18 results about "Plasma dna" patented technology

A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient.

The invention belongs to the technical field of noninvasive prenatal examination, and particularly relates to a preparation method of a pregnant woman simulated plasma standard substance capable of enriching fetal concentration through fragment size. The invention provides a preparation method of a pregnant woman plasma free DNA simulation sample, which is combined with a specific DNA fragmentation treatment technology to prepare the simulation sample which has high fidelity and stability and can accurately simulate the distribution proportion of fetal free DNA and pregnant woman free DNA in real pregnant woman plasma, and is used for quality control and evaluation of a noninvasive prenatal diagnosis technology. According to the method, the pregnant woman simulated plasma DNA with the corresponding fetal concentration can be accurately prepared according to requirements, the prepared pregnant woman simulated plasma can meet the application requirements of fetal concentration enrichment testing, and meanwhile the distribution condition of cfDNA fragments in the pregnant woman plasma is reduced to the maximum extent.

The invention discloses a lung nodule diagnosis method based on plasma DNA methylation characteristics and application, and the method comprises the following steps: S1, collecting peripheral blood of a subject in a special cfDNA preservation tube, carrying out centrifugal separation to obtain plasma, extracting cfDNA by adopting an optimized paramagnetic particle method or column extraction method, carrying out quality control on the cfDNA, then carrying out thorough hydrosulphite conversion treatment on the cfDNA, and carrying out purification treatment on the cfDNA to obtain the plasma; unmethylated cytosine is converted into uracil, and methylated cytosine is kept unchanged. The invention is derived from the selection of an early and stable epigenetic marker of DNA methylation, and replaces traditional dependent clinical parameters or mutation signals appearing at a late stage. According to the method, the problem of insufficient discrimination capability (AUClt; 0.60) caused by limited input information of an existing clinical prediction model (such as a MayoClinic model) is directly solved.

Massively parallel sequencing of cell-free maternal plasma DNA has recently been demonstrated to be a safe and effective method for screening for fetal chromosomal aneuploidy. Here, we report an improved sequencing method that significantly increases throughput and reduces costs by replacing the laborious sequencing library preparation step with PCR using a single primer pair. Using this method, samples containing as little as 4% trisomy 21 DNA can be readily distinguished from euploid samples.

Methods and kits are provided for determining the efficiency of separating plasma from whole blood using PCR amplification or high-throughput sequencing data of genomic loci present at different concentrations in plasma DNA and whole blood DNA.

A frequency of somatic mutations in a biological sample (e.g., plasma or serum) of a subject undergoing screening or monitoring for cancer, can be compared with that in the constitutional DNA of the same subject. A parameter can derived from these frequencies and used to determine a classification of a level of cancer. False positives can be filtered out by requiring any variant locus to have at least a specified number of variant sequence reads (tags), thereby providing a more accurate parameter. The relative frequencies for different variant loci can be analyzed to determine a level of heterogeneity of tumors in a patient.

The invention discloses a composition for detecting methylation of a human plasma RPS2 gene and a DCDC2 gene of liver cancer, which can be used for realizing early screening and early diagnosis of liver cancer through detection of plasma DNA (Deoxyribonucleic Acid). Meanwhile, the invention further provides a kit for methylation of the RPS2 gene and the DCDC2 gene, the sensitivity of detection of liver cancer patients reaches 85.88%, and the specificity is 92.23%.

Methods are provided to improve the positive predictive value for cancer detection using cell-free nucleic acid samples. Various embodiments are directed to applications (e.g., diagnostic applications) of the analysis of the fragmentation patterns and size of cell-free DNA, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, including viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).

The technology provided herein relates to amplification-based detection of bisulfite treated DNA, and in particular, but not exclusively, to methods and compositions for multiplex amplification of low levels of sample DNA prior to further characterization of the sample DNA. The technology also provides methods for isolating DNA from a blood or blood product sample, such as a plasma sample.

The invention relates to the field of library construction, in particular to an enzyme composition, a reagent, a kit and a library construction method for improving plasma DNA library construction efficiency and sensitivity. By improving a plasma DNA library construction method, the sensitivity of pathogen detection is improved. By adding specific ligase during traditional linker connection, enrichment of small fragment nucleic acid is enhanced, and detection sensitivity is improved. Afterwards, multiple rounds of magnetic bead purification steps after linker connection are omitted, a specific mixed enzyme treatment system is added for activation of PCR reaction, linker dimers, reagent residues and human source interference are effectively removed, meanwhile, the PCR reaction is optimized on the basis of a traditional library construction process, and the pathogen DNA detection effect is remarkably improved.

