Apparatus, systems, and methods for detecting intra-genic variants and loss-of-function events

A method to detect loss of function variants within one or more genes of interest in a subject suffering from, or suspected to suffer from, a cancer, the method comprising the steps of:

• (i) generating a whole-genome sequencing library from a plurality of DNA fragments derived from genomic DNA extracted from cells or cell-free DNA derived from bodily fluids;
• (ii) using high-throughput sequencing to obtain sequencing reads from the sequencing library;
• (iii) subjecting the sequencing reads to quality-based filters and mapping the resulting sequencing reads onto a reference genome;
• (iv) detecting, from the sequencing reads, genetic variants that belong to at least two distinct categories, such as single nucleotide variants (SNVs), short insertions/deletions (indels), intra-genic copy number variants (CNV), large copy number variants (CNVs), and structural rearrangements;
• and
• (v) combining information from at least two different types of genetic variants to determine whether the subject comprises loss of function of the one or more genes of interest.