All Posts By

GenomeScan

Competitive, fast, and adaptable RNA Sequencing services

By | News | No Comments

RNA sequencing is an affordable and dependable tool driving R&D and clinical projects. To answer scientific challenges, GenomeScan develops innovative methods to analyze RNA samples. Minute populations of sorted cells or FFPE samples are no longer hampering progression of your project. Get direct access to a wide range of RNA-seq services under ISO/IEC 17015 accreditation. Our experienced scientific team can determine with you the optimal solution to reach your objectives. Tell us more about your project to get started.

Recently, we co-authored a study involving RNASeq published in a high-impact journal. Read the full article in Cell.

You can review our RNASeq service portfolio on the website.

07.04.2019 RNAseq for all sample types 1 Competitive, fast, and adaptable RNA Sequencing services

Widespread RNA circularization events define clinically distinct tumor subtypes

By | Science article | No Comments

This article describes the results of a multidisciplinary prostate cancer study. Prof. dr. ir. Guido Jenster and his collaborators (NGS ProToCol consortium) showed that clinical roles of circular RNA’s are different from their linear counterparts, promoting cell proliferation in localized prostate cancer. GenomeScan contributed to the RNA sequencing and data processing.

Read full article: https://www.sciencedirect.com/science/article/pii/S0092867419300583

Prostate cancer article Widespread RNA circularization events define clinically distinct tumor subtypes

How to generate high-quality, alignable sequence data?

By | News | No Comments

Innovation Alert: Mid-read sequencing

Sequencing of PE250 reads on the NovaSeq 6000

 

PE250 reads fig.1 How to generate high quality, alignable sequence data?

Printing a book of more than 2 billion pages, every two days. Illumina’s NovaSeq 6000 has made it possible to
produce >6 Terabases of high-quality bases per sequencing run. This huge amount keeps the cost per base low and has allowed for the development of many new applications.

With such a complete solution, what is the drawback? Usually none; but to resolve certain research questions, 150 nucleotide (nt) sequencing is not sufficient. Some cases require generating fragments up to 250 nt to uniquely map most of the reads.

PE250 reads fig.2 How to generate high quality, alignable sequence data?

Now, GenomeScan offers PE250 sequencing under ISO/IEC 17025 accreditation. Longer reads can, for example, span the highly variable regions in T-cell or B-cell receptors (TCR, BCR). Or they form ‘larger puzzle pieces’, to resolve repetitive regions. This can be beneficial for resequencing of whole genomes or microbiome sequencing.

What is the quality of those longer runs?
As is shown in the figure above, the quality stays very high during the run and produces reads that are of superior quality (high % of Q30 reads). With PE250 sequencing on the NovaSeq, GenomeScan can offer cost-effective sequencing of up to 500 nt.PE250 Tab.1 1024x161 How to generate high quality, alignable sequence data?

PE250 reads fig.3 1024x296 How to generate high quality, alignable sequence data?

Do you have questions or want to know how NGS could benefit your project? Just leave your message below and André will contact you…

 

 

GenomeScan to offer two Bioinformatics PhD traineeships as part of the EU Horizon 2020 program

By | News | No Comments

logo GenomeScan to offer two Bioinformatics PhD traineeships as part of the EU Horizon 2020 program Two EU-funded Consortium Grants for PhD training at GenomeScan

GenomeScan has been granted two Marie Skłodowska-Curie Actions within the Innovative Training Network calls of the European Union-funded Horizon 2020 Program. These PhD traineeships are part of Horizon 2020 Grants acquired by two different Consortia where Academia and Industry collaborate closely together. Recruitment of PhD candidates with a focus on Bioinformatics will start near the end of 2019 (applications are welcome as of today).

The proEVLifeCycle Project (ID 860303) aims to study the life cycle of extracellular vesicles in prostate cancer – from biogenesis and homing, to functional relevance. Prostate cancer presents as a major health care problem for men, with EU-wide approximately 365,000 new cases annually (reference https://ec.europa.eu/jrc/en/publication/epidemiology-prostate-cancer-europe). Current means to identify rapid from slow progressing tumors are lacking specificity. There is an unmet need to means of non-invasive discrimination of these tumors and identification of novel targets for therapeutic intervention of high-risk tumors. The proEVLifeCycle Project will aid to the understanding of prostate cancer progression and consequently, to the implementation of novel biomarkers and therapeutic interventions to have a lasting impact on this indiscriminate and lethal disease.

The goal of the TrainCDKis Project (ID 860977) is to provide a multidisciplinary training programme to top-level young scientists to develop creative solutions for chronic kidney disease – from genetic modifiers to drug discovery. Chronic kidney disease is characterized by the progressive decline of renal function, associated with impaired quality of life and reduced life expectancy. It affects 10-15% of the worldwide population and is recognized as an increasing global health problem with a substantial burden on health-care budgets. The research projects within TrainCKDis will address key challenges focusing at genetic and epigenetic modifiers able of identifying patients that are predisposed to disease progression, biomarkers for disease monitoring and identification of novel therapeutic targets to impact the limited treatment options.

