| CPC C12Q 1/6886 (2013.01) [C12Q 1/686 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/156 (2013.01); C12Q 2600/16 (2013.01)] | 16 Claims |
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1. A method for treatment of lung squamous cell carcinoma in a subject, the method comprising:
a) sequencing all of a genome of the lung squamous cell carcinoma of the subject to define early clonal mutations in said lung squamous cell carcinoma, wherein said sequencing is carried out on one or more samples obtained from all or part of the lung squamous cell carcinoma or one or more subsections thereof and defining the early clonal mutations comprises:
1) calculating an observed cancer cell fraction (CCF) of each mutation (obsCCF) and a phylogenetic CCF of that mutation (phyloCCF);
2) timing a clonal or subclonal mutation using the phyloCCF, wherein mutations in parts of the genome with at least two copies of a major allele are preliminarily classified as early if a mutation copy number for the mutation is greater than 1 and as late if the mutation copy number for the mutation is less than or equal to 1; and
3) performing temporal analysis comprising classifying all clonal or all subclonal mutations that are preliminarily classified as early across all tumor regions as an early clonal mutation, classifying all clonal or all subclonal mutations that are preliminarily classified as late across all tumor regions as a late clonal or subclonal mutation, and classifying all clonal or all subclonal mutations not timed as early or late as being a clonal or subclonal untimed mutation;
b) clustering all the clonal and subclonal mutations;
c) identifying mutation clusters having at least five mutations assigned thereto;
d) producing a subject-specific fraction of DNA by identifying the lung squamous cell carcinoma samples having at least two mutation clusters identified therein;
e) performing phylogenetic analysis on the subject-specific fraction of the DNA, wherein the phylogenetic analysis comprises assembling the mutations into a phylogenetic tree defining the clonal and subclonal mutation profile of the lung squamous cell carcinoma;
f) analyzing DNA included in a sample of DNA obtained from the subject subsequent to the lung squamous cell carcinoma removal using a set of subject-specific reagents capable of detecting at least one early clonal mutation characteristic of a trunk of the phylogenetic tree and at least one subclonal mutation characteristic of a branch of the phylogenetic tree, wherein detecting the at least one subclonal mutation characteristic of the branch of the phylogenetic tree is indicative of the branch seeding a relapse of the lung squamous cell carcinoma in the subject; and
g) administering a treatment to the subject, wherein the treatment comprises adjuvant chemotherapy and is a personalized treatment chosen for the subject in order to target the branch seeding the relapse of the lung squamous cell carcinoma in the subject; and
h) monitoring a response of the subject to the treatment based on detection of the at least one early clonal mutation characteristic of the trunk of the phylogenetic tree.
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