Automated allele caller
AssigneeMillennium Pharmaceuticals, Inc.
InventorsMartha J. Hiller, John W. Martin, Alexander N. Parker, Richard A. Nicoletti, Christopher R. Page
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Abstract
An auto allele caller executed in a computer system for identifying alleles from a trace is described. The auto allele caller applies a typical shape of an allele for a marker to the trace to identify potential allele calls that match to the typical shape of the allele at the marker and assigns a quality factor to the allele calls.
Claims28
A method executed in a computer system for identifying potential alleles from a trace, the method comprising:
- retrieving pre-existing allele calls for a marker, forming an allele shape by determining an average shape of the pre-existing allele calls to provide a allele shape for an allele at the marker, said allele shape characterized by a height and shape that is expected for identification of the allele at a known base pair marker;
- applying the allele shape for an allele for the marker to the trace;
- identifying potential allele calls that match to the shape of the allele at the marker;
- assigning a quality factor to the potential allele calls;
- and
- rendering on an output device, an indication of whether portions of the trace correspond to alleles.
A method executed in a computer system for identifying alleles from a trace, the method comprising:
- retrieving pre-existing allele calls based on a marker corresponding to the trace data;
- forming from the pre-existing allele calls a shape for alleles at the marker;
- comparing the trace to the shape to identify an allele;
- and
- rendering on an output device, an indication of portions of the trace correspond to the allele.
A method executed in a computer system for identifying alleles from trace data, the method comprising:
- extracting trace data from a database;
- preprocessing the trace data to correct for peak errors in the trace data;
- comparing peaks in the trace data to an allele shape corresponding to an allele to produce at least one potential allele identification;
- postprocessing the at least one potential allele identification by applying at least one heuristic processing criteria to the at least one potential allele identification to determine whether the at least one potential allele identification should be an allele call;
- and
- rendering on an output device, an indication of whether portions of the trace correspond to potential alleles.
A computer program product residing on a computer readable medium for identifying potential alleles from a trace, comprising instructions for causing a computer to:
- retrieve pre-existing allele calls for a marker and forming a allele shape by forming an average shape of the pre-existing allele calls to provide the shape for an allele at the marker;
- apply the allele shape for an allele for the marker to the trace;
- identify potential allele calls that match to the shape of the allele at the marker;
- assign a quality factor to the potential allele calls and
- render on an output device, an indication of whether portions of the trace correspond to potential alleles.
A computer program product residing on a computer readable medium for identifying alleles from a trace, comprising instructions for causing a computer to:
- extract trace data from a database;
- preprocess the trace data to correct for errors in the trace data;
- compare peaks in the trace data to an allele shape to find potential allele calls;
- postprocess potential allele calls by applying at least one heuristic processing criterion to the at least one potential allele call to determine whether the at least one potential allele call should be an allele call;
- and
- render on an output device, an indication of whether portions of the trace correspond to alleles.
Dependencies are inferred from the claim text.