Synthetic nucleic acid spike-ins
AssigneeKarius, Inc.
InventorsFred C. Christians, Igor D. Vilfan, Michael Kertesz, Timothy A. Blauwkamp, Shivkumar Venkatasubrahmanyam, Michael Rosen, Rene Sit
Life of this patent
Estimating the term…
Abstract
This disclosure provides methods for determining relative abundance of one or more non-host species in a sample from a host. Also provided are methods involving addition of known concentrations of synthetic nucleic acids to a sample and performing sequencing assays to identify non-host species such as pathogens. Also provided are methods of tracking samples, tracking reagents, and tracking diversity loss in sequencing assays.
Claims49
A method of determining abundance of nucleic acids in an initial sample comprising target nucleic acids, the method comprising:
- (a) adding a known quantity of spike-in nucleic acids to the initial sample comprising target nucleic acids, wherein the spike-in nucleic acids comprise at least 1,000 spike-in nucleic acids with sequences that are unique to each other;
- (b) performing a sequencing assay on a portion of the target nucleic acids and a portion of the at least 1000 spike-in nucleic acids, thereby obtaining target nucleic acid sequence reads and spike-in nucleic acid sequence reads;
- and
- (c) using the spike-in nucleic acid sequence reads to calculate abundance of the target nucleic acids.
Dependencies are inferred from the claim text.