Human population admixture in Asia

Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers

Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

Ethnic disparities in demographic, clinicopathologic and biological behaviours and prognosis of gastric cancer in northwest China

This retrospective study aimed to investigate ethnic disparities in demographic, clinicopathologic, and biological behaviours of gastric cancer (GC) in a high GC incidence area of China. There were 5022 GC patients, including 3987 Han (79.4%) and 987 Hui (14.4%) patients from Northwest China. All patient data were retrieved from 2009 to 2017. Median survival was estimated using the Kaplan‐Meier method and compared using the log‐rank test. A Cox proportional hazards model was used to assess the impact of covariates. Similarly, low 5‐year OS rates were observed in both the Hui and Han groups (23.8% and 24.2% respectively). Hui patients with stage T1 or N0 or with tumours <5 cm had 2.144‐fold, 1.426‐fold and 1.305‐fold increased risks of poor prognosis compared with Han patients with these characteristics respectively (all p < 0.05). Further, Hui patients had 1.265‐fold, 1.364‐fold and 1.401‐fold increased risks of poor prognosis compared with Han patients among those with high expression of Ki67, EGFR and VEGF respectively (all p < 0.05). There are ethnic disparities in the prognosis of GC patients in Northwest China. Understanding the effects of ethnicity on GC will guide reasonable evaluations of prognosis and future interventions to equalise access to high‐quality care for GC patients of different ethnicities in China.

Heterogeneity in the distribution of 159 drug-response related SNPs in world populations and their genetic relatedness

Interethnic variability in drug response arises from genetic differences associated with drug metabolism, action and transport. These genetic variations can affect drug efficacy as well as cause adverse drug reactions (ADRs). We retrieved drug-response related single nucleotide polymorphism (SNP) associated data from databases and analyzed to elucidate population specific distribution of 159 drug-response related SNPs in twenty six populations belonging to five super-populations (African, Admixed Americans, East Asian, European and South Asian). Significant interpopulation differences exist in the minor (variant) allele frequencies (MAFs), linkage disequilibrium (LD) and haplotype distributions among these populations. 65 of the drug-response related alleles, which are considered as minor (variant) in global population, are present as the major alleles (frequency ≥0.5) in at least one or more populations. Populations that belong to the same super-population have similar distribution pattern for majority of the variant alleles. These drug response related variant allele frequencies and their pairwise LD measure (r²) can clearly distinguish the populations in a way that correspond to the known evolutionary history of human and current geographic distributions, while D' cannot. The data presented here may aid in identifying drugs that are more appropriate and/or require pharmacogenetic testing in these populations. Our findings emphasize on the importance of distinct, ethnicity-specific clinical guidelines, especially for the African populations, to avoid ADRs and ensure effective drug treatment.

Effect of multi-ethnicity and ancestry on prevalence of allergic disease

BACKGROUND/PURPOSE

Differences exist among racial and ethnic groups in the prevalence and severity of allergic diseases. However, influence of population admixing on allergic disease has not been studied. We examined the effect of population admixing on the occurrence of allergic disease.

METHODS

We reviewed the data of 68,043 adolescents who participated in the 11th Korea Youth Risk Behavior Web-based Survey, which provides a sample that is representative of the entire Korean middle school and high school student population. Multi-ethnic status was determined by using parental country of birth and prevalence of asthma, allergic rhinitis (AR), and atopic dermatitis (AD) was determined by questionnaire.

RESULTS

Multi-ethnic adolescents accounted for approximately 0.9% of the total adolescents. Prevalence of asthma was significantly higher in multi-ethnic group than non multi-ethnic group while that of AR and AD was significantly higher in non multi-ethnic group than multi-ethnic group. Parental region of country at birth showed a significant difference in prevalence of allergic disease. Univariate analysis found that urbanity, perceived economic status (PES), parental region of country at birth, and environmental tobacco smoke (ETS) showed a significant odds ratio (OR) in asthma, AR, and AD. Body mass index (BMI) showed a significant OR in asthma and AD. After adjusting for urbanity, PES, BMI and ETS, multiethnicity showed significantly lower OR in AR and AD.

CONCLUSION

Population admixing appears to have significant effect on the prevalence of allergic disease. Further study will be needed to clarify the effect of population admixing on prevalence of allergic disease.

