Inferring transcription factor activity from dna methylation and its application as a biomarker

A method comprising:

• (a) obtaining total DNA from a cell-free biological sample;
• (b) modifying the total DNA and amplifying the modified total DNA to obtain a genome-wide methylation profile at a plurality of transcription binding sites in the total DNA;
• (c) analyzing, including aligning and/or comparing the genome-wide methylation profile obtained in step (b) to a reference genome-wide methylation profile at the plurality of transcription binding sites in total DNA obtained from a cell-free reference sample;
• (d) determining alteration in methylation at the plurality of transcription binding sites based on the analysis in step (c);
• (e) generating a summary methylation profile for each of the plurality of transcription binding sites, wherein the summary methylation profile comprises a pattern of the total DNA that are methylated and/or unmethylated at the plurality of transcription binding sites in the total DNA of the cell-free biological sample;
• and
• (f) generating a metric/quantitative score,
• wherein the metric/quantitative score comprises generating a Transcription Factor Activity Score (TFAScore).

A method of treatment of prostate cancer, the method comprising:

• (i) determining a type of prostate cancer by analyzing total DNA obtained from a cell-free biological sample of a subject, wherein the subject is a human, the method comprising:
• (a) performing methylation-aware genome-wide sequencing for the total DNA to generate genome-wide sequence reads, wherein the genome-wide sequence reads comprise methylation status at a plurality of transcription binding sites of the total DNA;
• (b) analyzing, including aligning and/or comparing to a reference human genome the genome-wide sequence reads obtained in step (a) to identify each of a plurality of transcription binding sites, and using the analysis to obtain methylation status for each of the plurality of transcription binding sites in the total DNA;
• (c) generating a summary methylation profile from the methylation status for each of the plurality of transcription binding sites obtained in step (b), wherein the summary methylation profile comprises a pattern of the total DNA that are methylated and/or unmethylated at the plurality of transcription binding sites in the total DNA obtained from the cell-fee biological sample of the subject;
• and
• (d) determining the subject has a specific type of prostate cancer based at least in part on the summary methylation profile, wherein the step of determining the type of prostate cancer comprises analyzing differences between values of the summary methylation profile obtained in step (c) and values of one or more reference methylation profiles, and wherein at least one of the one or more reference methylation profiles is obtained from DNA of at least one biological sample obtained from a subject known to have the specific type of prostate cancer and/or a healthy subject;
• (ii) selecting at least one therapeutic modality based on the type of prostate cancer;
• and
• (iii) administering to the subject an effective amount of the at least one therapeutic modality.

A computer-implemented method of determining a phenotype in a sample from a subject, the method comprising:

• receiving, by a computing system, sequencing data for the sample;
• aligning, by the computing system, the sequencing data to a reference genome to generate alignment data;
• processing, by the computing system, the alignment data to create methylation data;
• processing, by the computing system, the methylation data to create summary methylation data for transcription factor binding sites associated with a first phenotype of interest and a second phenotype of interest;
• determining, by the computing system, a first transcription factor activity score for the first phenotype of interest and a second transcription factor activity score for the second phenotype of interest based on the summary methylation data;
• and
• determining, by the computing system, the phenotype in the sample based on the first transcription factor activity score and the second transcription factor activity score.