Friday, June 29, 2012

Arrayit versus Luminex



This is one of my most widely read posts, updated 6-19-2015
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Read and quantify 96 microarrays with hundreds of biomarkers in each microarray in less than 10 minutes...read on.....

There are many advantages of the Arrayit microarray platform over Luminex and Bioplex and bead based type equipment, herein after referred to as "bead arrays". It is the easy microarray manufacturing step of binding and immobilization of antibodies, antigens, peptides and other biomarkers that makes immunoassays easy to design and perform on the Arrayit Platform. Having a multiplexed panel of biomarkers of the assay immobilized to a 2 dimensional planar surface makes it easy to separate bound from non-bound material during the assay much more specifically than bead based assays. Our ability to wash away non-specifically bound materials in a complex mixture of proteins such as serum makes the Arrayit microarray platform a powerful tool for measuring specific analytes from a crude preparation such as serum, sweat, urine, a cell or tissue lysate.

Reduced cost and labor by multiplexing.
Arrayit microarrays multiplex, miniaturize and parallelize many more assay types and with much higher throughput. Ex-situ microarrays made at Arrayit have the ability to multiplex and miniaturize to a much greater degree. Bead arrays read by flow cytometry have a maximum of 500 different capture analytes (but 500 rarely work beads in solution have a lot of cross reactivity). A spotted microarray platform provided by Arrayit can simultaneously capture data from single analytes to tens of thousands of capture analytes in a single binding reaction using a microscope slide size piece of glass. These microarrays can be processed manually or with the use of automation. The 2-color fluorescent microarray scanner can be used to read the results, these instruments are all over the world and are provided by Arrayit. Single colorimetric systems cost less than $4K, SPR, TIFR real time, Chemiluminesence and other detection methods can also be used. Scanners using fluorescent dyes in the IR range are now available to even further enhance signal to noise ratio on nitrocellulose surfaces used in Reverse Phase Protein Microarrays (See our Innoscan IR scanner). Bead array platforms cannot use label free detection methods nor IR methods and are not capable of performing Reverse Phase Reactions.

Shortened time-to-results by favorable reaction kinetics, with smaller sample requirements.
Our platform can simultaneously measure thousands of analytes with less than 1 ul of serum.  The latest release on Luminex requires 50 ul of serum.  Additionally we can provide even smaller reaction areas than bead assays run in 96 or 384 well plates and run through a flow cytometer detection instrument. In miniaturized "array of arrays" format on activated glass slides, 192 microarrays of 25 capture analytes each can be run with reaction volumes of approximately 1 ul. 96 well formats compatible with standard ELISA assay processing equipment used (see catalog ID: AHC4x24 at www.araryit.com).  This tool has been extremely popular.  Every spot in the microarray is subjected to the same processing conditions, with positive and negative controls within each test. Common bead array plate based protocols use 50-100 ul reactions, each well is under separate processing and detection conditions. Smaller spots, less analyte and less detection reagents make Arrayit's microarray analysis platform less expensive to run than bead arrays.

Liquid reaction kinetics give faster, more reproducible results.
Capture analytes in both cases...beads and planar microarrays...the capture analytes are bound to a solid surface. Beads, like the surfaces of microarrays, are insoluble. However in the case of spotted planar microarrays, the capture analytes are covalently bound to the surface of the microarray. They cannot interact with each other in solution, as can capture analytes attached to beads in solution. All planar microarrays are reacted with liquids. The miniaturization of printed microarrays provide a platform where the detection proteins in solution are in far excess concentration than the capture analytes bound to the microarray. Increased concentration means faster binding kinetics and increased sensitivity. A properly executed microarray is always more sensitive and reproducible results than bead arrays.

Focused, flexible multiplexing in the range of 1 to tens of thousands of analytes meets the needs of a wide variety of applications.  Arrayit spotted microarrays have a higher degree miniaturization, number of capture analytes and faster data collection time (Full slide scans of 25,000 array elements can be scanned in 3.5 minutes). Microarrays have used antibodies, antigens, peptides, serum, amplified DNA, oligonucleotides, small molecules, carbohydrates, oligosaccarides, hybridomas, phage and others as capture analytes...many sample types that cannot be attached to beads. The microarray platform by ArrayIt is clearly a universal biochemistry assay platform for an almost infinite number of assay types.


5. Open architecture allows market leading companies to provide compatible kits and software. 


*Microarray data quality is checked by careful examination of the raw data of the microarray scan. Bead array flow cytometer dectection instruments do not provide any raw data. The raw data of flow cytometry bead array experiment cannot be examined and checked for quality. Bead array systems rely on the redundancy of the system to verify the quality of the data. With microarray the quality of the data can be physically examined by the end user with as much redundancy and controls built in as needed. Additionally, unlike beads, microarrays can be checked for quality prior to their use.

