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Similaire à Dr. Mike Evans — Chief Executive A unique targeted sequencing service providing meaningful results, not insurmountable data
Similaire à Dr. Mike Evans — Chief Executive A unique targeted sequencing service providing meaningful results, not insurmountable data (20)
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Dr. Mike Evans — Chief Executive A unique targeted sequencing service providing meaningful results, not insurmountable data
- 1. Dr. Mike Evans — Chief Executive A unique targeted sequencing service providing meaningful results, not insurmountable data
- 4. OGT’s key businesses IP Licensing 40 licence relationships Technologies For Molecular Medicine Clinical and Genomic Solutions Cytogenetics products and genomic services Diagnostic Biomarkers Genomic- and protein-based diagnostics
- 8. Customer Satisfaction… 20,000 samples. 1,000 samples / week “ In order to characterise genetic variants, reproducible performance and reliable processing of the high resolution microarrays is essential. We were pleased with OGT’s responsive approach and attention to producing high quality data to tight deadlines ” Dr Matt Hurles, Wellcome Trust Sanger Institute .”
- 9. OGT Collaborators and Customers
- 12. Delivering an Integrated, Comprehensive Service 30/06/11 1. Selection of most appropriate genomic regions for enrichment 2. Capture, sample multiplexing and sequencing 3. Data analysis and advanced filtering of variants
- 20. Read Depth Will Vary Across a Region of Interest *Sequence Depth >20x: ~82% for Single End How many times has a base been sequenced? *Agilent. 5990-4928EN
- 21. Read Depth Will Vary Across a Region of Interest *Sequence Depth >20x: ~82% for Single End ~90% for Paired End How many times has a base been sequenced? *Agilent. 5990-4928EN
- 26. Example of Design Bias - Insufficient Coverage Targeted gene sequencing can lead to some targets without the required depth of coverage *data kindly provided by C. Mattocks National Genetics Reference Lab, Salisbury, UK 14x (Q30) Inadequate Coverage
- 40. The Analysis Challenge Sequencer Hard drive with ~4Gb per exome Publication
- 46. Primary Analysis - Mapping and Alignment Raw Sequence Files FASTQ Format Mapping BWA/Bowtie Raw Alignment Files SAM/BAM Format Local Realignment (around InDels) GATK Duplicate marking Analysis-ready Alignment Picard SAM/BAM Format Quality score re-calibration Picard
- 47. Why Mark Duplicates and Realignment around Indels?
- 48. Why Mark Duplicates and Realignment around Indels? 3 incorrect calls within 40bp!
- 49. Primary Analysis - Mapping and Alignment Raw Sequence Files FASTQ Format Mapping BWA/Bowtie Raw Alignment Files SAM/BAM Format Local Realignment (around InDels) GATK Duplicate marking Analysis-ready Alignment Picard SAM/BAM Format Quality score re-calibration Picard
- 51. Base Quality Score Re-Calibration Source: The Broad Institute http://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_poplin.pdf Before Recalibration After Recalibration
- 52. Primary Analysis – Raw data and assembly QC Raw Sequence Files FASTQ Format Mapping BWA/Bowtie Raw Alignment Files SAM/BAM Format Local Realignment (around InDels) GATK Duplicate marking Analysis-ready Alignment Picard SAM/BAM Format Quality score re-calibration Picard
- 53. Primary Analysis – Raw data and assembly QC Raw Sequence Files FASTQ Format Mapping BWA/Bowtie Raw Alignment Files SAM/BAM Format Local Realignment (around InDels) GATK Duplicate marking Analysis-ready Alignment Picard SAM/BAM Format Quality score re-calibration Picard Sequence QC check Raw data QC Report FastQC AlignmentQC Report Alignment QC check Picard
- 58. OGT Processing Overview Data Information Individual Genome Analysis (Standard Level) Multi Genome Analysis, Data Gathering and Comparison (Advanced Level) Tailored analysis based on client’s individual requirements (Expert Level) Perform pairwise genome analysis Filter out variants present in any “baseline” exome (e.g. somatic tissue, healthy sibling) AND not all “case” exomes Study specific additional in-depth filtering and analysis
- 59. NGS Data Delivery Hard drive (or FTP) ship data browse Double click! Copy data to shared drive or local hard drive and...
- 60. NGS Data Delivery Hard drive (or FTP) ship data browse Comprehensive HTML analysis report Copy data to shared drive or local hard drive and...
- 61. NGS Data Delivery Hard drive (or FTP) ship data browse Comprehensive HTML analysis report Copy data to shared drive or local hard drive and... File location & share results
- 62. Analysis Report: Summary Section
- 63. Analysis Report: Summary Section
- 64. Analysis Report: Summary Section
- 65. Analysis Report: Summary Section
- 66. Analysis Report: QC Section – Read QC
- 67. Analysis Report: QC Section – Read QC
- 68. Analysis Report: QC Section – Read QC
- 69. Analysis Report: QC Section – Read QC
- 70. Analysis Report: QC Section – Read QC
- 71. Analysis Report: QC Section – Alignment QC
- 72. Analysis Report: QC Section – Alignment QC
- 73. Analysis Report: QC Section – Alignment QC
- 85. Alignment View of Selected Variant in IGV
- 86. Alignment View of Selected Variant in IGV
- 87. Alignment View of Selected Variant in IGV
- 91. Analysis Report: Supplementary Section
Notes de l'éditeur
- Mention all business areas and how the skill sets within each business area complement each other - especially in bioinformatics (over 9 dedicated, experienced employees) helping customers to not only design the right experiments but also access meaningful results. Could mention the ER group – lends additional credibility.
