Abstract: Provided herein, inter alia, are methods of detecting the presence of extrachromosomal DNA (ecDNA) in esophageal cells obtained from a subject who has esophageal cancer or who is at risk of developing esophageal cancer. Provided are methods for treating esophageal cancer, including detecting the presence of ecDNA and administering an esophageal cancer treatment.

Abstract: Provided herein are methods for treating uveal melanoma in a subject in need thereof, and methods of detecting high-risk uveal melanoma in a subject, the subject having been selected by a method comprising, or alternatively consisting essentially of, or yet further consisting of detection of high methyl ati on levels at one or more of: BAP-1, CCNG2 and/or FKBP14 and/or measuring the mRNA expression of JARID2 and TMEM173 and determining ratio of mRNA expression JARID2 to TMEM173 in a sample isolated from the subject. Further provided herein are methods of determining prognosis of a subject having uveal melanoma, wherein high methylation levels and/or the ratio of mRNA expression JARID2 to TMEM173 of less than about 1 indicate a decreased probability and/or duration of survival and low methylation levels and/or the ratio of mRNA expression JARID2 to TMEM173 of greater than about 1 indicate an increased probability and/or duration of survival.

Abstract: Provided herein are, inter alia, methods and compositions to detect, monitor and treat cancer, wherein the cancer includes amplified extrachromosomal oncogenes. The methods are useful for personalized treatment and exploit differential expression of amplified extrachromosomal oncogenes in cancer cells versus healthy cells.

Abstract: Provided herein are, inter alia, methods and compositions to detect, monitor and treat cancer, wherein the cancer includes amplified extrachromosomal oncogenes. The methods are useful for personalized treatment and exploit differential expression and chromatin structure of extrachromosomal oncogenes in cancer cells.

Abstract: Provided herein are, inter alia, methods and compositions to detect, monitor and treat cancer, wherein the cancer includes amplified extrachromosomal oncogenes. The methods are useful for personalized treatment and exploit differential expression of amplified extrachromosomal oncogenes in cancer cells versus healthy cells.

Abstract: Provided herein are, inter alia, methods of treating cancer in a subject having or being at risk of developing cancer, wherein the subject has an amplified extrachromosomal oncogene. The treatment methods provided herein target cancer cells that include extrachromosomal DNA by administering a therapeutically effective amount of a DNA repair pathway inhibitor (e.g., a PARP inhibitor). The methods provided herein are furthermore useful to indicate the progressiveness of cancer, and/or to facilitate evaluation of responsiveness to therapy.

Abstract: Provided herein are, inter alia, methods and compositions to detect, monitor and treat cancer, wherein the cancer includes amplified extrachromosomal oncogenes. The methods are useful for personalized treatment and exploit differential expression of amplified extrachromosomal oncogenes in cancer cells versus healthy cells.