Genetic diversity and ancestry of the Khmuic-speaking ethnic groups in Thailand: a genome-wide perspective

The Khmuic-speaking populations are believed to be the descendants of one of the earliest groups to settle in Mainland Southeast Asia. In Thailand, there are two agricultural Khmuic-speaking ethnic groups, the Khamu and Lua (Htin). These peoples primarily reside in scattered locations along the mountainous Thailand-Laos border in Nan province. In this study, we conducted genome-wide SNP analysis on 81 individuals from three Khamu and two Lua villages in northern Thailand. Our findings revealed that both the Khamu and Lua groups possess genetic structures that are distinct from other ethnicities in Southeast Asia, indicating a unique history of migration and settlement. Within the Khmuic group, the Khamu populations living in different locations exhibited similar genetic structures and displayed genetic affinities only with some hill-tribes and Tai-Kadai (Kra-Dai)-speaking groups in Thailand, suggesting potential intermixing or cultural exchange. Furthermore, the Lua people displayed a distinctive population structure, which could be attributed to the founder effect and endogamous marriage practices. Additionally, we discovered a relationship between the Khmuic-speaking populations in Thailand and a Neolithic ancient sample obtained from the Tham Pha Ling archaeological site in Laos. This study provides new insight into genetic substructure within the Khmuic-speaking people and their potential relationship to the indigenous inhabitants of Mainland Southeast Asia.

South Asian maternal and paternal lineages in southern Thailand and the role of sex-biased admixture

Previous genome-wide studies have reported South Asian (SA) ancestry in several Mainland Southeast Asian (MSEA) populations; however, additional details concerning population history, in particular the role of sex-specific aspects of the SA admixture in MSEA populations can be addressed with uniparental markers. Here, we generated ∼2.3 mB sequences of the male-specific portions of the Y chromosome (MSY) of a Tai-Kadai (TK)-speaking Southern Thai group (SouthernThai_TK), and complete mitochondrial (mtDNA) genomes of the SouthernThai_TK and an Austronesian (AN)-speaking Southern Thai (SouthernThai_AN) group. We identified new mtDNA haplogroups, e.g. Q3, E1a1a1, B4a1a and M7c1c3 that have not previously reported in Thai populations, but are frequent in Island Southeast Asia and Oceania, suggesting interactions between MSEA and these regions. SA prevalent mtDNA haplogroups were observed at frequencies of ~35-45% in the Southern Thai groups; both of them showed more genetic relatedness to Austroasiatic (AA) speaking Mon than to any other group. For MSY, SouthernThai_TK had ~35% SA prevalent haplogroups and exhibited closer genetic affinity to Central Thais. We also analyzed published data from other MSEA populations and observed SA ancestry in some additional MSEA populations that also reflects sex-biased admixture; in general, most AA- and AN-speaking groups in MSEA were closer to SA than to TK groups based on mtDNA, but the opposite pattern was observed for the MSY. Overall, our results of new genetic lineages and sex-biased admixture from SA to MSEA groups attest to the additional value that uniparental markers can add to studies of genome-wide variation.

Enhanced apoptosis of HCT116 colon cancer cells treated with extracts from Calotropis gigantea stem bark by starvation

