Interview: Human genome sequencing on PromethION: characterisation of structural variants and repetitive regions

Frontline Genomics Webinar

Date: Thursday 11th October

Time: 4pm BST/5pm CEST

Speakers: Arne De Roeck & Wouter De Coster

Arne De Roeck and Wouter De Coster are currently completing their PhDs at the Center for Molecular Neurology at the University of Antwerp, studying the genetic basis of neurodegenerative diseases, such as Alzheimer’s and frontotemporal dementia. Ahead of their webinar with Front Line Genomics on 11th October, we caught up with them to discuss their work and the impact whole-genome sequencing is having on our understanding of neurodegeneration.

What are you current research interests?

ADR: I’m studying repetitive structural variations in complex genetics of Alzheimer’s disease with the use of long-read sequencing.

WDC: I currently focus on structural variation in long-read sequencing data, especially repeat expansions. I want to see how capable PromethION and other recently developed sequencing tools are to detect these variants.

What first ignited your interest in Alzheimer’s and dementia research?

ADR: Dementia is one of the biggest challenges in modern medicine —50 million people currently suffer from dementia with no cure available, and these numbers will rapidly increase in the following decades. In addition, we know very little about the human brain and it is, in my opinion, the most interesting topic to study in biology. The big challenges that are part of studying Alzheimer’s disease and the potentially high impact on science and for society is what first ignited my interest to pursue a PhD in this field.

WDC: Due to our ageing population, neurodegenerative diseases are an increasing burden on people and society, and dementia research is challenging since the brain is relatively inaccessible. As neurodegeneration usually begins decades before the onset of symptoms, one of our best options to learn more about the pathomechanism is to identify initial contributing factors, such as involved genes.

Can you tell us more about how long-read sequencing technology is changing Alzheimer’s and dementia research? How has it benefited your work?

ADR: Neurological diseases are particularly affected by complex DNA mutations, for example tandem repeat expansions, and brain tissue contains the largest variety of transcript isoforms. Long-read sequencing can improve characterisation of these nucleotide sequences and will enable identification of novel disease-affecting variants in the future. We have previously used nanopore sequencing to phase splicing events with Alzheimer’s disease causing mutations, and observed that these alternative isoforms could rescue the transcript. More recently we identified a novel tandem repeat which affects Alzheimer’s disease, and we now have a PromethION-based assay to study this sequence in depth.

WDC: Due to technical limitations, structural variations have been underestimated and underrepresented in genetic research for decades, including large population sequencing projects. Nevertheless, we now know that these can have a profound impact on diseases, including neurodegeneration. Long-read sequencing can provide a comprehensive view, with high resolution on structural variation in the entire genome.

What impact could a deeper understanding of the genetic basis of neurodegenerative diseases have on patients?

ADR: Neurodegenerative diseases are extremely challenging to study due to our incomplete understanding of the human brain, the difficulty in accessing diseased tissue and unrepresentative model systems. The field is particularly struggling with distinguishing cause from consequence so identification of disease causing mutations is, in many cases, the only way to identify disease initiating mechanisms. Furthermore, it’s clear that prevention of Alzheimer’s disease, rather than treatment, will be the ultimate cure. To facilitate this, identification of individuals at risk through genetics will be needed.

WDC: Despite decades of research, the genetic cause in the majority of patients remains unexplained, hampering diagnosis, genetic counseling and development of therapeutics. A more comprehensive understanding of the genetic basis is crucial since it would accelerate genetic diagnosis, development of biomarkers and therapeutic interventions.

What have been the main challenges in your research and how have you approached them?

ADR: My biggest challenge was to identify and characterize a novel, expanded and challenging tandem repeat in Alzheimer ’s disease. To deal with this, I had to get out of my comfort zone and establish completely different methods in our department, including nanopore sequencing, Southern blotting, CRISPR, and bioinformatics.

WDC: New technologies and new software tools require a comprehensive evaluation to highlight strengths and weaknesses. By sequencing a well-characterised human genome to a high depth we had the opportunity to evaluate our current capacity to detect structural variation.

What’s next for your research?

ADR: Generating and analysing long-read datasets on large cohorts of dementia patients and healthy controls, possibly on brain DNA, to identify previously missed repetitive structural variations.

WDC: A comprehensive overview of structural variation in health and disease is currently lacking, requiring long-read sequencing of multiple individuals across populations. We also need novel reference genome structures to avoid substantial biases caused by using just a single composite reference genome for alignment.

Arne De Roeck and Wouter De Coster will be presenting ‘Human genome sequencing on PromethION: characterization of structural variants and repetitive regions’ on Thursday 11th October 4PM GMT/5PM CEST with Front Line Genomics.

Arne De Roeck is a PhD student in the Neurodegenerative Brain Diseases Group at the Center for Molecular Neurology (CMN), VIB – University of Antwerp. He studies the complex genetics of Alzheimer’s disease (AD) and identified a novel VNTR affecting AD. He is designing an algorithm to accurately determine length, sequence, and nucleotide modifications in this tandem repeat using whole genome sequencing on the PromethION.

Wouter De Coster is a bioinformatics PhD student in the lab of Christine Van Broeckhoven at the Antwerp VIB Center of Molecular Neurology. In his research, he investigates the genetic etiology of neurodegenerative diseases such as Alzheimer disease and frontotemporal dementia using long-read sequencing on the Oxford Nanopore MinION and PromethION platforms. He has developed NanoPack, a package of software tools for quality assessment and processing of long-read sequencing data. As an early adopter of new technologies, Wouter is exploring the possibilities of whole-genome sequencing on the PromethION, with the main objective of identifying structural variants underlying neurodegeneration.