Perkinelmer Las, Inc.

General Scanning, Inc.

Perkinelmer Health Sciences, Inc.

Packard Instrument Company, Inc.

Ultivue, Inc.

Packard Bioscience Corporation

Packard Biochip Technologies, LLC

Packard Bioscience Company

Mack J Schermer

Mark Norman Bobrow

Karl Edwin Adler, Jr

C Brian Candiloro

Avery Osgood

Michael J Natan

Mael Manesse

Todd J Stephan

Abdul Majeed Mohammed

Mona L Phaff

Karl Edwin Adler

Philip Richard Buzby

Roger Dowd

Carl Brian Candiloro

Paul St Cyr

Thomas R Mullinax

Donald T Regan

Jun Yang

Robert Milkowski

Hans Bengtsson

Paul E Glynn

Roger D Dowd

Rolland Zeleny

Marc Silvagni

C Todd Lombardo

Ron Achin

Markus Weber

Jr Karl Edwin Adler

Mark N Borrow

Marc Silvaghi

Compositions, kits and methods for detecting a plurality of targets are provided herein. A probe-set composition is provided, including one or more first probes and one or more second probes. Each of the first probe includes a nucleic acid sequence complementary to a nucleic acid barcode of a corresponding target-specific binding partner, a first label, and a cleavage site for a first cleavage agent, wherein the first cleavage agent is capable of releasing the first label. Each of the second probes includes a nucleic acid sequence complementary to a nucleic acid barcode of a corresponding target-specific binding partner, a second label, a quench moiety that renders the second label undetectable, and a cleavage site for the first cleavage agent. The first cleavage agent is capable of releasing the quench moiety, whereby the second label is rendered detectable.

Methods and compositions for sequentially detecting targets

Encoded bead multiplex assays for chromosomal gains and losses are provided that provide the benefits of complex, large template DNA sources, such as BAC DNA, as the probe material without bead networking or other assay performance problems. Reagents for assaying DNA are described herein which include a plurality of encoded particles having attached amplicons amplified from a template DNA sequence. Each individual attached amplicon includes a nucleic acid sequence identical to a random portion of the template DNA sequence, wherein the amplicons together represent substantially the entire template DNA and wherein the nucleic acid sequence identical to a random portion of the template DNA sequence of each individual amplicon is shorter than the entire template DNA.

Reagents and methods relating to DNA assays using amplicon probes on encoded particles

DNA assays using amplicon probes on encoded particles

A method and apparatus are provided for washing and drying pins in a microarray spotting instrument. The apparatus includes an array of chambers, each for receiving one of the pins of the spotting instrument. To wash the pins, streams of wash fluid are directed at the pins. To dry the pins, a gas such as air is flowed over pin surfaces.

Method for washing and drying pins in microarray spotting instruments

The invention provides an apparatus for interrogating an optical biosensor. The apparatus includes (a) locating means for positioning one or more optical biosensors; (b) calibration means for generating a reference measurement; (c) one or more biosensors for generating one or more sample measurements, the biosensors being substantially planar and removable from the apparatus; (d) a reading means for interrogating biosensor and calibration means, and (e) a transport means for moving one or more of a biosensor, the calibration means and the reading means, whereby the reading means is positioned to interrogate the biosensor and the calibration means.

Methods, apparatus and compositions for improved measurements with optical biosensors

A method and apparatus are provided for automatically sensing the presence (or absence) of spot dispensers such as pins in various possible mounting locations in the printhead of a microarray spotting instrument. Pin-location data obtained by the method and apparatus is provided to the computer controller of the instrument, which uses the data to control the motion of the printhead during operation of the instrument. A pin detection apparatus includes one or more sensor elements that automatically sense possible pin locations in the printhead for the presence of pins. The sensor elements are preferably arranged in an array corresponding to the array of pin locations in the printhead so that pin detection at each pin location can be performed simultaneously. Various types of sensor elements can be used to locate pins in a printhead. For example, sensors can be used that are remote from or attached to a printhead. Pin sensors can be used that sense pin locations from various positions relative to the printhead including above or below the printhead. Also, pin sensing can be by contact or non-contact mechanisms. The method and apparatus allow pin positions in a printhead to be quickly and accurately determined, and without significant risk of damaging the pins, which are fragile.

