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The Illumina Genome Network
The Illumina Genome Network links researchers interested in conducting large whole human genome sequencing projects with leading institutes worldwide that provide highly economical and rapid turnaround access to Illumina sequencing. Consisting of CSPro-certified organizations with proven expertise in generating high-quality, economical human genome data, the Illumina Genome Network enables researchers to complete their genome sequencing projects rapidly and confidently. Highest quality data with fast turnaround times: that is the promise of the Illumina Genome Network.
Entrust your study to some of the most recognized names in sequencing, all of whom rely upon the trusted and proven Illumina technology platform. Leverage their expertise to get fast access to comprehensive whole-genome assemblies, including:
- High quality variant calling of single nucleotide polymorphisms (SNPs) and insertions and deletions (Indels)
- Ability to identify Copy Number Variations (CNV) and other structural rearrangements
- Access to a comprehensive set of in-house and third-party analysis tools designed to support the system with the largest installed base in the industry
- Ability to reanalyze data sets over time
You can choose your Illumina Genome Network partner and create service packages based on your individual study requirements. Flexible turnaround times and a range of value-added services are available to meet the unique needs of every study. It’s a quick and reliable way to get your sequencing study started on the Illumina sequencing technology platform.
Whole Human Genome Sequencing Services Brochure
Illumina Genome Network Data Sheet
Technical Note-Leveraging Whole Human Genome Sequencing in Cancer
High-Quality Data
Sound research hinges on good data. While other service companies promise it, the Illumina Genome Network delivers high-quality data, using industry-leading HiSeq 2000 systems, TruSeq reagents, and experienced scientists to cost-effectively perform whole-human genome sequencing. We stand by the accuracy of our data. See how we compare.
More Useable Data
Whole-genome sequencing involves more than obtaining high coverage depth and quality reads. It’s the generation of usable, callable data for variant calling. The Illumina Genome Network runs each base pair through a usable genome test, providing you with the highest callable genome (>95%), even in the difficult-to-sequence regions (< 5%). Giving > 80% of all reads passing filter a quality score of Q30 or greater.
High Accuracy
Accuracy is vital for calling variants, especially the ones that are central to your research. The Illumina Genome Network delivers the TruSeq genome, the most accurate genome in the industry. Don’t take our word for it. See how the TruSeq genome delivers in the following tests:
1. Measuring consensus accuracy at the whole-genome level
| Services co. (60X) | Illumina (30X) | |
|---|---|---|
| Callable Sites Present in Trio (bp) “N-Excluded” | 2,575,974,378 | 2,530,389,955 |
| Mendelian Conflicts on Genotypes | 35,843 | 10,801 |
| Conflicts Per Mb | 13.91 | 4.27 |
2. Analyzing consensus calls
- More SNPs and fewer false positives (so you won’t waste time chasing false leads)
| Services co. (60X) | Illumina (30X) | |
|---|---|---|
| Called SNPs in Any One of Trio | 4,294,576 | 4,403,335 |
| Mendelian Conflicts on Genotypes | 35,843 | 10,801 |
| False Positive Rate | 0.83% | 0.25% |
- More SNPs and fewer false negatives (so you won’t miss a variant)
| Services co. (60X) | Illumina (30X) | |
|---|---|---|
| Called SNPs | 3,466,755 | 3,536,295 |
| Called SNPs from Gold Standard Set (95,005) | 87,474 | 87,965 |
| False Positive Rate | 7.93% | 7.41% |
Analyzing SNP concordance
We run every sample on a HumanOmni-2.5 BeadChip, demonstrating a hallmark of the TruSeq genome—concordance > 99%. To support your further studies, we provide this genotyping data, as well as all WGS data files, as part of the final report.
The Illumina Genome Network Partners
BC Cancer Agency Genome Sciences Centre
100-570 West 7th Avenue
Vancouv er, BC V5Z 4S6 Canada
Email: igninfo@bcgsc.ca
Web: www.bcgsc.ca
Canada’s Michael Smith Genome Sciences Centre (BCGSC) at the BC Cancer Agency is a leading international centre for genomics and bioinformatics research. Our mandate is to advance knowledge about cancer and other diseases, to improve human health through disease prevention, diagnosis and therapeutic approaches, and to realize the social and economic benefits of genomics research. Founded in 1999, BCGSC is the largest academic genome centre in Canada, and among the most productive in the world in the fields of cancer genomics and bioinformatics. We collaborate locally, nationally and internationally with partners in all ares of genome sciences.
Macrogen/Genomic Medicine Institute/Seoul National University
Rm 1002, 10th floor
World Merdian Venture Center
60-24, Gasan-dong, Geumchen-gu
Seoul, 153-781, South Korea
Phone: +82.2.2113.7000
Fax: +82.2.2113.7016
Email: chipinfo@macrogen.com
Web: www.macrogen.co.kr/eng
Genomic Medicine Institute (GMI) was founded in 1997 with the mission of providing Asian whole genome sequences and supporting the development of genomic technology for future personalized medicine and taking a role as the institute of excellence for Genomics in Korea.
