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.

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.

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.

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

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.

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

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.

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.

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.

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.

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.

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

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

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).

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

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

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.

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).

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.

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.