Bambam: parallel comparative analysis of high-throughput sequencing data
First Claim
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1. A method of deriving a differential genetic sequence object, the method comprising:
- providing access to a genetic database storing (a) a first genetic sequence string representing a first tissue and (b) a second genetic sequence string representing a second tissue, wherein the first and second sequence strings have a plurality of corresponding sub-strings;
providing access to a sequence analysis engine coupled with the genetic database;
producing, using the sequence analysis engine, a local alignment by incrementally synchronizing the first and second sequence strings using a known position of at least one of plurality of corresponding sub-strings;
using, by the sequence analysis engine, the local alignment to generate a local differential string between the first and second sequence strings within the local alignment; and
using, by the sequence analysis engine, the local differential string to update a differential genetic sequence object in a differential sequence database.
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Abstract
The present invention relates to methods for evaluating and/or predicting the outcome of a clinical condition, such as cancer, metastasis, AIDS, autism, Alzheimer'"'"'s, and/or Parkinson'"'"'s disorder. The methods can also be used to monitor and track changes in a patient'"'"'s DNA and/or RNA during and following a clinical treatment regime. The methods may also be used to evaluate protein and/or metabolite levels that correlate with such clinical conditions. The methods are also of use to ascertain the probability outcome for a patient'"'"'s particular prognosis.
76 Citations
51 Claims
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1. A method of deriving a differential genetic sequence object, the method comprising:
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providing access to a genetic database storing (a) a first genetic sequence string representing a first tissue and (b) a second genetic sequence string representing a second tissue, wherein the first and second sequence strings have a plurality of corresponding sub-strings; providing access to a sequence analysis engine coupled with the genetic database; producing, using the sequence analysis engine, a local alignment by incrementally synchronizing the first and second sequence strings using a known position of at least one of plurality of corresponding sub-strings; using, by the sequence analysis engine, the local alignment to generate a local differential string between the first and second sequence strings within the local alignment; and using, by the sequence analysis engine, the local differential string to update a differential genetic sequence object in a differential sequence database. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 48, 49, 50, 51)
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28. A method of providing a health care service, comprising:
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providing access to an analysis engine that is informationally coupled to a medical records storage device, wherein the storage device stores a differential genetic sequence object for a patient; producing, by the analysis engine, a patient-specific data set using presence of a local differential string or constellation of a plurality of local differential strings in the differential genetic sequence object for the patient; and producing, by the analysis engine, a patient-specific instruction based on the patient-specific data set. - View Dependent Claims (29, 30, 31, 32, 33, 34, 35)
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36. A method of analyzing a population, comprising:
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obtaining and storing a plurality of differential genetic sequence objects in a medical records database of a population, wherein the records database is informationally coupled to an analysis engine; identifying, by the analysis engine, a constellation of a plurality of local differential strings within the plurality of differential genetic sequence objects to produce a constellation record; and using, by the analysis engine, the constellation record to generate a population analysis record. - View Dependent Claims (37, 38, 39, 40, 41, 42, 43, 44)
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45. A method of analyzing a differential genetic sequence object of a person, comprising:
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storing a reference differential genetic sequence object in a medical records database that is informationally coupled to an analysis engine; calculating, by the analysis engine, a deviation between a plurality of local differential strings in the differential genetic sequence object of the person and a plurality of local differential strings in the reference differential genetic sequence object to produce a deviation record; using, by the analysis engine, the deviation record to generate a person-specific deviation profile. - View Dependent Claims (46, 47)
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Specification