Sequenom, Inc.

Progenity, Inc.

Other

Amin R Mazloom

Cosmin Deciu

Zeljko Dzakula

Mathias Ehrich

Sharat Singh

Sung Kyun Kim

Chen Zhao

Yijin Wu

Pankaj Oberoi

Taylor Jacob Jensen

Gregory Hannum

Christopher Ellison

Huiquan Wang

Youting Sun

Mostafa Azab

Matthew L Cooper

Richard Giulio Del Mastro

Tong Liu

Lyndal Hesterberg

John Allen Tynan

Mark Whidden

Karen A F Copeland

Yang Zhong

Michael Sykes

Mohammad Abbasi

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

Methods and processes for non-invasive assessment of genetic variations

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.

Methods for non-invasive assessment of copy number alterations

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.

Methods for non-invasive assessment of genetic alterations

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.

Methods and processes for assessment of genetic variations

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.

Copy number alteration and reference genome mapping

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.

Disclosed herein are methods, kits, tests, and systems for detecting, predicting, monitoring, or ruling out preeclampsia in pregnant women. Also provided herein are novel diagnostic markers, methods of data analysis, assay formats, and kits employing such markers to improve one or more characteristics of a test for identifying or ruling out preeclampsia based on biomarkers from patient samples.

Preeclampsia biomarkers and related systems and methods

Described herein are methods, compositions, kits, and systems for detecting free and bound PlGF, and using detection of such species to distinguish between pregnant women with or without preeclampsia or related conditions.

Assessment of preeclampsia using assays for free and dissociated placental growth factor

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.

Genetic copy number alteration classifications

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

Growing community of inventors

Del Mar, CA, United States of America

Amin R Mazloom