The adoption of personalized medicine is happening!

Adverse drug reactions are among the highest causes of death. Part of the work in personalized medicine is about developing drugs that include a genetic or other type of test to match the patient with the right drug and dosage. This will make drug therapies safer and more effective. We are seeing the needed changes to make this happen in all areas of our society. Regulatory requirements are being defined and insurance reimbursement for diagnostic tests linked to proper care are being approved. Congress is working on laws to to prevent genetic discrimination and our educational system is ramping up to incorporate genetic testing methods their curriculum. At Arrayit we are supporting a number of undergraduate microarray education programs with tools, kits and reagents for education purposes. The good graduate programs are working at it too. So it is clear a supportive public policy environment is helping to address the important issues to make Personalized Medicine a true medical dicipline...not just a buzz word. Our federal government has the power to provide addition incentives to business, investment banks, and insurance companies that would help accelerate the development of drugs and companion diagnostic tests. The American Society for Human Genetics published a nice synopsis March 07,...it is an interesting read to see how quickly the changes are really happening....Read more here..

Microarray Manufacturing - Outsourcing Makes Sense

I'm often asked if we print microarrays as a service and should someone try to do it themselves or outsource. Here at the ArrayIt Division at TeleChem we're so well know for microarray spotting pins, surface chemistry and processing tools, our high quality microarray manufacturing service gets overlooked.
As it's mentioned in previous blog entries our technology tool set empowers us to make a microarray from any biomolcule. If you are considering having microarray microarrays made, hire us to do it for you. Cost cutting is the major driver, but there are other considerations....

Reduce capital spending. Outsourcing your microarray manufacturing to us converts fixed costs into variable costs, since you can purchase microarrays as you need them. This releases capital for investment elsewhere in your business, and allows you to avoid large expenditures. Outsourcing can also make your firm more attractive to investors, since you're able to pump more capital directly into other R&D activities or revenue-producing activities such as sales and marketing.

Increase efficiency. Companies that do everything themselves have much higher research and development costs. Additionally marketing, and distribution expenses are higher, which are ultimately passed on to customers. We provide an affordable cost structure and since we supply so many users we have the economy of scale to give your organization the competitive advantage.

Reduce labor costs. Microarray manufacturing has gotten a lot easier over the years, primarily because the equipment and tools of the trade have improved tremendously. That said, hiring and training staff to make microarrays can still use up valuable time and money. These employees can be difficult to manage since managers don't know and don't want to know anything about making microarrays!! Microarray projects can be expensive, and temporary employees for microarray manufacturing don't exist. Outsourcing lets you focus your human resources where you need them most.

New projects come to fruition faster. We have the microarray resources to implement all major microarray applications in-house. Our experience can bring your new microarray ideas and applications to reality quickly. Tackling the microarray project in-house involves weeks or months to hire the right people, train them, and provide the support they need. Additionally, capital investments make the startup process even more difficult. We have the technology in-house to make any type of microarray.

Focus on your core business. All organizations have limited resources, and every project manager has limited time and attention. Outsourcing microarray manufacturing to us shifts the focus from peripheral activities toward work that that generates valuable data for your organization...the reason we use microarray in the first place!

Level the playing field. We've been making microarray for 12 years. Most firms simply can't match the in-house expertise that we have maintained over the years. Outsourcing gives your firm access to our vast experience, economies of scale, efficiency, and expertise that that we have built over many years. Since we make our own surface chemistry, microarrayers, micro spotting devices and more...you don't have to buy it!!

Reduce risk. Every business investment carries a certain amount of risk. Markets, competition, government regulations, financial conditions, and technologies all change very quickly. We assume and manage much of the risk for you, and we know how to avoid risk in the microarray industry.

Of course we're happy to empower you to make your own microarrays...but as we've examined here, outsourcing can make a lot of sense. Please contact us for your microarray manufacturing needs.

Kind regards,
Todd Martinsky
todd@arrayit.com

Microarray Spotter Worktables

Our NanoPrint microarrayer allows a user to setup an unlimited number of worktables to provide ultimate flexibility to the microarray robot. Current work tables that are designed and running at current customer sites are microscope slide size glass, micro-fluidic cartridges, microplates, and proplate glass. Any other type of sensors used in biology and/or material science applications can be custom designed and implemented quickly. The existing software of the on the NanoPrint is easy to use and flexible enough to print various targets. Once you own a NanoPrint there will be no need to purchase a new microarray robot if the size and shape of your substrate changes. Please contact us with your applications.

Multi-analyte Microarrays and ELISA

Standard ArrayIt Multi-analyte Protein Microarray Protocol

1. Print antigens at a final concentration of 0.3mg per ml as a final concentration in protein printing buffer onto SuperEpoxy 2 surface chemistryNanoPrint microarrayer. For colorimetric detection use SuperNitro. Consider immunoglobulin controls as a dilution series for quantitation "dose response" curves. After microarray manufacturing, let microarrays sit overnight on the deck microarrayer to dry. Stored printed microarrays clean, dry and at room temperature. Protein printing buffer will stabilize the printed proteins for long periods of time.

