Oncogenic splice variant determination
AssigneeIllumina, Inc.
InventorsJune Snedecor, Han-Yu Chuang, Gwenn Berry, Xiao Chen
Life of this patent
Estimating the term…
Abstract
Presented herein are systems and methods for identifying splice variants. The techniques include determining one or more sample splice junctions from a plurality of RNA sequence reads from a single biological sample, retrieving a set of baseline splice junctions determined from a plurality of healthy RNA samples and comparing the one or more sample splice junctions to the set of baseline splice junctions to identify one or more filtered sample splice junctions comprising sample splice junctions that do not overlap with the baseline splice junctions, wherein the one or more filtered sample splice junctions are candidate oncogenic events.
Claims20
A system for identifying splice variants from a patient comprising:
- a memory;
- at least one processor;
- and
- at least one non-transitory computer readable medium containing instructions that, when executed by the at least one processor, cause the at least one processor to perform operations comprising:
- determining one or more sample splice junctions from a plurality of RNA sequence reads from a single biological sample obtained from the patient;
- retrieving a set of baseline splice junctions, the set of baseline splice junctions determined from a plurality of healthy RNA samples not obtained from the same biological object as the single biological sample;
- comparing the one or more sample splice junctions to the set of baseline splice junctions;
- identifying one or more filtered sample splice junctions, wherein the filtered sample splice junctions are sample splice junctions that do not overlap with the set of baseline splice junctions;
- and
- determining that one or more of the identified filtered sample splice junctions are candidate oncogenic events.
(canceled)
A computer implemented method, comprising:
- determining, using at least one processor, one or more sample splice junctions from a plurality of RNA sequence reads from a single biological sample obtained from a patient;
- retrieving, by the at least one processor from a memory, a set of baseline splice junctions determined from a plurality of healthy RNA samples not obtained from the same biological object as the single biological sample;
- comparing the one or more sample splice junctions to the set of baseline splice junctions;
- identifying, by the at least one processor, one or more filtered sample splice junctions, wherein the filtered sample splice junctions are sample splice junctions that do not overlap with the baseline splice junctions;
- and
- determining that one or more of the identified filtered sample splice junctions are candidate oncogenic events.
(canceled)
Dependencies are inferred from the claim text.