23 results about "Fetal dna" patented technology

Compositions, methods, kits, systems, and software are provided for non-invasive prenatal testing for autosomal recessive diseases. Next generation sequencing is used to sequence maternal and fetal DNA isolated from maternal plasma by probe capture. The fetal fraction of the sequencing reads for DNA isolated from maternal plasma is estimated by counting single nucleotide polymorphisms (SNPs) for which an allele is detected that is present in the paternal haplotype but absent in the maternal haplotype, based on the assumption that SNPs having a paternal allele belong to the fetal DNA. The fetal fraction is bioinformatically enriched by excluding sequencing reads over a specified length via in-silico size selection, which increases fetal genotype prediction accuracy. Parental haplotype information together with the read ratios observed at the linked SNPs is used to predict the fetal genotype at a site of a mutation linked to the autosomal recessive disease.

The invention provides methods for non-invasive prenatal testing that allow for detecting risk of chromosomal and subchromosomal abnormalities, including but not limited to aneuploidies, microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures. The methods of the invention utilize a pool of TArget Capture Sequences (TACS) to enrich for sequences of interest in a mixed sample containing both maternal and fetal DNA, followed by massive parallel sequencing and statistical analysis of the enriched population to thereby detect the risk of a genetic abnormality in the fetal DNA. Kits for carrying out the methods of the invention are also provided.

The invention provides methods for assessment of fetal DNA samples using target-enriched multiplexed parallel analysis. The methods of the invention utilize TArget Capture Sequences (TACS) to thereby enrich for target sequences of interest, followed by massive parallel sequencing and statistical analysis of the enriched population. The methods can be used with fetal or embryonic DNA samples, for example for detection of the presence of genetic abnormalities, e.g., for purposes of IVF Pre-implantation Genetic Screening (PGS) and Diagnosis (PGD). Kits for carrying out the methods of the invention are also provided.

The present application relates to the field of paternity determination, and provides a non-invasive prenatal paternity relationship determination method and system and electronic equipment, the method comprising: obtaining a paternal DNA sample and a pregnant woman's plasma free DNA sample, the pregnant woman's plasma free DNA sample including a fetal DNA sample; performing genomic sequencing on the paternal DNA sample and the pregnant woman's plasma free DNA sample; after genotype filling, determining the paternal genotype and the fetal genotype; calculating the kinship coefficient of the paternal genotype and the fetal genotype; based on the kinship coefficient of the paternal genotype and the fetal genotype and a pre-constructed corresponding relationship between the kinship coefficient and the paternity relationship, determining the paternity relationship between the father and the fetus. The present application solves the defects of low detection efficiency and high technical cost in the related art, and is convenient to operate, completely non-invasive, and does not cause any physiological interference to the pregnant woman and the fetus; the detection can be carried out from the seventh week of pregnancy, and is suitable for precise identification of the biological father of the fetus and unrelated individuals.

A chromosomal aneuploidy analysis method and a use. The method comprises: using sequencing data of a sample to be tested and an alignment result thereof to calculate the fetal DNA concentration in said sample and the window depth of said sample within a set window; and calculating the average relative depth of all samples in a selected reference set within the set window as a correction baseline, using the correction baseline to correct the window depth of said sample, calculating a Z value of said sample on the basis of the corrected window depth, and on the basis of the Z value, determining whether an aneuploidy abnormality has occurred to a fetal chromosome of said sample. Using the selected reference set to calculate the correction baseline for correcting said sample enables more stable and accurate detection of the chromosomal aneuploidy abnormality in said sample under the condition that there are no samples in a same batch as references, thereby reducing inter-batch variability in testing.

A method of detecting fetal cell-free fetal DNA (cffDNA) in the breath of the pregnant woman is provided. The method includes condensation of the breath sample to liquefy; selection of the target genome region locus; selection of primers that amplify the selected locus; selection of probes that attach to the replicated locus; introducing the targeted site primers and the breath sample into the PCR cycle and amplifying the targeted locus, if present in the sample; binding the probes specific to the amplified region; detecting the fluorescent radiation with the PCR reader and presenting it as data, if there is a targeted region in the breath sample.

This application discloses a method, apparatus, and storage medium for detecting fetal chromosomal aneuploidy. The method for detecting fetal chromosomal aneuploidy includes calculating a new Z-value for the sample based on the fetal DNA concentration, Z-value, and chimerism of the cell-free DNA in the pregnant woman's blood; the new Z-value is used to determine whether fetal chromosomal aneuploidy has occurred. Chimerism is the ratio of abnormal fetal cells to all fetal cells. This application is the first to incorporate chimerism into the detection of fetal chromosomal aneuploidy, comprehensively considering three variables—fetal DNA concentration, chimerism, and Z-value—to calculate a new Z-value, which improves the accuracy of NIPT detection, provides excellent differentiation between true positive and false positive samples, and reduces false positives. The new Z-value conforms to a normal distribution, meeting current regulatory and clinical requirements, reducing data distribution volatility, thereby reducing the gray area rate, reducing the retest rate, and improving the stability of the test results.

