US 6,673,547 B2 · DNA analysis system

Abstract

A genome DNA analysis method and a genome DNA analysis system of the present invention generates multiply-charged ions with 5 or more electric charges by an ionization process using air atomization. Also, a mass spectrometric spectrum thereof is detected and compared with predicted mass spectrum patterns in the presence or absence of polymorphism to determine a base at a polymorphic point.

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Drawings

Claims20

Dependent claims

A DNA analysis method for analyzing DNA polymorphism, comprising the steps of:

generating plural kinds of multiply-charged ions of a test DNA fragment by ionization, where each of the multiply-charged ions has five or more charges;
performing a mass spectrometry an the multiply-charged ions formed by the ionization so as to measure a mass spectrum of the test DNA fragment;
predicting possible mass spectrum patterns in each of two cases, where one of the two cases is that the test DNA fragment is polymorphic and an other of the two cases is that the test DNA fragment is not polymorphic, based on both an information about the number of each of four different nucleic acid bases that constitute the test DNA fragment and an information about a polymorphism point;
and comparing a plurality of the predicted mass spectrum patterns with the measured mass spectrum to determine a nucleic acid base on the polymorphism point.

1 more element

A DNA analysis method for analyzing DNA polymorphism, comprising the steps of:

sampling by supplying a sample including a test DNA fragment for ionization intermittently at a predetermined time period;
generating plural kinds of multiply-charged ions of the test DNA fragment by ionization, where each of the multiply-charged ions has five or more charges;
for performing a mass spectrometry on the multiply-charged ions formed by the ionization so as to measure a mass spectrum of the test DNA fragment;
performing the following treatment to obtain S(i) for the measured mass spectrum (I(i)) at an ordinal number “i”, S ⁡ ( i ) = I ⁡ ( i ) - ∑ n = 1 m ⁢ ⁢ w ⁡ ( n ) ⁢ ⁢ I ⁡ ( i - n ) ⁢
wherein m represents a predetermined natural number and w(n) represents a factor for the measured mass spectrum of the sample measured at n-th before the measurement of the sample which is measured at i-th;
predicting possible mass spectrum patterns in each of two cases, where one of the two cases is that the test DNA fragment is polymorphic and an other of the two cases is that the test DNA fragment is not polymorphic, based on both an information about the number of each of four different nucleic acid bases that constitute the test DNA fragment and an information about a polymorphism point, wherein the step of predicting includes predicting a mass-to-charge ratio (m/z;
m is an ion mass, z is a number of electric charges) of each of the plural kinds of multiply-charged ions and a relative ion intensity corresponding to the mass-to-charge ratio (m/z) in each of the two cases;
and
comparing a plurality of the predicted mass spectrum patterns with the measured mass spectrum to determine a nucleic acid base on the polymorphism point, wherein the step of comparing includes comparing the predicted mass-to-charge ratio (m/z) of the predicted mass spectrum patterns with a mass-to-charge ratio (m/z) of the measured mass spectrum and compares the predicted relative ion intensities of the predicted mass spectrum patterns with relative ion intensities of the measured mass spectrum, and wherein the S(i) is compared with each of the predicted mass spectrum patterns.

6 more elements

A DNA analysis method for analyzing DNA polymorphism, comprising the steps of:

sampling by supplying a sample including a test DNA fragment for ionization intermittently at a predetermined time period;
generating plural kinds of multiply-charged ions of the test DNA fragment ionization, where each of the multiply-charged ions has five or more charges;
performing a mass spectrometry on the multiply-charged ions formed by the ionization so as to measure a mass spectrum of the test DNA fragment;
performing the following treatment to obtain S(i) for the measured mass spectrum (I(i)) at an ordinal number “i”, S ⁡ ( i ) = I ⁡ ( i ) - ∑ n = 1 m ⁢ ⁢ w ⁡ ( n ) ⁢ ⁢ I ⁡ ( i - n ) ⁢
wherein m represents a predetermined natural number and w(n) represents a factor for the measured mass spectrum of the sample measured at n-th before the measurement of the sample which is measured at I-th;
predicting possible mass spectrum patterns in each of two cases, where one of the two cases is that the test DNA fragment is polymorphic and an other of the two cases is that the test DNA fragment is not polymorphic, based on both an information about the number of each of four different nucleic acid bases that constitute the test DNA fragment and an information about a polymorphism point, wherein step of predicting includes predicting a mass-to-charge ratio (m/z;
m is an ion mass, z is a number of electric charges) of each of the plural kinds of multiply-charged ions and a relative ion intensity corresponding to the mass-to-charge ratio (m/z) in each of the two cases;
and
comparing including calculating a total ion intensity of each of the predicted mass spectrum patterns with respect to a plurality of peaks in the range of a predetermined mass-to-charge ratio (m/z) and for selecting the predicted mass spectrum pattern which has a highest total ion intensity and comparing the predicted mass spectrum patterns having the highest total ion intensity with the measured mass spectrum to determine a nucleic acid base on the polymorphism point, and wherein the S(i) is compared with the selected predicted mass spectrum patterns.

