High sample throughput SNP genotyping of cattle using
the Fluidigm EP1™ system
Ken Livak1, Min Lin1, Amy Hamilton1, John Hudson1, Rafal Iwasiow2, Ellen Maclean2, and Yong Yi1
1.
2.

Fluidigm Corporation, South San Francisco, CA USA
DNA Genotek, Ottawa, CanadaAbstract
The Fluidigm EP1™ system is the ideal
solution for high sample throughput SNP
genotyping for plant and animal studies
because it offers outstanding data quality
and the most efficient workflow available.
The system routinely achieves 99% orhigher call rates and takes only four hours
to obtain results.
The performance of the Fluidigm system isdemonstrated using cattle samples obtainedwith the Performagene™ kit from DNA Genotek.
The samples have been tested against aparentage panel of 96 SNPs that weredeveloped by a USDA-led cattle consortium.

Fluidigm 96.96 Dynamic ArrayTM
IFCs and the EP1 System
Dynamic Array IFCs are integrated fluidic
circuits (IFCs) including a network of
microfluidic channels, chambers, and valves.

Each 96.96 Dynamic Array IFC (left) is
capable of running 96 samples against 96
SNP assays generating a total of 9,216genotypes. The advantages include:• Outstanding data quality using gold
standard assays, e.g. TaqMan® assays.
• A fast and easy workflow that provides
results in only four hours.
• One hundred times reduced reagent andpipetting requirements.
• Better data from samples that may be
low in concentration or quality, throughthe optional use of Specific Target
Amplification (STA).

Fast and Easy Workflow

SNP Genotyping Results

The Fluidigm EP1 system runs 96.96
Dynamic Array IFCs, which offer a fast andeasy workflow that can be integrated into ahigh throughput laboratory.

The SNP genotyping results demonstrate
the excellent performance of the Fluidigm
system using cattle samples.
• Results have shown 99.3% call rates,with the majority of no calls comingfrom one sample.
• 99.9% call rates and 100% concordance
are achieved in duplicates after thatsample had been removed from theanalysis.

1. Samples are filled in theSample inlets.
SNP assays are filled theAssay inlets.

2. The 9,216 individual reactions
are assembled automatically by
the IFC controllers, requiring
100 times fewer pipetting steps
and reagents.

3. Samples are amplified ona thermal cycler using astandard program.

Figure 1. A call map view displays the overallcalls for the Dynamic Array IFC, displaying 9,216
results at one time.

4. The 96.96 Dynamic Arrayis imaged in the EP1
reader in a matter ofminutes.

• The format of the dynamic array iscompatible with the SBS (Society forBiomolecular Sciences) standards,
allowing the use of standard liquidhandling robots.
• The 384-style pitch between inlets means
there is no need to re-configure existing
96 or 384 sample layouts.

Performagene by DNA Genotek
All genetic applications start with thecollection of DNA samples. Blood samples
are expensive to collect, as well as complex
and costly to ship, store and process. Hairfollicles and ear punches are inefficient toprocess and can provide low quality andquantity DNA, resulting in failed samples
and a requirement to recollect, incurring
additional cost, effort and time.
Eliminate these challenges by collecting
superior samples with Performagene.
• Easy, reliable and cost effective
collection, transportation andprocessing.

SNP Genotyping Experiment
The Fluidigm system was used to genotype
48 cattle nasal samples in duplicate against
a 96 SNP parentage panel. The nasal
swab samples were obtained using thePerformagene kit from DNA Genotek and
STA was used, although not required.

• Barcoded for full sample traceability.
• Efficient sample preparation andextraction of high quality, high quantity
DNA.
• DNA is stable for 1 year at room
temperature.

• The SNP genotyping results wereobtained in only one half day and withminutes of actual hands-on time.
• 96 custom TaqMan assays weredesigned and ordered using standard
protocols.

Fluidigm Corporation
7000 Shoreline Court, Suite 100 • South San Francisco, CA 94080
Toll-free: 1.866.FLUIDLINE
www.fluidigm.com

Figure 2. Cluster plots for two of the 96 SNP
assays represent typical results obtained from
Fluidigm Dynamic Array IFCs.

Conclusions• SNP genotyping experiments using
Performagene cattle nasal samples havedemonstrated 99.9% call rates and 100
percent concordance on the Fluidigm system.
• The workflow for Fluidigm Dynamic Array IFCs
requires only a few hours of total time andminutes of actual hands on-time.
• The Fluidigm system has been designed to beeasily integrated into a high throughput
laboratory.

The Fluidigm system provides the ideal solution
for high sample throughput plant and animalstudies because is offers outstanding data
quality and the most efficient workflow.
Fluidigm, the Fluidigm logo , EP1, and Dynamic Array are trademarks orregistered trademarks of Fluidigm Corporation in the U.S. and/or othercountries. All other trademarks are the property of their respective
owners.
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