Methods for preparing nucleic acid libraries for sequencing
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.
Claims30
A method for preparing an enriched library of nucleic acids for sequencing, the method comprising:
- identifying a patient-specific set of six or more genomic regions that harbor a plurality of phased variants that are within 170 base pairs of each other;
- obtaining a personalized set of nucleic acid probes that have been designed to enrich for phased variant-containing nucleic acids from the six or more genomic regions;
- preparing cell-free nucleic acids from the patient for sequencing;
- and
- selectively enriching the prepared cell-free nucleic acids from the patient for phased variant-containing nucleic acids from the six or more genomic regions via hybridization capture or amplification to form an enriched library of nucleic acids for sequencing;
- wherein identifying the patient-specific set of six or more genomic regions that harbor a plurality of phased variants comprises comparing sequencing data from a either a diseased sample from the patient or a cell-free DNA sample from the patient to sequencing data from a non-diseased sample from the patient;
- wherein at least 10% of phased variant-containing nucleic acids from the library of nucleic acids have a first phased variant and a second phased variant that are separated from each other by at least one nucleotide.
A method for preparing an enriched library of nucleic acids for sequencing, the method comprising:
- identifying a patient-specific set of three or more genomic regions that harbor a plurality of phased variants that are within 170 base pairs of each other;
- preparing cell-free nucleic acids from the patient for sequencing;
- and
- selectively enriching the prepared cell-free nucleic acids from the patient for phased variant-containing nucleic acids from the three or more genomic regions to form an enriched library of nucleic acids for sequencing;
- wherein at least 10% of phased variant-containing nucleic acids from the enriched library of nucleic acids have a first phased variant and a second phased variant that are separated from each other by at least one nucleotide.
A method for detection or monitoring of a disease, the method comprising:
- identifying a patient-specific set of three or more genomic regions that harbor a plurality of phased variants that are within 170 base pairs of each other;
- preparing cell-free nucleic acids from the patient for sequencing;
- selectively enriching the prepared cell-free nucleic acids from the patient for phased variant-containing nucleic acids from the three or more genomic regions to form an enriched library of nucleic acids for sequencing;
- sequencing the enriched library of nucleic acids to produce sequencing data;
- and
- analyzing the sequencing data to detect or monitor a disease of the patient;
- wherein at least 10% of phased variant-containing nucleic acids from the library of nucleic acids have a first phased variant and a second phased variant that are separated from each other by at least one nucleotide.
Dependencies are inferred from the claim text.