Pancreatic adenocarcinoma has the worst overall mortality of any solid tumor, with only 7% of patients surviving after 5 years. To evaluate the clinical implications of genomic alterations in this low cellularity tumor type, we deeply sequenced the genomes of 101 enriched pancreatic adenocarcinomas from patients who underwent potentially curative resections and used non-invasive approaches to examine tumor specific mutations in the circulation of these patients. These analyses revealed somatic mutations in chromatin regulating genes including MLL and ARID1A in 20% of patients that were associated with improved survival. Liquid biopsy analyses of cell free plasma DNA revealed that 43% of patients with localized disease had detectable circulating tumor DNA (ctDNA) in their blood at the time of diagnosis. Detection of ctDNA after resection predicted clinical relapse and poor outcome, and disease recurrence by ctDNA was detected 6.5 months earlier than with standard CT imaging.

The invention discloses a composition for detecting methylation of a human plasma SOX15 gene and an EME1 gene for lung cancer, which can be used for realizing early screening and early diagnosis of the lung cancer through detection of plasma DNA (Deoxyribonucleic Acid). Meanwhile, the invention further provides a kit for methylation of the SOX15 gene and the EME1 gene, the sensitivity of detection of lung cancer patients reaches 83.49%, and the specificity is 92.10%.

The invention discloses a composition for detecting methylation of an EYA4 gene and an LCAT gene in human plasma, which can be used for realizing early screening and early diagnosis of gastric cancer through detection of plasma DNA (Deoxyribose Nucleic Acid). Meanwhile, the invention also provides a kit for methylation of EYA4 and LCAT genes, the sensitivity of the kit for detection of gastric cancer patients reaches 91.6%, and the specificity of the kit is 94.6%.

Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.

The present application belongs to the technical field of non-invasive prenatal testing, and particularly relates to a preparation method of a pregnant woman simulated plasma standard product capable of fetal concentration enrichment through fragment size. The present application provides a preparation method of a pregnant woman plasma free DNA simulation sample. The method combines specific DNA fragmentation processing technology to prepare a simulation sample with high fidelity and stability and capable of accurately simulating the fetal free DNA and pregnant woman free DNA distribution proportion in real pregnant woman plasma, for quality control and evaluation of non-invasive prenatal diagnosis technology. The method can accurately prepare the pregnant woman simulated plasma DNA with the corresponding fetal concentration according to the requirement, and the prepared pregnant woman simulated plasma can meet the requirement of the application of fetal concentration enrichment test, and at the same time, the cfDNA fragment distribution in the pregnant woman plasma is restored in the maximum range.

Methods and kits for determining the efficiency of plasma separation from whole blood are provided, which use PCR amplification or high-throughput sequencing data of genomic loci that are present at different concentrations in plasma DNA and in whole blood DNA.

Methods are provided to improve the positive predictive value for cancer detection using cell-free nucleic acid samples. Various embodiments are directed to applications (e.g., diagnostic applications) of the analysis of the fragmentation patterns and size of cell-free DNA, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, including viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).

The invention provides a plasma DNA rapid extraction method, and relates to the technical field of DNA separation and purification, and the plasma DNA rapid extraction method comprises the following steps: mixing plasma and a lysis solution, carrying out heating treatment, and injecting the plasma and the lysis solution into an extraction container at the same time; adding a magnetic bead suspension, and starting a motor to provide swing and oscillation effects; dNA is adsorbed to the surfaces of the magnetic beads in a high-salt environment to form a magnetic bead suspension; fixing the extraction container by using a magnetic frame, and controlling the magnetic beads to be concentrated; extracting supernate, and removing impurities; and adding a low-salt buffer solution to release DNA, controlling the magnetic beads to concentrate again, and extracting the released supernatant to obtain a purified DNA solution. When the motor controls the extraction container to rotate, a more uniform oscillation effect is provided, the mixing efficiency is improved, and when an internal solution is extracted, the internal solution can be far away from magnetic beads to the greatest extent, so that the purity of the finally extracted DNA solution is improved.