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US 10,706,956 B2Granted
Bambam: parallel comparative analysis of high-throughput sequencing data
AssigneeThe Regents of the University of California
InventorsDavid Haussler, John Zachary Sanborn
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Abstract
Methods are provided 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.
Claims22
A sequence analysis computer system comprising:
- a file system storing a first digital sequence file and a different, second digital sequence file wherein each file includes sequence short reads that are aligned with respect to sequence locations;
- and
- at least one computer operating as a sequence analysis engine that is configured to:
- identify in the first and second digital sequence files a first common sequence location from the sequence locations;
- read from the first digital sequence file a first set of sequence short reads that overlap with the first common sequence location, thereby forming a first pileup stored in a memory;
- read from the second digital sequence file a second set of sequence short reads that overlap with the first common sequence location, thereby forming a second pileup stored in the memory;
- identify at least one variant as a difference among inferred bases at the first common sequence location as a function of the sequence short reads in the first pileup and the sequence short reads in the second pileup that overlap the first common sequence location by optimizing likelihoods of the inferred bases based on observed bases of the first pileup and the second pileup at the first common sequence location;
- and
- output the at least one variant in a file as a sequence difference between the first digital sequence file and the second digital sequence file.
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