Copy number variation in Parkinson’s disease: An update from Sub-Saharan Africa

Genetic mutations, including copy number variations (CNVs), in well-established Parkinson’s disease (PD) genes, have been identified as causes of familial and sporadic PD.¹ These CNVs have primarily been detected in individuals of Asian and European ancestry^1,2 but have rarely been reported in individuals of African ancestry from Sub-Saharan Africa (SSA) (Table1).^3–7 This may in part be due to the scarcity of SSA studies screening for CNVs, with only 96 unrelated PD cases having been screened to date (Table 1).^3–10 To help address this critical knowledge gap, we employed the multiplex ligation-dependent probe amplification (MLPA) assay to investigate CNVs within known PD and parkinsonism genes in 131 PD cases of African ancestry from South Africa and Nigeria.

Table 1.

Studies screening for copy number variation in African ancestry Parkinson’s disease cases from Sub-Saharan Africa

Country	Study	CNV screening method	No. of unrelated African ancestry probands screened	Identified African ancestry CNV carriers
Nigeria	Okubadejo et al., 200810	Illumina Infinium HumanHap550 BeadChips	2	None
	Milanowski et al., 20218	P051 MLPA kit	15	None
South Africa	Keyser et al., 20104	P051 and P052 MLPA kits	12	A male proband (AAO = 45) with a heterozygous PRKN exon 2 duplication and a heterozygous PRKN exon 9 deletion. He had an affected sister with the same genotype.
	Haylett et al., 20125	P051 and P052 MLPA kits	5	A female proband (AAO = 56) with a heterozygous PRKN exon 4 deletion and a heterozygous PRKN point mutation (ss410758733:C>T). She had no reported family history.
	van der Merwe et al., 20169	P051 and P052 MLPA kits	21	None
	Mahne et al., 20166	P051 MLPA kit	11	A female proband (AAO = 50) with a heterozygous PRKN exon 4 deletion. She had no reported family history.
Tanzania	Dekker et al., 20207	P051 and P052 MLPA kits	1	A female proband (AAO = 24) with a homozygous PRKN exon 4 deletion. She had two affected sisters, one of whom was also screened using MLPA and had the same genotype.
Zambia	Yonova-Doing et al., 20123	P051 and P052 MLPA kits	29	A proband (AAO = 16) with a heterozygous PRKN exon 2 and a heterozygous PRKN exon 4 deletion. The sex and family history of the proband were not specified.
Nigeria & South Africa	The present study	P051 and P052 MLPA kits	131	None

CNV, Copy Number Variation; MLPA, Multiplex Ligation-dependent Probe Amplification; AAO, age at onset

Using MLPA kits (P051 and P052), that additionally detect the presence of the LRRK2 Gly2019Ser mutation, we screened 61 Nigerian and 70 South African PD cases for CNVs as described in the supplementary material. Neither the most common LRRK2 mutation nor known CNVs were detected. However, we acknowledge that CNVs in genomic regions not included in the MLPA kits may have been missed in this study. Initially, false-positive deletions were noted in two individuals (supplementary material) due to two single nucleotide variants (SNVs; rs566749983:C>T and rs226249:T>C) that are reported to be more common in African- than in European genomes.¹¹ These false-positive findings not only highlight the importance of confirmation of MLPA results using a different technique in genetically diverse and understudied populations, but also highlight the need for considering ancestry-specific markers in the design of genomic assays.

Most notably, we show that the genetic basis of PD in SSA is still severely understudied, given that with only 131 individuals, this is the largest SSA study to date screening African ancestry PD cases for CNVs. Combining our results with previous studies on African ancestry cases in SSA (Table 1), the frequency of CNV mutations in PRKN is 2.2% (5/227 unrelated cases) but remains 0% in other PD genes, including SNCA and PINK1. These findings (together with the fact that LRRK2 Gly2019Ser, one of the most common PD-associated mutations,¹² was not present in our study participants, and that it remains undetected in SSA individuals of African ancestry)^8,13,14 support the notion that PD genetics is understudied in SSA and reinforces that the genetic contributors to PD in SSA may differ from those identified in other ancestries. Therefore, although challenging,¹⁵ further research into the genetic causes, including CNVs, of PD in SSA is warranted. For this, we promote across-border collaborative research between clinicians and researchers (as illustrated in our study) to achieve greater sample sizes, and the use of next-generation sequencing or long-read sequencing of whole nuclear- and mitochondrial genomes.

Ultimately, the inclusion of diverse populations in future PD studies, as highlighted in the Aligning Science Across Parkinson’s/ Global Parkinson’s Genetics Program project (ASAP/GP2; https://parkinsonsroadmap.org/) and supporting consortia efforts (e.g. GEoPD and IPDGC), will be key to identifying novel genetic contributors to disease and gaining a better understanding of PD’s complex etiology on a global scale.

Data Availability Statement

Data that support the findings of this study are available in the supplementary material of this article. Additional data are available upon request.