Abstract: The present disclosure provides a method for genetic analysis for disease diagnoses, as well as a system for implementing such analysis. Provided is a comprehensive, scalable, biotechnology solution that solves diagnostic and therapeutic complications in rapidly progressive childhood genetic diseases. As such, the invention provides Genome-to-Treatment (GTRx?), which is an automated, virtual system for genetic disease diagnosis and acute management guidance.

Abstract: The present disclosure provides a method for genetic analysis disease diagnoses as well as a system for implementing such analysis.

Abstract: The method for genome analysis translates the clinical findings in the patient into a comprehensive test order for genes that can be causative of the patient's illness, delimits analysis of variants identified in the patient's genome to those that are “on target” for the patient's illness, and provides clinical annotation of the likely causative variants for inclusion in a variant warehouse that is updated as a result of each sample that is analyzed and that, in turn, provides a source of additional annotation for variants.

Abstract: The process of the present invention is used to perform nucleotide sequence variant detection using two or more independent analysis methods to produce a superset of highly sensitive variant calls. The process of the present invention is used for genetic disease diagnosis including the steps of genome sequencing, creating a superset of sensitive variant calls by using at least two independent analysis methods, comparing a database of genetic diseases with disease phenotype information to produce a prioritized list of probable genetic diseases, and integrating the superset of sensitive variant calls and the prioritized list of probable genetic diseases.

Abstract: The method for genome analysis translates the clinical findings in the patient into a comprehensive test order for genes that can be causative of the patient's illness, delimits analysis of variants identified in the patient's genome to those that are “on target” for the patient's illness, and provides clinical annotation of the likely causative variants for inclusion in a variant warehouse that is updated as a result of each sample that is analyzed and that, in turn, provides a source of additional annotation for variants.

Abstract: A method for determining prognosis, diagnosis and theronosis of a sepsis infection in a patient is disclosed. The method involves measuring the age, mean arterial pressure, hematocrit, patient temperature, and the concentration of one or more metabolites that are predictive of sepsis severity. The method can involve obtaining a blood sample from said patient and determining the concentration of the metabolite in the patient's blood; and then determining the severity of sepsis infection by analyzing the measured values in a weighted logistic regression equation.

Abstract: The present invention is directed to methods for diagnosis of sepsis and high risk of sepsis death. Such methods are directed to subjects presenting to healthcare facilities with symptoms for sepsis. Clinico-metabolomic classifiers are tested and compared in the methods of the present invention.

Abstract: Detection of expression of biomarkers (e.g., protein analytes) whose regulation is perturbed in COPD patients can be used to diagnose COPD, to confirm a diagnosis of COPD, and to assess or prognose progression of COPD. Test substances can be screened for the ability to affect levels of protein analyte expression, thereby identifying potential anti-COPD drugs.

Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. Amplification of the DNA circle is dependent on the presence of the primer. Thus, the disclosed method produces an amplified signal, via rolling circle amplification, from any analyte of interest. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. The disclosed method can be used to detect and analyze proteins and peptides. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. A rolling circle replication primer is then associated with the various proteins using a conjugate of the primer and a molecule that specifically binds the proteins to be detectable.

Abstract: Biomarkers for sepsis and resulting mortality can be detected by assaying blood samples. Changes in the concentration of the biomarkers can be used to indicate sepsis, risk of sepsis, progression of sepsis, remission from sepsis, and risk of mortality. Changes can be evaluated relative to data sets, natural or synthetic or semisynthetic control samples, or patient samples collected at different time points. Some biomarkers' concentrations are elevated during disease and some are depressed. These are termed informative biomarkers. Some biomarkers are diagnostic in combination with others. Individual biomarkers may be weighted when used in combinations. Biomarkers can be assessed in individual, isolated or assays, in parallel assays, or in single-pot assays.

Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. Amplification of the DNA circle is dependent on the presence of the primer. Thus, the disclosed method produces an amplified signal, via rolling circle amplification, from any analyte of interest. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. The disclosed method can be used to detect and analyze proteins and peptides. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. A rolling circle replication primer is then associated with the various proteins using a conjugate of the primer and a molecule that specifically binds the proteins to be detectable.

Abstract: Methods for the amplification of selected nucleic acids at high rate but with high specificity and control are disclosed using a secondary, tertiary, quaternary or higher order platform especially designed to amplify selected sequences within the primary product of linear or exponential rolling circle amplification and amplifying said sequences along with specialized detector or reporter molecules that serve to enhance the ability to detect the amplification products.

Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. Amplification of the DNA circle is dependent on the presence of the primer. Thus, the disclosed method produces an amplified signal, via rolling circle amplification, from any analyte of interest. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. The disclosed method can be used to detect and analyze proteins and peptides. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. A rolling circle replication primer is then associated with the various proteins using a conjugate of the primer and a molecule that specifically binds the proteins to be detectable.

Abstract: Disclosed are compositions and methods for detecting small quantities of analytes such as proteins and peptides. The method involves associating a primer with an analyte and subsequently using the primer to mediate rolling circle replication of a circular DNA molecule. Amplification of the DNA circle is dependent on the presence of the primer. Thus, the disclosed method produces an amplified signal, via rolling circle amplification, from any analyte of interest. The amplified DNA remains associated with the analyte, via the primer, and so allows spatial detection of the analyte. The disclosed method can be used to detect and analyze proteins and peptides. Multiple proteins can be analyzed using microarrays to which the various proteins are immobilized. A rolling circle replication primer is then associated with the various proteins using a conjugate of the primer and a molecule that specifically binds the proteins to be detectable.

Abstract: Methods for the amplification of selected nucleic acids at high rate but with high specificity and control are disclosed using a secondary, tertiary, quaternary or higher order platform especially designed to amplify selected sequences within the primary product of linear or exponential rolling circle amplification and amplifying said sequences along with specialized detector or reporter molecules that serve to enhance the ability to detect the amplification products.

Abstract: Methods for the amplification of selected nucleic acids at high rate but with high specificity and control are disclosed using a secondary, tertiary, quaternary or higher order platform especially designed to amplify selected sequences within the primary product of linear or exponential rolling circle amplification and amplifying said sequences along with specialized detector or reporter molecules that serve to enhance the ability to detect the amplification products.