Methods and Systems for Analyzing Nucleic Acid Molecules
AssigneeThe Board of Trustees of the Leland Stanford Junior University
InventorsDavid M. Kurtz, Maximilian Diehn, Arash Ash Alizadeh
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Abstract
Processes and materials to detect cancer, transplant rejection, or fetal genetic abnormalities from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences indicative of a neoplasm, transplant rejection, or fetal genetic abnormality. Detection of somatic variants occurring in phase and/or insertions and deletions (indels) can indicate the presence of cancer, transplant rejection, or fetal genetic abnormalities in a diagnostic scan, and a clinical intervention can be performed.
Claims21
1-20. (canceled)
A method comprising:
- (a) obtaining sequence reads of DNA derived from cell-free DNA extracted from a human plasma sample;
- and
- (b) identifying circulating tumor DNA based on concordant detection of at least two non-reference events in a single sequence read compared to a reference genome, wherein the at least two non-reference events (i) occur in the sequence read within 170 nucleotides of each other and (ii) are separated by at least 10 nucleotides in the sequence read;
- wherein the identifying does not involve deduplication of the sequence reads using a molecular barcode, wherein the method is capable of detecting a tumor fraction of 1 part per million.
A method comprising:
- (a) obtaining sequence reads derived from at least 10,000 cell-free DNA molecules extracted from a human plasma sample;
- (b) comparing the sequence reads corresponding to the at least 10,000 cell-free DNA molecules to a reference genomic sequence, and identifying one or more circulating tumor DNA molecules based on concordant detection of at least two non-reference events in a single sequence read compared to the reference genomic sequence, wherein the at least two non-reference events (i) occur in the sequence read within 170 nucleotides of each other and (ii) are separated by at least 10 nucleotides in the sequence read;
- wherein the method does not involve deduplication of the sequence reads using a molecular barcode, wherein the method is capable of detecting a tumor fraction of 1 part per million.
Dependencies are inferred from the claim text.