Arne De Roeck
Human genome sequencing on PromethION to investigate tandem repeats in dementia
About Arne De Roeck
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.
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