Bioo Scientific Honored for Increasing Austin’s Ability to Compete in the Global Marketplace

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Bioo Scientific received the British Airways International Trade, Investment & Expansion Award, recognizing the worldwide economic growth fueled by its international sales team and network of distributors. The British Airways International Trade, Investment & Expansion Award recognizes investments by international companies in Austin that create jobs locally, as well as Austin-based companies who have a global impact through products and services provided worldwide. Bioo Scientific is an Austin-based biotech company which manufactures food and feed safety test kits and products supporting life science research.

The awards, presented by the Austin Chamber, recognize local firms and organizations for achievements, community contributions and milestones. It is one of the largest business events in Central Texas, bringing together 1,000 business leaders, entrepreneurs, organizations, government officials and regional chambers.

About 300 companies were nominated for the Chamber’s Business Awards. Out of this group, Bioo Scientific was recognized for being a top exporter in the Austin area. All of Bioo Scientific’s products are manufactured in the United States; however, international sales make up over three quarters of Bioo Scientific’s business.  Bioo Scientific exports food and feed safety test kits and life science research products to more than 100 countries across Asia, Europe, the Middle East, Africa and Latin America.

Currently Bioo Scientific is focusing its attention on increasing its global presence, as exporting is essential to our future growth. The 2015 Greater Austin Business Export Awards recognizes the success of these efforts.

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Rapid Whole-Genome Sequencing of Bacteria

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Clinical personnel and health officials must rapidly identify potential pathogens in order to respond to suspected disease outbreaks to prevent public disturbances. Next-generation sequencing has the potential to complement conventional diagnostics in many instances, and whole genome sequencing is ideal for use as a typing tool to identify the causative agent behind diseases.

One recent example of NGS being used in a clinical setting is illustrated in the publication Rapid Metagenomic Diagnostics for Suspected Outbreak of Severe Pneumonia, a letter to Emerging Infectious Diseases, in which researchers describe the methodology their group used to identify the pathogen responsible for acute respiratory distress syndrome in their patients, using a NEXTflex™ Kit for library construction. This sequencing methodology was used to identify the etiologic agent of a suspected pneumonia outbreak among German police officers.

With a robust two-hour library prep protocol and up to 384 single-index barcodes, which facilitate high level multiplexing while reducing concerns about run-to-run sample carryover and sample crosstalk, the NEXTflex™ Rapid DNA-Seq Kit is ideal for rapid identification of disease-causing pathogens.

To demonstrate the efficacy of next generation sequencing for identification of pathogens, we present below Bioanalyzer traces of libraries constructed from varying inputs of DNA isolated from E. coli, Campylobacter and Salmonella bacteria.

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Figure 1. Bioanalyzer trace of a library constructed using the NEXTflex Rapid DNA-Seq Kit from 100 ng of E. coli bacteria in water.

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Figure 2. Bioanalyzer trace of a library constructed using the NEXTflex Rapid DNA-Seq Kit from 1 µg of Campylobacter bacteria in water.

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Figure 3. Bioanalyzer trace of a library constructed using the NEXTflex Rapid DNA-Seq Kit from 100 ng Salmonella bacteria in water.

Fischer, N., et al. (2014) Rapid metagenomic diagnostics for suspected outbreak of severe pneumonia [letter]. Emerg Infect Dis. doi: 10.3201/eid2006.131526.

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Featured Publication: Transcriptomic Analysis of Degraded Forensic Body Fluids

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Researchers Meng-Han Lin, Daniel F. Jones, and Rachel Fleming determined the NGS analysis of RNA obtained from various fluid samples is a reliable method for body fluid identification from the degraded samples frequently encountered at crime scenes, which can be difficult to analyze using the current detection methods, RT-PCR and qPCR.

These researchers have made significant advances in analysis of degraded RNA from forensically relevant fluids, generating significant high quality sequencing output from fresh, two and six week aged samples of oral mucosa/saliva (buccal samples), circulatory blood, menstrual blood and vaginal fluid. Libraries for sequencing were generated using the NEXTflex™ Rapid Directional RNA-Seq Kit, from total RNA which was not subjected to ribosomal RNA depletion. Due to the low concentration and degraded nature of some samples, 13 µL total RNA input was used for library preparation irrespective of concentration.

