Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations. Provided in certain aspects are systems for analyzing cell-free nucleic acid sequence reads. Provided in certain aspects are systems for detecting a chromosome aneuploidy. Provided in certain aspects are systems for detecting a chromosome aneuploidy based on an analysis of cell-free nucleic acid sequence reads for chromosomes 13, 18, and 21.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 30/20 - Sequence assembly

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of nucleic acid fragments from circulating cell free nucleic acid. Also provided herein are methods for partitioning one or more genomic regions of a reference genome into a plurality of portions according to one or more features.

IPC Classes  ?

• G16B 30/10 - Sequence alignmentHomology search
• C12Q 1/6869 - Methods for sequencing
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

The present disclosure relates to genetic copy number variation (CNV) detection. Particularly, aspects are directed to sequencing nucleic acid obtained from a biological sample obtained from a subject to generate sequencing data. The sequence reads are ordered by mapping the sequence reads to a reference genome and stored in an ordered format, A global segmentation of the target region is performed based on the stored sequence reads and a set of segments of the target region is identified and used to determine a copy number variation (CNV) metric. A first status of a genetic condition for the subject is determined based on the CNV metric, and a report of the corresponding genetic condition screening test is determined based on the CNV metric and the status.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for determining sequences of nucleotides for nucleic acid templates in a nucleic acid sample. The technology provide herein also relates in part to methods, processes, machines and apparatuses for counting nucleic acid templates. Nucleic acid templates of a sample are tagged with nonrandom oligonucleotide adapters that include predetermined non-randomly generated sequences. The use of these nonrandom oligonucleotide adapters provides an efficient method to reduce sequencing errors, and increase the sensitivity of detection of low-frequency single nucleotide alterations.

IPC Classes  ?

• C12Q 1/6855 - Ligating adaptors
• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/6869 - Methods for sequencing
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Provided are compositions and processes that utilize genomic regions that are differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer

Abstract

Provided herein are methods, processes, systems and machines for non-invasive assessment of genetic variations. In particular, provided herein are methods, processes, systems and machines for non-invasive assessment of copy number variations. In some aspects, copy number variations include aneuploidies (e.g., trisomy 13, 18, or 21). In some aspects, copy number variations include microdeletions or microduplications.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/10 - Ploidy or copy number detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search

Abstract

Provided herein are methods, processes, systems and machines for non-invasive assessment of genetic variations. In particular, provided herein are methods, processes, systems and machines for non-invasive assessment of copy number variations. In some aspects, copy number variations include aneuploidies (e.g., trisomy 13, 18, or 21). In some aspects, copy number variations include microdeletions or microduplications.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/10 - Ploidy or copy number detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Provided herein are methods, processes, systems, machines and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 30/10 - Sequence alignmentHomology search
• C12Q 1/6816 - Hybridisation assays characterised by the detection means
• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6872 - Methods for sequencing involving mass spectrometry
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16H 10/40 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
• G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems

Abstract

Provided herein are methods and compositions to extract and enrich by, physical separation or amplification, relatively short nucleic acids from a nucleic acid composition containing a high background of longer nucleic acids (e.g., host or maternal nucleic acids; genomic nucleic acid and the like).

IPC Classes  ?

• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12Q 1/6834 - Enzymatic or biochemical coupling of nucleic acids to a solid phase

Abstract

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C07K 16/18 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans
• C12Q 1/6804 - Nucleic acid analysis using immunogens

Abstract

Provided herein are bioinformatic tools and processes used to classify the presence or absence of genetic mosaicism for a copy number variation in one or more fetuses (e.g., predict whether one fetus or more than one fetus is affected with the copy number variation). Sample nucleic acid is subjected to a sequencing process and the resulting sequence reads are analyzed to identify a genetic copy number variation region. A genetic mosaicism for the copy number variation region is classified for one fetus or more than one fetus based on: (i) a mosaicism ratio of a fraction of nucleic acid having the copy number variation region to a fraction of fetal nucleic acid, and (ii) the chromosome having the genetic copy number variation region (e.g., the type of aneuploidy identified) or (ii) a number of fetuses being carried by the pregnant female.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection

Abstract

Provided herein are methods, compositions and kits to extract and relatively enrich by physical separation or amplification short base pair nucleic acid in the presence of a high background of genomic material (e.g., host or maternal nucleic acids).

IPC Classes  ?

• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/686 - Polymerase chain reaction [PCR]

Abstract

Provided herein are methods, processes, systems, machines and apparatuses for non-invasive assessment of chromosome alterations.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 30/20 - Sequence assembly

Abstract

Provided herein are methods of normalizing nucleic acid libraries. The method uses nucleic acid probes with nucleic acid sequences that are complementary to one or more of these adaptor sequences are added to the nucleic acids libraries. The probes can hybridize to the adaptor sequences in the single stranded nucleic acid molecules derived from the libraries to form hybridization complexes. The probes are conjugated to a first binding member, which can interact with a second binding member that is conjugated to solid supports. The solid supports can then be collected and the single stranded nucleic acid molecules can be recovered in a volume of elution buffer to reach a desired concentration. As compared to standard methods, the methods are more efficient and cost-effective.

IPC Classes  ?

• C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• C40B 40/06 - Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining nucleic acid fragments from a sample from a test subject; sequencing the sequence constructs to obtain sequence reads; demultiplexing the sequence reads to a first and a second subset of sequences reads; generating a first set of consensus reads that correspond to the first nucleic acid fragment based on SMBs associated with the first subset of sequences reads; generating a second set of consensus reads that correspond to the second nucleic acid fragment based on SMBs associated with the second subset of sequences reads; and determining a presence of one or more genetic alterations for the test subject based on the two sets of consensus reads.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• C12Q 1/6816 - Hybridisation assays characterised by the detection means
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/40 - Population geneticsLinkage disequilibrium
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 30/10 - Sequence alignmentHomology search

Abstract

The present invention relates to systems and methods for non-invasive assessment of genetic variation. In particular, aspects are directed to a computer-implemented method that includes ligating nucleic acid molecules with adapters to generate sequence constructs, sequencing the sequence constructs to obtain sequence reads, generating an alignment computer file including on-target sequence reads and associated genomic positioning data, generating a probe coverage data file for the sample using the on-target sequence reads and the associated genomic positioning data, generating segments and associated probe coverage quantification data for each segment using a segmentation model and the probe coverage data file, identifying genes overlapping with the segments, generating filtered segments based on the identified genes, and determining a presence or absence of a genetic variation in the sample based on the filtered segments.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Blood plasma of pregnant women contains fetal and (generally >90%) maternal circulatory extracellular DNA. Most of said fetal DNA contains ≤500 base pairs, said maternal DNA having a greater size. Separation of circulatory extracellular DNA of ≤500 base pairs results in separation of fetal from maternal DNA. A fraction of a blood plasma or serum sample of a pregnant woman containing, due to size separation (e.g. by chromatography, density gradient centrifugation or nanotechnological methods), extracellular DNA substantially comprising ≤500 base pairs is useful for non-invasive detection of fetal genetic traits (including the fetal RhD gene in pregnancies at risk for HDN; fetal Y chromosome-specific sequences in pregnancies at risk for X chromosome-linked disorders; chromosomal aberrations; hereditary Mendelian genetic disorders and corresponding genetic markers; and traits decisive for paternity determination) by e.g. PCR, ligand chain reaction or probe hybridization techniques, or nucleic acid arrays.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of nucleic acid fragment length information.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.

IPC Classes  ?

• C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
• C12Q 1/6844 - Nucleic acid amplification reactions

Abstract

Techniques are described for identifying a genetic variant in a test sample by comparing sequences reads obtained from the test sample to unique k-mers that are representative of a target genomic region. In one particular aspect, a method is described that includes generating a dictionary of a target genomic region having a set of unique k-mers by: accessing a sequence of the target genomic region, determining a set of k-mers for the target genomic region, comparing the set of k-mers for the target genomic region with one or more sets of k-mers for non-target genomic regions, and selecting the unique k-mers that do not appear in the one or more sets of k-mers for non-target genomic regions. The dictionary can then be used to identify a genetic variant in a test sample by comparing sequences reads obtained from the test sample to the unique k-mers in the dictionary.

IPC Classes  ?

• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment

Abstract

Technology provided herein relates in part to non-invasive classification of one or more genetic copy number variations (CNVs) for a test sample. Technology provided herein is useful for classifying a genetic CNV for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material

Abstract

The present disclosure relates to methods for enriching circulating tumor DNA (ctDNA) to enhance early disease detection or predictions of disease progression. The present disclosure also relates to methods for enriching circulating fetal cell free DNA (fetal cfDNA) to enhance early disease detection. In some embodiments, the method comprises enriching ctDNA or fetal cfDNA in a sample by selecting for cell-free nucleic acid fragments that are less than 150 bp prior to copy number alteration (CNA) analysis. Also disclosed are compositions, systems, and computer-program products for analyzing circulating cell free nucleic acids by any of the methods disclosed herein.

IPC Classes  ?

