One place for answers

Frequently Asked Questions

Below you will find answers to the questions we get asked the most about our NGS services. If you have any question that we haven’t been able to answer, please do not hesitate to contact our team.

Answers to common questions

You can browse the topics below to find the answer you are looking for. GenomeScan can perform your project under ISO/IEC 17025, ISO 15189, OECD GLP or GCLP.

Company Services

1. Which services do you offer?

GenomeScan offers a broad portfolio of DNA, RNA and epigenetic sequencing solutions and bioinformatics analysis services. Download overview >>

2. Can you provide proof of competence?

We can proudly say that multiple bodies, including the Dutch Accreditation Council (RvA), have endorsed our competence in genome analysis, transcriptomics, and epigenetics. In consecutive years, customers have rated our service with an average score of 8.9 (out of 10) or higher. GenomeScan has an ISO15189 accreditation (M309) for its diagnostic activities and an ISO/IEC17025 accreditation (L518) for all activities within its accreditation scope. Furthermore, the company can provide OECD GLP and GCLP services if required. Customers are welcome to visit and/or audit the GenomeScan laboratory to verify our quality standards.

3. Are you a certified service provider (e.g. Illumina, PacBio, Agilent)?

As stated above, GenomeScan is an accredited service provider and we do not make use of certificates delivered by instrument manufacturers. We value manufacturers commitment to maintaining a high-level service, but accreditation documents delivered by government agencies and regulation bodies are internationally recognized and far more stringent and thorough standards. The conformity of our laboratory and sequencing services is regularly audited and submitted to test, inspection and certification. For detailed information, please contact info@genomescan.nl

4. What is the price of your services?

Every project is unique and necessitates our full attention. Price greatly depends on number of samples, desired turnaround time, scope of your project and the sequencing strategy adopted to match your requirements. Whenever possible, we prefer to discuss the details of your project first and then provide you with the accurate, competitive pricing.

5. Do you offer DNA/RNA extraction services?

Conditions of the service can be discussed with our Customer Support or Project Manager. We do offer DNA and RNA extraction as a standard option for a selected types of starting material (e.g. saliva, blood, bacterial samples). Please contact us to discuss your needs.

6. How should I acknowledge the contribution of GS in publications?

For standard services, we appreciate being mentioned in the acknowledgments section, such as e.g. “We would like to thank GenomeScan for performing the NGS experiments.” For projects with a higher degree of involvement, such as the development of protocols or custom bioinformatic analyses, we appreciate a co-authorship on the resulting publications. This can be discussed during the initial planning or at later stages of the project, whenever applicable.

7. Are the Terms and Conditions available online?

We aim to match your expectations by clearly describing how we interact with you. Please read our Terms and Conditions.

Project Submission

1. Do I need a quote?

Yes, each sequencing project is tailored to your specific needs. Our colleagues will discuss your project in detail and provide you with a personal quotation. For long-term agreements to efficiently process batches of samples on regular basis, we provide the option for initiation of a Standing Order or Service Level Agreement.

2. Do you have an example of a project report?

Yes, we have several project reports demonstrating our previous work in areas such as gene expression, WES, WGS, methylation or metagenomics. Examples can be requested through email .

3. Who owns the intellectual properties of my project?

You do. GenomeScan is NGS service provider and as such we do not claim intellectual property on data we generate for our customers.

Sample Delivery

1. Where should I send my samples?

The sample submission form is mandatory when shipping samples to our laboratory. The shipping address is:

GenomeScan
Plesmanlaan 1d, 4th floor
2333 BZ LEIDEN, The Netherlands

2. Can I bring my sample to GenomeScan?

Yes. From Monday to Friday, between 9:00 and 16:00 hours, you can personally bring your sample, along with the sample submission form, to our laboratory. A technician will acknowledge receipt of it. While transporting, your samples should be stored at the correct temperature.

3. How should I prepare my samples?

View our Sample Submission Guide  for instructions on preparing and sending samples. You can ship your samples directly to our laboratory in Leiden in the appropriate conditions. The shipping address is listed on the sample submission form.

4. What if I cannot match the quantity and/or quality requirements?

We encourage you to connect with our Customer Support or Project Manager to discuss the quality and quantity requirements for your NGS project. They can provide you with guidelines or protocols to prepare your material.

5. How do I pack and ship my samples

Preferably deliver your samples in 96-well plates. To ensure optimal preservation of the samples, we recommend shipment of (g)DNA using ice packs and RNA samples on dry-ice. View the Sample Submission Guide for more details. 

