Methods and systems for genetic analysis

A method for personalized genetic testing, comprising:

• (a) performing a first assay on nucleic acid molecules extracted from at least one biological sample from a subject to produce a first set of nucleic acid sequence data;
• (b) extracting a plurality of genetic characteristics from the first set of nucleic acid sequence data;
• (c) obtaining a personalized probe set for the subject, wherein;
• (i) the personalized probe set comprises a plurality of nucleic acid probe molecules having a plurality of nucleic acid sequences or complements thereof, and
• (ii) the personalized probe set comprises nucleic acid probe molecules having oligonucleotide-directed genomic content comprising:
• (1) at least one variable portion comprising potential neoantigen-causing variants of the subject, wherein the potential neoantigen-causing variants are identified by alignment of the first set of nucleic acid sequence data to a reference genome from the subject, and
• (2) at least one fixed portion selected from a group comprising one or more of (a) cancer driver genes, (b) genes involved in the pharmacogenomics of cancer drugs, (c) genes involved in Mendelian immunological diseases, (d) genes related to inherited forms of cancer, (e) genes associated with tumor escape from a targeted or immune cancer therapy, (f) HLA typing, or (g) variants common in the population and used by B-allele methods to detect structural variation;
• (d) performing a second assay on nucleic acid molecules extracted from one or more additional biological samples using the personalized probe set to obtain a second set of nucleic acid sequence data;
• and
• (e) outputting biomedical information of the subject based on an analysis comparing results from the first assay with results from the second assay, wherein the biomedical information comprises one or more biomedical outputs, wherein the one or more biomedical outputs suggest, select, designate, recommend, or otherwise determine a course of treatment and/or prevention of a disease or condition, wherein the course of treatment comprises an anti-cancer therapy.