Clinical genetic screening assay with rescue minimization

A computer-implemented method for performing a clinical genetic screening assay comprising:

• obtaining a plurality of regions of interest (ROIs) comprising a set of variants, wherein the set of variants comprises pathogenic variants, likely pathogenic variants, and/or computationally predicted high impact variants;
• obtaining population allele frequency information for the set of variants, wherein the population allele frequency information comprises a population allele frequency for each variant of the set of variants;
• performing next generation sequencing (NGS) on a patient sample to generate NGS read data for the plurality of ROIs;
• determining a read coverage for each location of each ROI of the plurality of ROIs based on the NGS read data;
• obtaining a sensitivity profile, wherein the sensitivity profile provides a probability that a variant is detected based on a read coverage and a variant type of the variant;
• performing a rescue minimization process comprising:
• determining an expected false negative (EFN) value for each ROI of the plurality of ROIs based on the sensitivity profile and a population allele frequency of one or more variants in the ROI;
• determining a sample EFN value for the patient sample based on the EFN values of the plurality of ROIs,
• determining if the sample EFN value is greater than a predetermined threshold, and
• when the sample EFN value is greater than the predetermined threshold,
• sorting the plurality of ROIs based on the EFN values;
• and
• rescuing a number of ROIs from the plurality of ROIs based on the sorting, wherein a sum of the EFN values of remaining ROIs of the plurality of ROIs is less than or equal to the predetermined threshold;
• performing Sanger sequencing on the rescued ROIs, wherein the Sanger sequencing generates confirmatory read data for the one or more ROIs;
• and
• outputting a result of the clinical genetic screening assay based on the NGS read data and the confirmatory read data.

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

• obtaining a plurality of regions of interest (ROIs) comprising a set of variants, wherein the set of variants comprises pathogenic variants, likely pathogenic variants, and/or computationally predicted high impact variants;
• obtaining population allele frequency information for the set of variants, wherein the population frequency information comprises a population allele frequency for each variant of the set of variants;
• performing next generation sequencing (NGS) on a patient sample to generate NGS read data for the plurality of ROIs, wherein the patient is a subject of a clinical genetic screening assay;
• determining a read coverage for each location of each ROI of the plurality of ROIs based on the NGS read data;
• obtaining a sensitivity profile, wherein the sensitivity profile provides a probability that a variant is detected based on a read coverage and a variant type of the variant;
• performing a rescue minimization process comprising:
• determining an expected false negative (EFN) value for each ROI of the plurality of ROIs based on the sensitivity profile and a population allele frequency of one or more variants in the ROI;
• determining a sample EFN value for the patient sample based on the EFN values of the plurality of ROIs,
• determining if the sample EFN value is greater than a predetermined threshold, and
• when the sample EFN value is greater than the predetermined threshold,
• sorting the plurality of ROIs based on the EFN values;
• and
• rescuing a number of ROIs from the plurality of ROIs based on the sorting, wherein a sum of the EFN values of remaining ROIs of the plurality of ROIs is less than or equal to the predetermined threshold;
• performing Sanger sequencing on the rescued ROIs, wherein the Sanger sequencing generates confirmatory read data for the one or more ROIs;
• and
• outputting a result of the clinical genetic screening assay based on the NGS read data and the confirmatory read data.

A system comprising:

• one or more data processors;
• and
• a non-transitory computer readable medium storing instructions which, when executed on the one or more data processors, cause the one or more data processors to perform operations comprising:
• obtaining a plurality of regions of interest (ROIs) comprising a set of variants, wherein the set of variants comprises pathogenic variants, likely pathogenic variants, and/or computationally predicted high impact variants;
• obtaining population allele frequency information for the set of variants, wherein the population frequency information comprises a population allele frequency for each variant of the set of variants;
• performing next generation sequencing (NGS) on a patient sample to generate NGS read data for the plurality of ROIs, wherein the patient is a subject of a clinical genetic screening assay;
• determining a read coverage for each location of each ROI of the plurality of ROIs based on the NGS read data;
• obtaining a sensitivity profile, wherein the sensitivity profile provides a probability that a variant is detected based on a read coverage and a variant type of the variant;
• performing a rescue minimization process comprising:
• determining an expected false negative (EFN) value for each ROI of the plurality of ROIs based on the sensitivity profile and a population allele frequency of one or more variants in the ROI;
• determining a sample EFN value for the patient sample based on the EFN values of the plurality of ROIs,
• determining if the sample EFN value is greater than a predetermined threshold, and
• when the sample EFN value is greater than the predetermined threshold,
• sorting the plurality of ROIs based on the EFN values;
• and
• rescuing a number of ROIs from the plurality of ROIs based on the sorting, wherein a sum of the EFN values of remaining ROIs of the plurality of ROIs is less than or equal to the predetermined threshold;
• performing Sanger sequencing on the rescued ROIs, wherein the Sanger sequencing generates confirmatory read data for the one or more ROIs;
• and
• outputting a result of the clinical genetic screening assay based on the NGS read data and the confirmatory read data.