Genetic resolution of applied biosystems™ precision ID Ancestry panel for seven Asian populations

Massively parallel sequencing (MPS) offers additional information in cases that lack reference samples for comparison. The HID-Ion AmpliSeq Ancestry Panel is a forensic multiplex platform consisting of 165 autosomal markers designed to provide biogeographic ancestry information. We analyzed seven different population groups from Asia to assess the accuracy and reliability of analysis, using this panel. In this study, we have designated 750 unrelated Asians, from southern China (n = 99), Beijing (n = 100), Japan (n = 101), Korea (n = 100), Vietnam (n = 100), Nepal (n = 100), India (n = 51), and Pakistan (n = 99). The likelihood ratios of 750 Asians were calculated, using the Torrent Server and the HID SNP Genotyper Plugin Version 4.3.2. The results reveal that all Northeast Asians (China, Japan, and Korea), and Vietnamese, were predicted as East Asians with the highest ethnicity likelihood values from reference data. Although the samples from Nepal, India and Pakistan (Southwest Asians), were predominantly predicted as South Asians, there were seven cases of which results revealed as Europeans, with similar likelihood patterns. Population structure analysis indicated that Southwest Asians have a genetic profile that is distinguishable from those of other Asian populations. This panel was validated for potential usefulness in forensic analysis and the findings could be used as a basis for building additional Asian specific reference databases. Nevertheless, additional analyses comprising larger sample sizes will be necessary, especially Southeast Asians, to fully understand the Asian population structure, and to discriminate them with further details.

Analysis of the clinicopathological features and prognostic factors in 734 cases of Chinese Hui and Han patients with adenocarcinoma of the esophagogastric junction

OBJECTIVE

To explore the clinicopathological features and prognostic factors of 734 cases of Chinese Hui and Han patients with adenocarcinoma of the esophagogastric junction (AEG).

METHODS

In total, 734 patients were confirmed to have AEG by gastroscopy and pathology at the General Hospital of Ningxia Medical University between January 2002 and December 2012. Univariate and multivariate analyses of demographic, clinicopathological, and prognostic data were performed.

RESULTS

In total, 734 AEG patients underwent surgical intervention, including 169 Hui patients and 565 Han patients. The male to female ratio was 9.5:1 in Hui patients and 6.4:1 in Han patients, and the average age in both groups was approximately 61 years. The Han patients were more likely to have a cigarette smoking history and an alcohol consumption history than the Hui patients (58.8% vs. 29.4%, p = 0.000; 45.8% vs. 14.6%, p = 0.000). The 5-year survival rate in the Hui and Han patients was 54.3% and 39.9%, respectively (p = 0.024). Age (p = 0.005), sex (p = 0.015), pathologic T stage (p = 0.056), pathologic N stage (p = 0.000), pathologic M stage (p = 0.001), number of resected lymph nodes (p = 0.001) and adjuvant chemoradiotherapy (p = 0.002) were significant independent prognostic factors.

CONCLUSION

The AEG patients were primarily male and elderly in both Hui and Han groups with the prognosis of Hui patients better than Han patients. Age, sex, pathologic T3-4 stage, pathologic N stage, pathologic M stage, number of resected lymph nodes, and adjuvant chemoradiotherapy were significant independent factors predictive of the prognosis of AEG in both groups.

Genetic admixture and obesity: recent perspectives and future applications

The process of the colonization of the New World that occurred centuries ago served as a natural experiment, creating unique combinations of genetic material in newly formed admixed populations. Through a genetic admixture approach, the identification and genotyping of ancestry informative markers have allowed for the estimation of proportions of ancestral parental populations among individuals in a sample. These admixture estimates have been used in different ways to understand the genetic contributions to individual variation in obesity and body composition parameters, particularly among diverse admixed groups known to differ in obesity prevalence within the United States. Although progress has been made through the use of genetic admixture approaches, further investigations are needed in order to explore the interaction of environmental factors with the degree of genetic ancestry in individuals. A challenge to confront at this time would be to further stratify and define environments in progressively more granular terms, including nutrients, muscle biology, stress responses at the cellular level, and the social and built environments.