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

Claim 3:
4. 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 the repeat region further comprises identifying at least one gene-specific peak; and sizing the at least one gene-specific peak using the ladder of amplification products comprising
generating a dynamic threshold from a background model by piecewise scaling the background model to obtain the dynamic threshold;
determining gene-specific peak locations in a repeat profile using the dynamic threshold;
associating repeat sizes with the gene-specific peak locations using the ladder of amplification products; and
outputting an indication of the gene-specific peak sizes.