Calotropis gigantea stem bark extract, particularly the dichloromethane fraction (CGDCM), demonstrated the most potent antiproliferative effects on hepatocellular carcinoma HepG2 and colorectal HCT116 cells. The current study focused on enhancing the effectiveness of cancer treatment with CGDCM at concentrations close to the IC50 in HCT116 cells by reducing their nutrient supply. CGDCM (2, 4, and 8 μg/mL) treatment for 24 h under glucose conditions of 4.5 g/L without fetal bovine serum (FBS) supplementation or serum starvation (G+/F-), glucose 0 g/L with 10% FBS or glucose starvation (G-/F+), and glucose 0 g/L with 0% FBS or complete starvation (G-/F-) induced a greater antiproliferative effect in HCT116 cells than therapy in complete medium with glucose 4.5 g/L and 10% FBS (G+/F+). Nonetheless, the anticancer effect of CGDCM at 4 μg/mL under (G-/F-) showed the highest activity compared to other starvation conditions. The three starvation conditions showed a significant reduction in cell viability compared to the control (G+/F+) medium group, while the inhibitory effect on cell viability did not differ significantly among the three starvation conditions. CGDCM at 4 μg/mL in (G-/F-) medium triggered apoptosis by dissipating the mitochondrial membrane potential and arresting cells in the G2/M phase. This investigation demonstrated that a decrease in intracellular ATP and fatty acid levels was associated with enhanced apoptosis by treatment with CGDCM at 4 μg/mL under (G-/F-) conditions. In addition, under (G-/F-), CGDCM at 4 μg/mL increased levels of reactive oxygen species (ROS) and was suggested to primarily trigger apoptosis in HCT116 cells. Thus, C. gigantea extracts may be useful for the future development of alternative, effective cancer treatment regimens.

Women's wellness in the mountains: An exploration of medicinal plants among tibeto-burman groups in Thailand

Ethnopharmacological relevance

This study offers valuable insight into the traditional healing practices of women's healthcare within four Tibeto-Burman groups. By focusing on women's wellness, the research sheds light on the often-neglected yet significant contributions made by women in the field of traditional medicine.

Aims of the study

The study seeks to address the gap of studies on the ethnobotany of women healthcare of the Tibeto-Burman groups in Thailand and to analyst the factors that could affect the diversity of ethnobotanical knowledge.

Materials and methods

The study compiled data from 15 group-informants residing in 12 different villages. The information gathering process involved a combination of free-listing, semi-structured interviews, group discussion, and the walk-to-the-wood method. To analyze the data, the researchers used various methods such as use-reports, Relative Frequency of Citation (RFC), Relative Importance Index (RI), and Cluster analysis.

Results

This study identified 200 plant species used in traditional women's healthcare practices, with leaves being the most frequently used part. Drinking was the most common method for internal use, while bathing and steam were the most emphasized for external use. Blumea balsamifera and Buddleja asiatica had high RI and RFC. Cluster analysis revealed that group-informants were divided by ethnicity and geographical location.

Conclusion

This study contributes to the understanding of traditional healthcare practices among Tibeto-Burman groups in Thailand, with a particular focus on women's wellness. The results provide insight into the ethnobotanical knowledge of these communities and highlight the important role played by women in traditional medicine. The study underscores the need for continued research in this field to preserve and utilize this valuable knowledge.

Genetic Structure and Forensic Utility of 23 Autosomal STRs of the Ethnic Lao Groups From Laos and Thailand

The Lao Isan and Laotian are the major groups in the area of present-day northeastern Thailand and Laos, respectively. Several previous genetic and forensic studies indicated an admixed genetic structure of Lao Isan with the local Austroasiatic speaking groups, e.g. Khmer, whereas there is a paucity of reporting Laotian’s forensic short tandem repeats (STRs). Here, we newly generated 451 genotypes of seven Lao Isan and three Laotian populations (two Lao Lum and one Lao Thoeng) using 23 autosomal STRs embedded in Verifiler^TM plus PCR Amplification kit. We reported allelic frequency and forensic parameters in different dataset: combined ethnic Lao groups, combined Lao Isan populations and combined Laotians. Overall, the forensic parameter results indicate that this set of STRs is suitable for forensic investigation. The anthropological results revealed the genetic homogeneity of Tai-Kadai speaking Lao groups from Thailand and Laos, consistent with previous studies, while the Austroasiatic speaking groups from southern Laos showed genetic relatedness to both Lao Isan and Khmer. In sum, STRs allelic frequency results can provide the genetic backgrounds of populations which is useful for anthropological research and also strengthens the regional forensic database in both countries.