2. Prior to using the microarrays they must be blocked. Incubate microarray(s) in 1X blocking buffer from 1 hour to overnight. Blocking for less than 1 hour can compromise results. After blocking wash microarray 3 times 5 minutes each in PBS or PBST.

3. React primary antibody to the microarrays(s). Use diluted serum or other test sample diluted into 1X BlockIt Buffer, typical dilutions are 1 to 200. Because kinetics of microarrays are fast, incubations can be as short as 15 minutes or as long as overnight. Agitation and increased temperature can be used to speed up kinetics. Temperature can varied depending on the application from 4 C to 37 C.

4. Wash off reaction 3 time 5 minute each in 1X PBS or PBST.

5. React secondary antibody to the microarray. Secondary antibodies can be labeled with fluorescent markers for detection in microarray scanners or conjugated to AP and subsequently developed using an alkaline phosphatase development kit. Protect fluorescent reactions from light to avoid photo bleaching. Incubate 1 minute to 1 hour.

6. Wash microarray(s) in 1X PBS or PBST 3 times for 5 minutes. Rinse for 15 seconds in ddH20 and dry. A microarray centrifuge can be used to dry slide based microarrays. If using fluorescent detection, scan immediately.

Breaking Microarrays...how to avoid it.

The reason microarrays can occasionally break is primarily due to the fragile and brittle glass that some organizations have chosen for their substrate. At ArrayIt we have created a formulation of glass (harder than borosilicate and soda lime) and special cutting, grinding, polishing, and laser ablation procedures to avoid micro-fractures. Micro-fractures in glass are very problematic, since through vibration, direct pressure and other stress of microarray processing can cause a micro-fracture to become a major break. Our combination of hard glass and polishing procedures provides glass specifically designed to survive the entire life cycle a microarray substrate must live though. Microarray glass goes through many processing and manufacturing steps prior to the end user finally scanning their raw data. Steps include:

polishing
cutting
laser ablation (optional)
cleaning
surface chemistry
microarray manufacturing
pre-hybridization
hybridization
post hybridization
drying
scanning

Some microarray instruments are harder on the glass than others. The most severe stress is caused by gaskets in automated hybridization stations and multiplexed hybridization tools pressing a sealing gasket down hard on the glass. This is the time where failures are most common and most disastrous since not only is the microarray lost, but so are all the hybridizations. Other stress areas are on the nest or deck of the microarrayer...such as when glass is held down by vacuum pressure, clips or other holding mechanisms that place can place stress on the glass.

Accidents can always happen, but breakage is minimized by using the proper substrate. For more information on microarray substrates please see http://www.arrayit.com/Products/Substrates/

Location Helps the Success of our Organization

Having the ArrayIt Microarray Division located in Silicon Valley makes acquiring the resources needed to get our important work done a lot easier. Additionally it's a great place to visit, as watching this movie will show you. Please make an appointment and come see our microarray show room. We welcome students too. Contact Paul Haje, paul@arrayit.com about our educational outreach program.

Microarray Surface Chemistry

Many studies have been done to test what microarray surface is best for DNA and protein microarray applications. The principles that determine how microarray surface chemistries are used and interpreted are as follows:

Rule 1. Attach biomolecules in a stable manner.

A stable attachment is key to producing strong signals and accurate results. Capture molecules must be immobilized, remain in a specific location and essentially stay unchanged throughout all the pre and post printing procedures of the microarray experimental life cycle. Only a stable surface can meet this need.

Rule 2. Maintain activity of attached biomolecules

The binding, hybridization, epitope and enzymatic activity properties of biomolecules are essential to usability of the microarrays. Without the binding activity of the printed sample, there can be no experiment. Activity can be prolonged on a surface by using stabilizing printing buffers; therefore the activity of a biomolecule on a surface is not completely dependent on the surface chemistry.

Rule 3. The surface binding mechanism must have longevity.

The surface used in a microarray experiment must maintain its binding activity for at least several months, in some cases years. Time and flexibility is required to design experiments, plan manufacturing, procure product, prepare samples and store printed microarrays prior to binding reaction, data acquisition and analysis. Shelf life for a microarray after biomolecules have been spotted and attached can be years under proper storage conditions. That same surface may need to be spotted onto within several months after the surface chemistry has been made for best results.

Rule 4. Accurate biological representation of each sample

The density of reactive groups and/or attachment method on the surface must be uniform across the entire substrate to ensure identical coupling of biomolecules at each microarray location. The molecules attached to the surface must reflect an accurate representation of the sample from the source plates. Samples must not be allowed to attach to the source plate and reach the surface chemistry at the proper concentration. Lateral flow of the sample on the surface must be kept at a minimum to keep spots defined and the density of bound molecules within a spot to optimize reaction kinetics. "Too much of a good thing" is true when it comes to microarray spots...too little will compromise results as well. The surface must be completely homogenous. Without homogeneity, different amounts of biomolecule will attach in different areas of the substrate and compromise quantitation. Regardless of the printing technology (contact or non-contact), the samples being printed at a spot location are being deposited in saturating volumes to the attachment sites of each location. What does not attach to the surface in each spot washes away in the pre-processing steps of a microarray.

Rule 5. A microarray surface must be planar.

