Displaying publications 1 - 20 of 38 in total

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  1. Lou H, Lu Y, Lu D, Fu R, Wang X, Feng Q, et al.
    Am J Hum Genet, 2015 Jul 02;97(1):54-66.
    PMID: 26073780 DOI: 10.1016/j.ajhg.2015.05.005
    Tibetan high-altitude adaptation (HAA) has been studied extensively, and many candidate genes have been reported. Subsequent efforts targeting HAA functional variants, however, have not been that successful (e.g., no functional variant has been suggested for the top candidate HAA gene, EPAS1). With WinXPCNVer, a method developed in this study, we detected in microarray data a Tibetan-enriched deletion (TED) carried by 90% of Tibetans; 50% were homozygous for the deletion, whereas only 3% carried the TED and 0% carried the homozygous deletion in 2,792 worldwide samples (p < 10(-15)). We employed long PCR and Sanger sequencing technologies to determine the exact copy number and breakpoints of the TED in 70 additional Tibetan and 182 diverse samples. The TED had identical boundaries (chr2: 46,694,276-46,697,683; hg19) and was 80 kb downstream of EPAS1. Notably, the TED was in strong linkage disequilibrium (LD; r(2) = 0.8) with EPAS1 variants associated with reduced blood concentrations of hemoglobin. It was also in complete LD with the 5-SNP motif, which was suspected to be introgressed from Denisovans, but the deletion itself was absent from the Denisovan sequence. Correspondingly, we detected that footprints of positive selection for the TED occurred 12,803 (95% confidence interval = 12,075-14,725) years ago. We further whole-genome deep sequenced (>60×) seven Tibetans and verified the TED but failed to identify any other copy-number variations with comparable patterns, giving this TED top priority for further study. We speculate that the specific patterns of the TED resulted from its own functionality in HAA of Tibetans or LD with a functional variant of EPAS1.
  2. Hatin WI, Nur-Shafawati AR, Etemad A, Jin W, Qin P, Xu S, et al.
    Hugo J, 2014 Dec;8(1):5.
    PMID: 27090253 DOI: 10.1186/s11568-014-0005-z
    BACKGROUND: The Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago. The sub-ethnic groups can be divided based on the region they inhabit; the northern (Melayu Kedah and Melayu Kelantan), western (Melayu Minang) and southern parts (Melayu Bugis and Melayu Jawa) of Peninsular Malaysia. We analyzed 54,794 autosomal single nucleotide polymorphisms (SNPs) which were shared by 472 unrelated individuals from 17 populations to determine the genetic structure and distributions of the ancestral genetic components in five Malay sub-ethnic groups namely Melayu Bugis, Melayu Jawa, Melayu Minang, Melayu Kedah, and Melayu Kelantan. We also have included in the analysis 12 other study populations from Thailand, Indonesia, China, India, Africa and Orang Asli sub-groups in Malay Peninsula, obtained from the Pan Asian SNP Initiative (PASNPI) Consortium and International HapMap project database.

    RESULTS: We found evidence of genetic influx from Indians to Malays, more in Melayu Kedah and Melayu Kelantan which are genetically different from the other Malay sub-ethnic groups, but similar to Thai Pattani. More than 98% of these northern Malays haplotypes could be found in either Indians or Chinese populations, indicating a highly admixture pattern among populations. Nevertheless, the ancestry lines of Malays, Indonesians and Thais were traced back to have shared a common ancestor with the Proto-Malays and Chinese.

    CONCLUSIONS: These results support genetic admixtures in the Peninsular Malaysia Malay populations and provided valuable information on the enigmatic demographical history as well as shed some insights into the origins of the Malays in the Malay Peninsula.

