Patent ID: 11913068
Assignee: ASURAGEN, INC.
Field: Biotechnology (Chemistry)
Classification: CPC C | IPC C  G

Claim 7:
8. A method of sizing a repeat region of a nucleic acid, comprising:
i. providing a nucleic acid sample;
ii. amplifying a nucleic acid comprising a repeat region from the sample;
iii. performing capillary electrophoresis to obtain a ladder of amplification products;
iv. generating an internal sizing standard using the ladder of amplification products by:
identifying a repeat profile in a channel of the ladder of amplification products;
iteratively generating a set of repeat peak locations, the iterative generation comprising:
determining a predicted peak location in the repeat profile using a previous peak location and an interval value,
identifying a peak location within a window including the predicted peak location, and
adding the identified peak location to the set of repeat peak locations when a signal intensity at the identified peak location satisfies an amplitude criterion; and

estimating a linear relationship between repeat peak location and repeat fragment size using the set of repeat peak locations and a set of corresponding fragment sizes; and

v. sizing the repeat region using the internal sizing standard,, wherein sizing a repeat region further comprises:
(a) dynamically determining a threshold for calling peaks in a repeat profile;
(b) calling peaks in a repeat profile using a sliding window;
(c) interpolating peaks below an amplitude threshold in a repeat profile;
(d) generating a calibration curve that maps from sampling units to base pair units using estimated peak locations in a repeat profile;
(e) correcting a first channel for signal artifacts;
(f) extending the dynamic range of a first channel configured to detect a first electromagnetically detectable moiety; and/or
(g) determining satisfaction of sizing standard criteria, a repeat profile signal-to-noise criterion, a repeat profile contamination criterion, and/or a minor allele sensitivity criterion, and, wherein correcting a first channel for signal artifacts comprises:
a) identifying a window in the first channel including a potential air bubble location; determining a correlation between signal intensities for channels within the window; and replacing, based on the determined correlation, the signal intensities for the channels within the window; and/or
b) identifying a bleed-over location based on signal intensities for the first channel; determining a window including the bleed-over location based on signal intensities for a second channel; and replacing the signal intensities for the second channel.