BAMBAM: PARALLEL COMPARATIVE ANALYSIS OF HIGH-THROUGHPUT SEQUENCING DATA

摘要

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.

主权项

1. A computer-based genomic sequence analysis system comprising:
a memory storing at least two genomic sequence datasets including:
a tumor sequence dataset comprising genomic sequence strings of a tumor tissue sample of a patient; anda matched normal dataset comprising genomic sequence strings of a normal tissue sample of the same patient; and a sequence analysis engine coupled with the memory and configured to:
simultaneously and synchronously read a tumor sequence string from the tumor sequence dataset and a matched normal sequence string from the matched normal sequence dataset;wherein the tumor sequence string is incrementally synchronized with the matched normal sequence string based on a given genomic position;identify a genomic alteration associated with the given genomic position according to a probability derived from reads of the tumor sequence string and of the matched normal sequence string; andstore the genomic alteration in a device memory.