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US 2020/0048696 A1Published application
Methods for nucleic acid size detection of repeat sequences
AssigneeAsuragen, Inc.
InventorsEran Bram, Raghav Shroff, Andrew Hadd, Blake Printy
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Abstract
Disclosed herein are data processing and calculating annotation systems and devices, and corresponding methods, for nucleic acid analysis. In particular, disclosed herein are methods for sizing a repeat region of a nucleic acid sample. For example, the methods disclosed herein use a ladder of amplification products to determine nucleic acid size.
Claims23
1-90. (canceled)
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.
10 more elements
A method of reconstructing a genotype of a nucleic acid from a patient, comprising:
- i. providing a nucleic acid sample from the patient;
- 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;
- v. sizing the repeat region using the internal sizing standard;
- and
- vi. reconstructing a genotype of the nucleic acid using the repeat region size.
11 more elements
Dependencies are inferred from the claim text.