• C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genomic nucleic acid instability and genomic nucleic acid stability.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for determining sequences of nucleotides for nucleic acid templates in a nucleic acid sample. The technology provide herein also relates in part to methods, processes, machines and apparatuses for counting nucleic acid templates. Nucleic acid templates of a sample are tagged with nonrandom oligonucleotide adapters that include predetermined non-randomly generated sequences. The use of these nonrandom oligonucleotide adapters provides an efficient method to reduce sequencing errors, and increase the sensitivity of detection of low-frequency single nucleotide alterations.

IPC Classes  ?

• C12Q 1/6855 - Ligating adaptors
• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/6869 - Methods for sequencing
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/683 - Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 20/10 - Ploidy or copy number detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Provided are compositions and processes that utilize genomic regions that are differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of decision analyses. The decision analyses sometimes include segmentation analyses and/or odds ratio analyses.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G16B 30/10 - Sequence alignmentHomology search

Abstract

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G16B 25/20 - Polymerase chain reaction [PCR]Primer or probe designProbe optimisation
• G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• H01J 49/16 - Ion sourcesIon guns using surface ionisation, e.g. field-, thermionic- or photo-emission

Abstract

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6811 - Selection methods for production or design of target specific oligonucleotides or binding molecules

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 20/40 - Population geneticsLinkage disequilibrium
• G16B 30/20 - Sequence assembly
• G16B 30/10 - Sequence alignmentHomology search

Abstract

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C07K 16/18 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans
• C12Q 1/6804 - Nucleic acid analysis using immunogens

Abstract

Technology provided herein relates in part to methods, processes, compositions and apparatuses for analyzing nucleic acid.

IPC Classes  ?

• C12Q 1/6869 - Methods for sequencing
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/20 - Sequence assembly
• G16B 30/10 - Sequence alignmentHomology search

Abstract

Provided are methods for identifying the presence or absence of a chromosome abnormality by which a cell-free sample nucleic acid from a subject is analyzed. In certain embodiments, provided are methods for identifying the presence or absence of a fetal chromosome abnormality in a nucleic acid from cell-free maternal blood.

IPC Classes  ?

• C12Q 1/686 - Polymerase chain reaction [PCR]
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• G16B 25/20 - Polymerase chain reaction [PCR]Primer or probe designProbe optimisation

Abstract

This application provides methods and systems for determining transplant status. In some embodiments, the method comprises obtaining a biological sample from hematopoietic stem cell transplant (HSCT) recipient; measuring the amount of one or more identified recipient-specific nucleic acids or donor-specific nucleic acids in the sample; and (c) determining transplant status by monitoring the amount of the one or more identified recipient-specific nucleic acids or donor-specific nucleic acids after transplantation. In some approaches, the one or more recipient-specific or the donor-specific nucleic acids are identified based on the amount of one or more polymorphic nucleic acid targets, which can be used to determine the transplant status. Optionally, the biological sample is blood or bone marrow. Optionally the nucleic acid is genomic DNA.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 40/30 - Unsupervised data analysis

Abstract

Technology provided herein relates in part to non-invasive classification of one or more genetic copy number alterations (CNAs) for a test sample. Certain methods include sampling a quantification of sequence reads from parts of a genome, generating a confidence determination, and using the confidence determination to enhance classification. Technology provided herein is useful for classifying a genetic CNA for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G06N 7/00 - Computing arrangements based on specific mathematical models

Goods & Services

Medical services; genetic, prenatal and diagnostic testing for medical purposes; nucleic acid based testing for medical purposes; medical services in the fields of nucleic acid analysis and prenatal diagnosis and genetics, infertility testing, and testing of products of conception; medical diagnosis of patients through the use of nucleic acid analysis; medical reporting services; providing information relating to online medical records; all the foregoing provided before or during the pregnancy of the patient for the purpose of assessing the health of the fetus and does not include dna testing after the birth of the child.

Abstract

The present invention relates to an in vitro method for detecting methylated DNA comprising (a) coating a container with a polypeptide capable of binding methylated DNA; (b) contacting said polypeptide with a sample comprising methylated and/or unmethylated DNA; and (c) detecting the binding of said polypeptide to methylated DNA. In a preferred embodiment, said method further comprises step (d) analyzing the detected methylated DNA by sequencing. Another aspect of the present invention is a kit for detecting methylated DNA according to the methods of the invention comprising (a) a polypeptide capable of binding methylated DNA; (b) a container which can be coated with said polypeptide; (c) means for coating said container; and (d) means for detecting methylated DNA.

IPC Classes  ?