- The last 20 years has seen the rapid development of high-throughput, high-resolution molecular technologies for deciphering the genetic basis of disease. Keeping abreast of these new technologies is both expensive and time-consuming. Equipment quickly becomes obsolete as newer, more powerful platforms are developed. In addition, the sheer volume and complexity of the data generated using these technologies has placed great emphasis on the development of tools and services that can identify relevant genetic variation.
- Launched in October 2009, Genefficiency Microarray Services has quickly established OGT as the service provider of choice for high-throughput microarray processing and data analysis. Genefficiency provides a tailor-made service taking you though every step of the process from experimental and array design though to sample processing and comprehensive data analysis. Clinical and translational researchers have utilised our service in areas such as GWAS, cancer, molecular psychiatry and gene expression analysis. We place paramount importance on our quality control steps and provide complete reassurance though over 40 QC steps on each sample. Our bespoke Laboratory Information Management System records each QC step and provides a 360 degree audit trail on reagents, consumables and equipment. This attention to detail and proven delivery of high-quality results has been recognised by a number of independent organisations…….
- Including Agilent who named us as their first High-throughput Microarray Certified Service Provider. In addition, we are accredited by the International Organisation for Standardisation for a number awards essential for delivering high-quality genomic services
- We have processed over 40,000 aCGH samples (50,000 if we were to include Steve Rich [since 2008]) samples in our high-throughput lab including many high profile projects including the WTCCC (20,000 samples in <20 weeks).
- General outsourced services: CRUK, ICR Custom aCGH services: UVA,, Leuven, Wessex, Sanger, UCSD, CSHL Custom aCGH products: Karolinska, Emory, Greenwood Custom Methylation Services: Greenwood
- Our unique experience designing, processing, analysing and handling large-scale microarray projects provides us with the expertise required to deliver world-class genomic services for other technologies including….
- OGT’s new targeted sequencing services are designed to take you from project concept right through to qualified result. The decision to sequence is just the beginning. We can provide comprehensive services, tailored to suit your project. This includes flexible and expert design upstream, advanced data analysis, full support and advice throughout plus a dedication to quality which ensures that you can have confidence in the results you get back.
- OGT’s core expertise in the two key areas of probe design and data analysis allow us to focus on Steps 1 and 3 of the sequencing process: Step 1 is the selection of the most appropriate genomic content and design of capture probes to ensure efficiency and uniformity of capture; Step 3 is the analysis, filtering and prioritisation of variants, so that you receive information, not just data.
- Good project design is essential and it starts with selection of the most appropriate genomic content for your study. While whole genome sequencing holds much promise, a targeted approach is still the most commonly used and offers many benefits, including lower costs, faster turnaround time, and lower data complexity. Whole exome allows you to cover the regions which are most likely to be associated with many disorders (eg Mendelian) – indeed many of the findings from whole genome studies could also have been discovered with an exome-based approach. Sequencing cost is significantly lower, and data analysis is simpler than for whole genome. For small projects, a whole exome approach can be more cost-effective than a custom-based design, because you can use “off the shelf” exome kits. Custom region design also offers significant benefits for some studies: custom design allows you to include non-coding regions, or focus on particular candidate regions, post-GWAS for example. Shorter regions are most cost-effective to sequence because you can multiplex samples. Or you can benefit from much greater depth of sequencing coverage, to increase confidence of detection. Custom design requires optimisation of capture probe design, to ensure you capture all of the region of interest as evenly as possible. This is where OGT can add significant value, with our expertise in probe design – which will be covered by Jolyon later.
- “ The biggest bottleneck in sequencing is data analysis”.
- Through combination of internal validation and market feedback we chose the platforms above.
- Sanger format 0-93 ASCII encoding Illumina/Solexa 0-62 40 -60 mio such sequences per exome!
- Sanger format 0-93 ASCII encoding Illumina/Solexa 0-62
- Google images and you come across a wild rose and Kevin Rose, not quite what you expected. Same can happen in NGS data analysis – you don’t always get what you want
- Recalibration of quality scores
- Color coding?
- Color coding?
- Recalibration of quality scores
- Hard filtering like microarray analysis just looking for 2x up/down regulated genes
- Quality scores generated by sequencers are not very accurate! RMSE= root mean square error = is a measure of the differences between values estimated and the values actually observed Looking at millions of reads even little inaccuracies result in thousands of mistakes!
- Recalibration of quality scores
- Recalibration of quality scores
- SVs?
- Other components to add over time: alignment viewer, pathway information, GO annotation, genotype-based error rate
- Both hard drive and/or FTP possible!
- Both hard drive and/or FTP possible!
- Both hard drive and/or FTP possible!
- Let’s have a closer look at the report... Tabs, summary stats, variant overview,
- Let’s have a closer look at the report... Tabs, summary stats, variant overview,
- Let’s have a closer look at the report... Tabs, summary stats, variant overview,
- Let’s have a closer look at the report... Tabs, summary stats, variant overview,
- Excel or TXT download
- Excel or TXT download
- More links to come like OMIM; Excel or TXT download
- More links to come like OMIM; Excel or TXT download
- 2000 mutations to 200. Redundancy due to transcript level reporting
- 2000 mutations to 200. Redundancy due to transcript level reporting
- Quality and speed Filtering: you are the expert