Evidence map›Paper›PMID 32019516›Full record

ArticleBMC medical genetics2020

Targeted next-generation sequencing identifies novel variants in candidate genes for Parkinson's disease in Black South African and Nigerian patients.

Oluwafemi G Oluwole, Helena Kuivaniemi, Shameemah Abrahams, William L Haylett, Alvera A Vorster, Carel J van Heerden, Colin P Kenyon, David L Tabb, Michael B Fawale, Taofiki A Sunmonu and 9 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC medical genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing papers in PubMed
1.1field-weighted citation impact, top 19% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

10 citing papers in PubMed, 21 citations in OpenAlex.

  1. Article
  2. The identification of novel missense variant inOpen medicine (Warsaw, Poland) · 2025
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  6. The influence of 17q21.31 andFrontiers in aging neuroscience · 2022
    Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

19 authors at 6 institutions in 3 countries.

Oluwafemi G OluwoleDivision of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
Helena KuivaniemiDivision of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
Shameemah AbrahamsDivision of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
William L HaylettDivision of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
Alvera A VorsterDNA Sequencing Unit, Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa.
Carel J van HeerdenDNA Sequencing Unit, Central Analytical Facility, Stellenbosch University, Stellenbosch, South Africa.
Colin P KenyonDivision of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
David L TabbDivision of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa.
Michael B FawaleNeurology Unit, Department of Medicine, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria.
Taofiki A SunmonuNeurology Unit, Department of Medicine, Federal Medical Centre, Owo, Nigeria.
Abiodun AjoseDepartment of Chemical Pathology, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria.
Matthew O OlaogunDepartment of Medical Rehabilitation, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria.
Anastasia C RossouwDivision of Neurology, Department of Medicine, Faculty of Health Sciences, Walter Sisulu University, East London, South Africa.
Ludo S van HillegondsbergDivision of Neurology, Department of Medicine, Faculty of Health Sciences, Walter Sisulu University, East London, South Africa.
Jonathan CarrDivision of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
Owen A RossDepartment of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA.
Morenikeji A KomolafeNeurology Unit, Department of Medicine, College of Health Sciences, Obafemi Awolowo University, Ile-Ife, Nigeria.
Gerard TrompDivision of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa. gctromp@sun.ac.za.
Soraya BardienDivision of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University, Cape Town, South Africa. sbardien@sun.ac.za.ORCID 0000-0002-3508-3438
Stellenbosch University · ZAObafemi Awolowo University · NGSouth African Medical Research Council · ZAFederal Medical Centre · NGJacksonville College · USWalter Sisulu University · ZA

Funding

Neuropathology CoreP50NS072187 · NINDS · MAYO CLINIC JACKSONVILLE · PI DICKSON, DENNIS WILLIAM · 2010 to 2017
$8.7M
Capacity building in sub-Saharan Africa to conduct cutting-edge genetics research in Parkinson's disease.R21NS098862 · NINDS · STELLENBOSCH UNIVERSITY · PI BARDIEN, SORAYA · 2016 to 2017
$243k
NINDS NIH HHS P50 NS072187NINDS NIH HHS R21 NS098862
6 · The paper itself

Abstract

backgroundThe prevalence of Parkinson's disease (PD) is increasing in sub-Saharan Africa, but little is known about the genetics of PD in these populations. Due to their unique ancestry and diversity, sub-Saharan African populations have the potential to reveal novel insights into the pathobiology of PD. In this study, we aimed to characterise the genetic variation in known and novel PD genes in a group of Black South African and Nigerian patients.

methodsWe recruited 33 Black South African and 14 Nigerian PD patients, and screened them for sequence variants in 751 genes using an Ion AmpliSeq™ Neurological Research panel. We used bcftools to filter variants and annovar software for the annotation. Rare variants were prioritised using MetaLR and MetaSVM prediction scores. The effect of a variant on ATP13A2's protein structure was investigated by molecular modelling.

resultsWe identified 14,655 rare variants with a minor allele frequency ≤ 0.01, which included 2448 missense variants. Notably, no common pathogenic mutations were identified in these patients. Also, none of the known PD-associated mutations were found highlighting the need for more studies in African populations. Altogether, 54 rare variants in 42 genes were considered deleterious and were prioritized, based on MetaLR and MetaSVM scores, for follow-up studies. Protein modelling showed that the S1004R variant in ATP13A2 possibly alters the conformation of the protein.

conclusionsWe identified several rare variants predicted to be deleterious in sub-Saharan Africa PD patients; however, further studies are required to determine the biological effects of these variants and their possible role in PD. Studies such as these are important to elucidate the genetic aetiology of this disorder in patients of African ancestry.

Indexed as

Genetic Predisposition to DiseaseHigh-Throughput Nucleotide SequencingAdultAgedAged, 80 and overBlack PeopleFemaleGene FrequencyGenetic Association StudiesHumansMaleMiddle AgedMolecular Sequence AnnotationMutation, MissenseNigeriaParkinson DiseaseATP13A2 protein, humanProton-Translocating ATPasesNext-generation sequencingNigeriaParkinson’s diseaseScoring of sequence variantsSequence variantsSouth AfricaSub-Saharan Africa

Identifiers

PMID32019516
PMCPMC7001245
OpenAlexW3008901140

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.