Epigallocatechin gallate triggers apoptosis by suppressing de novo lipogenesis in colorectal carcinoma cells

The de novo lipogenesis (DNL) pathway has been identified as a regulator of cancer progression and aggressiveness. Downregulation of key lipogenesis enzymes has been shown to activate apoptosis in cancerous cells. Epigallocatechin gallate (EGCG) inhibits cancer cell proliferation without causing cytotoxicity in healthy cells. The aim of the present study is to investigate the effects of EGCG on the promotion of apoptosis associated with the DNL pathway inhibition in cancer cells, both in vitro and in vivo. We observed that two colorectal cancer (CRC) cell lines (HCT116 and HT-29) had a higher cytotoxic response to EGCG treatment than hepatocellular carcinoma cells, including HepG2 and HuH-7. EGCG treatment decreased cell viability and increased mitochondrial damage-triggered apoptosis in both HCT116 and HT-29 cancer cells. Additionally, we treated mice transplanted with HCT116 cells with 30 or 50 mg/kg EGCG for 7 days to evaluate the apoptotic effects of EGCN treatment in a xenograft mouse model of cancer. We observed a decrease in intracellular fatty acid levels, which suggested that EGCG-induced apoptosis was associated with a decrease in fatty acid levels in cancer. Suppression of adenosine triphosphate synthesis by EGCG indicated that cell death induction in cancer cells could be mediated by shared components of the DNL and energy metabolism pathways. In addition, EGCG-induced apoptosis suppressed the expression of the phosphorylation protein kinase B and extracellular signal-regulated kinase 1/2 signaling proteins in tumors from xenografted mice. Cytotoxic effects in unaffected organs and tissues of the mouse xenograft model were absent upon EGCG treatment.

Calotropis gigantea stem bark extract induced apoptosis related to ROS and ATP production in colon cancer cells

Conventional chemotherapeutic agents for colorectal cancer (CRC) cause systemic side effects and eventually become less efficacious owing to the development of drug resistance in cancer cells. Therefore, new therapeutic regimens have focused on the use of natural products. The anticancer activity of several parts of Calotropis gigantea has been reported; however, the effects of its stem bark extract on inhibition of cancer cell proliferation have not yet been examined. In this study, the anticancer activity of C. gigantea stem bark extract, both alone and in combination with 5-fluorouracil (5-FU), was evaluated. A crude ethanolic extract was prepared from dry, powdered C. gigantea barks using 95% ethanol. This was then partitioned to obtain dichloromethane (CGDCM), ethyl acetate, and water fractions. Quantitative analysis of the constituent secondary metabolites and calotropin was performed. These fractions exhibited cytotoxicity in HCT116 and HT-29 cells, with CGDCM showing the highest potency in both the cell lines. A combination of CGDCM and 5-FU significantly enhanced the cytotoxic effect. Moreover, the resistance of normal fibroblast, HFF-1, cells to this combination demonstrated its safety in normal cells. The combination significantly enhanced apoptosis through the mitochondria-dependent pathway. Additionally, the combination reduced adenosine triphosphate production and increased the production of reactive oxygen species, demonstrating the mechanisms involved in the induction of apoptosis. Our results suggest that CGDCM is a promising anti-cancer agent and may enhance apoptosis induction by 5-FU in the treatment of CRC, while minimizing toxicity toward healthy cells.

Reconstructing the Human Genetic History of Mainland Southeast Asia: Insights from Genome-Wide Data from Thailand and Laos

Thailand and Laos, located in the center of Mainland Southeast Asia (MSEA), harbor diverse ethnolinguistic groups encompassing all five language families of MSEA: Tai-Kadai (TK), Austroasiatic (AA), Sino-Tibetan (ST), Hmong-Mien (HM), and Austronesian (AN). Previous genetic studies of Thai/Lao populations have focused almost exclusively on uniparental markers and there is a paucity of genome-wide studies. We therefore generated genome-wide SNP data for 33 ethnolinguistic groups, belonging to the five MSEA language families from Thailand and Laos, and analyzed these together with data from modern Asian populations and SEA ancient samples. Overall, we find genetic structure according to language family, albeit with heterogeneity in the AA-, HM-, and ST-speaking groups, and in the hill tribes, that reflects both population interactions and genetic drift. For the TK speaking groups, we find localized genetic structure that is driven by different levels of interaction with other groups in the same geographic region. Several Thai groups exhibit admixture from South Asia, which we date to ∼600-1000 years ago, corresponding to a time of intensive international trade networks that had a major cultural impact on Thailand. An AN group from Southern Thailand shows both South Asian admixture as well as overall affinities with AA-speaking groups in the region, suggesting an impact of cultural diffusion. Overall, we provide the first detailed insights into the genetic profiles of Thai/Lao ethnolinguistic groups, which should be helpful for reconstructing human genetic history in MSEA and selecting populations for participation in ongoing whole genome sequence and biomedical studies.

