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Insertion sequence element single nucleotide polymorphism typing provides insights into the population structure and evolution of Mycobacterium ulcerans across Africa Instituut voor Tropische Geneeskunde Universiteit Antwerpen

Koen Vandelannoote, Kurt Jordaens, Pieter Bomans, Herwig Leirs, Lies Durnez, Dissou Affolabi, Ghislain Sopoh, Julia Aguiar, Delphin Mavinga Phanzu, Kapay Kibadi, et al.

Buruli ulcer is an indolent, slowly progressing necrotizing disease of the skin caused by infection with Mycobacterium ulcerans. In the present study, we applied a redesigned technique to a vast panel of M. ulcerans disease isolates and clinical samples originating from multiple African disease foci in order to (i) gain fundamental insights into the population structure and evolutionary history of the pathogen and (ii) disentangle the ...

Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants Instituut voor Tropische Geneeskunde Universiteit Antwerpen

Joachim Mertens, Jasmine Coppens, Katherine Loens, Marie Le Mercier, Basil Britto Xavier, Christine Lammens, Sarah Vandamme, Hilde Jansens, Herman Goossens, Veerle Matheeussen, et al.

OBJECTIVES: To evaluate a testing algorithm for the rapid identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that includes the use of PCR-based targeted single nucleotide polymorphism (SNP) detection assays preceded by a multiplex PCR sensitive to S-Gene Target Failure (SGTF).

METHODS: PCR SNP assays targeting SARS-CoV-2 S-gene mutations ΔH69-V70, L452R, E484K, N501Y, H655Y and P681R using melting ...

Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna KU Leuven

Luisa Orsini, Mieke Jansen, Erika Souche, Luc De Meester
BACKGROUND: Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, climate change, and antagonistic interactions with predators and parasites, which have all been demonstrated to induce ...

Gene-Based Single Nucleotide Polymorphism Markers for Genetic and Association KU Leuven

Carlos Galeano Mendoza, Jos Vanderleyden
BACKGROUND: In common bean, expressed sequence tags (ESTs) are an underestimated source of gene-based markers such as insertion-deletions (Indels) or single-nucleotide polymorphisms (SNPs). However, due to the nature of these conserved sequences, detection of markers is difficult and portrays low levels of polymorphism. Therefore, development of intron-spanning EST-SNP markers can be a valuable resource for genetic experiments such as genetic ...

Genomic library preparation and hybridization capture of formalin‐fixed tissues and allozyme supernatant for population genomics and considerations for combining capture‐ and RADseq‐based single nucleotide polymorphism data sets Universiteit Gent

Kyle A. O’Connell, Kevin Mulder, Addison Wynn, Kevin Queiroz, Rayna C. Bell
Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the ...

Emerging technologies for hybridization based single nucleotide polymorphism detection KU Leuven

Dragana Spasic, Kris Janssen, Jeroen Lammertyn
Detection of single nucleotide polymorphisms (SNPs) is a crucial challenge in the development of a novel generation of diagnostic tools. Accurate detection of SNPs can prove elusive, as the impact of a single variable nucleotide on the properties of a target sequence is limited, even if this sequence consists of only a few nucleotides. New, accurate and facile strategies for the detection of point mutations are therefore absolutely necessary for ...

The autoimmune-associated single nucleotide polymorphism within PTPN22 correlates with clinical outcome after lung transplantation Universiteit Antwerpen

Kevin Budding, Jessica van Setten, Eduard A. van de Graaf, Oliver A. van Rossum, Tineke Kardol-Hoefnagel, Johanna Kwakkel-van Erp, Erik-Jan D. Oudijk, C. Erik Hack, Henderikus G. Otten
Obstructive chronic lung allograft dysfunction (BOS) is the major limiting factor for lung transplantation (LTx) outcome. PTPN22 is described as the hallmark autoimmunity gene, and one specific single nucleotide polymorphism (SNP), rs2476601, is associated with multiple autoimmune diseases, impaired T cell regulation, and autoantibody formation. Taking into consideration the contribution of autoimmunity to LTx outcome, we hypothesized that ...

The CYP3A4*22 C>T single nucleotide polymorphism is associated with reduced midazolam and tacrolimus clearance in stable renal allograft recipients KU Leuven

Dirk Kuypers
Tacrolimus, a dual substrate of CYP3A4 and CYP3A5 has a narrow therapeutic index and is characterized by high between-subject variability in oral bioavailability. This study investigated the effects of the recently described CYP3A4*22 intron 6 C>T single nucleotide polymorphism on in vivo CYP3A4 activity as measured by midazolam (MDZ) clearance and tacrolimus pharmacokinetics in two cohorts of renal allograft recipients, taking into account ...

A rapid on-chip single nucleotide polymorphism detection directly from human blood KU Leuven

Lei Zhang, Benjamin Jones, Tim Stakenborg, Liesbet Lagae
© 2015 IEEE. This paper reports on a silicon/glass based microsystem for the fast detection of single nucleotide polymorphisms (SNPs) directly from on-chip filtered human blood. A crossflow micro-pillar filter is used for purifying lysed blood. It provides an easy solution for on-chip blood sample preparation. After purification, polymerase chain reaction (PCR) was no longer inhibited. The purified DNA solution is then tested for the detection ...