Human genome sequencing on PromethION to investigate tandem repeats in dementia
Expanded DNA tandem repeats can cause disease through their length, repeat unit sequence, and nucleotide modifications. However, these features are often difficult, if not impossible, to assess. We aim to tackle these issues with long-read human whole genome sequencing on PromethION. Starting with biomaterials obtained from dementia patients carrying C9orf72 repeat expansions (the most common cause of FTLD/ALS) or ABCA7 VNTR repeat expansions (a recently identified risk factor for Alzheimer’s disease), we consistently generate more than 90 Gigabase (> 25X human genome coverage) per sample on a single PromethION flow cell. First, we are evaluating whether the acquired long-sequencing reads can accurately measure repeat length. Secondly, we are looking into sequence differences and nucleotide modifications, and their relation to dementia. With this work, we aim to improve our understanding of repeat expansions in dementia and enable in-depth and high-throughput analysis of tandem repeats on a genome-wide scale.
Arne De Roeck is a PhD student in the Neurodegenerative Brain Diseases Group at the Center for Molecular Neurology (CMN), VIB – University of Antwerp, led by Prof. dr. Christine Van Broeckhoven. CMN has several decades of expertise in genetics of dementia and has been part of the Oxford Nanopore Technologies adventure from the beginning. In 2018, CMN sequenced several human whole genomes on PromethION, achieving some of the first and highest yield sequencing runs in the field.
PromethION: Unleash the power of nanopore sequencing
The recently available nanopore sequencing technology provides fantastic new possibilities in the field of DNA and RNA sequencing. It promises access to long sequence reads of DNA and RNA without significant investments in sequencing hardware and furthermore, direct detection of DNA and RNA modifications. More recently the PromethION was announced as the most powerful nanopore sequencer with an output in the range of 100GB per flow cell. Here, we provide insights in our experiences with the alpha version of the PromethION. Based on selected samples we will show the results obtained with the PromethION in the field of genetics, leukaemia and stem cell differentiation, and the challanges that we faced.
Helmut Blum heads the Genomics group in the Laboratory for Functional Genome Analyses at the Gene Center of the Ludwig-Maximilians-University of Munich. This group operates a technology platform for short and long-read sequencing and bioinformatic analysis. The platform provides a variety of library preparation methods and comprehensive sequencing for their own scientific projects and various collaborations in the field of life sciences. Currently the group extends its field of action towards high-output long-read sequencing with the PromethION sequencer.
Sequencing everything with PromethION
The York Genome Centre is based in a department with very wide-ranging research interests. As a result, we receive highly diverse samples to sequence, each with their own quirks. Our nanopore projects range from single microbial species to large plant genomes and metagenomes. We will discuss the requirements associated with sequencing and the analysis of such a broad range of samples, the library preparation methods we use, and discuss the challenges of analysing microbial communities from anaerobic digesters on the MinION and how these scale to the PromethION. Along the way, we will also describe a very efficient method for completely killing flow cells…
Sally is a Technical Specialist in Genomics for the University of York’s Bioscience Technology Facility. She completed her PhD in medical science at the University of Birmingham in 2008, and held post-doctoral positions studying stem cell biology and gene regulation at the University of Leeds, and then the University of York. She plays a key role in providing next-generation sequencing services and solutions to users within the University and further afield, and was an early adopter of nanopore sequencing technologies.