Autosomal Microsatellite Investigation Reveals Multiple Genetic Components of the Highlanders from Thailand

The hill tribes of northern Thailand comprise nine officially recognized groups: the Austroasiatic-speaking (AA) Khmu, Htin and Lawa; the Hmong-Mien-speaking (HM) IuMien and Hmong; and the Sino-Tibetan-speaking (ST) Akha, Karen, Lahu and Lisu. Except the Lawa, the rest of the hill tribes migrated into their present habitats only very recently. The Thai hill tribes were of much interest to research groups focusing on study of cultural and genetic variation because of their unique languages and cultures. So far, there have been several genetic studies of the Thai hill tribes. However, complete forensic microsatellite database of the Thai hill tribes is still lacking. To construct such database, we newly generated 654 genotypes of 15 microsatellites commonly used in forensic investigation that belong to all the nine hill tribes and also non-hill tribe highlanders from northern Thailand. We also combined 329 genotypes from previous studies of northern Thai populations bringing to a total of 983 genotypes, which were then subjected to genetic structure and population relationships analyses. Our overall results indicated homogenous genetic structure within the HM- and Tai-Kadai (TK)-speaking groups, large genetic divergence of the HM-speaking Hmong but not IuMien from the other Thai groups, and genetic heterogeneity within the ST- and AA-speaking groups, reflecting different population interactions and admixtures. In addition to establishing genetic relationships within and among these populations, our finding, which provides a more complete picture of the forensic microsatellite database of the multiple Thai highland dwellers, would not only serve to expand and strengthen forensic investigation in Thailand, but would also benefit its neighboring countries of Laos and Myanmar, from which many of the Thai hill tribes originated and where large populations of these ethnic groups still reside.

Harboyan syndrome: novel SLC4A11 mutation, clinical manifestations, and outcome of corneal transplantation

Harboyan syndrome or corneal dystrophy and progressive deafness (MIM #217400) is characterized by congenital hereditary endothelial dystrophy (CHED) and progressive, sensorineural hearing loss. Mutations in SLC4A11 are responsible for this rare genetic syndrome. Eight patients from seven unrelated families affected with Harboyan Syndrome with mean follow-up of 12.0 ± 0.9 years were thoroughly investigated for the ocular, hearing, and kidney function abnormalities and the outcome of penetrating keratoplasty (PK). Mutation analysis of SLC4A11 was performed. All patients presented with bilateral cloudy corneas since birth. Sensorineural hearing loss was detected in all patients. Seven patients (11 eyes) underwent PK with the median age at surgery of 10.1 years (7.1-22.9). The overall corneal graft survival rate after primary PK was 72.7% (8/11 eyes). The mean graft survival time was 94.6 months (95% CI 83.1-126.0). All patients had unremarkable kidney function. The c.2264G>A (p.Arg755Gln) mutation in SCL4A11 was detected in most patients (87.5%). All unrelated Karen tribe patients had p.Arg755Gln mutation, suggestive of founder effect. We found the allele frequency of this variant in the Karen population to be 0.01. The c.2263C>T (p.Arg755Trp) mutation was found in one patient with mild phenotype and the novel truncating protein mutation c.2127delG (p.Gly710fsx*25) in SCL4A11 was identified in two Thai sisters. Visual outcome and graft survival after PK were satisfactory. Our study shows that all studied patients with SLC4A11 mutations had CHED and sensorineural hearing loss, and SLC4A11 mutations were not related to the onset and severity of hearing loss or outcome of keratoplasty.