Method and apparatus for automatic pin detection in microarray spotting instruments

Detection apparatus for performing surface plasmon resonance (SPR) measurements on a sample includes a support having side walls and a bottom wall defining a plurality of adjacent wells. The bottom wall has integrated therein SPR detectors underlying the wells for detecting the refractive indexes of samples deposited in the wells. Each SPR detector includes a prism having an exterior entrance surface, an exterior exit facet and an interior sensing surface located at the bottom of the overlying well, and a thin metal layer coated on the sensing surface. The prism may be molded from a transparent polymer into the bottom of a standard-format microplate structure. That structure may be used in conjunction with an SPR measuring or reading instrument to perform label-less assay measurements on various samples in an efficient and reliable manner. A method of acquiring the assay measurements is also disclosed.

Plasmon resonance measuring method and apparatus

Methods and systems are disclosed that include an optical device for providing information about one or more samples. The system includes well(s) for holding the sample(s), and in one embodiment, the optical device(s) have non-parallel sidewalls optically contacting the well(s) for providing the information about the sample(s) in the well(s). In some embodiments the optical devices may be truncated prism(s). In some embodiments the optical devices are part of a unibody structure with the well(s).

Optical device integrated with well

A method and system are disclosed for automatically creating crosstalk-corrected data of a microarray utilizing calibration dye spots each of which comprises a single pure dye. A microarray scanner, such as a confocal laser microarray scanner, generates dye images, each of which contains at least one of the calibration dye spots for each of the output channels of the scanner. For each of the calibration dye spots, an output of each of the output channels is measured to obtain output measurements. A set of correction factors is computed from the output measurements to correct the data subsequently gathered from the microarray scanner. In other words, the correction factors are applied to quantitation or measurement data obtained from microarray images which contain spots having dyes of known or unknown excitation or emission spectra to obtain crosstalk-corrected data.

Method and system for automatically creating crosstalk-corrected data of a microarray

A scanner system analyses data plotted in a scatter plot in accordance with user-specified criteria or statistical measures from the data population, to produce a scatter plot that displays in the plotted data the boundaries for the selection of out-lyer points and/or otherwise visually denotes in the plotted data which points are the out-lyer points. The scanner system analyzes the underlying data based on user-specified differential expression ratios, or based on criteria associated with the statistics of the data population, to produce out-lyer boundaries that are represented by diverging lines. Alternatively, the system may analyze the underlying data based on absolute expression levels, to produce boundaries that are represented in the plot by lines that meet at an identity line of slope. The scanner system may also combine several criteria and produce boundaries that denote as out-lyers the data that, for example, show both sufficient differential expression and also include individual expressions that are sufficiently above an associated noise floor.

Interactive system for analyzing scatter plots

The disclosed pin-lifter can selectively lift pins partially out of a printhead of a spotting instrument and thereby prevent the lifted pins from contacting the substrate during any printing. Methods of using pin-lifters to increase the rate of production of compact microarrays are disclosed.

Method and apparatus for producing compact microarrays

The disclosed spotting instrument includes one or more sensors that are mechanically fixed to the instrument's printhead. The sensors enable the instrument to detect whether a substrate is mounted in a particular holder of the instrument's substrate station prior to attempting to print spots onto that substrate. Similarly, the sensors enable the instrument to detect whether a reservoir is mounted in a particular holder of the instrument's well station prior to attempting to collect a sample of target material from that reservoir. The sensors also enable the instrument to read bar code labels affixed to substrates or reservoirs mounted in the instrument.

Microarray spotting instruments incorporating sensors and methods of using sensors for improving performance of microarray spotting instruments

Growing community of inventors

Belmont, MA, United States of America

Mack J Schermer