Variant database
First Claim
1. A method of describing mutations in a patient genome, the method comprising using a computer system comprising a memory coupled to a processor for:
- receiving data representing a first mutation and a second mutation in the patient genome;
creating a first instance of an abstract class of genomic feature and storing in the first instance a number representing a start position in a reference human genome and at least one IUPAC character representing a nucleotide found in the patient genome at the start position and not found in the reference human genome;
creating a second instance of the abstract class and storing in the second instance a second number representing a second start position, different from the first start position, in the reference human genome and at least one second IUPAC character representing a nucleotide found in the patient genome at the second start position and not found in the reference human genome;
creating a third instance of the abstract class and storing in the third instance;
the first instance, the second instance, and a description of a relationship between the first instance and the second instance; and
describing the mutations in the patient genome based on the third instance.
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Accused Products
Abstract
The invention provides a system and method for describing polymorphisms or genetic variants based on information about mutations and relationships among them. The invention uses object-oriented concepts to describe variants as variant objects and relations among those variants as variant relation object, each object being an instance of an abstract class of genomic feature and able to contain any number of other objects. Information about genetic disorders is stored in association with the object that represents the pathogenic variant. Genetic test results are used to access corresponding objects to provide a report based on variants or polymorphisms in a patient'"'"'s genetic material.
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Citations
16 Claims
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1. A method of describing mutations in a patient genome, the method comprising using a computer system comprising a memory coupled to a processor for:
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receiving data representing a first mutation and a second mutation in the patient genome; creating a first instance of an abstract class of genomic feature and storing in the first instance a number representing a start position in a reference human genome and at least one IUPAC character representing a nucleotide found in the patient genome at the start position and not found in the reference human genome; creating a second instance of the abstract class and storing in the second instance a second number representing a second start position, different from the first start position, in the reference human genome and at least one second IUPAC character representing a nucleotide found in the patient genome at the second start position and not found in the reference human genome; creating a third instance of the abstract class and storing in the third instance;
the first instance, the second instance, and a description of a relationship between the first instance and the second instance; anddescribing the mutations in the patient genome based on the third instance. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
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9. A system for providing a description of a variant in a patient'"'"'s genome, the system comprising:
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a processor; and a computer-readable storage device containing instructions which when executed by the processor cause the system to receive data representing a first mutation and a second mutation in the patient'"'"'s genome; create a first instance of an abstract class of genomic feature and store in the first instance a number representing a start position in a reference human genome and at least one IUPAC character representing a nucleotide found in the patient genome at the start position and not found in the reference human genome; create a second instance of the abstract class and store in the second instance a second number representing a second start position—
different from the first start position—
in the reference human genome and at least one second IUPAC character representing a nucleotide found in the patient genome at the second start position and not found in the reference human genome comprising a description of the second mutation as a variant of the reference;create a third instance of the abstract class and store in the third instance;
the first instance, the second instance, and a description of a relationship between the first instance and the second instance; andprovide a description of the genome based on the third instance. - View Dependent Claims (10, 11, 12, 13, 14, 15, 16)
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Specification