US 12,073,921 B2
System for increasing the accuracy of non invasive prenatal diagnostics and liquid biopsy by observed loci bias correction at single base resolution
John Burke, Reno, NV (US); and Stephen Healy Sanders, Reno, NV (US)
Assigned to ECHELON DIAGNOSTICS, INC., Reno, NV (US)
Filed by Echelon Diagnostics, Inc., Reno, NV (US)
Filed on Nov. 7, 2018, as Appl. No. 16/183,617.
Claims priority of provisional application 62/582,842, filed on Nov. 7, 2017.
Prior Publication US 2019/0139627 A1, May 9, 2019
Int. Cl. G16B 30/10 (2019.01); G16B 20/00 (2019.01)
CPC G16B 30/10 (2019.02) [G16B 20/00 (2019.02)] 15 Claims
 
1. A method for measuring nucleic acid sequence abundances comprising:
a. obtaining on a processor first data that indicates a target sequence of nucleic acid bases at a plurality of loci, wherein the target sequence comprises a plurality of bins, each bin comprising thousands to millions of loci;
b. measuring a sample from a subject to obtain thousands of reads of DNA sequences along fragments in the sample, wherein read lengths are hundreds of nucleotides, which reads are input to the processor;
c. determining on the processor second data that indicates alignment with the target sequence of the reads;
d. obtaining on the processor third data that indicates locus dependent observed non-uniform biases in coverage;
e. determining on the processor a raw count of reads that start at each locus;
f. obtaining partition data that indicates, for a first partition, a window comprising a number of bases less than a number of loci in a bin and position relative to a current locus, and a plurality of strata based on a corresponding plurality of different contents of nucleic acid bases in the window;
g. attributing to each locus in the target sequence a stratum of the plurality of strata of the first partition based on the content of nucleic acid bases in the target sequence in the window relative to the locus;
h. determining an expected count of each stratum in the first partition based on the raw counts of each locus belonging to the stratum and based on a total number of loci in the target sequence belonging to the stratum;
i. determining on the processor a copy number of a first bin based on a sum over all loci in the first bin of the expected count of each stratum for the first partition with each expected count weighted by the locus dependent observed non-uniform biases in coverage; and
j. presenting on a display, output data that indicates the copy number of the first bin in the sample wherein the copy number of the first bin relative to a copy number of a different bin is indicative of a condition of interest.