Genetic Admixture in the Culturally Unique Peranakan Chinese Population in Southeast Asia

The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ∼300–500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ∼5.62% (95% confidence interval [CI]: 4.76–6.49%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.65–1.51%), southern Chinese (0.86%, 0.50–1.23%), and northern Chinese (0.25%, 0.18–0.32%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ∼1,612 (95% CI: 1,345–1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ∼190 (159–213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.     

Allelic variants of acidic proline-rich proteins observed in Japanese,Chinese, and Malays

Three new variants of acidic proline-rich proteins (At, Au, Aw) were found in human parotid saliva by isoelectric focusing and basic gel electrophoresis. Electrophoretic comparison of the purified proteins and their tryptic peptides suggested minor charge and size differences from other acidic PRPs. Genetic and biochemical studies indicate that the At and Aw proteins are allelic products of thePRH1 locus. Gene frequencies of the At productive allele (PRH1 ⁶) in Japanese, Chinese, and Malays were 0.008, 0.012, and 0.004, respectively. The Au protein was also found in Japanese (2 in 746 samples), Chinese (1 in 215 samples), and Malays (1 in 220 samples), however, the Aw protein was found only in one Japanese (n=746). These three proteins were not found in 106 Indian subjects.This study was supported in part by a grant from International Scientific Research Program of the Ministry of Education, Science and Culture of Japan, No. 62043071 (representative: K.S.).     

Helicobacter pylori Infection – A Boon or a Bane: Lessons from Studies in a Low‐Prevalence Population

Helicobacter pylori (H. pylori) infection is etiologically associated with gastric cancer and peptic ulcer diseases which are both important public health burdens which could be largely eliminated by H. pylori eradication. However, some investigators urge caution based on the hypothesis that eradication of H. pylori may result in an increase in the incidence of gastroesophageal reflux disease, esophageal adenocarcinoma, and childhood asthma. The ethnic Malays of northeastern Peninsular Malaysia have long had a low prevalence of H. pylori infection and, as expected, the incidence of gastric cancer and its precursor lesions is exceptionally low. The availability of a population with a low H. pylori prevalence and generally poor sanitation allows separation of H. pylori from the hygiene hypothesis and direct testing of whether absence of H. pylori is associated with untoward consequence. Contrary to predictions, in Malays, erosive esophagitis, Barrett's esophagus, distal esophageal cancers, and childhood asthma are all of low incidence. This suggests that H. pylori is not protective rather the presence of H. pylori infection is likely a surrogate for poor hygiene and not an important source of antigens involved in the hygiene hypothesis. Helicobacter pylori in Malays is related to transmission from H. pylori‐infected non‐Malay immigrants. The factors responsible for low H. pylori acquisition, transmission, and burden of H. pylori infection in Malays remain unclear and likely involves a combination of environmental, host (gene polymorphisms), and strain virulence factors. Based on evidence from this population, absence of H. pylori infection is more likely to be boon than a bane.     

Socio demographic and lifestyle factors of metabolic syndrome among adult rural indigenous Malaysian population from Perak State,Malaysia

Metabolic syndrome (MetS) is defined as a cluster of known disorders that increase the risk for morbidity and mortality from cardiovascular diseases (CVD) and type 2 diabetes mellitus. This cross sectional study was carried out to estimate the prevalence of MetS using Adult Treatment Panel 3 (ATP 3) classification and socio-demographic and lifestyle factors contributing to metabolic syndrome among rural indigenous Malaysian population from Perak state, Malaysia which included 148 rural Malay and 145 Orang Asli(OA) individuals. This community based cross-sectional study revealed that the prevalence of MetS was significantly higher among Malays (27.7%) as compared to Orang Aslis (13.8%). Overall Prevalence of Metabolic syndrome in the rural indigenous Malaysian population was 20.8%. Prevalence of abdominal obesity and high blood pressure were significantly higher among Malays as compared to OA population. Metabolic syndrome was significantly higher among those above 45 years of age group in overall rural indigenous Malaysian population and among OA. The prevalence of MetS was significantly higher among those who were obese and overweight and among Malays who were regularly taking snacks between meals. There was no significant association between other dietary risk factors, smoking, alcohol use or physical activity with metabolic syndrome.     

A whole genome analyses of genetic variants in two Kelantan Malay individuals

BackgroundThe sequencing of two members of the Royal Kelantan Malay family genomes will provide insights on the Kelantan Malay whole genome sequences. The two Kelantan Malay genomes were analyzed for the SNP markers associated with thalassemia and Helicobacter pylori infection. Helicobacter pylori infection was reported to be low prevalence in the north-east as compared to the west coast of the Peninsular Malaysia and beta-thalassemia was known to be one of the most common inherited and genetic disorder in Malaysia.ResultBy combining SNP information from literatures, GWAS study and NCBI ClinVar, 18 unique SNPs were selected for further analysis. From these 18 SNPs, 10 SNPs came from previous study of Helicobacter pylori infection among Malay patients, 6 SNPs were from NCBI ClinVar and 2 SNPs from GWAS studies. The analysis reveals that both Royal Kelantan Malay genomes shared all the 10 SNPs identified by Maran (Single Nucleotide Polymorphims (SNPs) genotypic profiling of Malay patients with and without Helicobacter pylori infection in Kelantan, 2011) and one SNP from GWAS study. In addition, the analysis also reveals that both Royal Kelantan Malay genomes shared 3 SNP markers; HBG1 (rs1061234), HBB (rs1609812) and BCL11A (rs766432) where all three markers were associated with beta-thalassemia.ConclusionsOur findings suggest that the Royal Kelantan Malays carry the SNPs which are associated with protection to Helicobacter pylori infection. In addition they also carry SNPs which are associated with beta-thalassemia. These findings are in line with the findings by other researchers who conducted studies on thalassemia and Helicobacter pylori infection in the non-royal Malay population.     

Sociocultural and dietary practices among Malay subjects in the north-eastern region of Peninsular Malaysia: a region of low prevalence of Helicobacter pylori infection

Background and Aim: The prevalence of Helicobacter pylori infection is exceptionally low among the Malays in the north‐eastern region of Peninsular Malaysia. The reasons are unknown. Our aim was to compare environmental factors that differed in relation to H. pylori prevalence among Malays born and residing in Kelantan. Methods: A case–control study was conducted among Malays in Kelantan who underwent upper endoscopy between 2000 and 2008. Helicobacter pylori status was determined by gastric histology. Sociocultural and dietary factors were assessed using a validated investigator‐directed questionnaire administered after 2008, and the data were analyzed using logistic regression analysis. Results: The study group consisted of 161 subjects (79 H. pylori positive and 82 controls). Univariable analysis identified five poor sanitary practices associated with an increased prevalence of H. pylori infection: use of well water, use of pit latrine, less frequent boiling of drinking water, and infrequent hand wash practice after toilet use and before meals. Multivariable logistic regression analysis identified three variables inversely associated with H. pylori infection: frequent consumption of tea (OR: 0.023, 95% CI: 0.01–0.07), frequent use of “budu” or local anchovy sauce (OR: 0.09, 95% CI: 0.1–0.7), and frequent use of “pegaga” or centenella asiatica (OR: 0.25, 95% CI: 0.1–0.65). Conclusions: Under the assumption that sanitary, sociocultural, and dietary habits have not changed over the years, we can conclude that an increased risk of H. pylori was associated with unsanitary practices whereas protection was associated with consumption of tea and locally produced foods, “pegaga” and “budu.” These dietary factors are candidates for future study on the effects on H. pylori transmission.