6 June 2019 in News

How to generate high-quality, alignable sequence data?

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4 June 2019 in News

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

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29 May 2019 in Blog

Some highlights from SMRT Meeting, Leiden, May 2019

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…

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23 May 2019 in Science article

Widespread and Functional RNA Circularizationin Localized Prostate Cancer.

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…

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Some highlights from SMRT Meeting, Leiden, May 2019

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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 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