• C12Q 1/6804 - Nucleic acid analysis using immunogens
• C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer

Abstract

Technology provided herein relates in part to non-invasive classification of one or more genetic copy number variations (CNVs) for a test sample. Technology provided herein is useful for classifying a genetic CNV for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection

Abstract

The present disclosure relates to methods for enriching circulating tumor DNA (ctDNA) to enhance early disease detection or predictions of disease progression. The present disclosure also relates to methods for enriching circulating fetal cell free DNA (fetal cfDNA) to enhance early disease detection. In some embodiments, the method comprises enriching ctDNA or fetal cfDNA in a sample by selecting for cell-free nucleic acid fragments that are less than 150 bp prior to copy number alteration (CNA) analysis. Also disclosed are compositions, systems, and computer-program products for analyzing circulating cell free nucleic acids by any of the methods disclosed herein.

IPC Classes  ?

• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

Abstract

This application provides methods and systems for determining transplant status. In some embodiments, the method comprises obtaining a biological sample from an organ transplant recipient who has received an organ; isolating cell-free nucleic acids from the biological sample; measuring the amount of each allele of one or more polymorphic nucleic acid targets in the biological sample; identifying the donor specific allele using a computer algorithm based on the measurements of the one or more polymorphic nucleic acid targets, whereby detecting one or more donor-specific circulating cell-free nucleic acids, detecting tissue injury based on the presence or amount of said one or more donor-specific nucleic acids, thereby determining transplant status.

IPC Classes  ?

• C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• G16B 30/10 - Sequence alignmentHomology search
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16H 10/40 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
• G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
• G16H 10/60 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for patient-specific data, e.g. for electronic patient records
• G16H 50/70 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients

Abstract

The invention generally relates to methods for analyzing nucleic acid sequence information. In some aspects, a sample is sequenced to obtain nucleic acid sequence information. In some aspects, an amount of GC bias in sequence information is determined. In some aspects, sequence information is corrected to account for the GC bias. In some aspects, corrected sequence information is analyzed.

IPC Classes  ?

• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/10 - Ploidy or copy number detection

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of nucleic acid fragments from circulating cell free nucleic acid. Also provided herein are methods for partitioning one or more genomic regions of a reference genome into a plurality of portions according to one or more features.

IPC Classes  ?

• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• C12Q 1/6869 - Methods for sequencing

Abstract

Blood plasma of pregnant women contains fetal and (generally >90%) maternal circulatory extracellular DNA. Most of said fetal DNA contains 500 base pairs, said maternal DNA having a greater size. Separation of circulatory extracellular DNA of <500 base pairs results in separation of fetal from maternal DNA. A fraction of a blood plasma or serum sample of a pregnant woman containing, due to size separation (e.g. by chromatography, density gradient centrifugation or nanotechnological methods), extracellular DNA substantially comprising 500 base pairs is useful for non-invasive detection of fetal genetic traits (including the fetal RhD gene in pregnancies at risk for HDN; fetal Y chromosome-specific sequences in pregnancies at risk for X chromosome-linked disorders; chromosomal aberrations; hereditary Mendelian genetic disorders and corresponding genetic markers; and traits decisive for paternity determination) by e.g. PCR, ligand chain reaction or probe hybridization techniques, or nucleic acid arrays.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

Abstract

Technology herein relates in part to methods, processes and apparatuses for analyzing nucleic acid sequence reads, where the sequence reads are partial sequence reads having one or more nucleotide species from a subset of the nucleotide species present in a sample nucleic acid at some but not all nucleotide positions of the partial sequence reads or one or more nucleobase classes at some or all nucleotide positions of the partial sequence reads.

IPC Classes  ?

• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 40/20 - Supervised data analysis

Abstract

Provided in part herein are methods and processes that can be used for non-invasive assessment of a genetic variation which can lead to diagnosis of a particular medical condition or conditions. Such methods and processes can, for example, identify dissimilarities or similarities for one or more features between a subject data set and a reference data set, generate a multidimensional matrix, reduce the matrix into a representation and classify the representation into one or more groups. Methods and processes described herein are applicable to data in biotechnology and other fields.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 40/20 - Supervised data analysis
• G16B 40/30 - Unsupervised data analysis

Abstract

A method and system for analyzing circulating cell-free nucleic acids from a pregnant female with reduced bias. Counts of sequence reads mapped to portions of a reference genome are obtained. A regression model is generated that models the relationship between the counts and the GC content. The read counts are normalized according to the regression model to remove the GC bias. The normalized counts are used for further analysis, such as the detection of fetal aneuploidy.

