Abstract: The present invention provides according to some aspects methods and kits for determining the efficiency of plasma separation from whole blood using quantitative PCR amplification of two amplicons, namely, a short amplicon of e.g. 70-150 bps and a long amplicon of e.g. 350-600 bps. The separation efficiency is determined based on the difference in amplification levels of the two amplicons. Advantageously, the separation efficiency is determined without absolute quantification of DNA and/or determination of copy number of any gene/locus.

Abstract: Methods for applying machine learning algorithms to nucleic acid sequencing-based diagnostics tests for detection of copy number variation and other genomic abnormalities are described.

Abstract: Compositions and methods for DNA amplification following a DNA digestion reaction are provided. In particular embodiments, reaction buffers comprising a chelating agent are provided. The provided reaction buffers obviate the need for a dilution and/or a purification step between the DNA digestion and the DNA amplification.

Abstract: Methods for the processing and analysis of blood samples obtained with blood collection tubes that reduce contamination of cfDNA by genomic DNA but that inhibit digestion by methylation-sensitive and/or methylation-dependent restriction enzymes.

Abstract: Methods and kits for determining the efficiency of plasma separation from whole blood are provided, using real-time PCR amplification of two amplicons, namely, a short amplicon of e.g. 70-150 bps and a long amplicon of e.g. 350-600 bps. The separation efficiency is determined based on the difference in amplification patterns of the two amplicons.

Abstract: Methods and systems for personalized cancer management and monitoring are provided, such as evaluating minimal residual disease (MRD), monitoring tumor recurrence, predicting and monitoring response to treatment and prognosis, based on detection and tracking of tumor-associated DNA methylation changes in cell-free DNA samples, particularly cell-free DNA from plasma samples.

Abstract: Methods and systems for highly sensitive detection of methylation changes in DNA samples are provided, particularly in DNA samples obtained from biological fluids such as plasma and urine.

Abstract: The invention provides methods for ultra-deep whole-genome sequencing of human DNA. The methods determine the methylation status of millions of sites in the human genome, wherein said methods use few (if any) DNA amplification cycles.

Abstract: Methods and systems for highly sensitive detection of methylation changes in DNA samples are provided, particularly in DNA samples obtained from biological fluids such as plasma and urine.

Abstract: Methods and kits for detection of cancer-related mutations in a DNA sample using enzymatic restriction and real-time PCR. A DNA sample is subjected to digestion with a restriction endonuclease to obtain restriction endonuclease-treated DNA, followed by co-amplification of a restriction locus comprising a cancer mutation site and a control locus. A ratio of signal intensities of the amplification products of the restriction locus and the control locus is used to detect the cancer-related mutation.

Abstract: Methods and kits for identification of lung cancer in a subject based on alterations in DNA methylation at selected genomic loci are provided.

Abstract: Methods and kits for detection of cancer-related mutations in a DNA sample using enzymatic restriction and real-time PCR. A DNA sample is subjected to digestion with a restriction endonuclease to obtain restriction endonuclease-treated DNA, followed by co-amplification of a restriction locus comprising a cancer mutation site and a control locus. A ratio of signal intensities of the amplification products of the restriction locus and the control locus is used to detect the cancer-related mutation.

Abstract: Methods and systems for assessing the presence of cancer in a subject and predicting the tissue source of the cancer are provided, by analyzing DNA methylation markers in cell- free DNA samples, particularly cell-free DNA from plasma samples.

Abstract: Methods and systems for genetic and epigenetic profiling of DNA samples and detecting genetic and epigenetic changes in DNA samples are provided, which involve digestion of DNA with methylation-sensitive restriction enzymes, followed by high-throughput sequencing and analysis of sequence reads. Advantageously, the methods and systems of the present invention are sensitive yet accurate, and enable working with very low amounts of DNA and receive vast amount of information, including methylation data, mutation data and more, based on sequencing data from a single run.

Abstract: Methods and kits for identification of lung cancer in a subject based on alterations in DNA methylation at selected genomic loci are provided.

Abstract: Methods and kits for determining the efficiency of plasma separation from whole blood are provided, using real-time PCR amplification of two amplicons, namely, a short amplicon of e.g. 70-150 bps and a long amplicon of e.g. 350-600 bps. The separation efficiency is determined based on the difference in amplification patterns of the two amplicons.

Abstract: Methods and systems for highly sensitive detection of methylation changes in DNA samples are provided, particularly in DNA samples obtained from biological fluids such as plasma and urine.

Abstract: Methods and kits for determining the efficiency of plasma separation from whole blood are provided, using real-time PCR amplification of two amplicons, namely, a short amplicon of e.g. 70-150 bps and a long amplicon of e.g. 350-600 bps. The separation efficiency is determined based on the difference in amplification patterns of the two amplicons.

Abstract: Methods and systems for highly sensitive detection of methylation changes in DNA samples are provided, particularly in DNA samples obtained from biological fluids such as plasma and urine.

Abstract: Methods and kits for identification of bladder cancer in a subject based on alterations in DNA methylation at selected genomic loci are provided.