Methods and Systems for Analyzing Nucleic Acid Molecules

Abstract

Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

What is claimed is: 
     
         1 . A method of monitoring progress of a condition, the method comprising:
 (a) obtaining, by a computer system, sequencing data for at least 1,000 DNA molecules obtained from a subject at a first timepoint;   (b) processing, by the computer system, the sequencing data for at least 1,000 DNA molecules obtained from the subject at the first timepoint to identify and determine genomic locations of a plurality of disease-derived phased-variant containing DNA molecules, wherein the identity and genomic locations of the disease-derived DNA molecules are determined based on alignment of reads corresponding to each of the at least 1,000 DNA molecules to a reference genomic sequence of at least 10 kb in length;   (c) obtaining, by the computer system, sequencing data for a plurality of cell-free DNA molecules obtained from the subject at a second timepoint that is subsequent to the first timepoint; and   (d) aligning, by the computer system, the sequencing data for the plurality of cell-free DNA molecules obtained from the subject at the second timepoint to the genomic locations of the at least 1,000 disease-derived phased-variant containing DNA molecules identified in (b) to assess an extent to which the cell-free DNA molecules from the subject at the second timepoint comprise disease-derived phased-variant containing cell-free DNA molecules.   
     
     
         2 . The method of  claim 1 , wherein the at least 1,000 DNA molecules obtained from the subject at the first timepoint are tumor-derived DNA molecules. 
     
     
         3 . The method of  claim 1 , wherein the at least 1,000 DNA molecules obtained from the subject at the first timepoint are cell-free DNA molecules. 
     
     
         4 . The method of  claim 1 , wherein the sequencing data comprises whole genome sequencing data. 
     
     
         5 . The method of  claim 1 , wherein the disease is a cancer. 
     
     
         6 . The method of  claim 1 , wherein the extent to which the cell-free DNA molecules from the subject at the second timepoint comprise disease-derived phased-variant containing cell-free nucleic acid molecules is used to determine minimal residual disease. 
     
     
         7 . The method of  claim 1 , wherein the second timepoint is at least 1 week subsequent to the first timepoint. 
     
     
         8 . The method of  claim 1 , wherein the subject is subjected to a treatment for the condition (i) prior to the second timepoint and (ii) subsequent to the first timepoint. 
     
     
         9 . The method of  claim 1 , further comprising enriching for cell-free DNA molecules corresponding to the genomic locations identified in (b) to obtain the least 1,000 cell-free DNA molecules obtained from the subject at the second timepoint. 
     
     
         10 . The method of  claim 1 , wherein the disease-derived phased variant-containing cell-free nucleic acid molecules identified in (b) each comprise a plurality of phased variants relative to the reference genomic sequence that are separated by at least one nucleotide. 
     
     
         11 . A method for altering a treatment of a human subject, the method comprising:
 (a) genotyping a subject having cancer to identify regions of a genome of the subject that have phased variants that are within 170 base pairs of each other;   (b) determining a condition of the subject based on analysis of phased variant content of cell-free nucleic acid molecules derived from the regions identified in (a), wherein the cell-free nucleic acid molecules are obtained from a biological sample from the subject after the subject has received at least a portion of a treatment regimen for the cancer; and   (c) altering the treatment regimen based on the condition determined in (b).   
     
     
         12 . The method of  claim 11 , wherein genotyping is performed by sequencing DNA derived from tumor cells. 
     
     
         13 . The method of  claim 11 , wherein genotyping is performed by sequencing cell-free nucleic acid molecules. 
     
     
         14 . The method of  claim 11 , wherein altering the treatment comprises canceling the treatment. 
     
     
         15 . The method of  claim 11 , wherein altering the treatment comprises canceling the treatment in factor of a new treatment, and wherein the new treatment is selected from the group consisting of chemotherapy, radiotherapy, chemoradiotherapy, immunotherapy, adoptive cell therapy, hormone therapy, targeted drug therapy, surgery, transplant, and transfusion. 
     
     
         16 . The method of  claim 11 , wherein the condition is cancer. 
     
     
         17 . The method of  claim 16 , wherein the cancer is selected from the group consisting of lymphoma, leukemia, sarcoma, breast cancer, colorectal cancer, pancreatic cancer, prostate cancer, multiple myeloma, kidney cancer and melanoma. 
     
     
         18 . The method of  claim 17 , wherein the cancer comprises a lymphoma and the lymphoma is diffuse large B cell lymphoma (DLBCL). 
     
     
         19 . The method of  claim 11 , wherein the phased variants comprise a first phased variant and a second phased variant that are separated from each other by at least one nucleotide. 
     
     
         20 . The method of  claim 11 , wherein the treatment regimen comprises all treatments of a treatment plan. 
     
     
         21 . A method for altering a treatment of a human subject, the method comprising:
 (a) determining a first state of a condition of a patient based on identification of a first set of one or more cell-free nucleic acid molecules having at least one set of phased variants from a first plurality of cell-free nucleic acid molecules that is obtained or derived from the subject;   (b) determining a second state of the condition of the patient based on identification of a second set of one or more cell-free nucleic acid molecules having at least one set of phased variants from a second plurality of cell-free nucleic acid molecules that is obtained or derived from the subject after a treatment;   (c) determining the progress of the condition based at least in part on the first state of the condition and the second state of the condition; and   (d) altering the treatment based at least in part on the progress of the condition.   
     
     
         22 . The method of  claim 21 , wherein the second state of the condition comprises a negative cancer status. 
     
     
         23 . The method of  claim 21 , wherein the progress of the condition comprises a worsening cancer status. 
     
     
         24 . The method of  claim 21 , wherein altering the treatment comprises increasing the dosage of the treatment. 
     
     
         25 . The method of  claim 21 , wherein altering the treatment comprises canceling the treatment in factor of a new treatment, and wherein the new treatment is selected from the group consisting of chemotherapy, radiotherapy, chemoradiotherapy, immunotherapy, adoptive cell therapy (e.g., chimeric antigen receptor (CAR) T cell therapy, CARNK cell therapy, modified T cell receptor (TCR) T cell therapy, etc.) hormone therapy, targeted drug therapy, surgery, transplant, transfusion, and medical surveillance. 
     
     
         26 . The method of  claim 21 , wherein the condition is cancer. 
     
     
         27 . The method of  claim 26 , wherein the cancer is selected from the group consisting of lymphoma, leukemia, sarcoma, breast cancer, colorectal cancer, pancreatic cancer, prostate cancer, multiple myeloma, kidney cancer and melanoma. 
     
     
         28 . The method of  claim 27 , wherein the lymphoma is diffuse large B cell lymphoma (DLBCL). 
     
     
         29 . The method of  claim 21 , wherein the at least one set of phased variants comprises a first phased variant and a second phased variant that are separated from each other by at least one nucleotide. 
     
     
         30 . The method of  claim 21 , wherein each of the plurality of phased variants is separated from each other by no more than 170 nucleotides.