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Mojca Strazisar
University of Antwerp
16Publications
8H-index
200Citations
Publications 19
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Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer’s disease-associated ABCA7 VNTR. The Guppy “flip-flop” base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessm...
1 CitationsSource
Summary: Modified nucleotides play a crucial role in gene expression regulation. Here we describe methplotlib, a tool developed for the visualization of modified nucleotides detected from Oxford Nanopore Technologies sequencing platforms, together with additional scripts for statistical analysis of allele specific modification within subjects and differential modification frequency across subjects. Availability and implementation: The methplotlib command-line tool is written in Python3, is compa...
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#1Wouter De Coster (University of Antwerp)H-Index: 4
#2Peter De Rijk (University of Antwerp)H-Index: 28
Last.C. Van Broeckhoven (University of Antwerp)H-Index: 113
view all 8 authors...
11 CitationsSource
#1Rita Cacace (University of Antwerp)H-Index: 6
#2Bavo Heeman (University of Antwerp)H-Index: 6
Last.C. Van BroeckhovenH-Index: 113
view all 29 authors...
Emerging evidence suggested a converging mechanism in neurodegenerative brain diseases (NBD) involving early neuronal network dysfunctions and alterations in the homeostasis of neuronal firing as culprits of neurodegeneration. In this study, we used paired-end short-read and direct long-read whole genome sequencing to investigate an unresolved autosomal dominant dementia family significantly linked to 7q36. We identified and validated a chromosomal inversion of ca. 4 Mb, segregating on the disea...
2 CitationsSource
#1Arne De Roeck (University of Antwerp)H-Index: 7
#2Wouter De Coster (University of Antwerp)H-Index: 4
Last.Kristel Sleegers (University of Antwerp)H-Index: 52
view all 11 authors...
Tandem repeats (TRs) can cause disease through their length, sequence motif interruptions, and nucleotide modifications. For many TRs, however, these features are very difficult - if not impossible - to assess, requiring low-throughput and labor-intensive assays. One example is a VNTR in ABCA7 for which we recently discovered that expanded alleles strongly increase risk of Alzheimer′s disease. Here, we investigated the potential of long-read whole genome sequencing to surmount these challenges, ...
9 CitationsSource
#1Wouter De CosterH-Index: 4
#2Arne De RoeckH-Index: 7
Last.C. Van BroeckhovenH-Index: 113
view all 8 authors...
Source
#1Wouter De CosterH-Index: 4
#2Arne De RoeckH-Index: 7
Last.C. Van BroeckhovenH-Index: 113
view all 8 authors...
We sequenced the Yoruban NA19240 genome on the Oxford Nanopore PromethION for benchmarking and evaluation of recently published aligners and structural variant calling tools. In this work, we determined the precision and recall, present high confidence and high sensitivity call sets of variants and discuss optimal parameters. The aligner Minimap2 and structural variant caller Sniffles are both the most accurate and the most computationally efficient tools in our study. We describe our scalable w...
10 CitationsSource
#1Wouter De CosterH-Index: 4
#2Tim De PooterH-Index: 12
Last.C. Van BroeckhovenH-Index: 113
view all 8 authors...
Source
#1Wouter De CosterH-Index: 4
#2Arne De RoeckH-Index: 7
Last.C. Van BroeckhovenH-Index: 113
view all 8 authors...
Source
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