Surface flatness is important to achieve high quality printing and detection. Accurate robotics and sophisticated printing devices are used to deposit array elements. That means the distance between the printing surfaces and printing mechanism must be calibrated within a minimum of tens of microns for high quality printing to take place. Surface roughness, parallelism, and flatness are all important characteristics. Unlike contacting printing with the 946 and Stealth Micro Spotting Devices, spot size of non-contact delivery systems is determined by how far away the delivery nozzle is from the printing surface. In other words, the farther a sample travels through the air, the bigger the spot gets. Surfaces that deviate in height will compromise spot quality. Additionally current microarray scanners have focal planes in the resolution range 5 to 50 microns. Accurate planarity of the substrate is required to maintain proper focus for acquisition. This is not a problem if your detection instrument as dynamic auto focus...many microarray detection instruments do not have this feature. Reacted microarrays must stay in focus during scanning and the physical properties of said substrate and reacted immobilized array elements should not change during or after scanning.

Rule 6.The surface must have low intrinsic background noise.

Fluorescent detection instruments dominates the microarray industry, however, colorimetric, chemiluminescent, light scattering, surface plasmon resonance, planar wave guides and others are being implemented. Regardless of the detector, the surface must not significantly contribute to the background noise of the detection system. For example, surfaces such as non-reflective clean white membranes read as zero background on the SpotWare Colorimetric Scanner. Glass is the preferred material for fluorescent-based detection devices, since white surfaces reflect photons into the PMT or CCD detector and cause high background.

Rule 7. Standard physical dimensions of the substrate are required.

The same physical size of each substrate facilitates automation for manufacturing and processing....thus dramatically increasing microarray usability. The standard in the microarray industry is 25 mm x 76 mm x ~1 mm. Affymetrix is one of the few examples of successful implementations of microarray technology outside this standard format. ArrayIt, Agilent, NimbleGen and many other organizations has standardized on the microscope size slide glass format. A standard format assures compatibly with open microarray platforms, reduces cost, promotes innovation and increases flexibility for the end user by empowering the use of products from multiple vendors.

Rule 8. Substrates require lot-to-lot, piece-to-piece consistency.

Each substrate must be the same to guarantee accurate results. A surface used in an experiment must work the same from one day to the next, one experiment to the next. Without consistency, it is impossible to plan, design, execute, analyze and compare experiments over time.

Rule 9. A microarray surface must be amenable to mass production

A lab running a microarray test could use dozens to hundreds of microarrays per day. That means that only one lab and one application requires ~25K substrates per year. Any surface must meet all the rules presented here and allow for mass production rates to guarantee availability. Surfaces prior to and after sample immobilization that do not require special storage conditions and have a long shelf life will be most desired. The ability for mass production allows for economies of scale, which leads to the most important characteristic, the product be affordable.

Case Study: Adhering to the rules

Our surface chemistry product development efforts adhere to this list of criteria. Our SuperEpoxy 2 surface is a good example. This surface is designed to bind biomolecules via free primary amine, thiol and hydroxyl groups covalently...making it useful for DNA, Protein and Peptide microarray applications. This type of reactive surface has tested favorably when compared to other 2D and 3D coupling strategies (see comparison below). To make the product we start with sheets of glass and manufacture it to be 25mm x 76mm x 0.96 mm size. Thickness is 0.96 mm for the reason that some of the surface of the glass is removed during our high precision polishing process. This polishing process makes the surface of the glass atomically homogenous. This homogeneity has been confirmed by AFM.

The surface is then cleaned, sterilized, and activated in class 100 cleanrooms. The surface is made active with primary amine binding reactive epoxide groups with covalent silane chemistry. Our precision in, precision out approach that takes advantage of the atomically homogenous glass and covalent chemistry assures our end result is homogenous. Without a perfect homogenous glass surface to start with, any chance of achieving a homogenous surface after silanization is lost. Our covalent approach allows us to easily remove reactive groups that do not bind in the activation process, leaving a pristine homogenous surface. It is an important to note the distinction between a treated and coated surface. A coating is a monolayer on top of the glass, and a treatment completely modifies the glass. All manufacturing processes are performed in a cleanroom setting to assure strict environmental control to further improve cleanliness and lot of lot consistency.

Advantages of 2 dimensional surface chemistry for microarray
(activated homogeneous glass)

• –Better defined spot morphology (no diffusion)
• –Inherent lower background (glass)
• –Compatible with SPR, planar wave guides, RLS and other exotic detection strategies
• –High specificity of binding
• –Non-porous surface (no place to trap any contaminate in processing) –Covalent and/or specific binding to avoid altering biological activity

Advantages of 3 dimensional surface chemistry for microarray

(membranes, filters & gels)

• –High binding capacity (absorption)
• –Compatible with fluorescent, chemiluminescent, and colorimetric detection
• –Longer history of use (comfort level for users such as nitrocellulose, nylon and PVDF
• –Less expensive labeling reagents and reading equipment (colorimetric) –3D capture to avoid altering biological activity

If you would like to discuss microarray surface selection, please contact me. 408-744-1331, todd@arrayit.com www.arrayit.com .