Fotos GenomeScan to offer two Bioinformatics PhD traineeships Post GenomeScan to offer two Bioinformatics PhD traineeships as part of the EU Horizon 2020 program

Some highlights from SMRT Meeting, Leiden, May 2019

By | Blog | No Comments

Some highlights from SMRT Leiden 2019

Innovation in long-read sequencing applications

SMRT Leiden – 7th -9th of May 2019

Arnoud Schmitz – PacBio® expert at GenomeScan

The yearly PacBio meeting brings together knowledgeable scientists who share the same enthusiasm for long reads. This two-days event is the perfect place to discuss innovative ideas, visions and meet with inspiring peoples. Here are my highlights.

1)   Improving personalized Medicine

Make your sequencing easier with high quality long reads.
For clinically relevant genes that are difficult to sequence, long reads are ideal. They are the method of choice when dealing with repeat structures, high GC content and/or highly similar pseudogenes. Examples included the highly diverse Immunoglobulin (Ig) genes and CYP2D6. The CYP2D6 enzyme metabolizes roughly 25% of all medications, typical substrates include antidepressants, antiarrhythmics, beta-blockers, and opioids. Patients could be classified into different groups based on the metabolization rate of CYP2D6 to improve drug dosing advises. It’s a nice example of how technology can be used to shape the future of personalized medicine.

Long reads make it possible to identify different haplotypes, find flaws in our current human reference, span unknow genetic territory and dig into other genome complexities.  Any information collected can help to diagnose diseases in patients for which common genetic analysis did not provide any answers. Prof. Euan Ashely from Stanford University Medical Center (part of Undiagnosed Diseases Network) showed some excellent cases in his keynote talk “Towards Precision Medicine”.

2)   Containing infectious disease outbreaks

How a Next Generation Sequencing (NGS) test can save you money?
Dr. Alexander Mellmann (Institute of Hygiene, University of Münster, Germany) showed how bacterial whole genome sequencing (WGS) helped infection prevention and control in hospitals. The spread of infection with multi drug resistant (MDR) bacteria could be tracked, leading to unexpected insights into contamination pathways.

3)   HiFi Reads – high quality innovation

A much-discussed topic: HiFi-reads!
Instead of going for super long reads with lower quality, why not using ±15 kb high quality CCS reads (Circular Consensus Sequencing) to accelerate mapping to a reference? The large CCS reads give much better base resolution without errors. Even though the reads are relative “shorter”, their high quality can help to span large repeat regions. This opens many possibilities, from various diagnostic tests to the assembly of organisms that have not been characterized yet.

4)   Conservation Genomics

Close to my heart and a recurrent topic during SMRT Leiden: Sequencing of organisms not referenced yet.
PacBio’s long reads are ideal for puzzling together “new genomes”. I always like research projects that take on endearing tasks. The International Barcode of Life consortium has set its mind to establishing a global biomonitoring system that will track ecosystems and reveal symbiomes. They aim to complete an “inventory of life” to map the global biodiversity (more on: www.ibol.org).Barcode of Life 1024x481 Some highlights from SMRT Meeting, Leiden, May 2019
Barcode of Life has established a method that uses a short genetic marker of the mitochondria (~650 bp) that sets species apart. They analyze amplicon pools from >9,000 DNA extracts in a single SEQUEL run, thereby greatly reducing sequencing costs in comparison to first (Sanger) generation and even short read platforms (read article).

On the same topic, Dr. Mara Lawniczak (Wellcome Sanger Institute, UK)  talked about the Earth BioGenome Project and Darwin Tree of Live consortium. In her talk she focused on their effort on sequencing Malaria carrying mosquito’s.

Arnoud Schmitz, GenomeScan (a.schmitz@genomescan.nl)

 

Interested, more details? Read the in depth blog on SMRT Leiden 2019.

Widespread and Functional RNA Circularizationin Localized Prostate Cancer.