6 more elements

A DNA analysis method for analyzing DNA polymorphism, comprising:

sampling by supplying a sample including a test DNA fragment for ionization intermittently at a predetermined time period;
generating plural kinds of multiply-charged ions of the test DNA fragment by ionization, where each of the multiply-charged ions has five or more charges;
performing a mass spectrometry on the multiply-charged ions formed by the ionization so as to measure a mass spectrum of the test DNA fragment;
performing the following treatment to obtain S(i) for the measured mass spectrum (I(i)) at an ordinal number “i”, S ⁡ ( i ) = I ⁡ ( i ) - ∑ n = 1 m ⁢ ⁢ w ⁡ ( n ) ⁢ ⁢ I ⁡ ( i - n ) ⁢
wherein m represents a predetermined natural number and w(n) represents a factor for the measured mass spectrum of the sample measured at n-th before the measurement of the sample which is measured at i-th;
predicting possible mass spectrum patterns in each of two cases, where one of the two cases is that the test DNA fragment is polymorphic and the other is that the test DNA fragment is not polymorphic, based on both an information about the number of each of four different nucleic acid bases that constitutes the test DNA fragment and an information about a polymorphism point, wherein the step of predicting includes predicting a mass-to-charge ratio (m/z;
m is an ion mass, z is a number of electric charges) of each of the plural kinds of multiply-charged ions and a relative ion intensity corresponding to the mass-to-charge ratio (m/z) in each of the two cases;
and
comparing a plurality of the predicted mass spectrum patterns with the measured mass spectrum to determine a nucleic acid base on the polymorphism point, wherein the step of comparing includes selecting the predicted mass spectrum pattern such that a sum of a square root of a difference between a relative intensity of the measured mass spectrum having the S(i) and a relative intensity of the predicted mass spectrum pattern is smallest.

6 more elements

A DNA analysis method for analyzing DNA polymorphism, comprising the steps of:

predicting mass spectrum patterns when plural kinds of multiply-charged ions generated from a test DNA fragment, where each of the multiply-charged ions has five or more charges, in each of two cases, where one of the two cases is that the test DNA fragment is polymorphic and an other of the two cases is that the test DNA fragment is not polymorphic, based on information of a number of each of four different nucleic acid bases that constitute the test DNA fragment and information of a polymorphism point;
generating plural kinds of multiply-charged ions from a sample containing the test DNA fragment, where each of the multiply-charged lone has five or more charges;
performing a mass spectrometry on the multiply-charged ions to measure a mass spectrum pattern;
selecting a predicted mass spectrum pattern that is most closely analogous to the measured mass spectrum pattern by comparing a plurality of the predicted mass spectrum patterns the measured mass spectrum pattern.

1 more element

Dependencies are inferred from the claim text.

Description10,335 words

Summary2,082 words

#1. Field of the Invention

#The present invention relates to measurements on biological materials, which require a high throughput. Specifically, the present invention relates to a method and system for analyzing DNA-polymorphisms in the human genome, such as single nucleotide polymorphisms (SNPs) that are single-base variations at a unique physical location among different individuals.

#2. Description of the Prior Art

Brief description of the drawings15 figures

#The above and other objects, features and advantages of the present invention will be apparent from the following detailed description of the preferred embodiments of the invention in conjunction with the accompanying drawings, in which:

#FIG. 1 is a schematic diagram that illustrates a genome DNA analysis system as a first embodiment of the present invention;

#FIG. 2 is a graphical representation that illustrates charts of mass spectra of outputs I(i), S(i), S(i−1), and S(i−2);

Detailed description7,922 words

#Preferred embodiments of the present invention will now be described with reference to the accompanying drawings.

#[First Embodiment]

#FIG. 1 is a schematic diagram that illustrates a genome DNA analysis system as one of preferred embodiments of the present invention. The genome DNA analysis system mainly includes three structural assemblies: a sample-preparation system, a measurement system, and a control system. The sample preparation system includes a sample treatment part 11 for preparing a sample, a container 12 in which a cleaning fluid is filled, a pump 14, and a sampling part 15. A sample prepared by the sample preparation system is transferred to the measurement system through the sampling part 15. The measurement system includes an ionization part 21 having a gas-supply part 22, and a mass spectrometric part 24 that carries out an analysis of multiply-charged ions 23 generated from the ionization part 21. Furthermore, the control system includes: an output prediction part 32 that predicts the results to be obtained from the analysis based on the sample information transmitted from the sample treatment part 11; an output analysis part 35 that analyzes an output from the mass spectrometric part 24 of the measurement system; a data analysis part 33 that generates the results of the sample analysis by performing a comparison between a predicted output from the output prediction part 32 and an actual output from the output analysis part 35; a recording part 34 that makes a record of the analyzing results from the data analysis part 33; and a control part 31 that controls the sampling part 15 of the sample preparation system and the output analysis part 35. Furthermore, as shown in FIG. 1, a display part 41 may be provided on the genome DNA analysis system. The display part 41 displays any information on its screen. The information includes the current analyzing status of the system (i.e., the information for defining whether the system functions normally or abnormally) and the latest analyzing results that include a mass spectrum.

Facts

Application

09/941,769Filed 30 Aug 2001

Priority

JP 2001-01035718 Jan 2001

Published

US 2002/0127566 A112 Sep 2002

Granted

6 Jan 2004

Term ended

30 Aug 2021

Estimated · how

20 years from earliest known nonprovisional domestic filing plus recorded patent term adjustment. Maintenance-fee lapses, terminal disclaimers and statutory extensions have not been checked. The continuity chain may be incomplete; this is not an enforceability determination.

Classification5 codes

H01J 49/10
Details: ion sources; Ion guns
C12Q 1/6827
Hybridisation assays: for detection of mutation or polymorphism
C12Q 1/6872
Methods for sequencing: involving mass spectrometry
H01J
Electric discharge tubes or discharge lamps

DNA analysis system

Life of this patent

DNA analysis system

Life of this patent

Life of this patent

Abstract

Drawings

Drawings

Claims20

Description10,335 words

Drawings

Classification5 codes

Life of this patent

Description10,335 words