Cultural variation impacts paternal and maternal genetic lineages of the Hmong-Mien and Sino-Tibetan groups from Thailand

The Hmong-Mien (HM) and Sino-Tibetan (ST) speaking groups are known as hill tribes in Thailand; they were the subject of the first studies to show an impact of patrilocality vs. matrilocality on patterns of mitochondrial (mt) DNA vs. male-specific portion of the Y chromosome (MSY) variation. However, HM and ST groups have not been studied in as much detail as other Thai groups; here we report and analyze 234 partial MSY sequences (∼2.3 mB) and 416 complete mtDNA sequences from 14 populations that, when combined with our previous published data, provides the largest dataset yet for the hill tribes. We find a striking difference between Hmong and IuMien (Mien-speaking) groups: the Hmong are genetically different from both the IuMien and all other Thai groups, whereas the IuMien are genetically more similar to other linguistic groups than to the Hmong. In general, we find less of an impact of patrilocality vs. matrilocality on patterns of mtDNA vs. MSY variation than previous studies. However, there is a dramatic difference in the frequency of MSY and mtDNA lineages of Northeast Asian (NEA) origin vs. Southeast Asian (SEA) origin in HM vs. ST groups: HM groups have high frequencies of NEA MSY lineages but lower frequencies of NEA mtDNA lineages, while ST groups show the opposite. A potential explanation is that the ancestors of Thai HM groups were patrilocal, while the ancestors of Thai ST groups were matrilocal. Overall, these results attest to the impact of cultural practices on patterns of mtDNA vs. MSY variation.

Microarray Analysis of Gene Expression Involved in Butyrate-Resistant Colorectal Carcinoma HCT116 Cells

BACKGROUND

Resistance to chemotherapeutic agents is usually found in cancer stem cells (CSCs) and cancer stem-like cells that are often regarded as the target for cancer monitoring. However, the different patterns of their transcriptomic profiling is still unclear.

OBJECTIVE

This study aims to illustrate the transcriptomic profile of CSCs and butyrate-resistant colorectal carcinoma cells (BR-CRCs), by comparing them with parental colorectal cancer (CRC) cells in order to identify distinguishing transcription patterns of the CSCs and BR-CRCs.

METHODS

Parental CRC cells HCT116 (HCT116-PT) were cultured and induced to establish the butyrate resistant cell model (HCT116-BR). Commercial enriching of the HCT116-CSCs were grown in a tumorsphere suspension culture, which was followed firstly by the assessment of butyrate tolerance using MTT and PrestoBlue. Then their gene expression profiling was analyzed by microarray.

RESULTS

The results showed that both butyrate-resistant HCT116 cells (HCT116-BR) and HCT116-CSCs were more tolerant a butyrate effects than HCT116-PT cells. Differentially expressed gene profiles exhibited that IFI27, FOXQ1, PRF1, and SLC2A3 genes were increasingly expressed in CSCs, and were dramatically overexpressed in HCT116-BR cells when compared with HCT116-PT cells. Moreover, PKIB and LOC399959 were downregulated both in HCT116-CSCs and HCT116-BR cells.

CONCLUSION

Our findings shed light on the transcriptomic profiles of chemoresistant CRC cells. This data should be useful for further study to provide guidelines for clinical prognosis to determine the guidelines for CRC treatment, especially in patients with chemoresistance and designing novel anti-neoplastic agents.

Genetic structure of the ethnic Lao groups from mainland Southeast Asia revealed by forensic microsatellites

PURPOSE

Laotians and Lao Isan are widely spread Lao groups who live in Laos and northeastern Thailand, respectively. We explored the genetic structure between them and other ethnic groups from Thailand to clarify historical patterns of admixture between Tai-Kadai and Austroasiatic speakers, and to expand the forensic reference database for the region.

