Contact us!


(DE) +49 (0) 7531 81 60 68

(FR) +33 (0) 97 04 46 743 

(GB) +44 (0) 207 691 4921

(SE) +46 (0) 8 655 3609

 

customerservice@gatc-biotech.com

 

Opening hours:
8 am - 6 pm CET (Mon-Fri)

Also available

 

InViewTM 1-Week Exome Diagnostic – meets the requirements in clinical setting. Results even faster!

Demodata

 

GATC Variant Analysis: Demo Data Analysis Report

Useful downloads

 

White Paper Target Specific Enrichments of Human Exomes (PDF, 450 KB)

 

Flyer InView Human Exon (PDF, 2,8 MB)

 

FAQs InView Human Exon (PDF, 230 KB)

Sequencing technologies


GATC has all the leading sequencing technologies available...more

InView™ Human Exon

Fastest variant detection for clinical research and translational studies

 

Exome enrichment and massively parallel sequencing of the coding regions is a versatile and economic tool for researches who want to identify relevant disease-causing mutations. InView™ 2-weeks Exome is a highly standardised complete solution for clinical and medical researchers to help them answer important questions faster.

 

Highlights

  • fast access within 10 business days, starting from one sample
  • applicable for genomic DNA from various sources (tissue, cells, blood and FFPE sample)
  • special protocol for low-input samples (please refer to Service & Specifications) 

 

InView™ 2-weeks Exome is a result of our customer-driven innovation process in close collaboration with partners from DKFZ (Deutsches Krebsforschungszentrum) or NCT (Nationales Centrum für Tumorerkrankungen) in Heidelberg, Germany. 

 

"GATC Biotech proved itself to be a reliable sequencing partner...

                                                      Prof. Dr. Peter Lichter, Head of Molecular Genetics, DKFZ, Heidelberg

 

InView™ 2-weeks Exome is the solution for your cutting-edge clinical research. Convince yourself and benefit as many other researchers already.  

 

 

Please choose your required service package

InView™ Human Exon



The exome accounts for ~1% of the human genome and consists of functionally relevant coding regions (exons) which are most likely to cause differences in phenotypes. Exome enrichment is a powerful tool for discovering relevant variations by sequencing only a fraction of the human genome. 


Exome analyses allow a closer insight in these target regions providing valuable information for:  

  • Disease studies
  • Pharmacogenomics
  • Pharmacogenetics
  • Clinical research
  • Genetic predisposition analyses
  • Evolutionary biology research (population-based studies within and between populations

 

GATC Biotech offers with InViewTM Human Exon a complete all-in-one service to support variant discovery for Mendelian diseases or population-based studies. The latest technologies for high throughput exome sequencing services are combined with streamlined workflows and highest quality standard. We offer a plurality of pre-sequencing services and a comprehensive self-explaining data report. A dedicated team of scientific project managers and bioinformaticians will ensure you receive reliable and reproducible results within fast turnaround time.

GATC Biotech offers an all-in-one service including quality control, library preparation and NextGen sequencing. Two delivery time options are available: InView™ 2-weeks Exome and InView™ 6-weeks Exome, each provided with a 30x60x120x guaranteed average on target coverage. 

 

Bioinformatics and a variety of pre-sequencing services are additionally available. GATC Biotech offers DNA isolation from FFPE tissue and provides an optimised protocol for high-quality low amount libraries. This special protocol enables processing of low-input samples of variable quality with predictable success rates in standard sample preparation pipelines. 

 

On request, your exome sequencing project can be performed under EN ISO/IEC 17025 standard.  

 

Starting material                        

  • genomic DNA (>= 500ng)
  • low amount DNA (>= 100ng)
  • various sources like tissue, cells, blood and formalin-fixed paraffin embedded (FFPE) samples 

 

Sequencing platform and enrichment

  • Illumina HiSeq 2500 system using 100bp paired-end sequencing
  • Agilent SureSelectXT Human All Exon V5 Kit (post-capture protocol)

 

GATC Biotech is Certified Service Provider for Agilent SureSelect Target Enrichment (CSP) and for Illumina NGS sequencing (CSPro). 

 

Guaranteed sequencing coverage

  • For InView™ 2-weeks and 6-weeks Exome: average on target coverage of 30x, 60x or 120x 

 

Delivery time 

  • InView™ 2-weeks Exome: 10 business days for up to 16 samples; >16 samples on request
  • InView™ 6-weeks Exome: 30 business days for up to 32 samples; >32 samples on request

Complete all-in-one service including DNA isolation, library preparation, amplification of target region, sequencing and data analysis through to delivery in common files. 

 

Pre-Sequencing Services

  • DNA isolation performed by GATC Biotech
  • DNA isolation from FFPE tissue 
  • optimised protocol for low amount library

 

Bioinformatics 

GATC Biotech applies optimised lab protocols and sophisticated parameters for data filtering to enable reliable detection of presumable variants providing 

  • highly accurate discovery and annotation of SNPs and InDels, with information on e.g., gene ID, amino acid change, functional class and additional statistics relating to the variants:
  • semiautomatic mapping against genomic reference
  • targeted region filtering 
  • detection of SNPs and InDels
  • annotation of detected SNPs and InDels (using dbSNP)
  • allocation of effects on protein level (using Ensembl)

  

Results delivered in common formats via your secured myGATC account 

  • alignment file (bam)
  • SNP and InDel tables including annotated variants and effects (vcf, tsv, bed)
  • Data Report (pdf)


Demodata and demo data report available on this website

References and customer testimonials

 

Our customers benefit from our expertise with NGS sequencing and rely on our high quality standard and certifications. Here you will find some selected references reporting on their experiences working with GATC Biotech.


Cooperation with MolecularHealth Inc. for personalised medicine with TreatmentMAP™
“…it’s essential that we put the best protocols in place for our lab.”


