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

Claim 9:
10. 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:
a) the sizing standard criteria comprise an internal sizing standard goodness-of-fit criterion, an external sizing standard goodness-of-fit criterion, and/or a consistency criterion that compares the internal sizing standard to the external sizing standard;
b) the repeat profile contamination criterion is failed when a repeat size associated with a location of a gene-specific peak is less than zero; and/or
c) the minor allele sensitivity criterion is satisfied when a ratio of a noise value of a repeat profile to a maximum of the values of the repeat profile at a location of a gene-specific peak exceeds a threshold value.