SYSTEM AND METHOD FOR ANALYZING GENOME DATA

• US 20100161607A1
• Filed: 11/06/2009
• Published: 06/24/2010
• Est. Priority Date: 12/22/2008
• Status: Abandoned Application

• Current Assignee: Roche NimbleGen, Inc. (Roche Holding AG)
• Original Assignee: Roche NimbleGen, Inc. (Roche Holding AG)
• Inventors: Singh, Jasjit, Heilman, Kurt
• Application Number:
  US12/613,776
• Publication Number:
  US 20100161607A1
• Time in Patent Office: Days
• US Class Current: 707/737
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/50 Compression of genetic data

Abstract

A system and method for analyzing genome data includes receiving genome analysis data generated by a genome analysis device, such as a microarray scanner, reducing the genome analysis data, and transmitting the reduced genome analysis data over a wide area network to a client computer. The reduced genome analysis data may provide a summary of the unreduced genome analysis data. One of several methods may be used to reduce the genome analysis data for transmittal over the wide area network.

Claims

1. A system for analyzing genome data, the system comprising:

a processor; and

a memory device communicatively coupled to the processor, the memory device having stored therein a plurality of instructions, which when executed by the processor, cause the processor to;

receive genome analysis data generated by a genome analysis device, the genome analysis data comprising a plurality of data points;

receive a request for genome analysis data from a client computer over a wide area network, the request identifying a location range of interest of the genome analysis data;

reduce the genome analysis data located in the location range to generate a reduced genome dataset, wherein the reduced genome dataset comprises (i) a first number of data points that is less than a second number of data points of the genome analysis data located in the location range and (ii) outlier metrics; and

transmit the reduced genome dataset to the client computer over the wide area network in response to the request.

2. The system of claim 1, wherein to receive genome analysis data comprises to receive genome analysis data generated from a microarray assay performed using a microarray scanner.

3. The system of claim 2, wherein the microarray assay is one of a nucleic acid microarray assay and a peptide microarray assay.

4. The system of claim 2, wherein the microarray assay is a nucleic acid microarray assay comprising genomic deoxyribonucleic acid samples.

5. The system of claim 1, wherein the request identifies a start location and a stop location of the genome analysis data, the location range extending from the start location to the end location.

6. The system of claim 1, wherein the first number of data points is no greater than ten percent of the second number of data points.

7. The system of claim 6, wherein the first number of data points is no greater than one percent of the second number of data points.

8. The system of claim 1, wherein the size in bytes of the reduced genome dataset is less than about one percent of the size in bytes of the genome analysis data located in the location range.

9. The system of claim 1, wherein the outlier metrics comprises data points that represent at least one of (i) values above a determined maximum and (ii) values below a determined minimum.

10. The system of claim 1, wherein the outlier metrics comprises data points having numerical values falling outside a predetermined deviation range of a determined average value.

11. The system of claim 1, wherein the reduced genome dataset comprises a mean data point value, a median data point value, a minimum data point value, and a maximum data value.

12. The system of claim 1, wherein to reduce the genome analysis data comprises:

to define a plurality of data bins, each data bin being assigned an associated sub-range of the location range;

to allocate each data point of the genome analysis data located in a sub-range of the location range to the corresponding data bin; and

to summarize the plurality of data bins by defining at least a mean data point value, a median data point value, a minimum data point value, and a maximum data point value for each data bin.

13. The system of claim 1, wherein the wide area network comprises the Internet.

14. The system of claim 1, wherein the genome analysis data comprises first genome analysis data generated from an analysis of a test nucleic acid sample and second genome data analysis data generated from a reference nucleic acid sample, and the plurality of instructions further cause the processor to:

identify at least one data point of the first genome analysis data that is different in value from a corresponding data point of the second genome analysis data, wherein the reduced genome dataset comprises the at least one data point.

15. A method for analyzing genome data, the method comprising:

receiving, with a computer system, a request for gnome analysis data from a client computer over the Internet, the request identifying a location range of interest of the genome analysis data;

reducing, on the computer system, the genome analysis data located in the location range to generate a reduced genome dataset such that (i) the reduced genome dataset summarizes the genome analysis data located in the location range and (i) the size in bytes of the reduced genome dataset is no greater than one percent of the size in bytes of the genome analysis data located in the location range; and

transmitting the reduced genome dataset from the computer system to the client computer over a wide area network.

16. The method of claim 15, wherein reducing the genome analysis data comprises determining outlier metrics, the outlier metrics including data points having numerical values falling outside a predetermined deviation range of a determined average value.

17. The method of claim 15, wherein reducing the genome analysis data comprises determining a mean data point value, a median data point value, a minimum data point value, and a maximum data value based on the genome analysis data located in the location range.

18. The method of claim 15, wherein reducing the genome analysis data comprises:

defining a plurality of data bins, each data bin being assigned an associated sub-range of the location range;

allocating each data point of the genome analysis data located in a sub-range of the location range to the corresponding data bin; and

summarizing the plurality of data bins by defining at least a mean data point value, a median data point value, a minimum data point value, and a maximum data point value for each data bin.

19. The method of claim 15, wherein transmitting the reduced genome dataset comprises transmitting the reduced genome dataset from the computer system to the client computer over the Internet during a first time period that is less than a time period required to transmit the genome analysis data located in the location range to the client computer.

20. A tangible, machine readable medium comprising a plurality of instructions, that in response to being executed, result in a computing system:

receiving genome analysis data comprising first genome analysis data generated from a microarray analysis of a test nucleic acid sample and second genome data analysis data generated from a reference nucleic acid sample;

identifying at least one data point of the first genome analysis data that is different in value from a corresponding data point of the second genome analysis data;

reducing the genome analysis data located in the location range to generate a reduced genome dataset, wherein the reduced genome dataset comprises (i) a first number of data points that is less than a second number of data points of the genome analysis data and (ii) the at least one data point; and

transmitting the reduced genome dataset to a client computer over a wide area network in response to a request received from the client computer.