By | Science article | No Comments

Widespread and Functional RNA Circularizationin Localized Prostate Cancer

Sujun Chen, Vincent Huang, Xin Xu, Julie Livingstone, Fraser Soares, Jouhyun Jeon, Yong Zeng, Junjie Tony Hua, Jessica Petricca, Haiyang Guo, Miranda Wang, Fouad Yousif, Yuzhe Zhang, Nilgun Donmez, Musaddeque Ahmed, Stas Volik, Anna Lapuk, Melvin L.K. Chua, Lawrence E. Heisler, Adrien Foucal, Natalie S. Fox, Michael Fraser, Vinayak Bhandari, Yu-Jia Shiah, Jiansheng Guan, Jixi Li, Michèle Orain, Valérie Picard, Hèlène Hovington, Alain Bergeron, Louis Lacombe, Yves Fradet, Bernard Têtu, Stanley Liu, Felix Feng, Xue Wu, Yang W. Shao, Malgorzata A. Komor, Cenk Sahinalp, Colin Collins, Youri Hoogstrate, Mark de Jong, Remond J.A. Fijneman, Teng Fei, Guido Jenster, Theodorus van der Kwast, Robert G. Bristow, Paul C. Boutros, and Housheng Hansen He.

Cell 2019 Feb 7; 176(4): 831-843

Erasmus MC and LUMC to co-participate in GenomeScan

By | News | 3 Comments

Erasmus MC and Leiden University Medical Center to co-participate in GenomeScan BV and extend their collaboration in the field of molecular diagnostics and R&D

 

Erasmus MC (Rotterdam, The Netherlands) announced today the acquisition of shares of the fast-growing genomics service provider GenomeScan BV based in Leiden (The Netherlands). Together with the Leiden University Medical Center (LUMC), another shareholder in GenomeScan, they are joining forces in the field of molecular diagnostics and research.

Ondertekening 190514 007 1024x683 Erasmus MC and LUMC to co participate in GenomeScanIn the fast-growing field of molecular diagnostics, it is critical to introduce and develop cutting-edge diagnostic technologies. One of these technologies is Next Generation Sequencing (NGS) that rapidly analyzes DNA and/or RNA of patients on a large scale.

GenomeScan is an ISO-accredited genomic service provider specialized in Next Generation Sequencing applications. The participation of Erasmus MC and LUMC in GenomeScan allows both UMCs to perform fast and sustainable molecular diagnostics under GenomeScan’s ISO-accreditation for NGS. Moreover, the collaboration will  increase the capacity to innovate, use new technologies and develop new applications for R&D and diagnostics in an international scientific environment.

GenomeScan’s expertise not only lies in molecular diagnostic, but also in developing customizable NGS solutions for pharmaceutical and biotech companies, academic centers and hospitals, mainly within Europe. In addition, GenomeScan collaborates with leading scientific institutes in a number of national and international research projects.

David Voetelink, vice-chairman of the Executive Board: “The Erasmus MC wants to drive innovation in healthcare and technology is becoming an increasingly important factor that requires consequent investments. Through our collaboration with the LUMC we optimize the use of capital equipment. As a result, not only we have access to the most advanced technologies, but also we have a chance to ensure that the healthcare costs remain affordable.”

Pancras Hogendoorn, vice-chairman of the Executive Board of LUMC: “The collaboration with GenomeScan and Erasmus MC fits perfectly with our strategy to develop cutting-edge applications to accelerate and improve diagnosis of patients in state-of-the art clinical research facilities. With the accession of Erasmus MC, we take a big step towards achieving this goal.”

Kees van den Berg, CEO GenomeScan: “Our partnership with both UMCs, allows GenomeScan to strengthen its engagement in developing new tools to diagnose genetic disorders quicker, affordably and more effectively. By sharing knowledge and regrouping facilities, this partnership helps the company to rapidly invest in costly emerging technologies, in a thoroughly sustainable manner, under ISO-accreditation for healthcare providers or academic research and under G(C)LP for the pharmaceutical market.”

 

About GenomeScan: As an ISO-accredited leading Dutch Next Generation Sequencing service provider, GenomeScan develops customizable NGS solutions for pharmaceutical and biotech companies, health care providers and academic institutions. By providing new tools to analyze genetic disorders quicker, affordably and effectively, GenomeScan fosters innovation through partnership with medical centers and research laboratories.

 

For more information please contact marketing@genomescan.nl

Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148.

By | Science article | No Comments

Functional characterization of a multi-cancer risk locus on chr5p15.33 reveals regulation of TERT by ZNF148.

Fang J, Jia J, Makowski M, Xu M, Wang Z, Zhang T, Hoskins JW, Choi J, Han Y, Zhang M, Thomas J, Kovacs M, Collins I, Dzyadyk M, Thompson A, O’Neill M, Das S, Lan Q, Koster R; PanScan Consortium; TRICL Consortium; GenoMEL Consortium, Stolzenberg-Solomon RS, Kraft P, Wolpin BM, Jansen PWTC, Olson S, McGlynn KA, Kanetsky PA, Chatterjee N, Barrett JH, Dunning AM, Taylor JC, Newton-Bishop JA, Bishop DT, Andresson T, Petersen GM, Amos CI, Iles MM, Nathanson KL, Landi MT, Vermeulen M, Brown KM, Amundadottir LT.

Nat Commun. 2017 May 2;8:15034.