NCGR (National Center for Genome Resources)
2935 Rodeo Park Drive East
Santa Fe, New Mexico 87505
Contact: Patricia Mena, Customer Relations Manager
Phone: 1.505.995.4444
Fax: 1.505.995.4432
Email: pmena@ncgr.org
Web: www.ncgr.org
NCGR, a non-profit research institute with extensive experience in Illumina DNA sequence data generation and analyses, provides sequencing, genotyping, and analysis services in a collaborative setting. Service offerings include whole-genome (including de novo), transcriptome, methylome, ChIP, smRNA, and exome (targeted or whole). Assistance with experimental design, custom data analysis, and visualization tools for de novo assembly, alignment, and variant detection are available. You can also contact us for Illumina genotyping services.
Service Details
When you send your project to an Illumina Genome Network Partner, you will receive whole human genome sequencing performed at 30X average coverage, from short-insert paired end reads, using a single library. Data analysis will be performed using CASAVA (consensus sequence from ELAND alignment, called SNPs, and small indels). The delivered data set will include reads and quality scores for further downstream analysis.
The following specifications are guaranteed for each sample:
- Average autosomal minimum fold coverage of 30X
- Percent of non-N reference coverage >90% for non-cancer samples
- Paired end sequencing at 2×100bp
- At least 3,000,000 SNPs detected for non-cancer samples
- Genotype Concordance >99.5% for non-cancer samples
Data will be delivered in standard formats for downstream visualization in Genome Studio or third-party open-source tools, as follows:
- All pass filter reads, alignments, and quality scores in an archival BAM format file, suitable for visualization and downstream analysis
- SNP calls, insertions and deletions with respect to the reference sequence, as well as an allele call and confidence score for every covered position in the reference
- Text reports for SNP calls for all SNPs in dbSNP for which sufficient coverage has been achieved
- Whole-genome genotyping array data and genotype report
Premium data analysis packages are also available through select Illumina Genome Network Providers. Please send questions directly to your Illumina Genome Network Partner.
Interested in Illumina Genome Network Services?
- Fill out web form to submit your project for the Illumina Genome Network
- Illumina provides a quote to you
(per your submitted project specifications, including a list of Illumina Genome Network Partners who can provide the service) - You confirm acceptance of subcontracting terms and rank Illumina Genome Network Partners of choice, including Illumina FastTrack Services
- Illumina approaches the Illumina Genome Network Partners according to your ranking order
- Illumina Genome Network Partner accepts your project
- You send samples to the Illumina Genome Network Partner to begin project
- Illumina Genome Network Partner notifies Illumina via email that data has been delivered to you to complete project
- You receive an invoice from Illumina
Whole Human Genome Sequencing Comes of Age
Advances in Whole Human Genome SequencingClick to enlarge »
In just 15 years, whole human genome sequencing has moved from an expensive, labor intensive, time consuming project costing $40 million, to a study that can be performed quickly and accurately by the Illumina Genome Network for $4,000 (50+ samples). Based on industry-leading TruSeq technology, Illumina sequencers are enabling whole genome sequencing (WGS) to become an integral part of human disease research, whether performed by researchers in their own laboratories, or by Illumina and its Illumina Genome Network partners.
See how whole human genome sequencing powered by Illumina sequencers is providing insight into the mechanisms of cancer and other life-threatening conditions, enabling researchers to visualize what's occurring at the genomic level to develop better therapeutics and improved diagnostics.
Research and Discovery
Cancer
Ley, TJ (2008) DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome
Mardis, ER (2009) Recurring mutations found by sequencing an acute myeloid leukemia genome
Ley, TJ (2010) DNMT3A mutations in acute myeloid leukemia
Chapman, MA (2011) Initial genome sequencing and analysis of multiple myeloma
Berger, MF (2011) The genomic complexity of primary human prostate cancer
Rafnar, T (2011) Mutations in BRIP1 confer high risk of ovarian cancer
Totoki, Y (2011) High-resolution characterization of a hepatocellular carcinoma genome
Mendelian, Rare Disease
Whole Human Genome Data Analysis
Bioinformatics and Methods
Baker, M (2011) Sorting out sequencing data
Earl, D (2011) Assemblathon 1: a competitive assessment of de novo short read assembly methods
Kinde, I (2011) Detection and quantification of rare mutations with massively parallel sequencing
Nguyen, T (2011) CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
Danacek P (2011) The variant call format and VCFtools
Bao, S (2011) Evaluation of next-generation sequencing software in mapping and assembly
Other Interesting WGS Publications
WGS and Methylation
Reviews and Commentaries
Reviews
Commentaries
Illumina Genome Network Partner Publications
Partners
At Illumina, our goal is to apply innovative technologies and revolutionary assays to the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. These studies will help make the realization of personalized medicine possible. With such rapid advances in technology taking place, it is mission critical to have solutions that are not only innovative, but flexible, scalable, and complete with industry-leading support and service. As a global company that places high value on collaborative interactions, rapid delivery of solutions, and prioritizing the needs of its customers, we strive to meet this challenge. Illumina's innovative, array-based solutions for DNA, RNA, and protein analysis serve as tools for disease research, drug development, and the development of molecular tests in the clinic.