BIOINFORMATICS SEARCH TOOL SYSTEM FOR RETRIEVING AND SUMMARIZING GENOTYPIC AND PHENOTYPIC DATA FOR DIAGNOSING PATIENTS

• US 20130212125A1
• Filed: 01/24/2013
• Published: 08/15/2013
• Est. Priority Date: 01/24/2012
• Status: Abandoned Application

• Current Assignee: The Board of Regents of the University of Colorado (University of Colorado System), University of Miami
• Original Assignee: The Board of Regents of the University of Colorado (University of Colorado System), University of Miami
• Inventors: Wierenga, Klaas Jan Johan, Jiang, Zhijie
• Application Number:
  US13/749,390
• Publication Number:
  US 20130212125A1
• Time in Patent Office: Days
• US Class Current: 707/769
• CPC Class Codes: G06F 16/245 Query processing
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/30 Data warehousing; Computing architectures

Abstract

A computer system having a processor, non-transitory memory and a communication system is described. The communication system is coupled to a network and communicates with one or more genetic databases using an internet protocol. The non-transitory memory stores processor executable code to cause the processor to (1) receive data indicative of genetic array data of a patient via the communication system, (2) conduct, via the communication system and the network, at least one query of one or more genetic databases of genotypic data and phenotypic data using the data indicative of patient genetic data and phenotypic data, and (3) provide results of the at least one query to provide a clinical synopsis of the patient.

Claims

1. A computer system, comprising:

a processor;

a non-transitory memory storing processor executable code to cause the processor to;

receive data indicative of genetic array from a patient representative of at least one chromosomal segment identifying at least one gene(s),

receive phenotypic data indicative of at least one physical characteristic of a patient, and

query, using search criteria including the data indicative of the genetic array and the phenotypic data, one or more gene databases containing data on diseases associated with the one or more gene(s) within the chromosomal segment and return results comprising one or more gene(s) and one or more phenotypic indicators for disease(s) associated with the one or more gene(s) within the chromosomal segment, and

a communication system transmitting the results via a network using an internet protocol.

2. The computer system of claim 1, wherein the processor executable code causes the processor to provide a data entry field for receiving the data indicative of the genetic array.

3. The computer system of claim 1, wherein the processor executable code causes the processor to provide a location unit input field to receive information indicative of a specific base pair location unit, and wherein the search criteria includes the information indicative of the specific base pair location unit.

4. The computer system of claim 1, wherein the processor executable code causes the processor to provide a genome assembly version input field to specify a genome assembly version of the data indicative of genetic array, and wherein the search criteria includes the genome assembly version.

5. The computer system of claim 1, wherein the processor executable code causes the processor to provide a query type input field, and wherein the search criteria includes the query type.

6. The query type input field of claim 5, wherein the query type is a query of runs of homozygosity.

7. The query type input field of claim 5, wherein the query type is a query of a microdeletion.

8. The query type input field of claim 5, wherein the query type is a query of a microduplication.

9. The computer system of claim 1, wherein the processor executable code causes the processor to provide a search type input field, and wherein the search criteria includes the search type.

10. The search type input field of claim 9, wherein the search type is a search for all genes within the at least one chromosomal segment.

11. The search type input field of claim 9, wherein the search type is a search for disorder associated genes within the at least one chromosomal segment.

12. The search type input field of claim 9, wherein the search type is a search for dominant inheritance pattern genes within the at least one chromosomal segment.

13. The search type input field of claim 9, wherein the search type is a search for recessive inheritance pattern genes within the at least one chromosomal segment.

14. The computer system of claim 1, wherein the processor executable code causes the processor to provide a data entry field for hierarchical phenotypic information, and wherein the search criteria include phenotypic information.

15. The computer system of claim 1, wherein the processor executable code causes the processor to provide a data entry field to receive clinical feature information, and wherein the search criteria include the clinical feature information.

16. A computer system, comprising:

a processor,

a communication system coupled to a network and communicating with one or more genetic databases using an internet protocol;

a non-transitory memory storing processor executable code to cause the processor to (1) receive data indicative of genetic array data of a patient via the communication system, (2) conduct, via the communication system and the network, at least one query of the one or more genetic databases of genotypic data and phenotypic data using the data indicative of patient genetic data and phenotypic data, and (3) provide results of the at least one query to provide a clinical synopsis of the patient.

17. A method, comprising the steps of:

receiving data indicative of at least a portion of a genetic array from a patient representative of at least one chromosomal segment identifying at least one gene(s);

receiving phenotypic data indicative of at least one physical characteristic of a patient;

querying one or more gene databases, using search criteria including the data indicative of the genetic array and the phenotypic data, the one or more gene databases containing data on diseases associated with the one or more gene(s) within the chromosomal segment;

returning a results set as one or more web pages comprising data indicative of one or more gene(s) and one or more phenotypic indicators for disease(s) associated with the one or more gene(s) within the chromosomal segment.

18. The method of claim 17, wherein the step of receiving phenotypic data includes the steps of generating a phenotype window having a standardized vocabulary of phenotypic abnormalities encountered in human disease.

19. The method of claim 18, wherein the standardized vocabulary is provided in a hierarchical format.