Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia

Liu, Xuanyao; Yunus, Yushimah; Lu, Dongsheng; Aghakhanian, Farhang; Saw, Woei Yuh; Deng, Lian; Ali, Mohammad; Wang, Xu; Nor, Fadzilah Mohd; Rahman, Thuhairah Hasrah Abdul; Shaari, Syahrul Azlin; Salleh, Mohd Zaki; Phipps, Maude E.; Ong, Rick Twee Hee; Xu, Shuhua; Teo, Yik Ying; Hoh, Boon Peng

doi:10.1007/s00439-014-1525-2

Cited by 22 publications

(26 citation statements)

References 76 publications

(77 reference statements)

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“…Traditionally leading a hunter-gatherer lifestyle in a tropical jungle environment, this indigenous people are also routinely exposed to malaria (7,16).…”

Section: Discussionmentioning

confidence: 99%

Perceptions and prevention practices on malaria among the indigenous Orang Asli community in Kelantan, Peninsular Malaysia

Munajat

Rahim

Wahid

et al. 2020

Preprint

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Background Malaysia is on track towards malaria elimination. However, several cases of malaria still occur in the country. Contributing factors and communal aspects have noteworthy effects on any malaria elimination activities. Thus, assessing the community’s knowledge, attitudes and practices (KAP) towards malaria is essential. This study was performed to evaluate KAP regarding malaria among the indigenous people (i.e. Orang Asli) in Peninsular Malaysia. Methods A household-based cross-sectional study was conducted in five remote villages (clusters) of Orang Asli located in the State of Kelantan, a central region of the country. Communities aged 6 years and above were interviewed. Demographic, socio-economic and KAP data on malaria were collected using a structured questionnaire and analysed using descriptive statistics. Results Overall, 536 individuals from 208 households were interviewed. Household indoor residual spraying (IRS) coverage and bednet ownership were 100% and 89.2%, respectively. A majority of respondents used mosquito bed nets every night (95.1%), but only 50.2% aware of bednets were use to prevent malaria. Nevertheless, almost all of the respondents (97.9%) were aware that malaria is transmitted by mosquitoes. Regarding practice for managing malaria, the most common practice adopted by the respondents was seeking treatment at the health facilities (70.9%), followed by self-purchase of medication from a local shop (12.7%), seeking treatment from a traditional healer (10.5%) and self-healing (5.9%). Concerning potential zoonotic malaria, about half of the respondents (47.2%) reported seeing monkeys from their house and 20.1% reported entering nearby forests within the last six months. Conclusion We conclude that most populations living in the villages have an acceptable level of knowledge and awareness about malaria. However, positive attitudes and practices with respect to managing malaria require marked improvement.

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“…Traditionally leading a hunter-gatherer lifestyle in a tropical jungle environment, this indigenous people are also routinely exposed to malaria (7,16).…”

Section: Discussionmentioning

confidence: 99%

Perceptions and prevention practices on malaria among the indigenous Orang Asli community in Kelantan, Peninsular Malaysia

Munajat

Rahim

Wahid

et al. 2020

Preprint

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“…In particular, at stronger bottlenecks corresponding to inbreeding coefficients of 0.2 and 0.3, haploPS reported false-positive rates of 5.8% and 13.3%, respectively, compared with those by iHS (17.2% and 55.3%, respectively) and XP-EHH (4.4% and 8.7%, respectively). Notably, the investigation into the sharing and differentiation of positive selection signals was only made possible with the advent of haploPS, 3,14,32,33 given the higher statistical power with accompanying lower type I errors. KCNN3, PMVK, PBXIP1, PYGO2, SHC1, CKS1B, MIR4258, FLAD1, LENEP, ZBTB7B, DCST2, DCST1, ADAM15, EFNA4, EFNA3, EFNA1, SLC50A1, DPM3, KRTCAP2, TRIM46, MUC1, MIR92B, THBS3, MTX1, GBAP1, GBA, FAM189B, SCAMP3, CLK2 Our study also presented multiple lines of evidence to suggest that South Asian populations were considerably different from the rest of the Asian populations, which concurred with previous findings that South Asia is considerably more diverse than other Asian regions.…”

Section: Discussionmentioning

confidence: 99%

Characterising private and shared signatures of positive selection in 37 Asian populations

Liu

Saw

et al. 2017

Eur J Hum Genet

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The Asian Diversity Project (ADP) assembled 37 cosmopolitan and ethnic minority populations in Asia that have been densely genotyped across over half a million markers to study patterns of genetic diversity and positive natural selection. We performed population structure analyses of the ADP populations and divided these populations into four major groups based on their genographic information. By applying a highly sensitive algorithm haploPS to locate genomic signatures of positive selection, 140 distinct genomic regions exhibiting evidence of positive selection in at least one population were identified. We examined the extent of signal sharing for regions that were selected in multiple populations and observed that populations clustered in a similar fashion to that of how the ancestry clades were phylogenetically defined. In particular, populations predominantly located in South Asia underwent considerably different adaptation as compared with populations from the other geographical regions. Signatures of positive selection present in multiple geographical regions were predicted to be older and have emerged prior to the separation of the populations in the different regions. In contrast, selection signals present in a single population group tended to be of lower frequencies and thus can be attributed to recent evolutionary events.

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“…It is associated with blood pressure regulation, atherosclerosis protection and regulation of adiponectin level [52,53]. Interestingly, this gene was also reported to be associated with malaria susceptibility [54], and consistently exerted as a signature of positive selection in the Negrito populations from Peninsular Malaysia [17,18].…”

Section: Estimating De Novo Mutation Ratesmentioning

confidence: 98%

“…However, these native populations are largely underrepresented in the whole-genome sequencing projects. The genomic architecture of these populations were characterized by a handful of SNP-array-based genome-wide studies [17][18][19][20][21][22]. Recently, using the whole genome sequencing data of 12 unrelated individuals, we have also revealed the population structure and divergence between native populations from Peninsular Malaysia and North Borneo [23].…”

Section: Introductionmentioning

confidence: 99%

Analysis of Five Deep-sequenced Trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo Populations

Deng

Lou

Zhang

et al. 2019

Preprint

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Background Recent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated. Results We analyzed the whole-genome deep sequencing data (~30×) of five native trios from Malaysia, and discovered approximately 6.9 million single nucleotide variants (SNVs), 1.2 million small insertions and deletions (indels), and 9,000 copy number variants (CNVs) in the 15 samples. We found 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify autosomal de novo variants and estimated the mutation rates to be 0.81×10-8–1.33×10-8 , 1.0×10-9–2.9×10-9, and ~0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for accurate haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example was a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples. Conclusion Our study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia.

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Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia

Cited by 22 publications

References 76 publications

Perceptions and prevention practices on malaria among the indigenous Orang Asli community in Kelantan, Peninsular Malaysia

Perceptions and prevention practices on malaria among the indigenous Orang Asli community in Kelantan, Peninsular Malaysia

Characterising private and shared signatures of positive selection in 37 Asian populations

Analysis of Five Deep-sequenced Trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo Populations

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