High throughput assay helps to manage screening data at Harvard Medical School
Fred Harbinski has a degree in plant biology from the University of California, Berkeley, where he studied fungal systematics.
He followed with two years of graduate work at Harvard University studying deep sea marine biology and bacterial evolution.
He currently manages a high throughput facility in the Tosteson Laboratory at Harvard Medical School, where they are screening for inhibitors of translation initiation for cancer therapy. "When I joined the Tosteson Laboratory at Harvard Medical School two years ago, our cancer biology group consisted of just seven individuals: two instructors, two students, two technicians, and one very driven PI.
"With two functional multi-pipettors between us, pushing fifty compounds a week through our series of biological assays was considered an accomplishment.
"A series of three-ring binders contained the sum of our labours: carried to every lab meeting, the relative merits of various scaffolds was debated blot by blot, page by page.
"A tripling in our laboratory size, coupled with the addition of a fully automated high-throughput screening facility, necessitated a revision of our information management system.
"After a careful review of the available options, we followed the advice of one of our NCI collaborators and became involved in the beta testing of CambridgeSoft's BioAssay HTS application.
"The backbone of BioAssay HTS is its virtual plate library, containing information on nearly every 96 and 384 well plate that passes through our screening facility.
"We began by populating our master plate library with the contents of the NCI Open Chemical Repository, a 3400-plate library containing more than 140,000 compounds.
"Organised by barcode designation, plates can be viewed in browse or edit mode, plate or chart form, complete with compound structure.
"A search function makes locating individual compounds relatively easy. "A click on any given well brings up a subwindow displaying relevant compound attributes such as molecular weight, formula, and solubility, as well as quantity remaining, solvent, and number of freeze-thaw cycles.
"Flexibility in the choice of fields displayed meant that we were also able to incorporate existing biological data, such as GI50 data from NCI's human tumour cell line screen.
"With the master library complete, tracking compounds to their final location on an assay plate is simply a matter of plate replication and reformatting.
Commonly used reformatting techniques, such as combining four 96-well plates to create a 384-well daughter plate, can be stored as templates in the form of a csv file, and later invoked with ease by following a series of menus following the 'create daughter plate' command.
By tailoring the 'plate format' folder, users can define the location of positive and negative controls, compound replicates, and compound concentrations to reflect actual assay formats used. "Drop-down menus available in edit mode then make application of these formats to daughter plates particularly straightforward.
"Plate management and compound tracking, however, is just the beginning of any high-throughput screening venture.
"The ultimate fate for almost every replicated plate, after all, is to be converted into a series of numbers representing either fluorescence polarisation, luminescence, or absorbance units, and each of these numbers in turn must then be interpreted for biological meaning.
"And it's here, in the analysis of overwhelming volumes of raw data, where we have found BioAssay HTS to be most useful.
"Each assay is initially defined with a series of nested tables, starting with a raw data or 'wells' table.
"Successive tables draw from values created in lower tables: for example, a wells table may subtract a background value, the next table may average wells of like concentration, and a third table may graph the averaged points along a sigmoidal dose-response curve.
"Once imported, the data can be examined at the level of any of these tables, from a Z factor for the entire run to the relative fluorescent units measured in well H1.
"In addition, information from any table can be displayed in plate or chart format, while user defined colour-coding allows for the rapid identification of either hits or invalid data points.
"Users can also view multiple plates side by side, or export the window contents to Excel with the click of a button.
"We found the plate import template flexible enough to accommodate the output from almost any plate reader on the market, be it columnar or block, tab or space delimited, with one or many plates per file. "The data import wizard guides the user through a brief series of steps connecting the raw data with the virtual assay plate or plates created in the plate library, after which the process is completely automatic.
"No matter how impressive an array of liquid handlers, robot arms, and plate readers a laboratory may possess, the paydirt invariably lies in the data. "And whether motivated by the race for a cure, that edge in the marketplace, or simply by the chemists down the corridor, efficiency in its analysis is always a must.
"To this end, I consider BioAssay HTS a cornerstone of our highthroughput screening effort, an invaluable asset and tool".
BioAssay HTS is supplied and supported in UK, Ireland, Germany, Denmark and the USA by Adept Scientific.
