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Genomic profiling: repid method for testing complex biological sample for presence of many types of organisms

A biological sample and genome technology, applied in the field of obtaining genetic information, can solve the problems of quantitative amplification methods that are difficult to design correctly and have no repeatability

Inactive Publication Date: 2002-09-18
基因描绘系统有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, quantitative amplification methods are extremely difficult to design correctly, may not be reproducible, and are currently only applicable to a single species at a time

Method used

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  • Genomic profiling: repid method for testing complex biological sample for presence of many types of organisms
  • Genomic profiling: repid method for testing complex biological sample for presence of many types of organisms
  • Genomic profiling: repid method for testing complex biological sample for presence of many types of organisms

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Experimental program
Comparison scheme
Effect test

Embodiment 5

[0151] Each of these steps is described in more detail below.

[0152] Step 1: Designate a collection of ID sequences including genomic difference sequences and group-specific sequences, which will be probed in a given test. This step involves selecting the organism to be tested and selecting a family of diagnostic ID sequences.

[0153] The first step in genomic profiling involves selecting the type of organisms to detect. For example, for medical applications, human pathogens can be selected; for detecting food spoilage, bacteria that cause food toxicity can be selected; for forensic purposes, multiple human individuals can be selected, and so on. Organisms selected for a particular test may vary widely in their genetic makeup, such as members of different kingdoms (i.e., viruses, bacteria, archaea, fungi, protozoa, plants, and animals); alternatively, the organisms selected may be a Smaller groups such as members of a species. An important application of genomic profilin...

Embodiment 2

[0319] Quantitative Analysis: What is the pathogen titer in the clinical sample? A powerful feature of genomic profiling assays is the ability to quantify pathogens in biological samples. Once target organisms have been identified by fingerprinting, their presence can be quantified by in situ hybridization with a portion of the original biological sample prepared according to standard methods (eg, Huang et al., Modern Pathology 11:971-977, 1998). I use a single molecule sensitive but simple method sufficient to detect nucleic acid sequences in a single organism (Huang et al., supra, 1998). This method is used with labeled probes for hybridization to the detection array. Alternatively, in situ hybridization can be performed using any of the biologically characteristic group-specific probes detectable by hybridization to the array. Example 2. Detection of the presence of pathogens in respiratory samples

[0320] pneumonia. Pneumonia is the most common cause of death from inf...

Embodiment 4

[0352] Identify pathogens present in blood samples. Blood samples were lysed and fingerprinted as described above for the reference strains, except ID probes from all bloodstream pathogen groups in Table 7 were included in the hybridization reaction. Pathogens present in the blood sample are identified by comparing the obtained fingerprints with those in a database of fingerprints of reference strains. Example 4. Forensic identification using genomic profiling assays

[0353] An overview of forensic identification. Identifying the origin of cellular samples is an important aspect of modern forensic analysis. Genetic identification of forensic samples requires amplification of DNA in cellular material, often only available in microscopic amounts, and comparison of the DNA with that of other individuals. Current methods of genetic identification generally require analytical gel electrophoresis, a step that is extremely time consuming and technically inappropriate for many for...

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Abstract

The present invention provides a method called genome distribution analysis, which simultaneously scans the nucleic acid sequences (including genome differential sequences, group-specific sequences, and DNA polymorphisms) of various types of biological characteristics in complex biological samples. exist. The invention also includes probes, detection assemblies and related molecules for use in the methods of the invention.

Description

Background of the invention [0001] The present invention relates to obtaining genetic information from complex biological samples such as body samples (eg blood, urine, sputum and feces). In medicine, identification of infectious organisms in such samples is important for optimal treatment of infections and maintenance of public health. Determining whether a patient has a genetic disease and forensic identification also rely heavily on the analysis of genetic information from body samples. [0002] Although current procedures for diagnosing infectious agents include complex panels of several hundred tests, a large proportion of infectious organisms often go undetected. For example, attempts to identify the infectious agent in patients with pneumonia, the most common cause of death from infectious diseases in the United States, have been successful only about half the time. [0003] Many diseases such as pneumonia, meningitis and acute gastrointestinal diseases are characteri...

Claims

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Application Information

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IPC IPC(8): C12N15/09C12Q1/68C12R1/01G01N33/566G01N33/53
CPCC12Q1/6827C12Q1/68Y02A50/30
Inventor D·斯特劳斯
Owner 基因描绘系统有限公司
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