IPC Classes  ?

• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G06F 17/18 - Complex mathematical operations for evaluating statistical data

Abstract

Provided herein are methods and compositions to extract and enrich by, physical separation or amplification, relatively short nucleic acids from a nucleic acid composition containing a high background of longer nucleic acids (e.g., host or maternal nucleic acids; genomic nucleic acid and the like).

IPC Classes  ?

• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12Q 1/6834 - Enzymatic or biochemical coupling of nucleic acids to a solid phase

Abstract

Provided herein are methods, processes, systems and machines for non-invasive assessment of genetic variations. In particular, provided herein are methods, processes, systems and machines for non-invasive assessment of copy number variations. In some aspects, copy number variations include aneuploidies (e.g., trisomy 13, 18, or 21). In some aspects, copy number variations include microdeletions or microduplications.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/10 - Ploidy or copy number detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Provided herein are bioinformatic tools and processes used to classify the presence or absence of genetic mosaicism for a copy number variation in one or more fetuses (e.g., predict whether one fetus or more than one fetus is affected with the copy number variation). Sample nucleic acid is subjected to a sequencing process and the resulting sequence reads are analyzed to identify a genetic copy number variation region. A genetic mosaicism for the copy number variation region is classified for one fetus or more than one fetus based on: (i) a mosaicism ratio of a fraction of nucleic acid having the copy number variation region to a fraction of fetal nucleic acid, and (ii) the chromosome having the genetic copy number variation region (e.g., the type of aneuploidy identified) or (ii) a number of fetuses being carried by the pregnant female.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection

Abstract

Improved solid supports and methods for analyzing target nucleotide sequences are provided herein. Certain improvements are directed to efficiently preparing nucleic acids that comprise nucleotide sequences identical to or substantially identical to one or more target nucleotide sequences, or complement thereof. The prepared nucleic acids include a reference sequence that facilitates sequence analysis. The solid supports and methods provided herein minimize the number of steps required by published sequence analysis methodologies, and thereby offer improved sequence analysis efficiency.

IPC Classes  ?

• C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6844 - Nucleic acid amplification reactions
• C12Q 1/6837 - Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips

Abstract

Provided are compositions and processes that utilize genomic regions differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6804 - Nucleic acid analysis using immunogens
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6888 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6879 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for sex determination
• G01N 33/53 - ImmunoassayBiospecific binding assayMaterials therefor

Abstract

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C07K 16/18 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans
• C12Q 1/6804 - Nucleic acid analysis using immunogens

Abstract

Provided herein are methods, compositions and kits to extract and relatively enrich by physical separation or amplification short base pair nucleic acid in the presence of a high background of genomic material (e.g., host or maternal nucleic acids).

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/686 - Polymerase chain reaction [PCR]

Abstract

Provided herein are methods, processes, systems, machines and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• C12Q 1/6816 - Hybridisation assays characterised by the detection means
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• C12Q 1/6872 - Methods for sequencing involving mass spectrometry
• C12Q 1/6869 - Methods for sequencing
• G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems

Abstract

This application provides methods and systems for determining transplant status. In some embodiments, the method comprises obtaining a biological sample from hematopoietic stem cell transplant (HSCT) recipient; measuring the amount of one or more identified recipient-specific nucleic acids or donor-specific nucleic acids in the sample; and (c) determining transplant status by monitoring the amount of the one or more identified recipient-specific nucleic acids or donor-specific nucleic acids after transplantation. In some approaches, the one or more recipient-specific or the donor-specific nucleic acids are identified based on the amount of one or more polymorphic nucleic acid targets, which can be used to determine the transplant status. Optionally, the biological sample is blood or bone marrow. Optionall the nucleic acid is genomic DNA.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of decision analyses. The decision analyses sometimes include segmentation analyses and/or odds ratio analyses.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 30/10 - Sequence alignmentHomology search
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation

Abstract

Provided are compositions and processes that utilize genomic regions that are differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

IPC Classes  ?

• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6888 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6804 - Nucleic acid analysis using immunogens

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 30/20 - Sequence assembly

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search

Abstract

Technology provided herein relates in part to non-invasive classification of one or more mosaic copy number variations (CNVs) for a test sample. Technology provided herein is useful for classifying a mosaic CNV for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example. In particular, a method is provided for classifying presence or absence of genetic mosaicism for a biological sample, the method includes identifying a genetic copy number variation region in sample nucleic acid from a subject, e.g. a pregnant female, determining a fraction of nucleic acid having the copy number variation in the sample nucleic acid, determining a fraction of a minority nucleic acid, e.g. fetal nucleic acid, in the sample nucleic acid, comparing the two fractions to generate a mosaicism ratio, and classifying a presence or absence of a genetic mosaicism for the copy number variation region according to the mosaicism ratio.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Abstract

This application provides methods and systems for determining transplant status. In some embodiments, the method comprises obtaining a biological sample from an organ transplant recipient who has received an organ; isolating cell-free nucleic acids from the biological sample; measuring the amount of each allele of one or more polymorphic nucleic acid targets in the biological sample; identifying the donor specific allele using a computer algorithm based on the measurements of the one or more polymorphic nucleic acid targets, whereby detecting one or more donor-specific circulating cell-free nucleic acids, detecting tissue injury based on the presence or amount of said one or more donor-specific nucleic acids, thereby determining transplant status.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 30/20 - Sequence assembly
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Provided herein are methods, processes, systems, machines and apparatuses for non-invasive assessment of chromosome alterations.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 30/20 - Sequence assembly

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for determining sequences of nucleotides for nucleic acid templates in a nucleic acid sample. The technology provide herein also relates in part to methods, processes, machines and apparatuses for counting nucleic acid templates. Nucleic acid templates of a sample are tagged with nonrandom oligonucleotide adapters that include predetermined non-randomly generated sequences. The use of these nonrandom oligonucleotide adapters provides an efficient method to reduce sequencing errors, and increase the sensitivity of detection of low-frequency single nucleotide alterations.

IPC Classes  ?

• C12Q 1/6855 - Ligating adaptors
• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/6869 - Methods for sequencing
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of copy number alterations. In particular, a method is provided for determining presence or absence of a copy number alteration for a test subject. The method includes providing a set of sequence reads. The sequence reads may be obtained from circulating cell free sample nucleic acid from a test sample obtained from the test subject, and the circulating cell free sample nucleic acid may be captured by probe oligonucleotides under hybridization conditions. The method further includes determining a probe coverage quantification of the sequence reads for the probe oligonucleotides and determining the presence or absence of a copy number alteration in the circulating cell free sample nucleic acid based on the probe coverage quantification of the sequence reads for the probe oligonucleotides for the test sample.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining a set of sequence reads. The sequence reads each include a single molecule barcode (SMB) sequence that is a non-random oligonucleotide sequence. The method further includes assigning the sequence reads to read groups according to a read group signature. The read group signature comprises an SMB sequence and a start and end position of a nucleic acid fragment from the circulating cell free sample nucleic acid. The sequence reads comprising start and end positions and an SMB sequence similar to the read group signature are assigned to a read group. The method further includes generating a consensus for each read group, and determining the presence or absence of a genetic alteration based on the consensus for each read group.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• C12Q 1/6816 - Hybridisation assays characterised by the detection means
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/40 - Population geneticsLinkage disequilibrium
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 30/10 - Sequence alignmentHomology search

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/10 - Sequence alignmentHomology search
• G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems

Abstract

Provided herein are methods for determining fetal ploidy according to nucleic acid sequence reads. Nucleic acid sequence reads may be obtained from test sample nucleic acid comprising circulating cell-free nucleic acid from the blood of a pregnant female bearing a fetus. Fetal ploidy may be determined according to genomic section levels and a fraction of fetal nucleic acid in a test sample.

IPC Classes  ?

• C12Q 1/683 - Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 20/10 - Ploidy or copy number detection
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material

Abstract

Provided herein are methods and compositions to extract and enrich by, physical separation or amplification, relatively short nucleic acids from a nucleic acid composition containing a high background of longer nucleic acids (e.g., host or maternal nucleic acids; genomic nucleic acid and the like).

IPC Classes  ?

• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12Q 1/6834 - Enzymatic or biochemical coupling of nucleic acids to a solid phase

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 20/40 - Population geneticsLinkage disequilibrium
• G16B 30/20 - Sequence assembly
• G16B 30/10 - Sequence alignmentHomology search
• G16B 20/10 - Ploidy or copy number detection

Abstract

Systems and methods for identifying a de novo mutation in a genome of a fetus are provided. Methods may include identifying a location of each of a plurality of cell-free nucleic acid molecules using sequence reads. Methods may also include identifying a first sequence in the sequence reads at a first location that is not present in the maternal or paternal sequences. Methods may additionally include determining a first fractional concentration of the first sequence in the biological sample at the first location. Further, methods may include determining a second fractional concentration of a fetal-specific second sequence. The second sequence may be inherited by the fetus from the father at the second location. In addition, methods may include classifying the first sequence as a de novo mutation at the first location in a fetal genome of the fetus if the first and second fractional concentrations are about the same.