* Microarrays are manufactured at very low cost.  For each . 100 um data size data points are made with a volume of little more than 500 picoliters of capture analyte.  The money that can be saved on protein can more than pay for the capital equipment required to read, process and manufacture microarrays.



* Microarrays are manufactured at very low cost.  For each . 100 um data size data points are made with a volume of little more than 500 picoliters of capture analyte.  The money that can be saved on protein can more than pay for the capital equipment required to read, process and manufacture microarrays.

*Microarrays do not need internal dyes to identify different capture analytes. Simple spot location identifies the capture analytes. Internal dyes makes detection of biomarkers more difficult and increases noise and crosstalk.

*Microarray elisa based assays are easy to implement and process, requiring no specialized equipment for processing. Microarrays in the bottoms of 96 well plates and on slides are amenable to existing IFA and ELISA type automation equipment.

* The proteins coated on beads stored in solution are not stable for long periods of time. Printed microarrays are stable for years at room temperature.

*Microarray elisa based assays are easy to implement and process, requiring no specialized equipment for processing. Microarrays in the bottoms of 96 well plates and on slides are amenable to existing IFA and ELISA type automation equipment.

* The proteins coated on beads stored in solution are not stable for long periods of time. Printed microarrays are stable for years at room temperature.

* The proteins coated on beads stored in solution are not stable for long periods of time. Printed microarrays are stable for years at room temperature.

*No expensive filter plates when you use microarray.

* Bead array detection of beads is done through a layer of liquid, that contributes to noise and reduces the sensitivity of the assay.  Microarrays spots are directly excited and read with confocal laser scanner for great signal to noise ratio.

It's my opinion that the spotted microarray platform is superior to flow cytometry based bead platforms. T




Printed microarray platform is an open architecture with microscope slide glass being the default substrate size used in microarray detection and processing instruments. Microarray detection is routinely done with fluorescent, colorimetric and chemiluminescent detection..providing a much more flexible and open operating environment. Both CCD and laser/PMT microarray scanner architectures are available based on the end users need for quantitation, cost and sensitivity. Very inexpensive colorimetric microarray detection can also be used. Bead arrays are limited to fluorescent detection and specialized equipment to read only specific bead types. Colorimetric detection, considered accurate and the least expensive of all types of detection, cannot be done with existing bead array technology.


Video showing quantification step is fast and easy.


What else is nice about Arrayit's microarray platform that bead array vendors don't want you to know? 

Colorimetric microarray detectors, that can capture 16bit quantitative data from analyte spots as small at 50 microns in diameter cost less than $4K and can be run in a 96 well format for less than $25K. (see SpotWare and ArrayPix colorimetric systems)  ArrayPix can read and quantify 96 microarrays in less than 10 minutes.




Microarrays do not need many readings of beads to validate data, only 1 image scan is required.

Beads in solution can aggregate together over time, rendering them useless. Microarray spots by their nature cannot aggregate.






Arrayit as an proprietary set of microarray manufacturing technology, surface chemistry, buffer systems and peptide synthesis methods it applies to delivering best in class peptide microarrays to it's customers.  One of Arrayit's key pieces of technology is their method and design patent on the microarray manufacturing device, USPTO 6,101,946.  Arrayit is the sole licensee and exclusive provider of this technology to the microarray industry. Since they are the inventors of microarray manufacturing methods, they are in the best position to deploy the technology.   In addition, the surface chemistry, peptide synthesis, buffer systems and ex-situ manufacturing methods are specifically engineered to work together to selectively attach the N terminus of the peptide covalently bound to the glass at the same time providing and amide C terminus to allow for easy binding of proteins in solution to the peptides on the microarray.  This covalent attachment method also allows for very stringent processing of the microarrays, critical for reporting the most accurate peptide microarray data possible.   Because Arrayit's microarray manufacturing methods are "ex-situ" every peptide on the microarray is quality controlled by mass spectrometry to assure that each peptide is correctly made.  To our knowledge Arrayit is the only manufacturer that provides this level of quality assurance and manufacturing methods, controlling the spotting device, surface chemistry, buffer system and peptide synthesis all designed specifically for this application.  Other companies may deploy other manufacturing manufacturing methods, but not manufacture their own devices, surface chemistry buffer systems. This provides Arrayit a unique and strategic advantage in quality control.  In-situ manufacturing methods are not capable of enabling this level of quality control. All microarray manufacturing is done in a class 100 clean room.  Arrayit's ex-situ microarray manufacturing methods are universal enough to meet the needs of any microarray hybridization and detection platform.  For our specific project, Arrayit agreed to provide specialized programming and formatting to meet our current Agilent microarray scanning and processing hardware for free.