Eureka AIR delivers breakthrough ideas for toughest innovation challenges, trusted by R&D personnel around the world.

Methods and apparatus for processing a sample of biomolecular analyte using a microfabricated device

a microfabricated device and biomolecular analyte technology, applied in the direction of fluid pressure measurement, liquid/fluent solid measurement, peptide, etc., can solve the problems of increasing the speed of str analysis, significant decreases in electrophoretic run-time, etc., to achieve baseline-resolved electrophoretic separation of single-locus str samples, improve speed, and improve the effect of speed

Inactive Publication Date: 2006-07-06
ADOURIAN ARAM S +4
View PDF19 Cites 36 Cited by
  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0014] In general, the term “biomolecular analyte” refers to both non-synthetic and synthetic nucleic acids (e.g., DNA and RNA) and portions thereof, and biological proteins. Described herein are practical ultra-fast techniques for allelic profiling of such biomolecular analyte. In particular, the techniques involve using a microfluidic electrophoresis device to analyze short tandem repeats (STRs) within a DNA sample. An assay method of the present invention has made it possible to rapidly achieve baseline-resolved electrophoretic separations of single-locus STR samples. In one embodiment, the assay permits baseline-resolved electrophoretic separations of single-locus STR samples in approximately 30 seconds. In addition, analysis of samples (e.g., PCR samples) containing loci defined or characterized by an STR which differs in the number or repeats is performed rapidly (e.g., at a rate which represents a 10-to-100-fold improvement in speed relative to capillary or slab gel systems) using the allelic profiling assay described herein. For example, analyses of PCR samples containing the four loci CSF1PO, TPOX, THO1 and vWA (abbreviated as CTTv) can be performed in less than two minutes. This constitutes a 10-to-100-fold improvement in speed relative to capillary or slab gel systems.
[0027] Preferably, the step of positioning the electromagnetic loading device includes the step of actuating a robotic assembly that supports the electromagnetic loading device such that the electromagnetic loading device moves to a programmed position relative to the test plate. This allows the sample to be positioned accurately and consistently from test to test.
[0031] Preferably, the test module assembly includes a heating device, supported by the housing, that provides heat to the dielectric plate member when power is provided to the heating device. The heat facilitates the separation of components within the sample during electrophoresis.
[0034] Preferably, the dielectric plate member includes multiple sets of channels. Each set of channels includes an injection channel and a separation channel. The injection channel of each set extends from the upper planar surface to the lower planar surface. The separation channel of each set extends within the dielectric plate member in a plane parallel with the upper and lower planar surfaces and intersects the injection channel of that set. The injection channels of the multiple sets of channels may be parallel with each other. These features of the invention increase the channel density (i.e., the number of channel sets per unit area of the plate member) of the dielectric plate member enabling more tests to be scanned by an individual scanner in a fixed position relative to the dielectric plate member. Furthermore, the orthogonal orientation of the injection channels (relative to the plane of the plate member) improves initial separation of the components within the sample during electrophoresis in the direction of the injection channel.

Problems solved by technology

Nevertheless, significant decreases in electrophoretic run-times would greatly increase the speed of STR analysis.

Method used

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
View more

Image

Smart Image Click on the blue labels to locate them in the text.
Viewing Examples
Smart Image
  • Methods and apparatus for processing a sample of biomolecular analyte using a microfabricated device
  • Methods and apparatus for processing a sample of biomolecular analyte using a microfabricated device
  • Methods and apparatus for processing a sample of biomolecular analyte using a microfabricated device

Examples

Experimental program
Comparison scheme
Effect test

example 1

Determination of Factors Which Influence the Speed of STR Analysis

[0130] Initially, the general operation of the microfabricated device for genotyping by STR analysis was characterized. The objective was to determine the factors which influence the ultimate speed of such analyzes in microchip devices. Device performance was followed for the STR system CTTv, which consists of the four loci CSF1PO, TPOX, THO1 and vWA, each of which contains STR alleles which differ in length by four base pairs. The four loci, CSF1PO, TPOX, THO1 and vWA, contain 9, 5, 7, and 8 common alleles respectively. FIG. 12A shows the separation of the CTTv ladder ranging from 140 to 330 bases by microchip gel electrophoresis using one of our devices. This ladder was used as an internal sizing standard for the allelic profiling. In FIG. 12A the alleles of all the four loci are well resolved in less than two minutes with measured resolution R,

R=([2 ln 2]1 / 2)(t2−t1) / (hw1+hw2),   (1)

where tn is the retention tim...

example 2

Assay of PCR Amplified Samples

[0136] The microchip device was used for genotyping of PCR amplified samples of eight individuals which were spiked with the CTTv ladder as the internal size standard and assayed on the microchip gel system. In all eight cases, the alleles could be identified with no ambiguity in under two minutes and the results were in complete agreement with data produced by traditional slab gel electrophoresis, which typically required 80, 94, 112 and 143 min to detect and resolve the alleles of vWA, THO1, TPOX, and CSF1PO respectively. The spiking experiment for one of the individuals is shown in FIG. 12B. The individual is clearly homozygous for vWA (allele 14) and heterozygous for THO1 (alleles 7 / 9), TPOX (alleles 8 / 9) and CSF1PO (alleles 10 / 14).

