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Precise Sizing and SMRT Sequencing Offer Unprecedented Read Length for Clinical Studies

Sage Science
19 Oct 2014

At the Icahn Institute for Genomics and Multiscale Biology at Mount Sinai in New York City, technology development expert Robert Sebra, Ph.D., sees tremendous need for long-read, high-accuracy clinical sequencing for use in microbial surveillance, detection of repeat expansions, and more. To meet that demand, he relies on Single Molecule, Real-Time (SMRT®) Sequencing from Pacific Biosciences with BluePippin™ automated DNA size selection from Sage Science. Together, these tools offer a powerful solution and industry-leading read lengths that allow Sebra and other researchers to resolve repeat elements and structural variants, rapidly close microbial genomes, and measure epigenetic marks.

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BluePippin Size Selection System

Sage Science

The BluePippin is a preparative electrophoresis platform for collection of size-selected DNA or protein samples. The system automates DNA or protein size selection using disposable, pre-cast agarose cassettes to extract fractions according to user-defined software input. Samples are electro-eluted from agarose and collected in buffer. The platform is used for the construction of next-gen sequencing libraries, or upstream of protein mass-spec. For DNA applications, the BluePippin features pulsed-field electrophoresis to collect high molecular weight targets, and can collect fragments (depending on gel type) between 90 bp- 50kb. For protein, the system uses SDS-agarose to collect targets between 18-200kDa. In both cases, a higher quality of sample is extracted, and more reproducibly, when compared to manual gel purification methods.

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ElectrophoresisElectrophoresis equipment is used to separate mixtures of protein, DNA or RNA, based on their electric charge, size and other physical characteristics, by passing them through a medium such as a polyacrylamide gel, an agarose gel or a capillary tube. Electrophoresis equipment includes horizontal and vertical gel electrophoresis chambers, isoelectric focusing systems, 2D electrophoresis and capillary electrophoresis instruments. Precast gels with a gradient can be used or gels can be hand cast. Samples are run alongside ladders or markers to identify the approximate size of a molecule. Separated proteins and nucleic acids in the gel can be stained or probed with fluorescent markers and then imaged and detected using gel documentation instruments, transilluminators, densitometers and scanners. Find the best electrophoresis equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Genome AnalysisGenomics, the study of genomes, includes functional genomics, evolutionary genomics and comparative genomics. There are many genomic technologies such as DNA sequencing of whole genomes, computational biology and bioinformatics. DNA and nucleic acids must be isolated and concentrated from cells for analysis with kits, automated analyzers and software. Other useful technologies for studying genomics include PCR, microarrays and electrophoresis.High-Throughput ScreeningHigh-throughput screening (HTS) is an automated drug discovery technique for identification of active compounds against a compound library. Use HTS readers and integrated assay preparation / analysis workstations to screen your compounds. Identify active compounds against various HTS libraries, including membranes, proteins and peptides and HTS cell lines. Find the best high-throughput screening products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.DNA SequencingDNA sequencing, such as sanger sequencing, is a biological technique that determines the precise order of nucleotide bases in a fragment or template of DNA. DNA sequencers and genetic analyzers are based on capillary electrophoresis, where labeled DNA fragments are electrophoretically separated by size as they migrate through a polymer. Find the best DNA sequencing products, including DNA sequencing kits, genomic libraries and genetic identity kits in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Gene Expression and Molecular CloningMolecular cloning is a set of techniques that utilizes vectors to transfer recombinant DNA into host cells and is an essential tool for investigating the expression of genes and proteins in bacterial or mammalian cells. A variety of vectors optimized for gene cloning and expression in a range of host organisms are available, alongside competent cells for genetic replication. Here, you can explore a range of molecular tools, high-quality genomic and cDNA libraries, premade clones, transformation and transfection reagents and mutagenesis or gene expression detection assays and expression arrays. Find the best gene expression and molecular cloning products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Clinical GeneticsMolecular Genetics covers the analysis of hereditary genetic disease and chromosomal abnormalities. Genetics can be analysed using DNA, RNA, and protein microarrays, PCR, RT PCR and DNA sequencing. Genetic equipment includes genetic workstations, thermal cyclers, cooling blocks and electrophoresis products. Diagnostic kits are used for DNA / RNA extraction and purification.Epigenetic AnalysisEpigenetic analysis products are used to study heritable phenotype changes that do not alter the DNA sequence, such as DNA modifications affecting gene activity. Determine whether genes have been methylated with DNA methylation quantification kits or methylation microarrays. Assess epigenetic regulation with histone modification kits or ChIP-on-chip microarrays. Kits are also available for bisulfite conversion and amplification of your samples, as well as epigenomic library preparation kits for next-generation sequencing (NGS). Find the best epigenetic products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Size SelectionHigh ThroughputHigh throughput experiments allow the simultaneous processing of several samples. This parallelization reduces the cost per experiment and increases reproducibility and output volume of data.

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Precise Sizing and SMRT Sequencing Offer Unprecedented Read Length for Clinical Studies