Using test patterns of chromosomal regions in plasma dna for detecting cancer

Abstract

Analysis of tumor-derived circulating cell-free DNA opens up new possibilities for performing liquid biopsies for solid tumor assessment or cancer screening. However, many aspects of the biological characteristics of tumor-derived cell-free DNA remain unclear. Regarding the size profile of plasma DNA molecules, some studies reported increased integrity of tumor-derived plasma DNA while others reported shorter tumor-derived plasma DNA molecules. We performed an analysis of the size profiles of plasma DNA in patients with cancer using massively parallel sequencing at single base resolution and in a genomewide manner. Tumor-derived plasma DNA molecules were further identified using chromosome arm-level z-score analysis (CAZA). We showed that populations of aberrantly short and long DNA molecules co-existed in the plasma of patients with cancer. The short ones preferentially carried the tumor-associated copy number aberrations. These results show the ability to use plasma DNA as a molecular diagnostic tool.

What is claimed is: 
     
         1 . A method of analyzing a biological sample of an organism, the biological sample including nucleic acid molecules originating from normal cells and potentially from cells associated with cancer, wherein at least some of the nucleic acid molecules are cell-free in the biological sample, the method comprising:
 identifying a plurality of chromosomal regions of the organism, each chromosomal region including a plurality of loci, wherein the plurality of chromosomal regions are subchromosomal;   for each of a plurality of nucleic acid molecules in the biological sample of the organism:
 identifying a location of the nucleic acid molecule in a reference genome of the organism; 
   for each of the plurality of chromosomal regions:
 identifying a respective group of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region; 
 calculating, with a computer system, a respective value of the respective group of nucleic acid molecules, the respective value defining a property of the nucleic acid molecules of the respective group; and 
 comparing the respective value to a respective reference value to determine a classification of whether the chromosomal region exhibits a deletion or an amplification; and 
   determining a test pattern of the chromosomal regions that exhibit a deletion or amplification, the test pattern including:
 a set of the chromosomal regions that exhibit a deletion or amplification; 
 a first subset of the set that exhibit an amplification; and 
 a second subset of the set that exhibit a deletion; 
   comparing the test pattern to a plurality of reference patterns of different types of cancer;   based on the comparison, determining a first amount of regions of the test pattern that exhibit a same deletion or amplification as a first reference pattern corresponding to a first type of cancer; and   comparing the first amount to a first threshold to determine a first classification of whether the biological sample exhibits the first type of cancer.   
     
     
         2 . The method of  claim 1 , wherein the plurality of chromosomal regions are non-overlapping. 
     
     
         3 . The method of  claim 1 , wherein the property of the nucleic acid molecules of at least one of the respective groups is of one haplotype of the chromosomal region, and wherein the respective reference value is of another haplotype of the chromosomal region. 
     
     
         4 . The method of  claim 1 , wherein the property of the nucleic acid molecules of at least one of the respective groups comprises a number of nucleic acid molecules with locations in the chromosomal region. 
     
     
         5 . The method of  claim 1 , wherein the property of the nucleic acid molecules of at least one of the respective groups comprises a size distribution. 
     
     
         6 . The method of  claim 5 , wherein the respective value comprises a mean of the size distribution, a median of the size distribution, a mode of the size distribution, or a proportion of nucleic acid molecules having a size below a size threshold. 
     
     
         7 . The method of  claim 1 , wherein the plurality of reference patterns are determined from reference samples of tissues and/or mixtures of cell-free nucleic acid molecules. 
     
     
         8 . The method of  claim 1 , wherein the first type of cancer is HCC, colorectal cancer, breast cancer, lung cancer, or nasopharyngeal carcinoma. 
     
     
         9 . The method of  claim 1 , wherein the first reference pattern includes a first number of regions, each having a defined status of amplification, deletion, or no aberration, wherein the first amount of regions is a percentage of the first number of regions to which the test pattern matches. 
     
     
         10 . The method of  claim 1 , further comprising:
 determining the first threshold by:
 clustering a set of reference patterns, wherein each cluster corresponds to a different type of cancer; 
 defining a centroid for a first cluster corresponding to the first type of cancer, wherein the centroid corresponds to regions of the reference patterns of the first cluster that are shared by at least a predetermined number of references patterns of the first cluster; and 
 defining a distance from a boundary of the first cluster and the centroid as the first threshold. 
   
     
     
         11 . The method of  claim 1 , further comprising:
 for each reference pattern of the plurality of reference patterns:
 determining a respective amount of regions of the test pattern that exhibit a same deletion or amplification as the reference pattern; and 
 determining a relative likelihood for each type of cancer by comparing the respective amounts to each other; and 
   identifying a matching type of cancer based on the relative likelihoods.   
     
     
         12 . The method of  claim 1 , further comprising:
 determining whether cancer exists in the organism using the first classification.   
     
     
         13 . A computer product comprising a computer readable medium storing a plurality of instructions for controlling a computer system to perform a method, the method comprising:
 identifying a plurality of chromosomal regions of an organism, each chromosomal region including a plurality of loci, wherein the plurality of chromosomal regions are subchromosomal;   for each of a plurality of nucleic acid molecules in a biological sample of the organism:
 identifying a location of the nucleic acid molecule in a reference genome of the organism; 
   for each of the plurality of chromosomal regions:
 identifying a respective group of nucleic acid molecules as being from the chromosomal region based on the identified locations, the respective group including at least one nucleic acid molecule located at each of the plurality of loci of the chromosomal region; 
 calculating a respective value of the respective group of nucleic acid molecules, the respective value defining a property of the nucleic acid molecules of the respective group; and 
 comparing the respective value to a respective reference value to determine a classification of whether the chromosomal region exhibits a deletion or an amplification; and 
   determining a test pattern of the chromosomal regions that exhibit a deletion or amplification, the test pattern including:
 a set of the chromosomal regions that exhibit a deletion or amplification; 
 a first subset of the set that exhibit an amplification; and 
 a second subset of the set that exhibit a deletion; 
   comparing the test pattern to a plurality of reference patterns of different types of cancer;   based on the comparison, determining a first amount of regions of the test pattern that exhibit a same deletion or amplification as a first reference pattern corresponding to a first type of cancer; and   comparing the first amount to a first threshold to determine a first classification of whether the biological sample exhibits the first type of cancer.