  3. Fu R, Mokhtar SS, Phipps ME, Hoh BP, Xu S
    Eur J Hum Genet, 2018 06;26(6):886-897.
    PMID: 29476164 DOI: 10.1038/s41431-018-0120-8
    Copy number variations (CNVs) are genomic structural variations that result from the deletion or duplication of large genomic segments. The characterization of CNVs is largely underrepresented, particularly those of indigenous populations, such as the Orang Asli in Peninsular Malaysia. In the present study, we first characterized the genome-wide CNVs of four major native populations from Peninsular Malaysia, including the Malays and three Orang Asli populations; namely, Proto-Malay, Senoi, and Negrito (collectively called PM). We subsequently assessed the distribution of CNVs across the four populations. The resulting global CNV map revealed 3102 CNVs, with an average of more than 100 CNVs per individual. We identified genes harboring CNVs that are highly differentiated between PM and global populations, indicating that these genes are predominantly enriched in immune responses and defense functions, including APOBEC3A_B, beta-defensin genes, and CCL3L1, followed by other biological functions, such as drug and toxin metabolism and responses to radiation, suggesting some attributions between CNV variations and adaptations of the PM groups to the local environmental conditions of tropical rainforests.
  4. Xu S, Kang Y, Soeharno H, Yeo N
    Malays Orthop J, 2020 Nov;14(3):194-197.
    PMID: 33403086 DOI: 10.5704/MOJ.2011.033
    Marjolin's ulcer is a rare and often overlooked diagnosis which can be encountered by a variety of specialities. Majority of the literatures describe long latency period of 11 to 75 years. The authors present two unusual cases of rapid progression to Marjolin's ulcer in patients with previously negative biopsy 8- and 10-month prior. This highlights the importance for clinicians to have a high degree of suspicion when encountered with any non-healing wound, especially one who's symptomatology and morphological features have undergone an acute change. Even with previous negative biopsy, patients should still be followed-up closely and clinicians should not hesitate to perform re-biopsy if the suspicion arises.
  5. Xu S, Lan H, Teng Q, Li X, Jin Z, Qu Y, et al.
    Int J Biol Macromol, 2023 Aug 12;251:126286.
    PMID: 37579904 DOI: 10.1016/j.ijbiomac.2023.126286
    H7 avian influenza virus has caused multiple human infections and poses a severe public health threat. In response to the highly variable nature of AIVs, a novel, easily regenerated DNA vaccine has great potential in treating or preventing avian influenza pandemics. Nevertheless, DNA vaccines have many disadvantages, such as weak immunogenicity and poor in vivo delivery. To further characterize and solve these issues and develop a novel H7 AIV DNA vaccine with enhanced stability and immunogenicity, we constructed nine AIV DNA plasmids, and the immunogenicity screened showed that mice immunized with pβH7N2SH9 elicited stronger hemagglutination-inhibiting (HI) antibodies than other eight plasmid DNAs. Then, to address the susceptibility to degradation and low transfection rate of DNA vaccine in vivo, we developed pβH7N2SH9/DGL NPs by encapsulating the pβH7N2SH9 within the dendrigraft poly-l-lysines nanoparticles. As expected, these NPs exhibited excellent physical and chemical properties, were capable of promote lymphocyte proliferation, and induce stronger humoral and cellular responses than the naked pβH7N2SH9, including higher levels of HI antibodies than naked pβH7N2SH9, as well as the production of cytokines, namely, IL-2, IFN-α. Taken together, our results suggest that the construction of an immune-enhanced H7-AIV DNA nanovaccine may be a promising strategy against most influenza viruses.
  6. Deng L, Lou H, Zhang X, Thiruvahindrapuram B, Lu D, Marshall CR, et al.
    BMC Genomics, 2019 Nov 12;20(1):842.
    PMID: 31718558 DOI: 10.1186/s12864-019-6226-8
    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 Peninsular Malaysia and North Borneo, and characterized the genomic variants, including single nucleotide variants (SNVs), small insertions and deletions (indels) and copy number variants (CNVs). We discovered approximately 6.9 million SNVs, 1.2 million indels, and 9000 CNVs in the 15 samples, of which 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 de novo variants and estimated the autosomal 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 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 is 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.

