INVIEW EPIGENOME BS-SEQ

SKU#B10140827

Study epigenetic changes across the entire genome

INVIEW EPIGENOME BS-Seq is an all-in-one, whole-genome bisulfite sequencing service. The product combines next-generation sequencing (NGS) of bisulfite-treated DNA and expert Bio-IT analysis to generate a detailed characterisation of the entire methylome of nearly any organism of interest.

Highlights of INVIEW EPIGENOME BS-Seq

  • Exceptionally high bisulfite conversion rate at true base level resolution
  • Flexible sequencing coverage
  • Applicable to all organisms with 5-methylcytosines

Service required

INVIEW EPIGENOME BS-SEQ incl. 5 Gb raw data (2 x 150 bp)

Additional data output

Pre-Sequencing

Bioinformatic analysis

INVIEW EPIGENOME BS-SEQ

INVIEW EPIGENOME BS-SEQ

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ISO9001 Certification - GATC BiotechISO17025 Accreditation - GATC BiotechIllumina Certified Service Provider Certificate

Product Details

Product Details

Full-service package offered by INVIEW EPIGENOME BS-Seq including:

  • Determination of cytosine methylation status at base-level resolution
  • Bisulfite treatment with an exceptionally high conversion rate
  • Optimised library preparation for Illumina technology
  • Comprehensive bioinformatics analysis
  • Diagnostic-quality processing under official accreditation
  • Fast delivery of ready-to-publish data

Accepted starting material for INVIEW EPIGENOME BS-Seq

  •  2 µg unamplified, high-quality DNA (20 ng/µL)
  • DNA isolation available as an additional service for tissue samples and cells

Please note that only S1-classified material is accepted for DNA isolation ordered online. More information about the current rules for classifying biological material can be found here. Please contact us for further information on isolating DNA from material classified as S2.

Sequencing platform used for INVIEW EPIGENOME BS-Seq

  •  Illumina

Sequencing mode for INVIEW EPIGENOME BS-Seq

  • 150 bp paired-end reads

Bioinformatic analysis included in INVIEW EPIGENOME BS-Seq

  • Available for human, mouse or rat; other organisms upon request
  • Sequence quality assessment and filtering
  • Mapping against genomic reference and refinement
  • SNP detection, including annotated variants
  • Methylation profiling and annotation
  • Comprehensive Data Analysis Report

Figure 1: Workflow bioinformatics pipeline

Deliverables of INVIEW EPIGENOME BS-Seq – Non-comparative mode

Genome alignment

  • Binary alignment map (BAM)
  • Indexed BAM

Methylation report  

  • Methylation rates (tsv)
  • Coverage and Methylation plots (png)
  • CpG methylation table including annotated variants and effects (vcf|tsv)

Variants – SNPs

  • Variant Call Format (vcf)
  • Tab Separated table (tsv)

Deliverables of INVIEW EPIGENOME BS-Seq –Comparative mode
(starting with 2 groups)

Genome alignment

  • Binary alignment map (BAM)
  • Indexed BAM

Methylation report  

  • Methylation rates (tsv)
  • Coverage and Methylation plots (png)
  • CpG methylation table (vcf|tsv)

Variants – SNPs

  • Variant Call Format (vcf)
  • Tab Separated table (tsv)

Differential Methylation Analysis

  • Correlation plots (png)
  • Annotation plots (png)
  • Hyper- and hypomethylated regions (tsv)

Delivery time

  • 25 days for up to 8 samples; >8 samples upon request

Optional Bio-IT for INVIEW EPIGENOME BS-Seq

  • Additional WGBS data packages of 5 Gb per samples without affecting delivery time

Additional Information

Whole-genome bisulfite sequencing with INVIEW EPIGENOME BS-Seq provides you with a complete and accurate picture of any DNA methylome. The method combines bisulfite treatment (Figure 2) with next-generation sequencing to attain both single-base resolution and genome-wide coverage. INVIEW EPIGENOME BS-Seq can be applied for all eukaryotes with 5-methylcytosines, as long as a genome reference is available.

Alterations in epigenetic markers have been demonstrated to be associated with diseases such as cancer, neurological disorders, and developmental abnormality. Therefore, epigenetic modifications are emerging as important diagnostic and prognostic biomarkers and as potential therapeutic targets.

Studies on epigenetic marker discovery and on gene expression regulation can greatly benefit from genome-wide bisulfite sequencing of the entire methylome. By providing the cytosine methylation status of all nucleotides in an organism of interest at single-base resolution, BS-Seq offers researchers the unique opportunity to explore epigenetic modifications in more depth and with more certainty.

Schematic view of bisulfite conversion
Figure 2: Bisulfite sequencing (BS-Seq) workflow
 
Specific applications of BS-Seq include:

  • Epigenetic mapping
  • Determining the function of epigenetic marks
  • Exploring mechanisms leading to aging and disease
  • Analysing gene-environment interactions
  • Investigating aberrant methylation patterns and their role in diseases such as cancer
  • Assigning prognostic value to specific methylation patterns that are indicative of cancer subtypes

 "GATC Biotech is a reliable partner, providing high-quality data for the epigenetic studies we perform within the FP7 EpiFemCare programme."     

Prof. Martin Widschwendter, Head of the Department of Women's Cancer, UCL

FAQs

1. Where do I obtain my results?
All raw data can be downloaded along with the analysed and assembled data via your secure myGATC online account. A demo data report for a typical BS-Seq project can be found under the section "Files".
 
2. What coverage should I use?
Sequencing results can vary depending on the composition of the analysed genome and the organism being sequenced. Typically, 30x average genome coverage is recommended.  
 
3. What starting material should I send and how much of it?
For sequencing on the Illumina platform, we require 2 µg of high-quality DNA that has not been amplified or bisulfite treated.
 
4. Do you guarantee a certain output?
We guarantee 20 million read pairs (+/- 10%) with 5 Gb raw data output (+/- 10%) per package.

5. What kind of quality controls do you perform?
The quality and quantity of each incoming sample will be determined by appropriate methods. Further quality controls are performed at various steps of the process.

6. Do you have any examples of successful joint ventures?
GATC Biotech is a partner in the EpiFemCare project. The project is partially funded by the EU’s Seventh Framework Programme (FP7) with the goal of using epigenetic-based methods to improve diagnosis and treatment measures for women with breast and ovarian cancer.
GATC Biotech manages sample processing, i.e., DNA isolation from serum/tissues, bisulfite treatment and library preparation. Cutting-edge technologies in epigenetics, next-generation sequencing and data management are applied for developing blood tests, with the aim of reliably detecting cancer and improving personalised treatment.
 
Learn more here or visit the EpiFemCare project website.

7. Where should I send my samples?
Please post your samples to:
GATC Biotech AG
European Genome and Diagnostics Centre
Jakob-Stadler-Platz 7
78467 Konstanz
Germany
 
Please do not use GATC Collection Points for shipping NextGen samples, because this will delay sample arrival at the appropriate destination!

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