[0137] Results, thus, have demonstrated that the quadruplex STR system CTTv can be analyzed with high accuracy in less than two minutes and a single locus in 30 seconds by microchip gel electrophoresis. Compared to capi...

example 3

Evaluation of the Feasibility of Loading Schemes

[0142] A glass microchip with laser-drilled injection ports leading to microchannels was interfaced with a 1 cm thick gasket fabricated from polydimethylsiloxane (PDMS) silicone elastomer material (Dow Coming Sylgard 184, Schenectady, N.Y.). Capillaries of inner diameter 100 μm and outer diameter 375 μm were molded into the gasket and set in place while the PDMS cured to a semi-rigid final state. No rigid support structure was used in these trials, and the capillary-gasket system was aligned to the injection holes on the microchip manually with the aid of a microscope. The free end of the 10 cm long capillary was inserted into a container of fluorescein and a voltage of 50 volts per centimeter was applied between the container and the microchip channels. The microchip was illuminated with an argon ion laser source operating at 488 nm, and the fluorescing fluorescein was observed flowing from its original container to the microchannels...

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

PUM

PropertyMeasurementUnit
diameteraaaaaaaaaa
angleaaaaaaaaaa
lengthaaaaaaaaaa
Login to View More

Abstract

A technique processes a sample of biomolecular analyte. The technique uses an apparatus having a support assembly that receives and supports a test module, a load assembly that loads the sample of biomolecular analyte onto the test module, an electrophoresis assembly that applies a current to the test module such that components within the sample separate by electrophoresis, and a controller that controls operations of the load assembly and the electrophoresis assembly. The load assembly and the electrophoresis assembly are coupled to the support assembly. The controller controls the operation of the load assembly in an automated manner. Preferably, the test module includes a dielectric plate member having an upper planar surface and a lower planar surface that is spaced apart from and coplanar with the upper planar surface. The dielectric plate member has at least one set of channels that includes an injection channel and a separation channel. The injection channel extends from the upper planar surface to the lower planar surface. The separation channel extends within the dielectric plate member in a plane parallel with the upper and lower planar surfaces and intersects the injection channel.

Description

RELATED APPLICATIONS [0001] This application is a divisional of application Ser. No. 09 / 768,075 filed Jan. 23, 2001 which is a divisional of application Ser. No. 09 / 153,215, filed Sep. 14, 1998 (now U.S. Pat. No. 6,207,031) which claims the benefit of U.S. Provisional Application No. 60 / 058,798, filed on Sep. 15, 1997. [0002] The entire teachings of the above applications are incorporated herein by reference.GOVERNMENT SUPPORT [0003] The invention was supported, in whole or in part, by Grant No. RO1 HG01389 from the National Institutes of Health and Grant No. F49620-95-1-0165 from the Defense Advanced Research Projects Agency / Air Force Office of Scientific Research. The Government has certain rights in the invention.BACKGROUND OF THE INVENTION [0004] The human genome includes stretches of DNA composed of short tandem repeats (STRs). The analysis of such STRs is an important tool for genetic linkage studies, forensics, and new clinical diagnostics because STRs are abundant and their ...

Claims

the structure of the environmentally friendly knitted fabric provided by the present invention; figure 2 Flow chart of the yarn wrapping machine for environmentally friendly knitted fabrics and storage devices; image 3 Is the parameter map of the yarn covering machine
Login to View More

Application Information

Patent Timeline
no application Login to View More
Patent Type & Authority Applications(United States)
IPC IPC(8): C07K1/26B01L3/00B01L99/00G01N27/447G01N35/10
CPCB01L3/0275Y10T436/2575B01L3/5025B01L3/5027B01L3/502715B01L3/502753B01L2200/027B01L2200/0605B01L2200/0647B01L2200/0657B01L2300/0803B01L2300/0816B01L2400/0415B01L2400/0421B01L2400/043B01L2400/0442G01N27/44743G01N27/44782G01N35/10B01L3/0289
Inventor ADOURIAN, ARAM S.EHRLICH, DANIEL J.KOUTNY, LANCE B.MATSUDAIRA, PAUL T.SCHMALZING, DIETER R.
Owner ADOURIAN ARAM S
Who we serve
  • R&D Engineer
  • R&D Manager
  • IP Professional
Why Eureka
  • Industry Leading Data Capabilities
  • Powerful AI technology
  • Patent DNA Extraction
Social media
Eureka Blog
Learn More
PatSnap group products