  7. Shahzad MF, Xu S, Lim WM, Yang X, Khan QR
    Heliyon, 2024 Apr 30;10(8):e29523.
    PMID: 38665566 DOI: 10.1016/j.heliyon.2024.e29523
    The advancement of artificial intelligence (AI) and the ubiquity of social media have become transformative agents in contemporary educational ecosystems. The spotlight of this inquiry focuses on the nexus between AI and social media usage in relation to academic performance and mental well-being, and the role of smart learning in facilitating these relationships. Using partial least squares-structural equation modeling (PLS-SEM) on a sample of 401 Chinese university students. The study results reveal that both AI and social media have a positive impact on academic performance and mental well-being among university students. Furthermore, smart learning serves as a positive mediating variable, amplifying the beneficial effects of AI and social media on both academic performance and mental well-being. These revelations contribute to the discourse on technology-enhanced education, showing that embracing AI and social media can have a positive impact on student performance and well-being.
  8. Xu S, Deo RC, Soar J, Barua PD, Faust O, Homaira N, et al.
    Comput Methods Programs Biomed, 2023 Nov;241:107746.
    PMID: 37660550 DOI: 10.1016/j.cmpb.2023.107746
    BACKGROUND AND OBJECTIVE: Obstructive airway diseases, including asthma and Chronic Obstructive Pulmonary Disease (COPD), are two of the most common chronic respiratory health problems. Both of these conditions require health professional expertise in making a diagnosis. Hence, this process is time intensive for healthcare providers and the diagnostic quality is subject to intra- and inter- operator variability. In this study we investigate the role of automated detection of obstructive airway diseases to reduce cost and improve diagnostic quality.

    METHODS: We investigated the existing body of evidence and applied Preferred Reporting Items for Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to search records in IEEE, Google scholar, and PubMed databases. We identified 65 papers that were published from 2013 to 2022 and these papers cover 67 different studies. The review process was structured according to the medical data that was used for disease detection. We identified six main categories, namely air flow, genetic, imaging, signals, and miscellaneous. For each of these categories, we report both disease detection methods and their performance.

    RESULTS: We found that medical imaging was used in 14 of the reviewed studies as data for automated obstructive airway disease detection. Genetics and physiological signals were used in 13 studies. Medical records and air flow were used in 9 and 7 studies, respectively. Most papers were published in 2020 and we found three times more work on Machine Learning (ML) when compared to Deep Learning (DL). Statistical analysis shows that DL techniques achieve higher Accuracy (ACC) when compared to ML. Convolutional Neural Network (CNN) is the most common DL classifier and Support Vector Machine (SVM) is the most widely used ML classifier. During our review, we discovered only two publicly available asthma and COPD datasets. Most studies used private clinical datasets, so data size and data composition are inconsistent.

    CONCLUSIONS: Our review results indicate that Artificial Intelligence (AI) can improve both decision quality and efficiency of health professionals during COPD and asthma diagnosis. However, we found several limitations in this review, such as a lack of dataset consistency, a limited dataset and remote monitoring was not sufficiently explored. We appeal to society to accept and trust computer aided airflow obstructive diseases diagnosis and we encourage health professionals to work closely with AI scientists to promote automated detection in clinical practice and hospital settings.

  9. Gao Y, Hu Y, Xu S, Liang H, Lin H, Yin TH, et al.
    J Helminthol, 2024 Apr 15;98:e33.
    PMID: 38618902 DOI: 10.1017/S0022149X24000221
    We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.
  10. Liu X, Lu D, Saw WY, Shaw PJ, Wangkumhang P, Ngamphiw C, et al.
    Eur J Hum Genet, 2017 04;25(4):499-508.
    PMID: 28098149 DOI: 10.1038/ejhg.2016.181
    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.
  11. Maran S, Lee YY, Xu S, Rajab NS, Hasan N, Mustaffa N, et al.
    Hepatogastroenterology, 2013 Jan-Feb;60(121):124-8.
    PMID: 22829558
    Using genome-wide case-control association approach, the current study aimed to determine whether genetic polymorphism(s) is/are associated with H. pylori infection among ethnic Malays from the north-eastern region of Peninsular Malaysia, a region with an exceptionally low prevalence for H. pylori infection and gastric cancer.
  12. Yu M, Xu S, Hu H, Li S, Yang G
    Behav Brain Res, 2023 Apr 12;443:114209.
    PMID: 36368444 DOI: 10.1016/j.bbr.2022.114209
    OBJECTIVE: We investigated brain activity associated with executive control attention network in elite, expert, and novice female ice hockey athletes during the revised lateralized attention network tast to determine whether the neural correlates of performance differ by skill level.

