The document summarizes research evaluating the performance of TaqMan Low Density Arrays for gene expression analysis. It finds that assays on arrays can discriminate 2-fold changes as well as plate assays, and assay results are highly reproducible both within and across arrays. The study also uses a TaqMan Low Density Human Endogenous Control Array to examine housekeeping gene expression across 32 tissues, identifying genes with consistent expression levels suitable for normalization.

1. Kathy Y Lee, Glo-Stella Concepcion, Kelly Li, Jake Freudenthal, Kathleen Shelton, Nico Tuason; Applied Biosystems, Foster City, CA 94404
TaqMan® Low Density Array: Performance Parameters Across
Arrays and Human Endogenous Control Panel Application
ABSTRACT
The TaqMan® Low Density Array allows for rapid
screening of many samples with 10s to100s of
TaqMan® Gene Expression Assays. The
researcher can easily move from gene lists and
single assays in tubes to large scale real-time
PCR gene expression profiling without the the
need for liquid handling robots. Of particular concern to customers is assay performance
on the Low Density Array relative to plates, as well as the precision within arrays, across
arrays and between manufactured lots. Over the past two years we have accumulated a
large amount of data on TaqMan® Array performance via our QC process and we used
this to evaluate its performance. In these studies we show the performance parameters
of TaqMan Arrays and the results of 32 tissues run on the TaqMan® Low Density Human
Endogenous Control Array.
INTRODUCTION
The TaqMan Low Density Array, designed to be used with the Applied Biosystems
7900HT Fast Real-Time PCR System, is a consumable consisting of 384 wells
connected by a series of microfluidic channels. During the manufacturing process
selected TaqMan Gene Expression Assays are loaded and dried in the array wells as
specified by the customer or as defined by a fixed Array Gene Panel (Immune Profiling
Array or Endogenous Control Panel). Each manufactured lot is tested for reproducibility
by running Universal RNA across all wells; replicates must meet certain criteria before
the arrays are released to the customer. To compare performance between plate and
low density array, we looked at QC data generated from > 3,000 TaqMan® Assays that
were run in parallel on TaqMan Low Density Arrays and 384-well plates. These data
show that assays on the array can discriminate 2-fold change with similar sensitivity as
on plates. We used data from multiple manufactured lots of the Immune Profiling Array
to determine assay reproducibility and found that across arrays reproducibility was very
good; across manufacturing lots the standard deviation increased but was well within
the QC standards set for within array reproducibility As a demonstration of the TaqMan®
Low Density Human Endogenous Control Array (P/N 4347601) performance, we
screened 32 different tissues and show the variation of expression of 16 common
housekeeping genes across these tissues.
METHODS
• Arrays from 6 different manufacturing lots of the Immune Profiling Array
(Fig. 2) were used to test assay performance. cDNA was prepared from commercially
available total RNA (Stratagene), using Applied Biosystems High Capacity cDNA
Archive Kit for reverse transcription. cDNA was mixed with Universal Master Mix and
loaded into the fill ports, 100ng cDNA/port (Fig. 1). The Array was then centrifuged to
load the sample specific reaction mixes into the individual wells of the microfluidic card,
and sealed before loading into the Applied Biosystems 7900HT System. CT (cycle
threshold) values were used to measure reproducibility (4 replicates/gene/sample/card).
• RT-PCR was performed on total RNA samples from 32 different tissues (Ambion) and
loaded into fill ports on 4 TaqMan® Human Endogenous Control arrays (Fig. 8). The
average CT (3 replicates/gene/sample) was used to calculate the average CT and StDev
across the 32 tissues.
Figure 1.
Figure 2. TaqMan® Low Density Immune Profiling Array
Running The Low Density Array
SealLoad Spin Run Real-Time PCR
Figure 3. Uniformity across an Array
384 wells containing TGFB1CT Stdev
of CT = 0.097
Figure 4a. GAPD (Hs99999905_m1)
8 replicates across 4 cards
Figure 4b. Reproducibility Across
Arrays
10
15
20
25
30
35
G
A
PD
H
IL-8
M
C
P-1
R
antes
B
ax
PG
K
1
C
D
86
IL-18
Ct
Card1
Card2
Card3
Card4
Figure 5. Reproducibility of Individual
Wells Across Lots
Figure 6. Reproducibility Across
Lots Immune Profiling Card
R2
= 0.9708
0
5
10
15
20
25
30
35
40
5 10 15 20 25 30 35 40
CT wells Lot_1
CTwellsLot_2
0
5
10
15
20
25
30
35
GAPD IL8 MCP-1 Rantes BAX PGK1 CD86 IL18
Assay
CT
Lot 1
Lot 2
Lot 3
Lot 4
Figure 7. Ability of TaqMan Low Density Arrays to Discriminate Fold Change
in Gene Expression
3 CT
TaqMan Low Density Arrays and
384-well plates for different
threshold cycles (CT) is shown
below.The results are based on a
statistical model of precision
(standard deviation) derived from
measurement of thousands of
TaqMan Assays across hundreds
of each consumable. The
expression level measured as CT
value is shown on the X-axis; the
Y-axis shows the fold-change in
expression that is measured with
95% confidence at a given CT.
