INVIEW HUMAN EXOME ADVANCE
Extract profound knowledge. Unlock your exome.
INVIEW HUMAN EXOME ADVANCE combines the latest technologies with upstream and downstream automation to provide a complete, pre-designed package with robust stability and enhanced eﬃciency.
Extract profound knowledge for a wide variety of variant-analysis studies including single-nucleotide variants, structural variants, copy-number variants and delicate tumour profiling. INVIEW HUMAN EXOME ADVANCE offers great flexibility in terms of data output and delivery time, depending on your needs. The all-in-one human exome sequencing service includes quality control, library preparation and next-generation sequencing using Illumina Sequencing technology. Regarding bioinformatics, INVIEW HUMAN EXOME ADVANCE can be complemented with QIAGEN’s Ingenuity® Variant Analysis™.
- Improved coverage of hard-to-capture regions
- Optimised protocol for superior, uniform exome coverage
- Whole-exome sequencing under diagnostics standards (ISO 17025)
- Guaranteed sequencing amount in multiples of 30x
- Rapid variant detection and prioritisation of variants with QIAGEN‘s Ingenuity® Variant Analysis™
First-rate data quality, analysis and security offered by INVIEW HUMAN EXOME ADVANCE
- GATC fully automated production under diagnostic standards
- Established know-how and expertise
- Delivery of .vcf files ready for QIAGEN’s Ingenuity® Variant Analysis™
- Comprehensive Data Analysis Report including raw data for your own analysis tools
- ISO 17025 accredited
Highly flexible sequencing service for INVIEW HUMAN EXOME ADVANCE
- Individual batch size starting with one sample
- Guaranteed on-target coverage in steps of 30x depending on your needs
- Protocols for various sources
Figure 1: Latest GATC Biotech exome enrichment strategy based on Custom Automation produces maximised variant information output and coverage uniformity. Compared to the former V5 design, using Agilent SureSelect V6 for target capturing, considerably reduces the proportion of under- and over-represented enriched targets. Proportion of targets with normal capture efficiency thereby is enlarged significantly. R1 and R2 are replicates of the experimental design.
Figure 2: Comparison of whole-exome sequencing and whole-genome sequencing (WGS). Coverage profile of BRCA1 exons is displayed as an example for showing the effect of deeper sequencing on increased target capture, leading to exceptional coverage uniformity across the entire exome. With its notably deeper coverage, compared to WGS, the assay is preferably used for analysis of inherited and somatic diseases with locus and allelic heterogeneity.
- At least 100 ng double-stranded, purified, high-molecular-weight, RNA-free DNA (concentration ≥ 1 ng/µL; OD 260/280 ≥ 1.8; OD 260/230 ≥ 2.0), at least 200 ng per sample for DNA from FFPE samples
- DNA isolation available as additional service for tissue, cell, blood and FFPE samples
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 HUMAN EXOME ADVANCE
Sequencing mode and enrichment method used for INVIEW HUMAN EXOME ADVANCE
- 150 bp paired-end sequencing
- Latest Agilent SureSelect Human All Exon V6 Kit (post-capture indexing format)
Bioinformatics offered for exome analysis by GATC Biotech
- Fully optimised bioinformatics pipeline for exome variant filtering, annotation and interpretation.
- Highly accurate discovery and annotation of SNPs and InDels, with information including gene ID, amino acid change, functional class and additional statistics relating to genetic variants
- Semiautomatic mapping against a 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)
- Comprehensive Data Analysis Report (pdf)
Bioinformatics analysis using Ingenuity® Variant Analysis
Detection of causative variants from sequencing data
Ingenuity® Variant Analysis™ allows for rapid identification of the most relevant variants in human exome sequencing. A combination of powerful analytical tools and content from the Ingenuity® Knowledge Base™ enables:
- Rapid variant analysis within hours
- Variant prioritisation based on biologically relevant filter criteria
- Variant filtering based on profound data from several cancers, kindred, proband and cohort studies
If you complement INVIEW HUMAN EXOME with QIAGEN’s Ingenuity Variant Analysis, GATC Biotech will provide you with an account and log-in data to QIAGEN’s web-based software platform. Your vcf-files are directly uploaded into this account – ready for analysis. This combination provides an integrated solution for discretely analysing and interpreting your exome sequencing data in order to detect causal variants in sequenced human DNA. Ingenuity Variant Analysis is intended for molecular biology applications and is not intended for the diagnosis, prevention or treatment of disease.
