The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics

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1 The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics

2 The GS Junior System The Power of Next-Generation Sequencing on Your Benchtop Proven technology: Uses the same long read GS FLX Titanium chemistry as the GS FLX System to deliver high-quality, bioinformatics-friendly long reads. Accessible: Small instrument size, along with low entry and operating costs, enables any lab to take advantage of next-generation sequencing. Easy to use: Move quickly from data to results using the comprehensive suite of dedicated data analysis software. GS Junior System Long Reads GS Junior System System Type Throughput HQ Reads per Run Average Read Length Accuracy Run Time Sample Input Computing Data Analysis Software Dimensions Weight Power Supply Benchtop instrument ~35 Mb ~70,000 amplicon, 100,000 shotgun ~400 bases Q20 read length of 400 bases (99% accuracy at 400 bases and higher for preceding bases) 10 hours Genomic DNA, PCR products (amplicons) or cdna, depending on the application High-performance desktop PC for run processing and analysis included GS Reference Mapper GS De Novo Assembler GS Amplicon Variant Analyzer 40 cm x 60 cm x 40 cm 25 kg 100 VAC-240 VAC 50/60 Hz 400 VA Typical performance. Actual results depend on specifi c sample and genomic characteristics. Example read length distribution from a GS Junior instrument run. Average read length is 488 bp with a modal read length of 496 bp. An Integrated Solution from Sample Prep to Data Analysis GS Junior Titanium Reagents & Accessories Benchtop Instrument & Computer Data Processing & Analysis Software 2

3 From Sample to Result in 72 Hours The Complete Workflow Sample Diversity Day 1 Highest Nucleic Acid Quality using Standardized Protocols Manual sample prep (Roche High Pure) or MagNA Pure Compact (8 samples) MagNA Pure LC 2.0 (32 samples) MagNA Pure 96 (96 samples) Sequencing on the GS Junior System Day 2 Day 3 Digital Data Output of the Individual Long Reads Isolate DNA from any kind of sample, such as blood or tissue, using manual or standardized automated protocols yielding high quality nucleic acids. Prepare your amplicon or shotgun sequencing library yet the same day and clonally amplify the library overnight using the empcr procedure. Start sequencing your samples on day two and analyze the results in depth with powerful and user-friendly bioinformatics software tools developed by 454 on day three. See page 4 for a detailed description of the 454 Sequencing workflow. 3

4 454 Sequencing Workflow Four Steps to Meaningful Results 1. Library Preparation For shotgun librairies, start with as little as 500 ng of sample DNA, fragment using nebulization, and ligate Rapid Library Adapters to enable subsequent purification, quantitation, amplification and sequencing steps. For amplicon libraries, create PCR products by amplifying with specific fusion primers containing 454 Sequencing adaptor sequences. 2. empcr Amplification Anneal the library to 454 DNA Capture Beads and create water-in-oil emulsion to trap individual beads in amplification microreactors. Amplify the entire emulsion in parallel to create millions of clonal copies of each library fragment on each bead. 3. Sequencing Load the beads onto the PicoTiterDevice which allows only one bead per well and place it into the GS Junior Instrument along with sequencing reagents. Start the sequencing run individual nucleotides are flowed in sequence across the wells. Each incorporation of a nucleotide complementary to the template strand on any given bead results in a chemiluminescent light signal recorded by the camera. 4. Data Processing & Analysis Process the raw data automatically on the accompanying desktop computer the software uses the signal intensity at each well position to determine the sequence of 70,000 amplicon, or 100,000 shotgun reads simultaneously. Analyze results in depth with powerful and user-friendly bioinformatics software, e.g. for amplicon variant analysis. 4