Provided are a method and apparatus for determining a concentration of fetal DNA. The method for determining the concentration of fetal DNA includes: acquiring multiple sequencing reads of a cell-free DNA (cfDNA) sample under test; aligning the multiple sequencing reads with a reference genome to obtain alignment results; and determining the concentration of fetal DNA based on the alignment results. The concentration of fetal DNA can be determined based on the alignment results between the sequencing reads and the reference genome so that applications to various sequencing platforms including a single-molecule sequencing platform can be satisfied, and the accuracy of determination of the concentration of fetal DNA can be improved.

Systems, apparatuses, and method are provided for determining the contributions of different tissues to a biological sample that includes a mixture of cell-free DNA molecules from various tissues types, e.g., as occurs in plasma or serum and other body fluids. Embodiments can analyze the methylation patterns of the DNA mixture (e.g., methylation levels at particular loci) for a particular haplotype and determine fractional contributions of various tissue types to the DNA mixture, e.g., of fetal tissue types or tissue types of specific organs that might have a tumor. Such fractional contributions determined for a haplotype can be used in a variety of ways.

The invention discloses a chromosome aneuploid analysis method and application, and the method comprises the following steps: calculating the fetal DNA concentration in a to-be-detected sample and the window depth of the to-be-detected sample in a set window by adopting the sequencing data of the to-be-detected sample and the comparison result of the to-be-detected sample; and calculating the average value of the relative depths of all the samples in the selected reference set in the set window as a correction baseline, correcting the window depth of the to-be-detected sample by adopting the correction baseline, calculating the Z value of the to-be-detected sample according to the corrected window depth, and judging whether the aneuploid abnormality occurs in the fetal chromosome of the to-be-detected sample according to the Z value. According to the method, the to-be-detected sample is corrected by calculating the correction baseline by selecting the reference set, so that the chromosome aneuploid abnormality of the to-be-detected sample can be more stably and accurately detected under the condition that no sample in the same batch is taken as a reference, and the batch fluctuation of detection is reduced.

Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists in a biological sample. One or more cutoff values ​​are selected to determine an imbalance, for example, the ratio of two sequences (or sets of sequences). The cutoff value can be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, that contains a background of maternal nucleic acid sequences. 1 [ cutoff value can be determined based on an average concentration of a sequence per reaction. In one aspect, the cutoff value is determined by a proportion of informative wells that are estimated to contain a particular nucleic acid sequence, wherein the proportion is determined based on the aforementioned percentage and / or average concentration. The cutoff value can be determined using many different types of methods, such as sequential likelihood ratio testing (SPRT).

This invention relates to a method for non-invasive prenatal screening using cell-free DNA extraction. Specifically, the invention provides a method and system for extracting cell-free DNA from liquid biological samples. The method can be used for determining fetal DNA fractions and for non-invasive prenatal screening of fetal aneuploidy and analysis of other types of cell-free DNA.

A method for evaluating fetal DNA concentration (cffDNA) in maternal blood during pregnancy through polymorphic locus linkage block, comprising: obtaining low-depth WGS sequencing data of the sample; obtaining a mapping relationship between the locus and the linkage polymorphism; and calculating the concentration according to the low-depth WGS sequencing data and the mapping relationship between the locus and the linkage polymorphism and taking a plurality of loci constituting the linkage polymorphism as a unit. Wherein, the mapping relationship between the locus and the linkage polymorphism can be obtained by processing public genome WGS data, processing public linkage polymorphism block data or processing a large amount of high-depth WGS measured data. The present application is based on low-depth WGS data, and the heterozygosity of the linkage SNP block can be used to calculate the cffDNA concentration in the maternal blood during pregnancy, which is not affected by the fetal gender in the actual application of NIPT, does not require the father's sample and does not require additional experiments, has high stability, high performance and low cost.

Methods, systems, and apparatus are provided for determining whether a nucleic acid sequence imbalance exists within a biological sample. One or more cutoff values for determining an imbalance of, for example, the ratio of the two sequences (or sets of sequences) are chosen. The cutoff value may be determined based at least in part on the percentage of fetal DNA in a sample, such as maternal plasma, containing a background of maternal nucleic acid sequences. The percentage of fetal DNA can be calculated from the same or different data used to determine the cutoff value, and can use a locus where the mother is homozygous and the fetus is heterozygous. The cutoff value may be determined using many different types of methods, such as sequential probability ratio testing (SPRT).