SUBJECTS AND METHODS

We combined new genetic data for 554 individuals from 12 populations, typed for 15 autosomal short tandem repeats, with available data from 14 populations from Thailand, for a total of 1,153 raw genotypes belonging to 26 populations. We calculated forensic parameters and performed various analyses on genetic diversity, genetic structure, genetic admixture, and genetic relationships among the studied populations.

RESULTS

Forensic estimators suggest a good power of discrimination with the combined power of exclusion ranging from 0.993628 to 0.999991 and a combined power of discrimination value greater than 0.99999999. Generally, the two Laotian groups were genetically similar, but the central Laotians from Vientiane have a closer genetic relationship to the Lao Isan than the northern Laotians from Luang Prabang. The Lao genetic ancestry forms the majority of the Lao Isan genetic makeup, while Austroasiatic ancestry is present at ∼10%-50%.

CONCLUSIONS

Lao Isan populations show signs of Lao ancestry and admixture with local Austroasiatic ancestry, which reflect historical migrations from Laos to Thailand. Lao speakers are genetically more homogeneous than Austroasiatic speakers, suggesting differential historical processes.

Contrasting Paternal and Maternal Genetic Histories of Thai and Lao Populations

The human demographic history of Mainland Southeast Asia (MSEA) has not been well studied; in particular, there have been very few sequence-based studies of variation in the male-specific portions of the Y chromosome (MSY). Here, we report new MSY sequences of ∼2.3 mB from 914 males and combine these with previous data for a total of 928 MSY sequences belonging to 59 populations from Thailand and Laos who speak languages belonging to three major Mainland Southeast Asia families: Austroasiatic, Tai-Kadai, and Sino-Tibetan. Among the 92 MSY haplogroups, two main MSY lineages (O1b1a1a* [O-M95*] and O2a* [O-M324*]) contribute substantially to the paternal genetic makeup of Thailand and Laos. We also analyze complete mitochondrial DNA genome sequences published previously from the same groups and find contrasting pattern of male and female genetic variation and demographic expansions, especially for the hill tribes, Mon, and some major Thai groups. In particular, we detect an effect of postmarital residence pattern on genetic diversity in patrilocal versus matrilocal groups. Additionally, both male and female demographic expansions were observed during the early Mesolithic (∼10 ka), with two later major male-specific expansions during the Neolithic period (∼4–5 ka) and the Bronze/Iron Age (∼2.0–2.5 ka). These two later expansions are characteristic of the modern Austroasiatic and Tai-Kadai groups, respectively, consistent with recent ancient DNA studies. We simulate MSY data based on three demographic models (continuous migration, demic diffusion, and cultural diffusion) of major Thai groups and find different results from mitochondrial DNA simulations, supporting contrasting male and female genetic histories.

Gene Combination of CD44 rs187116, CD133 rs2240688, NF-κB1 rs28362491 and GSTM1 Deletion as a Potential Biomarker in Risk Prediction of Breast Cancer in Lower Northern Thailand

Background:

Biomarkers play an important role in oncology, including risk assessment, treatment prediction, and monitoring the progression of disease. In breast cancer, many genes are used as biomarkers. Since, several SNP variations of hallmark – related genes have been reported to be of value in risk prediction in various cancers and populations, some genetic polymorphism loci were combined and reported as biomarkers for use in the risk assessment of breast cancer in Thai people.

Methods:

Twelve cancer gene hallmarks (15 polymorphic loci) were selected and genotyped in 184 breast cancer patients and 176 healthy individuals in Phitsanulok, Thailand.

Results:

AA genotype of CD44 rs187116 (c.67+4883G>A), the C allele of CD133 rs2240688 (c.*667A>C), the *2 allele (4 bp deletion) of NF-κB1 rs28362491 and the homozygous null allele genotype of GSTM1 were significantly associated with an increased risk of breast cancer (p<0.05). A combination of these 4 significant loci showed that AA-AA-*1*1-homozygous null allele genotype has the greatest correlation with increased risk of breast cancer (OR = 21.00; 95% CI: 1.77 to 248.11; p = 0.015), followed by GA-AA-*2*2- homozygous null allele genotype (p = 0.037) and GG-AC-*1*2- homozygous null allele genotype (p = 0.028).

