US 12,456,552 B2
Dynamic risk management for breast cancer with multi-factor genetic testing
Alexandre Bolze, San Francisco, CA (US); and Joseph J. Grzymski, San Mateo, CA (US)
Assigned to Helix, Inc., San Mateo, CA (US)
Filed by Helix, Inc., San Mateo, CA (US)
Filed on May 1, 2024, as Appl. No. 18/652,745.
Claims priority of provisional application 63/467,250, filed on May 17, 2023.
Prior Publication US 2024/0387051 A1, Nov. 21, 2024
Int. Cl. G16H 50/30 (2018.01); G16B 30/00 (2019.01); G16B 40/00 (2019.01); G16H 10/60 (2018.01)
CPC G16H 50/30 (2018.01) [G16B 30/00 (2019.02); G16B 40/00 (2019.02); G16H 10/60 (2018.01)] 20 Claims
OG exemplary drawing
 
1. A method of determining breast cancer risk level for a patient, the method comprising:
obtaining or having obtained a biological sample from the patient and performing or having performed sequencing on the biological sample to acquire sequenced genetic data for the patient, wherein the sequenced genetic data is accessible via a memory of a genomics server according to at least one file format selected from the group consisting of: a FASTQ format, a browser extensible data (BED) format, a binary alignment map format (BAM), a compressed reference oriented alignment map (CRAM) format, and a variant call format (VCF);
analyzing, by the genomics server, genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 represented in the sequenced genetic data;
determining, by the genomics server, that the patient does not have a qualifying variant in the analyzed genes BRCA1, BRCA2, PALB2, ATM, and CHEK2, wherein the qualifying variant includes at least one of a pathogenic variant, or a variant of uncertain significance (VUS), wherein a memory of the genomics server stores indications of variants included in the analyzed genes, and wherein a memory of the genomics server stores a location of the sequenced genetic data;
in response to determining that the patient does not have a qualifying variant in any of genes BRCA1, BRCA2, PALB2, ATM, and CHEK2, calculating, by the genomics server, a polygenic risk score (PRS) of the patient by analyzing the sequenced genetic data to determine a presence or absence of single nucleotide polymorphisms (SNPs) indicating breast cancer susceptibility that are located at predefined locations within a human genome; and
based on a comparison of the PRS to a predetermined threshold, classifying, by the genomics server, the patient as low risk for breast cancer.