6. What type of DNA do you accept?

We offer NGS services on any type of non-hazardous DNA extract (including human, animal, plant, microorganism). Whether you work with high-quality or degraded material, your samples should always meet our standard submission requirements as described in the Sample Submission Guide. If this is not the case, you can discuss your options with our Customer Support team or your assigned Project Manager.

7. What type of RNA do you accept?

We recommend submitting total RNA for NGS services. Please refer to the Sample Submission Guide for more details about input material for RNA sequencing services. 

8. Do you accept self-prepared libraries?

Yes, we do. You should provide GenomeScan with a minimum concentration of [2nM], estimates of the library size and an overview of the indexes you used (if any). We will QC your library using RT-PCR. Detailed requirements can be discussed with Customer Support or your Project Manager.

Delivery Times

1. What is the turnaround time for your NGS services?

Timelines for the delivery of the project can vary from three days to several weeks depending on the project size. Service includes sample QC, library preparation, hybridization, sequencing, data QC and reporting. Each project is unique, and we always strive to deliver the expected results within the agreed timeline. Please refer to the Sample Submission Guide for the indicative turnaround time per service.

Sequencing Platforms

1. Which sequencing platform do you use?

The sequencing platforms currently used at GenomeScan include Illumina NovaSeq 6000 and NextSeq500, PacBio Sequel II, IonTorrent, GeneStudio S5 prime and Oxford Nanopore Technologies.

2. Which sequencing primers do you use?

While it is possible to design primers using a variety of tools, GenomeScan commonly uses standard Illumina primer sets.

3. Which factors can impact the quality of my data?

Quality of your sequencing data directly reflects the quality of your DNA/RNA samples. However, a number of factors are critical to the quality of your data:

  • Proper storage conditions will reduce nucleic acids degradation
  • Shipping condition will affect the integrity and quality of your sample
  • Sequencing depth will improve the sensitivity
  • Read length will determine the specificity
  • Number of replicates will increase the confidence

4. What is the expected quality of the sequencing data?

When sequencing human samples in 150 bp paired-end mode, GenomeScan regularly achieves over 80% of base calls (Illumina threshold) with a quality value significantly higher than Q30 (>99.9% accurate).

5. How do you determine the sequencing depth/coverage?

Sample type Project type Recommended depth/coverage
DNA WGS x30
WES x150
Panel X400
RNA Transcript 40 M reads
Expression 20 M reads
Small RNA 15 M reads
Ultra-low input 20 M reads
Single Cell 35K reads / cell

To define the optimal coverage for your sample, we suggest you build on our existing experience and discuss this with our bioinformatics team.

6. Why are you using Unique Molecular Identifiers (UMIs)?

UMIs are mostly used to recognize duplicate reads (PCR duplicates). Other advantages of implementing UMIs in DNA-based studies include error correction and reduction of the false-positive rate, from single gene panels to Whole Exome Sequencing (WES) projects. True PCR duplicates can be used to correct PCR and sequencing errors, so pathologists and oncologists can reliably report on low frequency variants. Data-analysis pipelines that include corrections using UMIs can more reliably detect Copy Number Variations (CNVs). If the UMIs are used to remove duplicates, this results in a cleaner data set. If UMIs and duplicates are used to correct the data, they contribute to a higher level of sensitivity and specificity of all NGS-based methods.

7. How do you prevent excessive numbers of PCR duplicates?

The rate of PCR duplicates correlates with the quantity and quality of the starting material. However, with our proprietary library preparation process we can limit the number of PCR cycles while increasing library complexity. The use of UMIs also helps to detect and correct for PCR duplicates in your data.

8. What happens when sequencing of my samples fails?

To minimize sequencing failure, we run a QC after every major step of your project. Unfortunately, sequencing can sometimes fail due to various reasons (e.g. instrument malfunction, technical error, sample issue). If our assessment indicates that the failure is caused by our laboratory, we will repeat the analysis at our cost.

Data Delivery

1. How does GenomeScan deliver the data?

All raw data (FASTQ files) as well as the analyzed and assembled data i.e. VCF files, can be downloaded 24/7 via your secure web-portal accountMy Project. Other delivery options can be discussed with your assigned Project Manager.

2. How can I monitor the progress of my project?

We provide you with an easy monitoring of your NGS project progress and secure access to the result data through our secure web-portal My Project”. This online portal is available 24/7 and continuously supported by our team.