Figure 8. TaqMan®
Low Density Human Endogenous Control Array
Col 1- 3 Col 4 - 6 Col 7 - 9 Col 10 - 12 Col 13 - 15 Col 16 - 18 Col 19 - 21 Col 21 - 22
A 18S ACTB B2M GAPD GUSB HMBS HPRT1 IPO8
B PGK1 POLR2A PPIA RPLPO TBP TFRC UBC YWHAZ
C 18S ACTB B2M GAPD GUSB HMBS HPRT1 IPO8
D PGK1 POLR2A PPIA RPLPO TBP TFRC UBC YWHAZ
E 18S ACTB B2M GAPD GUSB HMBS HPRT1 IPO8
F PGK1 POLR2A PPIA RPLPO TBP TFRC UBC YWHAZ
G 18S ACTB B2M GAPD GUSB HMBS HPRT1 IPO8
H PGK1 POLR2A PPIA RPLPO TBP TFRC UBC YWHAZ
I 18S ACTB B2M GAPD GUSB HMBS HPRT1 IPO8
J PGK1 POLR2A PPIA RPLPO TBP TFRC UBC YWHAZ
K 18S ACTB B2M GAPD GUSB HMBS HPRT1 IPO8
L PGK1 POLR2A PPIA RPLPO TBP TFRC UBC YWHAZ
M 18S ACTB B2M GAPD GUSB HMBS HPRT1 IPO8
N PGK1 POLR2A PPIA RPLPO TBP TFRC UBC YWHAZ
O 18S ACTB B2M GAPD GUSB HMBS HPRT1 IPO8
P PGK1 POLR2A PPIA RPLPO TBP TFRC UBC YWHAZ
Figure 9. CT values for 32 tissues, 4 Candidate Endogenous Controls
0
5
10
15
20
25
30
18S GAPDH HPRT RPLPO
CT
UHR
Brain
Liver
Lung
Testis
Pancreas
Placenta
Thymus
Thyroid
Salivary Gland
Mammary Gland
Colon
Heart
Kidney
Skeletal Muscle
Prostate
Spleen
Spinal Cord
Fetal Kidney
Fetal Thymus
Fetal Liver
Fetal Brain
Adrenal Gland
Bone Marrow
Retina
PBL*
Tonsil
Trachea
Uterus
Small Intestine
Skin
Table 1. CT and StDev for 32 tissues with16 candidate endogenous
control genes
Gene ID CT StDev Gene ID CT StDev
RPLPO 20.48 0.68 POLR2A 23.85 1.07
18S 7.06 0.72 TBP 27.00 1.15
HMBS 26.43 0.72 ACTB 19.47 1.27
UBC 20.94 0.79 B2M 19.74 1.27
PPIA 21.45 0.94 HPRT 25.55 1.29
PGK1 23.01 0.96 TFRC 25.38 1.35
IPO8 26.44 1.00 GAPDH 19.77 1.42
GUSB 24.09 1.04 YWHAZ 26.92 1.44
Conclusions
• Gene expression measurements on TaqMan Low Density Arrays are
highly reproducible, both within and across arrays (Figs. 3, 4, 5, 6).
• The high precision of the TaqMan Low Density Array allows
discrimination of relative gene expression changes of two-fold or greater
(Fig. 7).
•The Human Endogenous Control Array can be used to quickly screen a
large number of samples to identify candidate normalization genes (Figs.
8, 9; Table 1).
For Research Use Only. Not for use in diagnostic procedures.
The PCR process and 5' nuclease process are covered by patents owned by Roche Molecular Systems, Inc. and F.
Hoffmann-La Roche Ltd. Applied Biosystems is a registered trademark and AB (Design) and Applera are trademarks of
Applera Corporation or its subsidiaries in the US and/or certain other countries.TaqMan is a registered trademark of
Roche Molecular Systems, Inc. Micro Fluidic Card developed in collaboration with 3M Company.
© 2005 Applied Biosystems. All rights reserved.
127PR15-01