Paragon Genomics, Inc.

Zhitong Liu

Guoying Liu

David Debruyne

Tao Chen

Kalyani Patankar

Jack Dong

Chenyu Li

Jeffrey Juehui Liu

Vidushi Kapoor

Yutao Fu

Michael Clark

Fang Xie

Logan Tom

Juehui Liu

Methods and compositions for making DNA libraries for massive parallel next generation sequencing (NGS), comprises two parts. These methods may be referred to as Triseq sequencing. The first part includes ligating a UMI adapter, amplifying the DNA fragments in the presence of dUTP, enriching the target molecules through primer extension by using a panel of both forward and reverse primers, and removing the dU-containing template DNA. The DNA molecules are organized to primary clones and subclones, labeled by the UMI on 5' and 3′ end of the DNA fragments, respectively. The second part includes sequencing the DNA library by NGS, deducing consensus sequence from each subclone, and from within each primary clone, and between the consensus sequences obtained from both forward and reverse primers.

Methods and compositions for reducing base errors of massive parallel sequencing using triseq sequencing

Methods, apparatuses and compositions for generating highly sensitive and accurate sequencing results of massive parallel sequencing (NGS). The methods and compositions may be referred to as SubDivision-Seq, and may comprise two parts. The first part includes making a target-enriched DNA library, organizing the UMIs on DNA molecules to form primary clones and subdividing the primary clones into subclones. The second part includes sequencing the DNA library by NGS, deducing consensus sequence from each subclone, then deducing consensus sequence in each primary clone.

Methods and compositions for amplifying DNA and generating DNA sequencing results from target-enriched DNA molecules

Laboratory-based high throughput methods and compositions (e.g., kits) for the detection of pathogen mRNA, including in particular, for the detection of SARS-CoV-2 RNA from up to 85,000 samples in one Illumina NovaSeq sequencing run. These methods may include barcoding cDNA, indexing pools of libraries and intensive use of automatic liquid handling, providing a ready-to-sequence library mix. These methods and compositions may allow a very inexpensive per sample cost and an assay that may be performed in about one day or less.

High throughput detection of pathogen RNA in clinical specimens

Methods, compositions, systems and kits to amplify or improve amplification of target-specific amplification products by reducing non-specific amplification products (e.g., primer-dimers) when amplifying multiple different nucleotide regions. The methods, compositions, systems and kits described herein may include, or include the use of, one or more resolvases that recognize and bind to and/or cut an aberrant DNA structure.

Methods and compositions for reducing non-specific amplification products

Methods, compositions, systems and kits to introduce a controlled-number of molecular barcodes onto DNA fragments by reducing redundant molecular barcodes formed in template-dependent primer extension reactions, and to find variant frequencies from both strands of DNA. The methods, compositions, systems and kits described herein may include, or include the use of, one or more single-stranded DNA specific nucleases that cleave the single-stranded regions containing unmatched base pairs in amplification products.

Methods and compositions for reducing redundant molecular barcodes created in primer extension reactions

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Foster City, CA, United States of America

Zhitong Liu