping options, visit
www.illumina.com/agrigenomics.

1.

Perkins TT, Tay CY, Thirriot F, Marshall B. Choosing a benchtop sequencing
machine to characterize Helicobacter pylori genomes. PLoS One.
2013;8:e67539.

2.

Quail MA, Smith M, Coupland P, et al. A tale of three next generation
sequencing platforms: comparison of Ion Torrent, Pacific Biosciences andIllumina MiSeq sequencers. BMC Genomics. 2012;13:341.

3.

Ross MG, Russ C, Costello M, et al. Characterizing and measuring bias insequence data. Genome Biol. 2013;14:R51.

4.

Jünemann S, Sedlazeck FJ, Prior K, et al. Updating benchtop sequencing
performance comparison. Nat Biotechnol . 2013;31:294–296.

5.

Loman NJ, Misra RV, Dallman TJ, et al. Performance comparison ofbenchtop high-throughput sequencing platforms. Nat Biotechnol .
2012;30:434–439.

6.

Wong SQ, Fellowes A, Doig K, et al. Assessing the clinical value of targeted
massively parallel sequencing in a longitudinal, prospective population-based
study of cancer patients. Br J Cancer. 2015;112:1411–1420.

Illumina, Inc. • 1.800.809.4566 toll-free (US) • +1.858.202.4566 tel • techsupport@illumina.com • www.illumina.com
For Research Use Only. Not for use in diagnostic procedures.
© 2017 Illumina, Inc. All rights reserved. Illumina, MiniSeq, MiSeq, NextSeq, TruSeq, and the pumpkin orange color are trademarks of Illumina, Inc. and/or itsaffiliate(s) in the U.S. and/or other countries. All other names, logos, and other trademarks are the property of their respective owners. Pub. No. 1370-2017002-A