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Method and system for DNA analysis

a dna analysis and method technology, applied in the field of dna analysis process, can solve the problems of over-examination of assay results, significant error in dna fragment size and concentration, and inability to achieve the desired tolerance of assays,

Inactive Publication Date: 2010-01-14
PERLIN MARK W
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

"The present invention is related to methods and systems for analyzing nucleic acid samples. The technical effects of the invention include improved accuracy and efficiency in analyzing genetic data, as well as improved resolution of DNA mixtures. The invention also provides a way to generate revenue from computer scoring of genetic data."

Problems solved by technology

However, these assays inherently produce data that have significant error with respect to the size and concentration of the characterized DNA fragments.
In spite of these improvements, the variability of these properties (between different instruments, runs, or lanes) can exceed the desired tolerance of the assays.
One inexact peak area method simply records the area under the curve; this approach does not account for band overlap between different peaks.
However, even with such advanced scoring technology, artifacts can obscure the results.
More importantly, insufficient data calibration can preclude the achievement of very low (e.g., <1%) data error rates, regardless of the scoring methods.
This problem is worse when different instruments are used, or when size separation protocols are not entirely uniform.
The result is that fragments can be incorrectly assigned to allele bins in a way that cannot be corrected without recourse to additional information (e.g., pedigree data) completely outside the STR sizing assay.

Method used

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  • Method and system for DNA analysis
  • Method and system for DNA analysis
  • Method and system for DNA analysis

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Embodiment Construction

Data Generation

[0044]In the most preferred embodiment, genotyping data is generated using STR markers. These tandem repeats include mono-, di-, tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, deca- (and so on) nucleotide repeat elements. STRs are highly abundant and informative marker distributed throughout the genomes of many species (including human). Typically, STRs are labeled, PCR amplified, and then detected (for size and quantity) on an electrophoretic gel.

[0045]The laboratory processing starts with the acquisition of a sample, and the extraction of its DNA. The extraction and purification are typically followed by PCR amplification. Labelling is generally done using a 5′ labeled PCR primer, or with incorporation labeling in the PCR. Prior to loading, multiple marker PCR products in k−1 different fluorescent colors are pooled, and size standards (preferably in a kth different color) is added. Size separation and detection is preferably done using automated fluorescent DNA ...

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Abstract

The present invention pertains to a process for automatically analyzing nucleic acid samples. Specifically, the process comprises the steps of forming electrophoretic data of DNA samples with DNA ladders; comparing these data; transforming the coordinates of the DNA sample's data into DNA length coordinates; and analyzing the DNA sample in length coordinates. This analysis is useful for automating fragment analysis and quality assessment. The automation enables a business model based on usage, since it replaces (rather than assists) labor. This analysis also provides a mechanism whereby data generated on different instruments can be confidently compared. Genetic applications of this invention include gene discovery, genetic diagnosis, and drug discovery. Forensic applications include identifying people and their relatives, catching perpetrators, analyzing DNA mixtures, and exonerating innocent suspects.

Description

FIELD OF THE INVENTION[0001]The present invention pertains to a process for analyzing a DNA molecule. More specifically, the present invention is related to performing experiments that produce quantitative data, and then analyzing these data to characterize a DNA fragment. The invention also pertains to systems related to this DNA fragment information.BACKGROUND OF THE INVENTION[0002]With the advent of high-throughput DNA fragment analysis by electrophoretic separation, many useful genetic assays have been developed. These assays have application to genotyping, linkage analysis, genetic association, cancer progression, gene expression, pharmaceutical development, agricultural improvement, human identity, and forensic science.[0003]However, these assays inherently produce data that have significant error with respect to the size and concentration of the characterized DNA fragments. Much calibration is currently done to help overcome these errors, including the use of in-lane molecula...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): G06F19/00G01N33/48G16B25/10C12Q1/68G16B20/20
CPCG06F19/18C12Q1/6809G16B20/00G16B20/20G16B25/10
Inventor PERLIN, MARK W.
Owner PERLIN MARK W
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