In these studies, body fluid-specific markers were detected across different body fluid types and aging intervals and FPKM values for body fluid-specific markers corresponded to the target body fluid type. The availability of this type of is contextual information may have significant implications for the investigation of crimes.

Read the entire publication here: http://www.fsigenetics.com/article/S1872-4973(15)00042-3/fulltext

Lin, M.-H., Jones, D. F. and Fleming, R. (2015) Transcriptomic analysis of degraded forensic body fluids. Forensic Science International: Genetics, Volume 17.  35-42. dio: 10.1016/j.fsigen.2015.03.005.

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Automated Sciclone Protocol for mRNA Purification from Total RNA Now Available

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The NEXTflex™ Poly(A) Beads offer the best available mRNA recovery rate, while providing a convenient method for batch purification of pure, intact mRNA from total RNA. An automation protocol for the Sciclone® NGS and NGSx Workstations is now available, allowing researchers to automate mRNA isolation upstream of RNA-Seq library preparation and other applications.

Download the Sciclone NGS and NGSx Workstation Automation Guide to simplify your mRNA purification: NEXTflex™ Poly(A) RNA Beads Sciclone Automation Guide

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Featured Publication – Genomic Variations in Plasma Cell Free DNA Differentiate Early Stage Lung Cancers from Normal Controls

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Drs. Shu Xia and others recently determined that early stage lung cancer can be detected in patients, using noninvasive, blood-based genomic and genetic assays which sensitively distinguish early stage disease when combined with other existing screening strategies, including low-dose CT scanning.

To evaluate copy number variations (CNV) and identify potential mutations, they performed low-pass whole-genome sequencing and targeted sequencing of 50 cancer genes. The NEXTflex™ Cell Free DNA-Seq Kit was used to construct libraries from cfDNAs and tumor tissue DNAs isolated from lung adenocarcinoma patients, and from cfDNAs isolated from normal controls for low-pass whole-genome Illumina sequencing. Targeted sequencing was performed using the Ion AmpliSeq™ Cancer Hotspot Panel V2.

To accurately reflect the tumor-associated genomic abnormality burden in plasma, Xia et al. developed a new scoring algorithm, plasma genomic abnormality (PGA) score, by summarizing absolute log2 ratios in most variable genomic regions. Digital PCR and allele-specific PCR was performed to validate mutations detected by targeted sequencing.

Read the entire publication here: http://www.sciencedirect.com/science/article/pii/S0169500215300088

Xia, S. et al. (2015) Genomic variations in plasma cell free DNA differentiate early stage lung cancers from normal controls. Lung Cancer. doi: 10.1016/j.lungcan.2015.07.002.

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Featured Publication – Rapid Metagenomic Diagnostics for Suspected Outbreak of Severe Pneumonia

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Researchers from the University Medical Centre Hamburg–Eppendorf, the German Center for Infection Research, and the Heinrich Pette Institute Leibniz Institute for Experimental Virology used the NEXTflex™ ChIP-Seq Kit and NEXTflex™ ChIP-Seq Barcodes in a clinical diagnostic setting to identify the etiologic agent of a suspected pneumonia outbreak among German police officers. Nucleic acids were extracted from bronchoalveolar lavage (BAL) specimens from two patients and used in next generation sequencing. The pneumonia cases were found to result from different etiologic agents and were not part of a larger outbreak.

Read the entire publication here: http://wwwnc.cdc.gov/eid/article/20/6/13-1526_article

Fischer, N., et al. (2014) Rapid metagenomic diagnostics for suspected outbreak of severe pneumonia [letter]. Emerg Infect Dis. doi: 10.3201/eid2006.131526.

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Small RNA-Seq Library Prep Incorporating Bias Reducing Randomized Adapter Technology Simplified with Pippin Prep Protocol

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A Pippin Prep protocol is now available for automated size selection of small RNA libraries constructed using the NEXTflex™ Small RNA Sequencing Kit v2. This kit uses a proprietary approach to overcoming ligation bias in small RNA-Seq libraries; using a pool of adapters having randomized sequences at the ligation site. Most of the bias in adapter ligation is due to the sequence of the nucleotides adjacent to the target junction, because no single adapter sequence is able to efficiently ligate to all small RNAs. The randomized adapter technology incorporated into the NEXTflex Small RNA-Seq Kit V2 allows small RNAs of any sequence to ligate to their corresponding optimal adapters, resulting in small RNA-Seq libraries that show a dramatic reduction in bias.

