Sequenom, Inc.

Other

Sequenom Center for Molecular Medicine

Taylor Jacob Jensen

Mathias Ehrich

Sung Kyun Kim

Cosmin Deciu

Dirk Johannes Van Den Boom

Christopher Ellison

Zeljko Dzakula

Amin R Mazloom

Jennifer Geis

Youting Sun

Anders Olof Herman Nygren

John Allen Tynan

Sung J Kim

Mostafa Azab

Michael Sykes

Amin Mazloom

Christopher K Ellison

Timothy S Burcham

Technology provided herein relates in part to 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 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

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

Systems for non-invasive assessment of chromosome alterations using changes in subsequence mappability

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.

Methods and processes for non-invasive detection of a microduplication or a microdeletion with reduced sequence read count error

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.

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.

Sequence adapter manufacture and use

Methods and compositions for identifying presence or absence of hypermethylation or hypomethylation locus

Non-invasive assessment of chromosome alterations using change in subsequence mappability

Reducing sequence read count error in assessment of complex genetic variations

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 aneuplodies.

Growing community of inventors

San Diego, CA, United States of America

Taylor Jacob Jensen