5 Targeted Resequencing Detect Variants at High Resolution Zoom into critical genomic regions using amplicon sequencing of PCR products and sequence capture technologies. Quickly perform haplotyping, genotyping, rare variant detection, structural variant detection, and heterozygote calling. Analyze disease-associated regions in oncology and immunogenetics, or viral quasispecies present within infected populations in infectiology. The Long Read Advantage Long reads enable long amplicons Link distant variants in regions up to 400 bp long with a single amplicon for high-resolution haplotyping, or even larger regions with tiled amplicons. Clonal reads without cloning Long, clonal reads provide results in just a few days by parallel-processing thousands of amplicons. Detect variants to <1% frequency without the need to individually clone and sequence each sample, a process that takes weeks with standard technologies. Applications Unambiguously resolve highly complex genomic regions (e.g., HLA, IgH) (Figure 1) Discover germline or somatic mutations in oncology (e.g., EGFR, KRAS, BRAF, PI3K, BRCA) hematology (e.g., TET2, CBL, RUNX1, RAS) metabolic diseases (e.g., CFTR, MODY) Detect low-frequency variants such as rare drugresistant viral mutations (e.g., HIV) Unambiguous Haplotyping Capillary Sequencing TTCMRCARAYTTRG 1: AA A C A 2: CA A C A 3: AG A C A 4: CG A C A 31: AG G T G 32: CG G T G Physically separate alleles by cloning (insert, grow, pick, grow, isolate plasmid DNA, sequence) 4+ days 454 Sequencing Systems Digitally separate alleles with AVA software (click) seconds Figure 1. Non-clonal sequencing of amplicons can lead to ambiguous results due to the difficulty in confidently haplotyping loci with more than one variant. For example, this short 14-base region of the HLA DQA1 exon 2 locus contains five variants resulting in 32 possible allelic combinations. Haplotyping involves physical separation of the two alleles by cloning, a time-consuming and labor-intensive process. In contrast, the 454 Sequencing approach yields hundreds to thousands of clonal reads for each amplicon. Haplotyping can be accomplished completely in software without any need for additional sequencing. In addition, the large number of clonal reads also allows for confident calling of low-frequency variations. 5

6 Amplicon Sequencing Highly Sensitive Detection of Genomic Variations The GS Junior System allows to focus on specific genomic regions of interest through PCR amplicon sequencing using target specific fusion primers to assess a broad set of variations, including single nucleotide polymorphisms, insertions and deletions. Long-Read Amplicon Resequencing Typically, amplicon fusion primers must contain a directional 454 Primer A or Primer B sequence, a four-base library «key» sequence, and a template-specific sequence at the 3-prime end (Figure 2). An optional Multiplex Identifier (MID) sequence may be added to allow for automated software identification of samples after pooling and sequencing, also referred to as «barcoding» of individual samples. Using 14 predefined standard MIDs in each of the two fusion primers will enable multiplexing of up to 196 samples per run. For your convenience, the 14 standard MID sequences have been preloaded in the Amplicon Variant Analyzer (AVA) Software developed by 454, enabling the alignment and analysis of amplicons against a reference sequence, and automatic demultiplexing of the reads. A A key MID MID key B B Forward primer (Primer A-Key): 5 -CGTATCGCCTCCCTCGCGCCATCAG-{MID}-{template-specific-sequence}-3 Reverse primer (Primer B-Key): 5 -CTATGCGCCTTGCCAGCCCGCTCAG-{MID}-{template-specific-sequence}-3 Figure 2. Amplicon structure (A) and nucleotide sequences of the GS Junior Titanium fusion primers (B), including the key, which is underlined and highlighted in red. These sequences are followed by an optional MID and your template-specific sequence. GS Amplicon Variant Analyzer (AVA) Software Identify haplotypes over distances of up to 400 bp or longer. Detect and quantify known or novel variants, including SNPs and indels. Perform simultaneous heterozygote calling on large number of amplicons. Detect low-frequency variants in complex samples, such as rare somatic mutations or viral quasispecies, based on ultra-deep sequencing of amplicons. 6

7 Service and Support Our global support team is dedicated to 454 Sequencing Systems from application knowledge to product expertise, the Roche team is committed to making your projects a success. Whether you are interested in training, service, hardware, software, or applications, we provide the support you need when you need it. 454 Sequencing Support is available Monday to Friday, from 8:00 am to 6:00 pm. Additional support, including manuals, software tutorials, and workflow videos, is available online through the my454 Web site at Products Products GS Junior System includes desktop PC and data analysis software GS GType HLA Medium Resolution Primer Set contains 4 basic microplates for medium resolution genotyping (40 tests per set) GS GType HLA High Resolution Primer Set contains 4 additional microplates for high resolution genotyping (40 tests per set) Cat. No

8 Restriction of Use Purchaser is only authorized to use 454 Sequencing System Instruments with PicoTiterPlate devices supplied by 454 Life Sciences Corporation and in conformity with the operating procedures contained in the 454 Sequencing System manuals and guides. 454, 454 SEQUENCING, 454 LIFE SCIENCES, GS JUNIOR, GS FLX, EMPCR, PICOTITERPLATE, HIGH PURE, and MAGNA PURE are trademarks of Roche. Other brands or product names are trademarks of their respective holders Roche Roche Diagnostics (Switzerland) Ltd CH-6343 Rotkreuz ARD

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