SEQUENOM, INC.

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.

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.

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.

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.

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

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.

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

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.

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.

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.