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US 11,634,779 B2Granted
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 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 derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.
Claims14
A method comprising:
- (a) obtaining a biological sample from a subject;
- (b) selectively enriching the biological sample for at least 1,000 cell-free DNA molecules from genomic regions known to harbor phased variants;
- (c) obtaining, by a computer system, sequencing data for the at least 1,000 cell-free DNA molecules from a subject;
- and
- (d) processing, by the computer system, the sequencing data to identify one or more cell-free DNA molecules of the at least 1,000 cell-free DNA molecules, wherein identifying the one or more cell-free DNA molecules comprises aligning reads corresponding to each of the at least 1,000 cell-free DNA molecules to a reference human genome, wherein each of the one or more cell-free DNA molecules comprises a plurality of phased variants relative to a sequence from the reference genome, wherein at least 10% of the one or more cell-free DNA molecules comprises a first phased variant of the plurality of phased variants and a second phased variant of the plurality of phased variants that are separated by at least one nucleotide.
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Dependencies are inferred from the claim text.