Qiagen Sciences, LLC

Qiagen Gaithersburg Inc.

Sabiosciences Corporation

Qiagen Gmbh

Yexun Wang

Quan Peng

Vikram Devgan

Qiong Jiang

John DiCarlo

Zhong Wu

Daniel Y Kim

Guozhen Liu

Samuel J Rulli

Jing-Yi Lo

Rachel Gardner

Martin Schlumpberger

Grace J Kim

John Dicarlo

Daniel Kim

The present disclosure provides oligonucleotides that comprise semi-random barcode sequences. Such oligonucleotides may be incorporated into reverse transcription primers, PCR primers, or portions of sequencing adapters in preparing sequencing libraries. The resulting sequencing libraries can be used for accurate sequencing, including DNA or RNA counting and mutation detection. Methods and kits for preparing sequencing adapters and sequencing libraries are also provided.

Semi-random barcodes for nucleic acid analysis

The present disclosure provides primers, primer sets, kits and methods for multiple displacement amplification, especially in combination with nucleic acid sequencing. The primers comprise self-complementary sequences at their 5' termini and random or semi-random sequences at their 3′ termini. Use of such primers facilitates handling of multiple samples, increases sequence coverage uniformity, and improves sequencing error corrections.

Primers with self-complementary sequences for multiple displacement amplification

The invention relates to integrated DNA and RNA library preparations and methods of making and uses thereof, wherein the DNA molecules are labelled with a tag identifying the molecule as being a DNA molecule and the RNA molecules are labelled with a tag identifying the molecule as being a RNA molecule. The methods do not require physical separation of DNA and RNA. The methods output two separate libraries from DNA and RNA, respectively, which helps flexible manipulation on downstream sequencing platforms. The application also claims the DNA library and the cDNA library produced by the method and the DNA tag and the RNA tag used in the method.

Integrative DNA and RNA library preparations and uses thereof

The present disclosure provides methods, sets of substantially complementary double-stranded adapters, and kits for performing nucleic acid sequencing. The substantial complementary double-stranded adapters comprise fully complementary molecular tag regions but one or more mismatches in other regions. Such adapters are ligated to double-stranded target nucleic acids, the obtained ligation products are amplified, and the generated amplification products are sequenced. The methods according to the present disclosure allow both strands of double-stranded target nucleic acids to be sequenced from one end of the target nucleic acids.

Single end duplex DNA sequencing

The present disclosure provides primers, primer sets, kits and methods for multiple displacement amplification, especially in combination with nucleic acid sequencing. The primers comprise self-complementary sequences at their 5' termini and random or semi-random sequences at their 3&#x2032; termini. Use of such primers facilitates handling of multiple samples, increases sequence coverage uniformity, and improves sequencing error corrections.

The present disclosure provides methods and kits for highly multiplex single primer extensions using a MutS protein and Mg2+ at a concentration higher than that in a typical PCR reaction. Also disclosed is the use of such methods and kits in next generation sequencing.

Methods and kits for highly multiplex single primer extension

The present disclosure provides methods and kits for performing high multiplex PCR using molecular barcodes. The methods disclosed herein separately extend a set of primers (BC primers) that each comprise a target-specific sequence, a molecular barcode and a universal sequence, and amplify the resulting extension products using another set of primers (LA primers) that each comprise another target-specific sequence and a universal sequence. The methods may further comprise amplification using universal primers (preferably comprising an adapter).

High multiplex PCR with molecular barcoding

The present disclosure provides methods, arrays and kits for assessing the quality of genomic DNA samples, especially those obtained from formalin-fixed paraffin-embedded (FFPE) samples. The methods, arrays and kits provided herein use primer pairs specific to regions in the genomes of the organisms from which genomic DNA samples are obtained that have identical or nearly identical copies distributed across multiple chromosomes.

DNA quality assessments using repetitive sequences

The present invention relates to a set of biomarkers, microarrays that provide for detection thereof, an expression signature comprising 16 genes or a subset thereof, and the use thereof in determining the regulation status of IL-6/STAT3 signaling pathway in a cell sample or subject, as well as compositions for the detection thereof. The regulation status of IL-6/STAT3 signaling pathway in a cell sample or subject may be assayed based on the level of expression of one or more of these genes. The methods and compositions provided herein may be used to evaluate IL-6/STAT3 pathway regulation status in a sample; classify a cell sample as having a deregulated or regulated IL-6/STAT3 signaling pathway; determine whether an agent modulates the IL-6/STAT3 signaling pathway; predict the response of a subject to an agent that modulates the IL-6/STAT3 signaling pathway; assign treatment to a subject; and/or evaluate the pharmacodynamic effects of therapies designed to regulate IL-6/STAT3 pathway signaling. Expression of the biomarkers is preferably determined by RT-PCR using SYBR Green methods, and the expression data analyzed and compared to a control sample by use of the random forest method.

Gene expression signature for IL-6/STAT3 signaling pathway and use thereof

Using repetitive sequences for DNA quality assessments

The present application relates to Multicomponent Nucleic Acid Enzymes (MNAzymes), which may be used for detecting, identifying and/or quantifying targets. More particularly, this application provides methods of designing and making more reliable MNAzymes, as well as compositions comprising MNAzyme components and methods of using MNAzymes.

Methods and compositions for nucleic acid detection

Improved methods that increase the specificity and sensitivity of detection of small RNAs, including miRNAs, using oligonucleotide primers and nucleic acid amplification, are provided. Reaction conditions that result in preferential decrease in cDNA synthesis of RNAs other than the small RNA molecules targeted for detection during miRNA tailing and reverse transcription reactions are described. Using these reaction conditions greater sensitivity and specificity of amplification of small RNAs including miRNAs is achieved.

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Ellicott City, MD, United States of America

Yexun Wang