Conclusion:

These findings suggest that the polymorphisms of CD44 rs187116 (c.67+4883G>A), CD133 rs2240688 (c.*667A>C), NF-κB1 rs28362491 and GSTM1 homozygous null allele genotype might be associated with an increased risk of breast cancer, and this gene combination could possibly be used as biomarkers for risk prediction, which would be of benefit in planning health surveillance and cancer prevention.

Association of Tissue-Specific DNA Methylation Alterations with α-Thalassemia Southeast Asian Deletion

In the wild-type allele, DNA methylation levels of 10 consecutive CpG sites adjacent to the upstream 5′-breakpoint of α-thalassemia Southeast Asian (SEA) deletion are not different between placenta and leukocytes. However, no previous study has reported the map of DNA methylation in the SEA allele. This report aims to show that the SEA mutation is associated with DNA methylation changes, resulting in differential methylation between placenta and leukocytes. Methylation-sensitive high-resolution analysis was used to compare DNA methylation among placenta, leukocytes, and unmethylated control DNA. The result indicates that the DNA methylation between placenta and leukocyte DNA is different and shows that the CpG status of both is not fully unmethylated. Mapping of individual CpG sites was performed by targeted bisulfite sequencing. The DNA methylation level of the 10 consecutive CpG sites was different between placenta and leukocyte DNA. When the 10th CpG of the mutation allele was considered as a hallmark for comparing DNA methylation level, it was totally different from the unmethylated 10th CpG of the wild-type allele. Finally, the distinct DNA methylation patterns between both DNA were extracted. In total, 24 patterns were found in leukocyte samples and 9 patterns were found in placenta samples. This report shows that the large deletion is associated with DNA methylation change. In further studies for clinical application, the distinct DNA methylation pattern might be a potential marker for detecting cell-free fetal DNA.

Genetic and linguistic correlation of the Kra-Dai-speaking groups in Thailand

The Kra-Dai linguistic family includes Thai and Lao as well as a great number of languages spoken by ethnic minorities in Southeast Asia. In Thailand, a dozen of other Kra-Dai languages are spoken in addition to Thai, the national language. The genetic structure of the Kra-Dai-speaking populations in Thailand has been studied extensively using uniparentally inherited markers. To extend this line of genetic investigation, this study used 15 autosomal microsatellites of 500 individuals from 11 populations, belonging to nine Kra-Dai ethnicities, namely, the Kaleung, Phu Thai, Saek, Nyo, Lao Isan, Yuan, Black Tai, Phuan and Lue. These ethnolinguistic groups are dispersed in three different geographic regions of Thailand, that is, Northern, Northeastern and Central. The results show a very low average of pairwised F(st) (0.0099), as well as no population substructure based on STRUCTURE analysis, indicating genetic homogeneity within the Kra-Dai-speaking group, possibly owing to shared linguistic ancestry. The Mantel test, an analysis of molecular variance, and the approximate Bayesian computation procedure employed to evaluate potential factors for driving genetic diversity revealed that language is the predominant factor affecting genetic variations, whereas geography is not. The result of distance-based clustering analyses and spatial analysis of molecular variance revealed genetic distinctions of some populations, reflecting the effects of genetic drift and gene flow on allele frequency within populations, in concordance with the result of R-matrix regression. The genetic and linguistic affiliations of the contemporary Kra-Dai-speaking groups are consistent with each other despite certain deviation due to various evolutionary factors that may have occurred during their migrations and resettlements.

