Fragile X Syndrome AGG Interruption 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 Fragile X Syndrome (FXS) assay performed on a sample using a genetic analyzer, wherein the raw data comprises gene-specific (GS) polymerase chase reaction (PCR) data and AGG interruption PCR data resolved by capillary electrophoresis;
• determining an expected AGG peak size for a first allele identified in the raw data;
• iteratively searching the raw data and identifying one or more AGG peaks on the first allele using a first set of search spaces determined based on the expected AGG peak size;
• determining a number of CGG repeats downstream of a final AGG interruption on the first allele based on the GS PCR data and the one or more AGG peaks identified on the first allele;
• determining a number of CGG repeats preceding a first AGG interruption on the first allele based on the GS PCR data and the one or more AGG peaks identified on the first allele;
• generating a AGG genotype for the first allele based on the number of CGG repeats downstream of the final AGG interruption and the number of CGG repeats preceding the first AGG interruption;
• and
• providing the AGG genotype for the first allele.

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 Fragile X Syndrome (FXS) assay performed on a sample using a genetic analyzer, wherein the raw data comprises gene-specific (GS) polymerase chase reaction (PCR) data and AGG interruption PCR data resolved by capillary electrophoresis;
• determining an expected AGG peak size for a first allele identified in the raw data;
• iteratively searching the raw data and identifying one or more AGG peaks on the first allele using a first set of search spaces determined based on the expected AGG peak size;
• determining a number of CGG repeats downstream of a final AGG interruption on the first allele based on the GS PCR data and the one or more AGG peaks identified on the first allele;
• determining a number of CGG repeats preceding a first AGG interruption on the first allele based on the GS PCR data and the one or more AGG peaks identified on the first allele;
• generating a AGG genotype for the first allele based on the number of CGG repeats downstream of the final AGG interruption and the number of CGG repeats preceding the first AGG interruption;
• and
• providing the AGG genotype for the first allele.