BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA
First Claim
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1. A parallel genomic comparative analysis system comprising:
- a memory; and
an sequence analysis engine coupled with the memory and configured to;
identify a genomic position within a reference genome;
access a first file storing tumor sequence data including short reads associated with a tumor tissue;
access a second file storing match normal sequence data short reads associated with a matched normal tissue;
store in the memory a tumor dataset having tumor short read sequences from the first file where the tumor short read sequences overlap the genomic position;
store in the memory a matched normal dataset having matched normal short read sequences from the second file and that overlap the genomic position;
select a tumor genotype and a matched normal genotype that maximize a joint probability as a function of the tumor short read sequences and the match normal short read sequences at the genomic position; and
store a difference between the tumor genotype and the matched normal genotype in a device memory.
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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.
16 Citations
20 Claims
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1. A parallel genomic comparative analysis system comprising:
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a memory; and an sequence analysis engine coupled with the memory and configured to; identify a genomic position within a reference genome; access a first file storing tumor sequence data including short reads associated with a tumor tissue; access a second file storing match normal sequence data short reads associated with a matched normal tissue; store in the memory a tumor dataset having tumor short read sequences from the first file where the tumor short read sequences overlap the genomic position; store in the memory a matched normal dataset having matched normal short read sequences from the second file and that overlap the genomic position; select a tumor genotype and a matched normal genotype that maximize a joint probability as a function of the tumor short read sequences and the match normal short read sequences at the genomic position; and store a difference between the tumor genotype and the matched normal genotype in a device memory. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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16. A parallel genomic comparative analysis system comprising:
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a memory; and a sequence analysis engine coupled with the memory and configured to; access a first file storing tumor sequence data including short reads associated with a tumor tissue; access a second file storing matched normal sequence data short reads associated with a matched normal tissue; align, relative to a first genomic position within a reference genome, the short reads associated with the tumor tissue with the short reads associated with the matched normal tissue; process at the same time all aligned short reads to determine a difference between the tumor sequence data and the matched normal sequence data; and store a difference between the tumor sequence data and the matched normal sequence data in a device memory. - View Dependent Claims (17, 18, 19, 20)
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Specification