Gen-probe, Inc.

Biomerieux Sa

Other

Pacific Biosciences of California, Inc.

Blomorloux S.a.

Steven T Brentano

James D Carlson

Michael McClellan Becker

Norman C Nelson

Dmitry Lyakhov

Lyle J Arnold, Jr

Philippe L Cleuziat

Markus T Jucker

Francisco D Delgado

Nick Mark Carter

Mehrdad R Majlessi

Philip W Hammond

Daniel Kolk

Gary P Schroth

Patricia C Gordon

Yeasing Y Yang

Guy Vernet

Nathalie Tran

Odile Babola

Daniel P Kolk

Kristin W Livezey

Margarita Batranina-Kaminsky

Marc Rodrigue

Christopher C Adams

Cynthia S Hasselkus-Light

Astrid R Schroder

Lyle J Arnold

Reinhold B Pollner

Wai-Chung Lam

Astrid R W Schroder

Matthew C Friedenberg

Roger L Lankford

Anne-Laure Shapiro

Philippe Cleuziat

Eugene Tu

Kandaswamy Vijayan

Jennifer Jill Bungo

Yi Zhang

Sherrol Hoffa McDonough

William G Weisburg

Jijumon Chelliserry

Xianqun Wang

Kiyotada Nunomura

Irene Andruszkiewicz

Jay H Shaw

Tongjia Yin

Michael Hadjisavas

Caroline F Knott

Astrid Rw Schroder

Reinhold Pollner

James Carlson

The invention provides methods of determining a consensus sequence from multiple raw sequencing reads of a nucleic acid target. The nucleic acid target includes an anchor segment of known sequence and an adjacent segment of unknown sequence. The anchor segment provides a means to assess the quality of a raw target sequencing read. Raw target sequencing reads meeting or exceeding a threshold are assigned to an accepted class. The consensus sequence of the adjacent segment can be determined from raw target sequencing reads in the accepted class. Successive polling steps determine successive consensus nucleobases in a nascent sequence of the adjacent segment. Raw target sequencing reads can be removed or reintroduced from the accepted class depending on their correspondence to the most recently determined consensus nucleobase and/or the nascent sequence.

Algorithms for sequence determinations

The invention provides an improved stem-loop target capture oligomer and methods of use. Such a target capture oligomer has a target-binding segment forming a loop flanked by stem segments forming a stem. The stem segments are of unequal length. Such probes show little or no binding to immobilized probes in the absence of a target nucleic acid but offer good target sensitivity. The probes are particularly useful in multiplex methods of detection in which multiple target capture oligomers are present for detecting of multiple target nucleic acids (for example, detecting multiple polymorphic forms of a target gene).

Asymmetric hairpin target capture oligomers

The present disclosure provides compositions, methods and systems for quantifying target sequences and identifying target sequence variants.

Methods of quantifying target nucleic acids and identifying sequence variants

Nucleic acid oligomeric sequences and in vitro nucleic acid amplification and detection methods for detecting the presence of HAV RNA sequences in samples are disclosed. Kits comprising nucleic acid oligomers for amplifying and detecting HAV nucleic acid sequences are disclosed.

Compositions and methods for detection of hepatitis A virus nucleic acid

The invention provides compositions and methods for making closed nucleic acid structures in which one or both strands are continuous. The closed nucleic acid structures can be used as sequencing templates among other applications.

Closed nucleic acid structures

The invention provides methods of forming a circular template for sequencing a target nucleic acid. The circular template is generated by amplification of a segment of the target nucleic acid with chimeric primers with complementary 5' ends. The circular template has a single nick or gap providing a site for initiation of template-directed extension for sequence analysis. Sequencing of a single template generates reads of alternating segments of the same strand of the target nucleic spaced by primer segments. The different reads of the same strand of the target nucleic acid can be compiled to generate a consensus sequence. Because only one strand of the target nucleic acid is sequenced per reaction, the present method avoids errors introduced by unwittingly combining sequences of both strands of a heteroduplex PCR product. Because only one strand of the target nucleic acid is sequenced per reaction, the present method avoids errors introduced by unwittingly combining sequences of both strands of a heteroduplex PCR product.

Circularized templates for sequencing

Compositions, reaction mixtures, and methods for performing an amplification reaction, including multiplex amplification reaction, wherein the method comprises using one or more amplification oligomer complexes comprising linked first and second amplification oligomer members. In one aspect, the amplification oligomer complex is hybridized to a target nucleic acid, the target nucleic acid with hybridized amplification oligomer complex is then captured, and other components are washed away. Target sequences of the target nucleic acids are pre-amplified to generate a first amplification product. The first amplification product is amplified in one or more secondary amplification reactions to generate second amplification products.

Methods and compositions for nucleic acid amplification

Compositions that are used in nucleic acid amplification in vitro are disclosed, which include a target specific universal (TSU) promoter primer or promoter provider oligonucleotide that includes a target specific (TS) sequence that hybridizes specifically to a target sequence that is amplified and a universal (U) sequence that is introduced into the sequence that is amplified, by using a primer for the universal sequence. Methods of nucleic acid amplification in vitro are disclosed that use one or more TSU oligonucleotides to attached a U sequence to a target nucleic acid in a target capture step and then use a primer for a U sequence in subsequent amplification steps performed in substantially isothermal conditions to make amplification products that contain a U sequence that indicates the presence of the target nucleic acid in a sample.

Growing community of inventors

Santee, CA, United States of America

Steven T Brentano