Using a Pippin Prep protocol with the NEXTflex Small RNA-Seq Kit V2 offers a significant savings of labor while producing a high-quality sample, as it automates the manual gel purification step which is otherwise required as the last step of small RNA library prep.

The protocol for automated size selection of small RNA libraries is available for download here: http://www.biooscientific.com/Portals/0/NGS/NEXTflex_Small_RNA_v2_Pippin_Prep_Supplement.pdf

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Increase Your Multiplexing Capabilities with 384 Single-index Barcodes for Illumina Sequencing

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The NEXTflex-HT Barcodes are the largest set of single-index barcodes available for high-throughput Illumina sequencing. The NEXTflex-HT Barcodes each contain 12 nt unique index sequences with Hamming Distances of five or greater, permitting dual error correction to enable proper differentiation between samples by preventing ambiguity from PCR errors or sequencing instrument miscalling. Additionally, each pair of consecutive barcodes are fully color balanced and suitable for low level multiplexing.

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Slideshow – Improving NGS Library Prep Automation on the Sciclone NGS Workstation

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While the use of the Sciclone NGS Workstation simplifies library prep by offering increased throughput and uniformity and decreased costs, it can also be a limiting factor if the latest library prep technology is not incorporated into the kits which are automated on the platform. Bioo Scientific has developed automation protocols for the Sciclone NGS and NGSx for a number of the NEXTflex library prep kits, so that the latest innovations available to reduce bias and increase library quality are now easily available for use with the Sciclone. With automation protocols and user guides available, these rapid and robust library prep solutions also are easy to deploy and greatly increase the end user’s multiplexing capabilities.


 

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Sequencing Ion Amplicon-Seq PCR Products on the Illumina MiSeq Reduces Mean Turnaround Time for Diagnosis While Augmenting the Number of Targets Analyzed in a Clinical Setting

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In a recent study published in Journal of Thoracic Oncology, the Network Genomic Medicine Lung Cancer, which was set up to rapidly translate scientific advances into early clinical trials of targeted therapies in lung cancer, performing molecular analyses of patients, demonstrates the feasibility of using a highly multiplexed targeted resequencing assay for detecting somatic mutations in patients for lung cancer diagnosis.

These researchers decided that an Ion AmpliSeq Custom DNA Panel containing 102 amplicons of 12 different genes (Life Technologies) was ideal for their needs because of the flexibility of the CP design, and initial testing which indicated that previously determined variants could be detected in routine diagnostics.

However, the Network Genomic Medicine Lung Cancer also wanted to sequence the multiplex PCR product obtained from the Ion AmpliSeq panel on a MiSeq Benchtop sequencer. Using the MiSeq they multiplex 44 patients with a mean coverage of 4000×, a quality Q30 score of over 95% and a minimal coverage of 500 in 99% of the amplicons. They were able to do this by incubating the PCR products with NEXTflex DNA Adenylation Mix and then ligating NEXTflex DNA Barcode adapters to the fragments. 10 cycles of PCR were then run and the samples were sequenced on an Illumina MiSeq (Fig. 1). Using this protocol, sample preparation was reduced by 4 ½ hours and turnaround time was reduced from 12 days to 10 days when compared to conventional dideoxy-sequencing, while augmenting the number of targets.

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This comprehensive biomarker testing provided novel information in addition to histological diagnosis and clinical staging. In 2657 consecutively analyzed lung cancer samples, the Network Genomic Medicine Lung Cancer identified driver mutations at the expected prevalence. Furthermore they found potentially targetable DDR2 mutations at a frequency of 3% in both adenocarcinomas and squamous cell carcinomas.

Overall, these data demonstrate the utility of NGS analysis in a clinical routine setting, and highlight the dramatic impact of such an approach on the availability of therapeutic strategies for the targeted treatment of individual cancer patients.

König, K. et al. (2015) Implementation of Amplicon Parallel Sequencing Leads to Improvement of Diagnosis and Therapy of Lung Cancer Patients. Journal of Thoracic Oncology. 10 :7, 1049–1057. doi: 10.1097/JTO.0000000000000570.

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