Visit www.ingenuity.com/variants to learn more about the variant analysis services offered. For up-to-date licensing information and product-specific disclaimers, see the corresponding QIAGEN product site. Further information can be requested from firstname.lastname@example.org
Delivery times for INVIEW HUMAN EXOME ADVANCE
- 30 days for up to 32 samples (excluding additional services)
- Express delivery available: 12 days for up to 16 samples
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 provide greater insight into these target regions providing valuable information for the following:
- Disease studies
- Clinical research
- Genetic predisposition analyses
- Evolutionary biology research (population-based studies within and between populations
When combined with the latest Agilent post-capture enrichment methods, GATC Biotech-specific protocols for fully automated lab workflows allow you to perform advanced exome analysis that provide the following:
- More targeted genes from current annotation databases, including hard-to-capture exonic regions
- Unbiased, deeper sequencing information
- Exceptional coverage uniformity across the entire exome
- Balanced coverage of active genes
Our customers benefit from our expertise with next-generation sequencing and rely on our high quality standard and certifications. INVIEW HUMAN EXOME ADVANCE is the result of our customer-driven innovation process in close collaboration with partners from the DKFZ (Deutsches Krebsforschungszentrum) and the NCT (Nationales Centrum für Tumorerkrankungen) in Heidelberg, Germany.
“With INVIEW HUMAN EXOME we found the perfect tool for our clinical exome sequencing. High-quality exome sequencing data from GATC Biotech allows us to achieve an average diagnostic success rate of about 70%. The remarkable coverage uniformity retained by the latest chemistry as well as the flexibility in terms of delivery times and the data generated are particularly invaluable for our application in diagnostics. Prof. Dr. Wolfgang Schmidt, Lab head of Neuromuscular Research Dept., Medical University of Vienna, Vienna
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
1. What is the data handling process, including QIAGEN’s Ingenuity Variant Analysis?
All raw data are analysed and converted into a vcf file, which is uploaded directly to QIAGEN’s web-based software platform. Log-in data to your account will be provided by GATC Biotech.
Furthermore, the alignment file (BAM), the SNP and InDel tables (vcf and tsv) and the Data Analysis Report (pdf) from GATC Biotech will be delivered in the formats indicated via your myGATC account (see below).
Please note: Customers must accept the QIAGEN End-User License Agreement before access will be granted to the Variant Analysis product or to the results generated by this product.
2. How long is my data accessible at my QIAGEN account?
The license grants you initial access to the analysis software for 6 months. After that period you have the option of renewing the license, but you may only purchase a renewal offline – please contact us.
3. Where do I get my results, if I only choose the optional BioIT from GATC Biotech?
All raw data as well as the analysed data can be downloaded via your secured myGATC account.
4. 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. Confidently discovering genetic variants in inhomogeneous samples, such as DNA extracted from normal and tumour cells, requires higher overall coverage. The amount of data needed to reach a certain coverage on the DNA of interest depends on the ratio of normal-to-tumour DNA. Please note that due to varying efficiency of the enrichment baits, the targeted regions are not covered evenly (see below).
5. 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.
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 obtain PCR duplicate rates of approximately 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.
6. Which starting material should I send? In what quantities?
Guarantees of raw data output currently only apply to freshly isolated, unamplified, pure human DNA samples (minimum 100 ng - 500 ng). Contamination by DNA from other species (> 3%; especially from closely related species) 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, such as Formalin-Fixed Paraffin Embedded (FFPE) samples, is usually accepted. Please contact us if you need any details.
7. What do you mean by overlapping reads?
The fragmentation of genomic DNA according to the Agilent SureSelectXT protocol and subsequent 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 250 bp. Sequencing those library fragments with 150 bp paired-end reads will generate partially overlapping reads that cover the same bases and hence create an artificial doubling of coverage at those positions. To assure accurate analyses, those bases are excluded from further downstream analyses, such as single-nucleotide variant and insertion and deletion detection. Furthermore, GATC is continuously optimising its protocols to minimise the number of overlapping bases.
8. What is the quality of the data?
When sequencing human samples in 150 bp paired-end mode, GATC Biotech typically achieves over 80% of base calls with a quality value higher than Q30 ( >99.9% accurate).
9. Do you guarantee a specific on-target output?
For samples that have successfully passed the initial quality check at GATC Biotech, we will guarantee the on-target output you have ordered. Average on-target coverage is calculated as the sum of the mapped bases at each target position, divided by the number of bases in the target (bases on-target / size of target region).
10. Which genes are enriched?
The target region corresponds to the bait coordinates of the Agilent SureSelectHuman All Exon V6 Kit: approx. 60 Mbp of exonic bases (>93% of the targets are covered with >20x, 90% of the genes are completely covered – all exons – 10% of the genes are partially covered)
11. Are all genes covered at 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 (V6) with improved design algorithms to better capture difficult regions and provide superior coverage uniformity.
12. How much starting material should I provide?
For optimum results we require at least 100 ng double-stranded, purified, high-molecular-weight, RNA-free DNA (concentration ≥ 1 ng/µL; OD 260/280 ≥ 1.8; OD 260/230 ≥ 2.0). For DNA from FFPE samples we need at least 200 ng of DNA.
13. 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.
14. Where should I send my samples?
Please post your samples to:
GATC Biotech AG
European Genome and Diagnostics Centre
Please do not use GATC Collection Points for shipping NextGen samples, because this will delay sample arrival at the appropriate destination!