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Chen C.-Y.,Illumina
Frontiers in Microbiology | Year: 2014

Next-generation sequencing (NGS) technologies have revolutionized modern biological and biomedical research. The engines responsible for this innovation are DNA polymerases; they catalyze the biochemical reaction for deriving template sequence information. In fact, DNA polymerase has been a cornerstone of DNA sequencing from the very beginning. Escherichia coli DNA polymerase I proteolytic (Klenow) fragment was originally utilized in Sanger's dideoxy chain-terminating DNA sequencing chemistry. From these humble beginnings followed an explosion of organism-specific, genome sequence information accessible via public database. Family A/B DNA polymerases from mesophilic/thermophilic bacteria/archaea were modified and tested in today's standard capillary electrophoresis (CE) and NGS sequencing platforms. These enzymes were selected for their efficient incorporation of bulky dye-terminator and reversible dye-terminator nucleotides respectively. Third generation, real-time single molecule sequencing platform requires slightly different enzyme properties. Enterobacterial phage φ29 DNA polymerase copies long stretches of DNA and possesses a unique capability to efficiently incorporate terminal phosphate-labeled nucleoside polyphosphates. Furthermore, φ29 enzyme has also been utilized in emerging DNA sequencing technologies including nanopore-, and protein-transistor-based sequencing. DNA polymerase is, and will continue to be, a crucial component of sequencing technologies. © 2014 Chen.

Haplotype-resolved genome sequencing enables the accurate interpretation of medically relevant genetic variation, deep inferences regarding population history and non-invasive prediction of fetal genomes. We describe an approach for genome-wide haplotyping based on contiguity-preserving transposition (CPT-seq) and combinatorial indexing. Tn5 transposition is used to modify DNA with adaptor and index sequences while preserving contiguity. After DNA dilution and compartmentalization, the transposase is removed, resolving the DNA into individually indexed libraries. The libraries in each compartment, enriched for neighboring genomic elements, are further indexed via PCR. Combinatorial 96-plex indexing at both the transposition and PCR stage enables the construction of phased synthetic reads from each of the nearly 10,000 'virtual compartments'. We demonstrate the feasibility of this method by assembling >95% of the heterozygous variants in a human genome into long, accurate haplotype blocks (N50 = 1.4–2.3 Mb). The rapid, scalable and cost-effective workflow could enable haplotype resolution to become routine in human genome sequencing. © 2014 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.

O'Daniel J.M.,Illumina | Lee K.,University of North Carolina at Chapel Hill
Cancer Journal (United States) | Year: 2012

The incorporation of whole-genome and whole-exome sequencing into clinical practice will undoubtedly change the way genetic counselors and other clinicians approach genetic testing. Enabling the analysis of essentially all human genes in one comprehensive test, this new technology can result in reduced testing cost and time to diagnosis. Another consequence of this broad scope, however, is the increased amount, complexity, and variety of results a clinician may need to discuss with a patient. The purpose of this article is to review the technology and outline some of the benefits and challenges of whole-genome and whole-exome sequencing in hereditary cancer practice. Copyright © 2012 by Lippincott Williams & Wilkins.

Luo S.,Illumina
Methods in Molecular Biology | Year: 2012

Direct sequencing of RNA molecules using next-generation sequencing (NGS) technology has revolutionized the analysis of transcriptome with its massively parallel throughput and low cost. Here, we describe Illumina's microRNA-Seq, a method for sequencing microRNA using the Illumina Genome Analyzer system. The sequence data generated from this method enables direct identifying and profiling of microRNAs in any given organism. It also sheds light in understanding the biogenesis and modification of microRNA. © 2012 Springer Science+Business Media, LLC.

Fluidic cartridge including a liquid container having a reservoir configured to hold a liquid. The liquid container includes an interior surface. The fluidic cartridge also includes a transfer tube that extends from the interior surface to a distal end. The distal end includes a fluidic port that is in flow communication with the reservoir through the transfer tube. The transfer tube has a piercing segment that includes the distal end. The fluidic cartridge also includes a movable seal that is engaged to the piercing segment of the transfer tube and configured to slide along the piercing segment from a closed position to a displaced position during a mating operation. The movable seal blocks flow of the liquid through the fluidic port when in the closed position. The piercing segment extends through the movable seal when in the displaced position.

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