Assay for Hemoglobin A (HBA) Detection and Genotyping

A system comprising:

• one or more data processors;
• and
• a non-transitory computer readable storage medium containing instructions which, when executed on the one or more data processors, cause the one or more data processors to perform actions including:
• obtaining raw data from a Hemoglobin A (HBA) assay performed on a plurality of samples, wherein the HBA assay is performed using a plurality of probes capable of detection of copy number losses or gains in a α-globin gene cluster region of each sample of the plurality of samples, and the raw data comprises HBA copy number data for the plurality of probes resolved by capillary electrophoresis for each sample of the plurality of samples;
• selecting a reference sample from the plurality of samples;
• calculating a first set of probe ratios for each sample of the plurality of samples based on the raw data from the HBA assay and the reference sample;
• identifying a predetermined number of reference samples to be combined as a synthetic reference sample for the plurality of samples based on the first set of probe ratios;
• generating the synthetic reference sample based on the predetermined number of reference samples;
• calculating a second set of probe ratios for each sample of the plurality of samples based on the raw data from the HBA assay and the synthetic reference sample;
• iteratively inputting the second set of probe ratios for each sample into a decision tree matrix;
• determining, by the decision tree matrix, a HBA genotype for each sample based on the second set of probe ratios for each sample and copy number calling thresholds for sample probe/reference probe ratios associated with each probe of the plurality of probes;
• and
• providing the HBA genotype for each sample.

A computer-program product tangibly embodied in a non-transitory machine-readable storage medium, including instructions configured to cause one or more data processors to perform actions including:

• obtaining raw data from a Hemoglobin A (HBA) assay performed on a plurality of samples, wherein the HBA assay is performed using a plurality of probes capable of detection of copy number losses or gains in a α-globin gene cluster region of each sample of the plurality of samples, and the raw data comprises HBA copy number data for the plurality of probes resolved by capillary electrophoresis for each sample of the plurality of samples;
• selecting a reference sample from the plurality of samples;
• calculating a first set of probe ratios for each sample of the plurality of samples based on the raw data from the HBA assay and the reference sample;
• identifying a predetermined number of reference samples to be combined as a synthetic reference sample for the plurality of samples based on the first set of probe ratios;
• generating the synthetic reference sample based on the predetermined number of reference samples;
• calculating a second set of probe ratios for each sample of the plurality of samples based on the raw data from the HBA assay and the synthetic reference sample;
• iteratively inputting the second set of probe ratios for each sample into a decision tree matrix;
• determining, by the decision tree matrix, a HBA genotype for each sample based on the second set of probe ratios for each sample and copy number calling thresholds for sample probe/reference probe ratios associated with each probe of the plurality of probes;
• and
• providing the HBA genotype for each sample.