Methods for early detection of cancer

Abstract

Disclosed herein are methods, compositions, and devices for use in early detection of cancer. The methods include sequencing a panel of regions in cell-free nucleic acid molecules and detecting one or more tumor markers that are indicative of a cancer.

1 . A method comprising:
 (a) providing a sample comprising cell-free nucleic acid (cfNA) molecules from a subject, wherein the subject does not detectably exhibit a cancer;   (b) capturing from the sample cfNA molecules covered by a sequencing panel, wherein the sequencing panel comprises one or more regions from each of a plurality of different genes, wherein:
 i. the sequencing panel is no greater than 50,000 nucleotides; 
 ii. a presence of a tumor marker in any one of the different genes indicates that the subject has the cancer; and 
 iii. at least 80% of subjects having the cancer have a tumor marker present in at least one of the plurality of different genes; and 
   (c) sequencing the captured cfNA molecules to a read depth sufficient to detect the tumor markers at a frequency in the sample as low as 1.0%, 0.75%, 0.5%, 0.25%, 0.1%, 0.075%, 0.05%, 0.025%, 0.01%, or 0.005%.   
     
     
         2 . The method of  claim 1 , wherein the cfNA molecules are derived from blood, serum, or plasma. 
     
     
         3 . The method of  claim 1 , wherein the sample comprises between 10 nanograms and 300 nanograms of cfNA, and wherein the cfNA is circulating cell-free DNA (cfDNA). 
     
     
         4 . The method of  claim 1 , wherein the cancer is selected from the group consisting of ovarian cancer, pancreatic cancer, breast cancer, colorectal cancer, and non-small cell lung carcinoma (NSCLC), or a combination thereof. 
     
     
         5 . The method of  claim 1 , wherein the cancer is non-small cell lung carcinoma (NSCLC), and the non-small cell lung carcinoma (NSCLC) is squamous cell carcinoma or adenocarcinoma. 
     
     
         6 . The method of  claim 1 , wherein the subject does not detectably exhibit the cancer as shown by one or more imaging methods selected from the group consisting of positron emission tomography scan, magnetic resonance imaging, X-ray, computerized axial tomography scan, and ultrasound. 
     
     
         7 . The method of  claim 1 , wherein the subject has previously undergone treatment for the cancer. 
     
     
         8 . (canceled) 
     
     
         9 . The method of  claim 1 , wherein the plurality of genes is between 2 to 30 different genes. 
     
     
         10 . The method of  claim 1 , wherein the plurality of genes is no more than any of 10, 9, 8, 7, 6, or 5 different genes. 
     
     
         11 . The method of  claim 1 , wherein the panel comprises a plurality of genes selected from the group consisting of AKT1, ALK, APC, ATM, BRAF, CTNNB1, EGFR, ERBB2, ESR1, FGFR2, GATA3, GNAS, IDH1, IDH2, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, PTEN, RB1, SMAD4, STK11, and TP53. 
     
     
         12 . The method of  claim 1 , wherein the sequencing panel is about 15,000 nucleotides to about 30,000 nucleotides. 
     
     
         13 . The method of  claim 1 , wherein the tumor marker is selected from the group consisting of a single base substitution, an insertion or deletion (indel), a gene fusion, a transversion, a translocation, an inversion, a deletion, aneuploidy, partial aneuploidy, polyploidy, chromosomal instability, chromosomal structure alterations, chromosome fusions, a gene truncation, a gene amplification, a gene duplication, a chromosomal lesion, a DNA lesion, abnormal changes in nucleic acid chemical modifications, abnormal changes in epigenetic patterns and abnormal changes in nucleic acid methylation. 
     
     
         14 . The method of  claim 1 , wherein at least 85%, at least 90%, at least 93%, at least 95%, at least 97%, at least 98%, or at least 99% of subjects having the cancer have a tumor marker present in at least one of the plurality of different genes. 
     
     
         15 . The method of  claim 1 , comprising sequencing the captured cfNA molecules to a read depth sufficient to detect the tumor markers at a frequency in the sample as low as 0.005%, 0.001%, or 0.0005%. 
     
     
         16 . The method of  claim 1 , wherein the one or more regions are selected for the sequencing panel to detect one or more differentially methylated regions. 
     
     
         17 . The method of  claim 1 , wherein the one or more regions comprise sequences differentially transcribed across one or more tissues of the subject. 
     
     
         18 . The method of  claim 1 , wherein the sequencing panel is selected to detect the one or more tumor markers with a theoretical sensitivity of 85% or greater. 
     
     
         19 . The method of  claim 1 , wherein the panel is selected to achieve a sensitivity of 85% or greater for one or more cancers selected from the group consisting of colorectal cancer, ovarian cancer, lung cancer, and pancreatic cancer. 
     
     
         20 . The method of  claim 1 , wherein assaying the cfNA molecules comprises subjecting the cfNA molecules to sequencing in the one or more regions in the sequencing panel to generate sequence reads. 
     
     
         21 - 87 . (canceled) 
     
     
         88 . A method for identifying treatment for a subject with non-small cell lung carcinoma (NSCLC), comprising:
 (a) sequencing cell-free DNA (cfDNA) molecules derived from a cell-free DNA (cfDNA) sample obtained from the subject;   (b) analyzing sequence reads derived from the sequencing to identify (i) circulating tumor DNA (ctDNA) among the cfDNA molecules and (ii) a copy number amplification (CNA) of the MET gene in the ctDNA with a specificity of at least 99%; and   (c) identifying, based at least on the identified CNA of the MET gene, an anti-MET therapy to be administered to the subject to treat the NSCLC.   
     
     
         89 - 102 . (canceled) 
     
     
         103 . A method for monitoring breast cancer in a subject, comprising:
 (a) sequencing cell-free DNA (cfDNA) molecules derived from a cell-free DNA (cfDNA) sample obtained from the subject; and   (b) analyzing sequence reads derived from the sequencing to identify (i) circulating tumor DNA (ctDNA) among the cfDNA molecules and (ii) one or more mutations in the ctDNA from the subject selected from:   EGFR, Exon 19 deletion; TP53, E286K mutation; AR, N706S mutation; ALK, G1137R mutation; MAP2K2, E66K mutation; and TP53, K164E mutation.   
     
     
         104 - 136 . (canceled)