Methods, systems, and devices are provided for determining whether a nucleic acid sequence imbalance is present in a biological sample.SOLUTION: One or more cutoff values for determining imbalance are selected, e.g., a ratio of two sequences (or sets of sequences). This cutoff value can be determined based, at least in part, on the percentage of fetal DNA in the sample that contains a background of maternal nucleic acid sequences, such as maternal plasma. The cutoff value can also be determined based on the average concentration of sequences per reaction. In one aspect, this cutoff value is determined from the proportion of informative wells that are likely to contain a particular nucleic acid sequence, where the proportion is determined based on the percentages and / or average concentrations described above. This cutoff value can be determined using many different types of methods, such as a sequential probability ratio test (SPRT).SELECTED DRAWING: Figure 1

Provided are a method and device for determining fetal DNA concentration. The method for determining the concentration of fetal DNA includes: acquiring multiple sequencing reads of a cell-free DNA (cfDNA) sample under test; aligning the multiple sequencing reads with a reference genome to obtain alignment results; and determining the concentration of fetal DNA based on the alignment results. The concentration of fetal DNA can be determined based on the alignment results between the sequencing reads and the reference genome so that applications to various sequencing platforms including a single-molecule sequencing platform can be satisfied, and the accuracy of determination of the concentration of fetal DNA can be improved.

The present disclosure relates to methods, compositions, and kits for concentrating and purifying at least one target analyte from a clinical biological sample. In some embodiments, the methods involve one or more aqueous two-phase system (ATPS) compositions and at least one solid phase medium. Some embodiments provide a kit comprising one or more ATPS compositions, a binding buffer; and a solid phase medium. Other embodiments provide methods of treating cancers or infectious diseases in a patient in need thereof.

A system and method for determining the genetic data for one or a small set of cells, or from fragmentary DNA, where a limited quantity of genetic data is available, are disclosed. Genetic data for the target individual is acquired and amplified using known methods, and poorly measured base pairs, missing alleles and missing regions are reconstructed using expected similarities between the target genome and the genome of genetically related subjects. In accordance with one embodiment of the invention, incomplete genetic data is acquired from embryonic cells, fetal cells, or cell-free fetal DNA isolated from the mother's blood, and the incomplete genetic data is reconstructed using the more complete genetic data from a larger sample diploid cells from one or both parents, with or without genetic data from haploid cells from one or both parents, and / or genetic data taken from other related individuals.

The invention relates to a free fetal DNA enrichment and quantitative analysis method based on a nano magnetic bead. The method comprises the following steps: preparing the nano magnetic bead of which the surface is modified with a polyethylene glycol (PEG) chain brush, regulating and controlling the density and spatial arrangement of the PEG chain, forming a structure screening layer adaptive to free DNA with the length of 140-160bp on the surface of the magnetic bead, and capturing short fragment DNA to finish selective enrichment; adding the functionalized nano magnetic beads into a pregnant woman plasma reaction system, and applying a directional electric field to guide negatively charged DNA to migrate to the surfaces of the magnetic beads to form a local focusing area of free fetal DNA; after adsorption and enrichment are completed, the pH value or temperature of a reaction system is adjusted, the structural tension gradient of a PEG chain brush area is excited, target fetal DNA with medium binding force is released from the surfaces of the magnetic beads, and specific desorption is completed; and introducing the released DNA solution into a microcavity structure provided with a micro-resistance flow channel, and only collecting DNA components which are relatively high in diffusion speed and high in leading edge centrality to carry out subsequent fluorescent quantitative PCR or digital PCR analysis so as to finish high-purity quantitative detection of the target fetal DNA.

Methods for non-invasive prenatal paternity testing are disclosed herein. The method uses genetic measurements made on plasma taken from a pregnant mother, along with genetic measurements of the alleged father, and genetic measurements of the mother, to determine whether or not the alleged father is the biological father of the fetus. This is accomplished by way of an informatics based method that can compare the genetic fingerprint of the fetal DNA found in maternal plasma to the genetic fingerprint of the alleged father.

The present methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample. Digital analysis is then be used to detect aneuploidy, such as the trisomy that causes Down Syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, e.g., 10,000 genome equivalents.

Systems, methods, and apparatus are provided for determining at least a portion of the fetal genome. DNA segments from a maternal sample (maternal and fetal DNA) can be analyzed to identify gene alleles at specific loci. The amounts of DNA segments of the corresponding gene alleles at these loci can be analyzed together to determine relative amounts of haplotypes for these loci and to determine which haplotypes have been inherited from the parental genomes. The loci where the parents are a specific combination of homozygous and heterozygous can be analyzed to determine regions of the fetal genome. Reference haplotypes that are common in the population can be used in conjunction with the analysis of DNA segments from the maternal sample to determine the maternal and paternal genomes.The determination of mutations, a fractional concentration of fetal DNA in a maternal sample, and a coverage rate of a sequencing determination of the maternal sample may also be provided.