Cell-free dna methylation patterns for disease and condition analysis

Abstract

Disclosed herein are methods and systems of utilizing sequencing reads for detecting and quantifying the presence of a tissue type or a disease type in cell-free DNA prepared from blood samples.

1 . A method of for treating a subject, comprising:
 (a) receiving a plurality of sequencing reads for a cell-free deoxyribonucleic acid (cfDNA) sample obtained or derived from the subject, wherein each of the plurality of sequencing reads comprises methylation sequencing data obtained from a nucleic acid sequence;   (b) determining a methylation pattern for a sequencing read in the plurality of sequencing reads, wherein the methylation pattern comprises a genomic region corresponding to the nucleic acid sequence and methylation status of one or more motifs in the genomic region;   (c) comparing the methylation pattern with each of one or more pre-established methylation signatures to compute one or more likelihood scores, wherein each of the one or more pre-established methylation signatures correlates with a cancer, and wherein each pre-established methylation signature comprises at least one pre-determined signature region and pre-determined methylation rate associated therewith;   (d) characterizing the cfDNA sample as containing cfDNAs derived from the cancer tissue, based at least in part on at least one of the one or more likelihood scores, thereby identifying the subject as having the cancer; and   (e) administering a treatment to the subject based on the identifying the subject as having the cancer, wherein the treatment comprises a member selected from the group consisting of a chemotherapy, a radiation therapy, an immunotherapy, and a tumor resection.   
     
     
         2 . The method of  claim 1 , further comprising:
 performing (b), (c), and (d) for each sequencing read in the plurality of sequencing reads.   
     
     
         3 . The method of  claim 1 , further comprising:
 establishing the one or more pre-established methylation signatures based on existing methylation sequencing data.   
     
     
         4 . The method of  claim 2 , wherein further comprising:
 determining a level of the cfDNAs derived from the cancer tissue based at least in part on a number of sequencing reads derived from the cancer tissue in the plurality of sequencing reads.   
     
     
         5 . The method of  claim 3 , wherein the existing methylation sequencing data is selected from the group consisting of tissue-specific sequencing data, disease-specific sequencing data, individual sequencing data, population sequencing data, and combinations thereof. 
     
     
         6 . The method of  claim 1 , wherein the cfDNA sample is obtained or derived from a plasma sample, a blood sample, a saliva sample, an amniotic fluid sample, a cystic fluid sample, a spinal fluid sample, a brain fluid sample, a urine sample, a sweat sample, or a tears sample from the subject. 
     
     
         7 . The method of  claim 1 , wherein the cancer tissue comprises a member selected from the group consisting of, liver cancer tissue, lung cancer tissue, kidney cancer tissue, colon cancer tissue, small intestines cancer tissue, pancreas cancer tissue, adrenal glands cancer tissue, esophagus cancer tissue, adipose cancer tissue, heart cancer tissue, brain cancer tissue, placenta cancer tissue, and combinations thereof. 
     
     
         8 . The method of  claim 7 , wherein the cancer tissue comprises a member selected from the group consisting of liver cancer tissue, lung cancer tissue, kidney cancer tissue, colon cancer tissue, pancreas cancer tissue, brain cancer tissue, and combinations thereof. 
     
     
         9 . The method of  claim 1 , wherein the methylation status and pre-determined methylation status are determined at bin level. 
     
     
         10 . The method of  claim 1 , wherein the methylation status and pre-determined methylation status are determined at CpG site level. 
     
     
         11 . The method of  claim 1 , wherein the one or more motifs is-comprises a CpG site. 
     
     
         12 . The method of  claim 4 , further comprising:
 comparing the level of the cfDNAs derived from the cancer tissue to a first reference level derived from a reference subject with cancer.   
     
     
         13 . The method of  claim 4 , further comprising:
 comparing the level of the cfDNAs derived from the cancer tissue to a second reference level derived from a reference subject without cancer.   
     
     
         14 . The method of  claim 13 , further comprising:
 determining the second reference level at least in part by:
 receiving a second plurality of sequencing reads for a second cfDNA sample obtained or derived from the reference subject without cancer, wherein each of the second plurality of sequencing reads comprises second methylation sequencing data obtained from a second nucleic acid sequence; 
 determining a second methylation pattern for a sequencing read in the second plurality of sequencing reads, wherein the second methylation pattern comprises a second genomic region corresponding to the second nucleic acid sequence and methylation status of one or more motifs in the second genomic region; 
 comparing the second methylation pattern with each of the one or more pre-established methylation signatures to compute one or more second likelihood scores; 
 characterizing the second cfDNA sample as containing cfDNAs derived from the cancer tissue, based at least in part on at least one of the one or more second likelihood scores; 
 repeating the determining, comparing and characterizing for each sequencing read in the second plurality of sequencing reads; and 
 determining a level of the cfDNA derived from the cancer tissue in the reference subject without cancer, based at least in part on a number of sequencing reads derived from the cancer tissue in the second plurality of sequencing reads. 
   
     
     
         15 .- 155 . (canceled) 
     
     
         156 . The method of  claim 1 , wherein each of the plurality of sequencing reads comprises methylation sequencing data obtained from a consecutive nucleic acid sequence of 50 or more nucleic acids. 
     
     
         157 . The method of  claim 1 , wherein (d) further comprises characterizing the cfDNA sample as containing cfDNAs derived from the cancer tissue, based at least in part on whether the at least one of the one or more likelihood scores exceeds a threshold value. 
     
     
         158 . The method of  claim 6 , wherein the cfDNA sample is obtained or derived from the plasma sample. 
     
     
         159 . The method of  claim 6 , wherein the cfDNA sample is obtained or derived from the blood sample. 
     
     
         160 . The method of  claim 8 , wherein the cancer tissue comprises liver cancer tissue. 
     
     
         161 . The method of  claim 8 , wherein the cancer tissue comprises lung cancer tissue. 
     
     
         162 . The method of  claim 8 , wherein the cancer tissue comprises kidney cancer tissue. 
     
     
         163 . The method of  claim 8 , wherein the cancer tissue comprises colon cancer tissue. 
     
     
         164 . The method of  claim 8 , wherein the cancer tissue comprises breast cancer tissue.