Next Generation Sequencing. Fast, accurate data analysis

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1 Next Generation Sequencing Fast, accurate data analysis

2 Source BioScience is a leading provider of genomic research service in the UK, offering you next generation sequencing using the Illumina HiSeq 2000 and Genome Analyzer II Systems to support your sequencing requirements. Over a decade of experience in the sequencing field We have the largest commercial capacity for Illumina sequencing in the UK with both HiSeq 2000 and GAIIx platforms, providing you with the fastest turnaround time. Dedication to providing the highest quality service to our clients Our service is certified to the Illumina sequencing CSPro status and operates a robust quality management system. In addition, we are also GLP, GCP and CPA certified, ensuring that you enjoy the highest quality of data and service. Individual project managers for every project We understand the importance of your project. An individual project manager is assigned to every project to efficiently complete your project. Genome finishing incorporating Sanger sequencing Our expertise in Sanger sequencing complements the next generation sequencing to support genome finishing. Advanced bioinformatic solutions We offer comprehensive advanced bioinformatics solutions for every application to assist in the analysis of the vast amounts of data produced by the Illumina sequencing system. Expert advice We are happy to talk to you about experimental designs and to assist you in grant applications.

3 Introducing Next Generation Sequencing HiSeq 2000 The Illumina HiSeq 2000 and Genome Analyzer IIx systems are groundbreaking platforms for genetic analysis and functional genomics. The unmatched combination of ultra-high output and read length enables the broadest range of genomic applications including: Genome de novo sequencing and re-sequencing Targeted resequencing ChIP sequencing Small RNA analysis Whole transcriptome sequencing: RNA-seq All you need to supply us is high quality DNA or RNA and our comprehensive service enables us to sequence template from any source to your specifications. The Illumina Sequencing Work Flow The work flow starts with quality control of input material, library preparation, quality control of library followed by cluster generation on a flow cell through to sequencing and data analysis. Each application requires specific sample preparation for the sequencing and the sample library is prepared according to the recommended Illumina protocol: 1 Preparation of samples for small RNA analysis, RNA sequencing and ChIP sequencing 2 Preparation of samples for single, paired end, or mate-paired read sequencing 3 Preparation of multiplexed sequencing 4 Sequence capture (exome and selected regions) and sequencing. Alternatively, we offer Run Only service and we can accept libraries that you have prepared. A range of read lengths is available, ranging from 38bp to 150bp to suit your project needs. GAIIx

4 Comprehensive advanced bioinformatics data analysis At the forefront of next generation sequencing, Source BioScience understands the importance of making sense of the vast amount of data generated. Our bioinformatics team regularly investigate novel algorithms for their suitability to data analysis, and can offer advice on the particular application that will be most appropriate for your data. Some of most popular bioinformatics solutions include: Reference Alignment maps your sequenced reads against any sequence, from individual genes to entire genomes, showing depth of coverage. It is an essential pre-requisite to many downstream analyses. De novo Assembly of paired-end reads allows assembly of your novel sequenced reads in the absence of a suitable reference. Variant Detection searches for significant changes between reference DNA and the reads that map to it. Our software scans the mapped reads and compares the consensus at each base with the known reference base, reporting polymorphisms at regions when a significant change is detected (figure 1). RNA Sequencing Analysis to quantify absolute gene expression levels, within and between samples. Whole transcriptome analysis allows accurate detection of alternative splicing events and quantification of individual transcripts (figure 2). Small RNA analysis enables the discovery and differential expression analysis of the identified small RNA, functional analysis of the small RNA target genes and identification of novel small RNAs. ChIP sequencing analysis to determine genomic regions and peaks of high binding density to the protein of interest. Data visualisation enriches the data analysis process by allowing our customers to quickly focus on regions in which they are most interested (figure 3). Annotation integrates the data analysis with addtional information from public resources to enrich the final result.

5 Figure 1 Variant Detection Screenshot of our Variant Detection report tool, showing single nucleotide and deletion-insertion polymorphisms, overlaid annotation, with links to ensemble databases Figure 2 RNA-Seq Analysis Screenshot of excel spreadsheet showing total number of reads which map to specific genes. The graph shows a simple graphical comparison between two samples of the expression levels across all genes. Each dot represents a single gene, and x/y values correspond to the expression value of that gene in each sample Figure 3 Data Visualisation Screenshot of ChIP-Seq data mapped against the current Mouse genome (mm9), visualised using the UCSC Genome Browser. The complete lists of all ChIP-Seq regions and peaks identified are provided as tab-delimitted text files and Excel files

6 Our service workflow We provide complete support to you during the lifetime of the project. The project starts with our sequencing experts discussing your needs to ensure that the most appropriate strategies are adopted to achieve the desired goals. Detailed information on the project specifications will be provided prior to the commencement of the project. Our service work flow consists of the following: Project discussion and finalise strategy Issue of project proposal detailing specifications and how the project will be carried out Quality control of input material Library preparation, quality control and sequencing according to validated in-house SOPs Run performance quality control Basic/advanced data analysis Our deliverables Once all analysis has been completed, all data is returned to you on an external hard drive. This will include: Finalised, documented output data generated by bioinformatics data analysis, as well as all intermediate files generated during sequencing. Retention of the intermediate files by you allows further experiments to be carried out in the future without a need to resequence samples. Lab QC report detailing the integrity of the samples and libraries that were used for sequencing. Bioinformatics report, explaining metrics used to assess the quality of the data, and details of all bioinformatics analyses that have been performed, explaining the methods used and results obtained. Compilation and delivery of reports.

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8 Source BioScience LifeSciences 1 Orchard Place Nottingham Business Park Nottingham NG8 6PX Tel: +44 (0) Fax: +44 (0) lifesciences@sourcebioscience.com Source BioScience 2010