“GATC Biotech’s proven expertise will be invaluable to our team, as we work to provide personalized, actionable information to cancer patients and their medical teams.“ 

Lloyd Everson, M.D., CEO MolecularHealth Inc. 

 

 

ICGC Initiative: Sequencing for the International Cancer Genome Consortium
“…we are continuing this successful collaboration (with GATC Biotech)“ 

Prof. Dr. Peter Lichter, Head of Molecular Genetics, DKFZ, Heidelberg 

 

NCT IMPROVE – Initiative of Molecular tumor PROfiling and Validation of the therapy recommendation

Study with more than 1,000 cancer patients funded with 15 Mio. EUR 

 

1. Where do I get my results and what do they look like?

All raw data as well as the analysed data can be downloaded via your secured myGATC account. Example analysed data of 30x coverage are available for download after login.

 

Global Analysis_report.pdf

 

InDel Table

demo.AllExonV5.HAPMAP_30x.indel.bed

demo.AllExonV5.HAPMAP_30x.indel.tsv

demo.AllExonV5.HAPMAP_30x.indel.vcf

 

SNP table

demo.AllExonV5.HAPMAP_30x.snp.bed

demo.AllExonV5.HAPMAP_30x.snp.tsv

demo.AllExonV5.HAPMAP_30x.snp.vcf

 

TargetRegion 

SureSelect_AllExon_V5_Genes

SureSelect_AllExon_V5_hg19_target_coordinates

 

2. What coverage should I use?

For SNP calling in heterozygote organisms we recommend at least 30x coverage. A higher coverage will increase the confidence of SNP calling. To confidently discover variants in inhomogeneous samples like e.g., DNA extracted from normal and tumor cells, a higher overall coverage should be chosen. The amount of data needed to reach a certain coverage on the DNA of interest depends on the ratio normal/tumor DNA. Please note, that due to varying efficiency of the enrichment baits, the targeted regions are not covered evenly (see below).

 

3. How do you handle PCR duplicates?

PCR duplicate rates are directly correlated to the quality and amount of starting material provided. Library preparation with less than the recommended amount of DNA requires additional PCR cycles to generate enough material to load the sequencer. Hence, the PCR duplicate rate is dependent on the sample and cannot be influenced by GATC Biotech. The duplicates are not excluded from the calculation of the average on-target coverage. Based on our experience with the sequencing of human samples we typically receive PCR duplicate rates of approx. 5% for high-quality DNA.
If further bioinformatics are ordered (e.g. SNP identification) only one copy of the duplicate read pair is kept in the alignment. The rest are excluded from further analysis to prevent any bias.

 

4. Which and how much starting material should I send?

Raw data output guarantees currently only apply for freshly isolated, unamplified and pure human DNA samples (minimum 3 µg). Contamination by DNA of other species (> 3%; especially from closely related ones) might interfere with the enrichment of the human DNA and also reduces the total amount of human DNA in the provided sample. Whole genome amplified (WGA) DNA or DNA from archived tissue like e.g., Formalin-Fixed Paraffin Embedded (FFPE) samples is usually accepted. Please contact us if you need any details.

 

5. What do you mean by overlapping reads?

The fragmentation of genomic DNA according to the Agilent SureSelectXT protocol and following downstream processing produces a Gaussian distribution of DNA fragments with different lengths. A small percentage of the resulting library fragments have an insert size below 200bp. Sequencing of those library fragments with 100bp paired end reads will generate partially overlapping reads which cover the same bases and hence create an artificial doubling of coverage at those positions. To assure accurate analyses those bases are excluded from the calculation of the average on target coverage and further downstream analyses. Furthermore GATC is continuously optimising its protocols to minimise the number of overlapping bases.

 

6. What is the quality of the data?

When sequencing human samples in 100bp paired-end mode GATC Biotech typically achieves over 80% of base calls with a quality value higher than Q30 ( >99.9% accurate).

 

7. Do you guarantee a certain on target output?

For samples which have successfully passed initial quality check at GATC Biotech, we will guarantee the on target output ordered by you. Average on target coverage is calculated as the sum of the mapped bases (without overlapping bases) at each target position, divided by the number of bases in the target (bases on-target / size of target region).

 

8. Which genes are enriched?

The target region corresponds to the bait coordinates of the Agilent SureSelectXT Human All Exon V5 Kit (approx. 50 Mb, comprising 21.522 genes and 357.999 exons). Target region (bed file) of Exon V5 Kit are available here.

 

9. Are all genes covered with 30x?

Due to varying efficiency of the enrichment baits (e.g., GC / AT content) targeted regions are covered differently and the range and uniformity of coverage varies over the target region. GATC Biotech applies the most recent Agilent Human All Exon kit design (V5) with improved design algorithms to better capture difficult regions and increase coverage uniformity.

 

10. How much starting should I provide?

For optimal results we require at least 3 µg double-stranded, purified, high molecular and RNA-free DNA (concentration approx. 200 ng/µl; OD 260/280 ≥ 1.8; OD 260/230 ≥ 1.9).

 

11. What kind of quality controls do you perform?

The quality and quantity of each incoming sample will be determined by appropriate methods (e.g. agarose gel analysis / Qubit® Fluorometer / NanoDrop / Agilent 2100 Bioanalyzer). Further quality controls are performed at various steps of the process.

 

12. Where should I send my samples?

Please post your samples to:
GATC Biotech AG
European Genome and Diagnostics Centre
Jakob-Stadler-Platz 7
D-78467 Konstanz, Germany

Please don't use GATC Collection Points for shipment of NextGen samples because this will cause delay in sample arrival at the appropriate destination!

Copyright © 2014 GATC Biotech AG. All rights reserved.
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