3. How many people can have an access to the GenomeScan web-portal My Project?

When starting your project, you receive a personal login and password. Upon your request, we can authorize other member(s) of your team or your lab to view your project(s). Please, contact your Project Manager or our Bioinformatic team to grant access to the new users.

4. Whom can I contact during the course of my project?

Your sequencing project is assigned to a Project Manager (Principal Investigator) as single point of contact. The Project Manager closely monitors the progress of your project and will contact you if needed. If you have questions, please do not hesitate to get in touch with your assigned Project Manager anytime.

Bioinformatics

1. What kind of Bioinformatic services do you offer?

GenomeScan provides services and expertise to assist scientists in and experimental planning and data analysis. Since NGS technologies change quite rapidly, we recommend that our customers discuss the project prior to start with our bioinformaticians.

2. Do I need specific software to view my data?

You will receive/download a zip file containing your sequencing data. You can unzip the file and then view and analyze the data using a genome browser (we recommend using Interactive Genome Viewer – IGV).

3. Which pipeline do you use for the analysis?

We use the state-of-the-art and industry-compliant software tools (commercial, FOSS, and in-house developed tools) to deploy our validated as well as custom workflows. Each tool has been evaluated and thoroughly validated. Tools and their functions are documented in a comprehensive data analysis report.

4. Should I provide a reference genome for data analysis?

For human genomes, the reference is defined in consultation with the customer, as additional annotations of a reference genome allows deeper analysis. For other species, you may provide (a link to) the appropriate reference.

5. How long do you store the data?

To maintain a WGBO-compliant data policy, your data are archived for a period of 20 years free of charge. After expiration of this period your data are permanently deleted. If you require a longer storage, please contact your Project Manager. During the 20-year retention period, the data will be kept safely in compliance with GDPR and NEN 7510 regulations and Good Laboratory Practice.

6. Whom do I contact if I have additional questions or need software support?

Your assigned Project Manager is your point of contact at GenomeScan and can be contacted via email, phone, or chat. He or she drives your project forward will be happy to address all your questions.

Quality and Privacy

1. What kind of quality control do you perform?

We use QC steps with strict measures to monitor the quality of starting material (e.g. Fragment Analyzer for DNA/RNA integrity analysis and Qubit fluorescent quantification for DNA/RNA concentration), intermediate products and final libraries.

2. Do I have an access to the QC report of my samples?

Yes, the QC report of each sample is made available via our web-portal. Go to “My Project and log in to view the results.

3. What if my samples do not pass QC?

If, for any reason, your sample does not pass our QC, we will contact you and discuss the options. You will determine whether we stop the project workflow and wait for you to submit a replacement sample or we move forward with the remaining samples. 

4. How long do you store the samples (after the project is finished)?

In the sample submission form, you are asked to indicate whether you wish that your samples are returned. If not, we store your samples for at least six months after completion of your project. You can, at any time after completion of your project, request a return shipping of your samples. Please feel free to contact us if you would like to make specific arrangements for your samples.

5. How do you ensure the security of the data?

Data is physically located within our facility or externally stored at a certified archive facility. All systems are backed up daily. All data is kept safely in compliance with NEN 7510 regulations.

6. How do you guarantee the privacy of my data?

GenomeScan is committed to protecting your privacy. Any information you provide to us is subjected to the European directives on personal data protection and privacy (GDPR). If you have questions or doubts related to privacy, please contact our Data Protection Officer at dpo@genomescan.nl.

7. What does ISO/IEC 17025 (or ISO 15189) mean?

For many preclinical and clinical analyses, the minimal laboratory quality level is legally determined. It is essential that testing is conducted by trained personnel without any delays and that results are reliable. The steps required to produce these results should be fully traceable. The ISO/IEC 17025 and ISO15189 criteria guarantee a level of quality assurance that is equal (and sometimes superior) to GLP. ISO/IEC 17025 is also the preferred quality level for GMP (Good Manufacturing Practice). 

8. Can you run a service under G(C)LP conditions?

GenomeScan is an accredited ISO/IEC 17025 (L518) and ISO 15189 (M308) laboratory and it is also possible to perform OECD GLP or GCLP compliant studies to meet your unique needs.

We are here to help bring your project to the next level.

06.2019 Portrait of Andre V1 Frequently Asked Questions

Andre Wijfjes

Manager Customer Support