The right answers to frequently asked questions
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What kind of samples can be processed with Inview Human Exome Explore?
We accept tissue, cells and blood as starting material for INVIEW Exome Explore. 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.
How much starting material should I send?
Data output only applies for freshly isolated, unamplified and pure human DNA samples (minimum 100 ng). Please note that contamination by DNA of other species (> 3 %; especially from closely related organisms) reduces the total amount of human DNA in the provided sample and it might interfere with the enrichment of the exonic region.
Which genes are enriched?
The target region corresponds to the bait coordinates of the Agilent SureSelect Human All Exon V6 Kit: 60.7 Mbp of exonic bases covering >20,000 genes in the human genome.
How do you handle PCR duplicates?
PCR duplicate rates are directly correlated to the quality and amount of the provided starting material. Hence, the PCR duplicate rate is dependent on the sample and cannot be influenced by Eurofins Genomics.
Are all genes covered with 10 Mio read pairs?
Due to varying efficiencies of the enrichment baits (e.g., GC / AT content) targeted regions are covered differently and the range and coverage varies over the target region. Eurofins Genomics applies the latest Agilent Human All Exon kit design (V6) with improved design algorithms to better capture hard-to-capture regions providing superior coverage uniformity.
Based on our experience with the sequencing of human samples we typically receive 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 remaining duplicates are excluded from further analysis to prevent bias.
What do you mean by overlapping reads?
The fragmentation of genomic DNA according to the Agilent SureSelectXT2 protocol and downstream processes produces a Gaussian distribution of DNA fragment sizes. A small percentage of the resulting fragments have an insert size below 300 bp. Sequencing of these small library fragments with 150 bp 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, these bases are excluded from further downstream analyses including single nucleotide variant (SNV) and insertion and deletion (InDel) detection. Eurofins Genomics is continuously working on optimising protocols in order to minimise the number of overlapping reads.
What is the quality of the data?
For human samples sequenced with 150 bp paired-end mode, Eurofins Genomics typically achieves over 80 % of base calls with a quality value higher than Q30 ( >99.9 % accurate).
Where do I get my results and in which form are they delivered?
The alignment file (bam), the SNP and InDel tables (vcf and tsv) and the Data Analysis Report (pdf) will be delivered in the given formats via your Ecom account.
How does data processing with QIAGEN’s Ingenuity Variant Analysis work?
Should you choose optional access to QIAGEN’s Ingenuity Variant Analysis platform, all raw data will be analysed and converted into a vcf file, and then directly uploaded to QIAGEN’s web-based software platform. Log-in data to your personal account will be provided by Eurofins Genomics.
Please note! Customer must accept QIAGEN’s End User License Agreement before access is granted to Ingenuity Variant Analysis and any data generated from the service.
How long is my data accessible at my QIAGEN account?
The license grants access to the analysis software for six months. After this period, an optional renewal of the license can be purchased offline exclusively – please contact us.
How should I choose between Inview Exome Explore and Inview Exome Advance?
Both Inview Exome Explore and Inview Exome Advance are excellent one-stop solutions for whole exome sequencing. The products offer sequencing according to diagnostic standards (ISO17025) and comparable BioIT pipelines for data analysis. Both services also offer complementary data processing with QIAGEN’s Ingenuity Variant Analysis. The two products vary slightly in their workflows, applications and associated costs
Inview Exome Explore is the most cost-efficient solution for whole exome sequencing. The product is ideal for analysis of germline mutations.
Inview Exome Advance is a more flexible whole exome sequencing solution. Inview Exome Advance is offered with guaranteed average on target coverage in multiples of 30x. The product can be used for analysis of both germline and somatic mutations.
Where should I send my samples?
Eurofins Genomics Europe Sequencing GmbH