Abstract: Ultra-sensitive detection of cancer by algorithmic analysis. In various embodiments, a sample comprising a plurality of polynucleotides is analyzed. A plurality of sequences of the plurality of polynucleotides is received. The plurality of sequences is provided to a trained classifier. The trained classifier is adapted to accept a plurality of sequences and output a class label indicative of the presence of a somatic variant within the plurality of sequences. A class label is received from the trained classifier indicative of the presence of a somatic clone within the plurality of sequences.

Abstract: Methods and apparatus for inferring purity and ploidy from a sample of cells (e.g., a sample comprising cancer and normal cells) are described. Copy number per cell of interest (e.g., cancer cell) is determined by optimizing purity and ploidy for the sample based, at least in part, on relative copy number profile information. One or more likelihood fit scores are determined for each of a plurality of candidate solutions generated by the methods described herein. A solution is selected based, at least in part on the likelihood fit score(s) and the copy number per cancer cell is determined in accordance with the selected solution.

Abstract: A method for diagnosis of different stages of endometrial cancer and for evaluating the probability of survival for an individual suffering from endometrial carcinoma, and for stratification of a therapy regimen for an endometrial tumor or monitoring therapeutic efficacy in an individual suffering considers the expression status of STMN1 gene or protein. A kit for use in the methods allows for determining amplifications and deletions of chromosomal regions 3q26.32 and 12p12.1, determining alterations of the gene expression profile of the genes (gene signature): upregulation of the genes PLEKHK1, ATP10B, NMU, MMP1, ATAD2, NETO2, TNNI3, PHLDA2, OVOL1 and down-regulation of the genes: NDP, KIAA1434, MME, CFH, MOXD1, SLC47A1, RBP1, PDE8B, ASRGL1, ADAMTS19, EFHD1, ABCA5, NPAS3, SCML1, TNXB, ENTPD3, AMY1A, ENPP, RASL11B, PDZK3, or the expression status of the STMN1 gene or protein.

Abstract: The present invention relates to a method for diagnosis of different stages of endometrial cancer in an individual. Further, the present invention relates to a method for evaluating the probability of survival for an individual suffering from endometrial carcinoma. In another aspect, the present invention relates to the stratification of therapy regimen of endometrial tumor, ovarian cancer, breast cancer, non-small lung cancer or hormone refractory prostate cancer therapy in an individual or monitoring therapeutic efficacy in an individual suffering from the same based on the expression status of STMN1 gene or protein. Moreover, the present invention relates to a kit for use in any of the above referenced methods comprising a means for determining amplifications and deletions of chromosomal regions 3q26.32 and 12p12.

Abstract: The present teachings provide methods for predicting the clinical outcome of the treatment of human solid tumors. In some embodiments, the method includes measuring in the cells of a tumor the expression level of a set of genes whose change is related to chromosomal instability; taking a statistical measure of the expression level of the set of measured genes; and if the statistical measure of the expression level of the set of measured genes is elevated, determining that the prognosis is poor. Another aspect of the present teachings is the sets of genes, which are useful in predicting the outcome of treatment of solid tumors.