Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Abstract: Methods for creating a selector of mutated genomic regions and for using the selector set to analyze genetic alterations in a cell-free nucleic acid sample are provided. The methods can be used to measure tumor-derived nucleic acids in a blood sample from a subject and thus to monitor the progression of disease in the subject. The methods can also be used for cancer screening, cancer diagnosis, cancer prognosis, and cancer therapy designation.

Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Abstract: Processes and materials to detect cancer, transplant rejection, or fetal genetic abnormalities from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences indicative of a neoplasm, transplant rejection, or fetal genetic abnormality. Detection of somatic variants occurring in phase and/or insertions and deletions (indels) can indicate the presence of cancer, transplant rejection, or fetal genetic abnormalities in a diagnostic scan, and a clinical intervention can be performed.

Abstract: Disclosed herein are polynucleotide adaptors and methods of use thereof for identifying and analyzing nucleic adds, including cell-free nucleic acids from a patient sample. Also disclosed herein are methods of using the adaptors to detect, diagnose, or determine prognosis of cancers.

Abstract: Disclosed herein are polynucleotide adaptors and methods of use thereof for identifying and analyzing nucleic acids, including cell-free nucleic acids from a patient sample. Also disclosed herein are methods of using the adaptors to detect, diagnose, or determine prognosis of cancers.

Abstract: Processes and materials to detect cancer from a biopsy are described. In some cases, cell-free nucleic acids can be sequenced, and the sequencing result can be utilized to detect sequences derived from a neoplasm. Detection of somatic variants occurring in phase can indicate the presence of cancer in a diagnostic scan and a clinical intervention can be performed.

Abstract: Disclosed herein are polynucleotide adaptors and methods of use thereof for identifying and analyzing nucleic acids, including cell-free nucleic acids from a patient sample. Also disclosed herein are methods of using the adaptors to detect, diagnose, or determine prognosis of cancers.

Abstract: Methods are provided for diagnosis and prognosis of disease by analyzing expression of a set of genes obtained from single cell analysis. Classification allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like. Single cell analysis also provides for the identification and development of therapies which target mutations and/or pathways in disease-state cells.

Abstract: Methods, kits, devices, and computer systems are provided for obtaining an NSCLC marker level representation for an individual with non small cell lung carcinoma (NSCLC); and/or for providing a prognosis for an individual with NSCLC. The methods can include measuring expression levels, in a biological sample, of 2 or more NSCLC markers selected from: MAD2L1, GINS1, SLC2A1, KRT6A, FCGRT, TNIK, BCAM, KDM6A, and FAIM3; calculating an NSCLC marker level representation based on the measured expression levels; comparing the NSCLC marker level representation of the individual to a reference marker level representation; providing a prognosis based on the comparison; and/or generating a report that includes at least one of: (i) an NSCLC marker level representation, (ii) an NSCLC marker level representation and a reference NSCLC marker level representation, (iii) a prognosis, and (iv) guidance to a clinician as to a treatment recommendation based on the prognosis.

Abstract: Methods are provided for diagnosis and prognosis of disease by analyzing expression of a set of genes obtained from single cell analysis. Classification allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like. Single cell analysis also provides for the identification and development of therapies which target mutations and/or pathways in disease-state cells.

Abstract: Methods are provided for diagnosis and prognosis of disease by analyzing expression of a set of genes obtained from single cell analysis. Classification allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like. Single cell analysis also provides for the identification and development of therapies which target mutations and/or pathways in disease-state cells.

Abstract: Methods for creating a selector of mutated genomic regions and for using the selector set to analyze genetic alterations in a cell-free nucleic acid sample are provided. The methods can be used to measure tumor-derived nucleic acids in a blood sample from a subject and thus to monitor the progression of disease in the subject. The methods can also be used for cancer screening, cancer diagnosis, cancer prognosis, and cancer therapy designation.

Abstract: Methods for creating a library of recurrently mutated genomic regions and for using the library to analyze cancer-specific and patient-specific genetic alterations in a patient are provided. The methods can be used to measure tumor-derived nucleic acids in patient blood and thus to monitor the progression of disease. The methods can also be used for cancer screening.

Abstract: Improved 4D imaging reconstruction is provided for a freely breathing patient. 3D patient images from an imaging dataset are binned according to respiratory displacement or phase. The bins are defined by ranges, so every image in the raw 3D data set is included in a bin. Since binning in this manner often results in two or more images per bin, the 4D reconstruction is determined by selecting one 3D image from each bin at each patient position. This selection is performed so as to maximize the anatomical similarity of 3D images at adjacent patient positions. In cases where the 3D images include multiple slices, a 2D comparison of the closest slices can be used to determine anatomical similarity of the 3D images.

Abstract: Methods are provided for diagnosis and prognosis of disease by analyzing expression of a set of genes obtained from single cell analysis. Classification allows optimization of treatment, and determination of whether on whether to proceed with a specific therapy, and how to optimize dose, choice of treatment, and the like. Single cell analysis also provides for the identification and development of therapies which target mutations and/or pathways in disease-state cells.

Abstract: Improved 4D imaging reconstruction is provided for a freely breathing patient. 3D patient images from an imaging dataset are binned according to respiratory displacement or phase. The bins are defined by ranges, so every image in the raw 3D data set is included in a bin. Since binning in this manner often results in two or more images per bin, the 4D reconstruction is determined by selecting one 3D image from each bin at each patient position. This selection is performed so as to maximize the anatomical similarity of 3D images at adjacent patient positions. In cases where the 3D images include multiple slices, a 2D comparison of the closest slices can be used to determine anatomical similarity of the 3D images.

Abstract: Cancer stem cells (CSCs) have been prospectively isolated or identified from primary tumor samples, and shown to possess the unique properties of self-renewal and differentiation, and can form unique histological microdomains useful in cancer diagnosis. Such cancer stem cells are shown herein to have the phenotype of containing decreased levels of reactive oxygen species (ROS) relative to non-tumorigenic (non-stem cell) cancer cells, as well as expression of other protective pathways. The CSCs are further shown to be more resistant to ionizing radiation (IR) and certain chemotherapies and to express high levels of ROS genes.