    METHODS: We collected and analyzed functional near-infrared spectroscopy data of 38 participants while performing the revised lateralized attention network tast.

    RESULTS: Elite players were significantly faster than novices (p = .005), and the experts' overall accuracy rate (ACC) was higher than that of novices (p = .001). The effect of the executive network on reaction time was higher in novices than in elite players (p = .008) and experts (p = .004). The effect of the executive network on the ACC was lower in elite players than in experts (p = .009) and novices (p = .010). Finally, elite player had higher flanker conflict effects on RT (p = .005) under the invalid cue condition. the effect of the alertness network and orientation on the ACC was lower in elite players than in novices (p = .000) and experts (p = .022). Changes in the blood oxygen level-dependent signal related to the flanker effect were significantly different in the right dorsolateral prefrontal cortex (F=3.980, p = .028) and right inferior frontal gyrus (F=3.703, p = .035) among the three groups. Elit players showed more efficient executive control (reduced conflict effect on ACC) (p = .006)in the RH.The changes related to the effect of blood oxygen level on orienting were significantly different in the right frontal eye fields (F=3.883, p = .030) among the three groups, Accompanied by significant activation of the right dorsolateral prefrontal cortex(p = .026).

    CONCLUSION: Our findings provide partial evidence of the superior cognitive performance and high neural efficiency of elite ice hockey players during cognitive tasks. These results demonstrate the right hemisphere superiority for executive control.We also found that specific brain activation in hockey players does not show a clear and linear relationship with skill level.

  13. Liu X, Yunus Y, Lu D, Aghakhanian F, Saw WY, Deng L, et al.
    Hum Genet, 2015 Apr;134(4):375-92.
    PMID: 25634076 DOI: 10.1007/s00439-014-1525-2
    The indigenous populations from Peninsular Malaysia, locally known as Orang Asli, continue to adopt an agro-subsistence nomadic lifestyle, residing primarily within natural jungle habitats. Leading a hunter-gatherer lifestyle in a tropical jungle environment, the Orang Asli are routinely exposed to malaria. Here we surveyed the genetic architecture of individuals from four Orang Asli tribes with high-density genotyping across more than 2.5 million polymorphisms. These tribes reside in different geographical locations in Peninsular Malaysia and belong to three main ethno-linguistic groups, where there is minimal interaction between the tribes. We first dissect the genetic diversity and admixture between the tribes and with neighboring urban populations. Later, by implementing five metrics, we investigated the genome-wide signatures for positive natural selection of these Orang Asli, respectively. Finally, we searched for evidence of genomic adaptation to the pressure of malaria infection. We observed that different evolutionary responses might have emerged in the different Orang Asli communities to mitigate malaria infection.
  14. Deng L, Hoh BP, Lu D, Saw WY, Twee-Hee Ong R, Kasturiratne A, et al.
    Sci Rep, 2015 Sep 23;5:14375.
    PMID: 26395220 DOI: 10.1038/srep14375
    The Malay people are an important ethnic composition in Southeast Asia, but their genetic make-up and population structure remain poorly studied. Here we conducted a genome-wide study of four geographical Malay populations: Peninsular Malaysian Malay (PMM), Singaporean Malay (SGM), Indonesian Malay (IDM) and Sri Lankan Malay (SLM). All the four Malay populations showed substantial admixture with multiple ancestries. We identified four major ancestral components in Malay populations: Austronesian (17%-62%), Proto-Malay (15%-31%), East Asian (4%-16%) and South Asian (3%-34%). Approximately 34% of the genetic makeup of SLM is of South Asian ancestry, resulting in its distinct genetic pattern compared with the other three Malay populations. Besides, substantial differentiation was observed between the Malay populations from the north and the south, and between those from the west and the east. In summary, this study revealed that the genetic identity of the Malays comprises a mixed entity of multiple ancestries represented by Austronesian, Proto-Malay, East Asian and South Asian, with most of the admixture events estimated to have occurred 175 to 1,500 years ago, which in turn suggests that geographical isolation and independent admixture have significantly shaped the genetic architectures and the diversity of the Malay populations.
  15. Jia J, Ma Y, Xu S, Zheng J, Ma X, Zhang Y, et al.
    Psychol Res Behav Manag, 2023;16:2417-2424.
    PMID: 37426390 DOI: 10.2147/PRBM.S413382
    OBJECTIVE: This study aimed to investigate the impact of academic self-efficacy on test anxiety among higher vocational students, as well as the role of sense of life meaning, fear of failure, and gender difference in mediating this relationship.