IPC Classes  ?

• C12Q 1/6876 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 30/10 - Sequence alignmentHomology search
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Abstract

Technology provided herein relates in part to non-invasive classification of one or more mosaic copy number variations (CNVs) for a test sample. Technology provided herein is useful for classifying a mosaic CNV for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example. In particular, a method is provided for classifying presence or absence of genetic mosaicism for a biological sample, the method includes identifying a genetic copy number variation region in sample nucleic acid from a subject, e.g. a pregnant female, determining a fraction of nucleic acid having the copy number variation in the sample nucleic acid, determining a fraction of a minority nucleic acid, e.g. fetal nucleic acid, in the sample nucleic acid, comparing the two fractions to generate a mosaicism ratio, and classifying a presence or absence of a genetic mosaicism for the copy number variation region according to the mosaicism ratio.

IPC Classes  ?

• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection

Abstract

Provided are methods for identifying the presence or absence of a chromosome abnormality by which a cell-free sample nucleic acid from a subject is analyzed. In certain embodiments, provided are methods for identifying the presence or absence of a fetal chromosome abnormality in a nucleic acid from cell-free maternal blood.

IPC Classes  ?

• C12Q 1/686 - Polymerase chain reaction [PCR]
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• G16B 25/20 - Polymerase chain reaction [PCR]Primer or probe designProbe optimisation

Abstract

Technology provided herein relates in part to methods, processes, compositions and apparatuses for analyzing nucleic acid.

IPC Classes  ?

• C12Q 1/6869 - Methods for sequencing
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/20 - Sequence assembly
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR

Abstract

Technology provided herein relates in part to non-invasive classification of one or more genetic copy number variations (CNVs) for a test sample. Technology provided herein is useful for classifying a genetic CNV for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.

IPC Classes  ?

• G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genetic alterations. In particular, a method is provided for that includes obtaining a set of sequence reads. The sequence reads each include a single molecule barcode (SMB) sequence that is a non-random oligonucleotide sequence. The method further includes assigning the sequence reads to read groups according to a read group signature. The read group signature comprises an SMB sequence and a start and end position of a nucleic acid fragment from the circulating cell free sample nucleic acid. The sequence reads comprising start and end positions and an SMB sequence similar to the read group signature are assigned to a read group. The method further includes generating a consensus for each read group, and determining the presence or absence of a genetic alteration based on the consensus for each read group.

IPC Classes  ?

• G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
• G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for determining sequences of nucleotides for nucleic acid templates in a nucleic acid sample. The technology provide herein also relates in part to methods, processes, machines and apparatuses for counting nucleic acid templates. Nucleic acid templates of a sample are tagged with nonrandom oligonucleotide adapters that include predetermined non-randomly generated sequences. The use of these nonrandom oligonucleotide adapters provides an efficient method to reduce sequencing errors, and increase the sensitivity of detection of low-frequency single nucleotide alterations.

IPC Classes  ?

• C12Q 1/6855 - Ligating adaptors
• C12Q 1/6869 - Methods for sequencing
• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of copy number alterations. In particular, a method is provided for determining presence or absence of a copy number alteration for a test subject. The method includes providing a set of sequence reads. The sequence reads may be obtained from circulating cell free sample nucleic acid from a test sample obtained from the test subject, and the circulating cell free sample nucleic acid may be captured by probe oligonucleotides under hybridization conditions. The method further includes determining a probe coverage quantification of the sequence reads for the probe oligonucleotides and determining the presence or absence of a copy number alteration in the circulating cell free sample nucleic acid based on the probe coverage quantification of the sequence reads for the probe oligonucleotides for the test sample.

IPC Classes  ?

• G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions

Abstract

Provided herein are methods and compositions to extract and enrich by, physical separation or amplification, relatively short nucleic acids from a nucleic acid composition containing a high background of longer nucleic acids (e.g., host or maternal nucleic acids; genomic nucleic acid and the like).

IPC Classes  ?

• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

Abstract

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Technology provided herein relates in part to non-invasive classification of one or more genetic copy number alterations (CNAs) for a test sample. Certain methods include sampling a quantification of sequence reads from parts of a genome, generating a confidence determination, and using the confidence determination to enhance classification. Technology provided herein is useful for classifying a genetic CNA for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G06N 7/00 - Computing arrangements based on specific mathematical models

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genomic nucleic acid instability and genomic nucleic acid stability. The method comprises providing a set of genomic portions each coupled to a copy number alteration quantification for a test sample, wherein the genomic portions comprises portions of a reference genome to which sequence reads obtained for nucleic acid from a test sample obtained from the subject have been mapped, and the copy number alteration quantification coupled to each genomic portion has been determined from a quantification of sequence reads mapped to the genomic portion; and determining, by a computing device, presence or absence of genomic instability for the subject according to the copy number alteration quantifications coupled to the genomic portions.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 10/00 - ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis

Abstract

Technology provided herein relates in part to non-invasive classification of one or more genetic copy number alterations (CNAs) for a test sample. Certain methods include sampling a quantification of sequence reads from parts of a genome, generating a confidence determination, and using the confidence determination to enhance classification. Technology provided herein is useful for classifying a genetic CNA for a sample as part of non-invasive pre-natal (NIPT) testing and oncology testing, for example.

IPC Classes  ?

• G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for non-invasive assessment of genomic nucleic acid instability and genomic nucleic acid stability.

IPC Classes  ?

• G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions

Abstract

Provided in part herein are methods and processes that can be used for non-invasive assessment of a genetic variation which can lead to diagnosis of a particular medical condition or conditions. Such methods and processes can, for example, identify dissimilarities or similarities for one or more features between a subject data set and a reference data set, generate a multidimensional matrix, reduce the matrix into a representation and classify the representation into one or more groups. Methods and processes described herein are applicable to data in biotechnology and other fields.

IPC Classes  ?

• G16H 20/00 - ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

Abstract

Methods for non-invasive assessment of genetic variations that make use of nucleic acid fragment length information, in particular length of fragments in circulating cell-free nucleic acids and compares the number of counts from fragments with different length.

IPC Classes  ?

• G16B 20/10 - Ploidy or copy number detection
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 30/10 - Sequence alignmentHomology search

Abstract

Technology provided herein relates in part to methods, processes, machines and apparatuses for detecting genetic variations. In some embodiments, the technology is related to non-invasive assessment of aneuploidies.

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)

Abstract

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C07K 16/18 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans
• C12Q 1/6804 - Nucleic acid analysis using immunogens

Abstract

Provided are compositions and processes that utilize genomic regions that are differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12Q 1/6869 - Methods for sequencing
• C12Q 1/6804 - Nucleic acid analysis using immunogens
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6888 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms

Abstract

Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of nucleic acid fragments from circulating cell free nucleic acid. Also provided herein are methods for partitioning one or more genomic regions of a reference genome into a plurality of portions according to one or more features.

IPC Classes  ?

• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• C12Q 1/6869 - Methods for sequencing

Abstract

Provided herein are methods and compositions to extract and enrich by, physical separation or amplification, relatively short nucleic acids from a nucleic acid composition containing a high background of longer nucleic acids (e.g., host or maternal nucleic acids; genomic nucleic acid and the like).

IPC Classes  ?

• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

Abstract

Provided herein are methods, processes, systems, machines and apparatuses for non-invasive assessment of genetic variations.

IPC Classes  ?

• G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
• G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

Abstract

Technology provided herein relates in part to methods, processes and apparatuses for non-invasive assessment of genetic variations. In particular the invention relates to methods and kits for detecting aneuploidy of a fetal chromosome by determining the amounts of differentially methylated regions in each of chromosomes 13, 18 and 21 in circulating cell-free nucleic acid from a human pregnant female.

IPC Classes  ?

• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G16B 25/20 - Polymerase chain reaction [PCR]Primer or probe designProbe optimisation
• H01J 49/16 - Ion sourcesIon guns using surface ionisation, e.g. field-, thermionic- or photo-emission

Abstract

Provided are compositions and processes that utilize genomic regions that are differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
• C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes

Abstract

Provided herein are methods, compositions and kits to extract and relatively enrich by physical separation or amplification short base pair nucleic acid in the presence of a high background of genomic material (e.g., host or maternal nucleic acids).

IPC Classes  ?

• C12N 15/00 - Mutation or genetic engineeringDNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purificationUse of hosts therefor
• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/686 - Polymerase chain reaction [PCR]

Goods & Services

Medical services; genetic testing for medical purposes; providing on-line medical record services; medical diagnostic testing, monitoring and reporting services; medical diagnostic services in the field of nucleic acid analysis; medical diagnosis and monitoring of patients through the use of nucleic acid analysis; nucleic acid based testing for medical purposes; genetic, prenatal and diagnostic testing for medical purposes; medical services in the fields of nucleic acid analysis and prenatal diagnosis and genetics; medical diagnostic testing, monitoring and reporting services in the field of oncology; medical diagnostic services in the field of nucleic acid analysis.