Non-unique barcodes in a genotyping assay
AssigneePersonal Genome Diagnostics Inc.
InventorsMark Sausen, Victor Velculescu, Luis Diaz
Life of this patent
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Abstract
The present disclosure involves ctDNA assays that interrogate many regions from a single sample with high precision and accuracy, while evaluating multiple forms of cancer-related genomic alterations including sequence mutations and structural alterations. The disclosure provides simplified yet robust methods that achieve high sensitivity and specificity by analyzing cancer genes using a limited pool of non-unique barcodes in combination with endogenous barcodes. Samples are captured and sequenced using high coverage next-generation sequencing to allow tumor-specific somatic mutations, amplifications, and translocations to be identified.
Claims21
-23. (canceled)
The method of claim 24, wherein the identifying the mutations in the nucleic acid fragments from the sample comprises identifying tumor-specific sequence mutations, amplifications, and/or translocations in a plurality of genes.
A method of analyzing a sample comprising nucleic acid fragments, the method comprising:
- introducing a limited pool of non-unique exogenous barcodes to the nucleic acid fragments to generate a genomic library comprising barcoded fragments, wherein the limited pool comprises twenty or fewer sets of non-unique exogenous barcodes, and wherein each of the nucleic acid fragments includes an endogenous barcode;
- identifying end portions of the barcoded fragments based on the endogenous barcodes;
- sequencing the barcoded fragments to generate sequence reads;
- aligning the sequence reads to a reference human genome sequence based on the non-unique exogenous barcodes and the endogenous barcodes;
- and
- identifying mutations in the nucleic acid fragments from the sample based on the alignment.
The method of claim 25, wherein the plurality of genes includes ALK, BCR, BRAF, EGFR, NTRK1, PDGFRA, PDGFRB, RARA, RET, and ROS1.
Dependencies are inferred from the claim text.