    METHODS: A total of 2231 higher vocational students from Shandong Province were surveyed by means of Academic Self-efficacy Questionnaire, Meaning in Life Questionnaire, and Test Anxiety Scale.

    RESULTS: There were significant negative correlations among academic self-efficacy, sense of life meaning, and test anxiety. Fear of failure was positively correlated with test anxiety. Sense of life meaning and fear of failure played a mediating role in the relationship between academic self-efficacy and test anxiety. The chain mediating effect was significant only in the female group, not in the male group. In contrast, academic self-efficacy indirectly predicted test anxiety by the independent mediating effect of sense of life meaning or fear of failure in the male group.

    CONCLUSION: Academic self-efficacy may influence test anxiety through the independent mediating effect of sense of life meaning, fear of failure, and the chain mediating effect, and there is a gender difference in these effects.

  16. Hoh BP, Deng L, Julia-Ashazila MJ, Zuraihan Z, Nur-Hasnah M, Nur-Shafawati AR, et al.
    Hum Genomics, 2015 Jul 22;9:16.
    PMID: 26194999 DOI: 10.1186/s40246-015-0039-x
    Fine scale population structure of Malays - the major population in Malaysia, has not been well studied. This may have important implications for both evolutionary and medical studies. Here, we investigated the population sub-structure of Malay involving 431 samples collected from all states from peninsular Malaysia and Singapore. We identified two major clusters of individuals corresponding to the north and south peninsular Malaysia. On an even finer scale, the genetic coordinates of the geographical Malay populations are in correlation with the latitudes (R(2) = 0.3925; P = 0.029). This finding is further supported by the pairwise FST of Malay sub-populations, of which the north and south regions showed the highest differentiation (FST [North-south] = 0.0011). The collective findings therefore suggest that population sub-structure of Malays are more heterogenous than previously expected even within a small geographical region, possibly due to factors like different genetic origins, geographical isolation, could result in spurious association as demonstrated in our analysis. We suggest that cautions should be taken during the stage of study design or interpreting the association signals in disease mapping studies which are expected to be conducted in Malay population in the near future.
  17. Maran S, Lee YY, Xu S, Rajab NS, Hasan N, Syed Abdul Aziz SH, et al.
    World J Gastroenterol, 2013 Jun 21;19(23):3615-22.
    PMID: 23801863 DOI: 10.3748/wjg.v19.i23.3615
    To identify genes associated with gastric precancerous lesions in Helicobacter pylori (H. pylori)-susceptible ethnic Malays.
  18. Deng L, Pan Y, Wang Y, Chen H, Yuan K, Chen S, et al.
    Mol Biol Evol, 2022 Feb 03;39(2).
    PMID: 34940850 DOI: 10.1093/molbev/msab361
    Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.
  19. Yew CW, Hoque MZ, Pugh-Kitingan J, Minsong A, Voo CLY, Ransangan J, et al.
    Ann. Hum. Genet., 2018 07;82(4):216-226.
    PMID: 29521412 DOI: 10.1111/ahg.12246
    The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the "North Borneo"-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non-Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST ) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non-Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s).
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