Methods and systems for abnormality detection in the patterns of nucleic acids

A method for processing a nucleic acid sample of a subject, comprising:

• (a) using a probe set comprising probes having sequence complementarity with a plurality of regulatory elements to enrich for nucleic acid sequences in said nucleic acid sample, wherein said nucleic acid sequences comprise at least a subset of said plurality of regulatory elements, thereby providing an enriched nucleic acid sample;
• (b) directing said enriched nucleic acid sample or a derivative thereof to nucleic acid sequencing to generate a plurality of sequence reads comprising sequences that align with said subset of said plurality of regulatory elements;
• (c) computer processing said plurality of sequence reads to determine an expression profile of genes operably linked to said subset of said plurality of regulatory elements;
• and
• (d) using said expression profile of genes to identify a disease in said subject at an accuracy of at least 90%.

A system comprising a computer processor, wherein said computer processor is programmed to:

• (a) enrich for nucleic acid sequences in a nucleic acid sample from a subject, wherein said nucleic acid sequences comprise at least a subset of a plurality of regulatory elements, thereby providing an enriched nucleic acid sample;
• (b) sequence said enriched nucleic acid sample or a derivative thereof to generate a plurality of sequence reads comprising sequences that align with said subset of said plurality of regulatory elements;
• (c) process said plurality of sequence reads to determine an expression profile of genes operably linked to said subset of said plurality of regulatory elements;
• and
• (d) using at least said expression profile of genes to identify a disease in said subject at an accuracy of at least 90%.