Admixed origin of the Kayah (Red Karen) in Northern Thailand revealed by biparental and paternal markers

This study analyzes the autosomal short tandem repeats (STRs) variation and the presence of Y chromosomal haplogroups from 44 individuals of the Kayah or Red Karen (KA) in Northern Thailand. The results based on autosomal STRs indicated that the KA exhibited closer genetic relatedness to populations from adjacent regions in Southeast Asia (SEA) than populations from Northeast Asia (NEA) and Tibet. Moreover, an admixed origin of the KA forming three population groups was observed: NEA, Southern China, and Northern Thailand. The NEA populations made a minor genetic contribution to the KA, while the rest came from populations speaking Sino-Tibetan (ST) languages from Southern China and Tai-Kadai (TK) speaking groups from Northern Thailand. The presence of six paternal haplogroups, composed of dual haplogroups prevalent in NEA (NO, N, and D1) and SEA (O2 and O3) as well as the intermediate genetic position of the KA between the SEA and NEA also indicated an admixed origin of male KA lineages. Our genetic results thus agree with findings in linguistics that Karenic languages are ST languages that became heavily influenced by TK during their southward spread. A result of the Mongol invasions during the 13th century A.D. is one possible explanation for genetic contribution of NEA to the KA.

Thailand mutation and variation database (ThaiMUT)

With the completion of the human genome project, novel sequencing and genotyping technologies had been utilized to detect mutations. Such mutations have continually been produced at exponential rate by researchers in various communities. Based on the population's mutation spectra, occurrences of Mendelian diseases are different across ethnic groups. A proportion of Mendelian diseases can be observed in some countries at higher rates than others. Recognizing the importance of mutation effects in Thailand, we established a National and Ethnic Mutation Database (NEMDB) for Thai people. This database, named Thailand Mutation and Variation database (ThaiMUT), offers a web-based access to genetic mutation and variation information in Thai population. This NEMDB initiative is an important informatics tool for both research and clinical purposes to retrieve and deposit human variation data. The mutation data cataloged in ThaiMUT database were derived from journal articles available in PubMed and local publications. In addition to collected mutation data, ThaiMUT also records genetic polymorphisms located in drug related genes. ThaiMUT could then provide useful information for clinical mutation screening services for Mendelian diseases and pharmacogenomic researches. ThaiMUT can be publicly accessed from http://gi.biotec.or.th/thaimut.

Genetic evidence supports linguistic affinity of Mlabri--a hunter-gatherer group in Thailand

Background

The Mlabri are a group of nomadic hunter-gatherers inhabiting the rural highlands of Thailand. Little is known about the origins of the Mlabri and linguistic evidence suggests that the present-day Mlabri language most likely arose from Tin, a Khmuic language in the Austro-Asiatic language family. This study aims to examine whether the genetic affinity of the Mlabri is consistent with this linguistic relationship, and to further explore the origins of this enigmatic population.

Results

We conducted a genome-wide analysis of genetic variation using more than fifty thousand single nucleotide polymorphisms (SNPs) typed in thirteen population samples from Thailand, including the Mlabri, Htin and neighboring populations of the Northern Highlands, speaking Austro-Asiatic, Tai-Kadai and Hmong-Mien languages. The Mlabri population showed higher LD and lower haplotype diversity when compared with its neighboring populations. Both model-free and Bayesian model-based clustering analyses indicated a close genetic relationship between the Mlabri and the Htin, a group speaking a Tin language.

Conclusion

Our results strongly suggested that the Mlabri share more recent common ancestry with the Htin. We thus provided, to our knowledge, the first genetic evidence that supports the linguistic affinity of Mlabri, and this association between linguistic and genetic classifications could reflect the same past population processes.

Mapping human genetic diversity in Asia

Asia harbors substantial cultural and linguistic diversity, but the geographic structure of genetic variation across the continent remains enigmatic. Here we report a large-scale survey of autosomal variation from a broad geographic sample of Asian human populations. Our results show that genetic ancestry is strongly correlated with linguistic affiliations as well as geography. Most populations show relatedness within ethnic/linguistic groups, despite prevalent gene flow among populations. More than 90% of East Asian (EA) haplotypes could be found in either Southeast Asian (SEA) or Central-South Asian (CSA) populations and show clinal structure with haplotype diversity decreasing from south to north. Furthermore, 50% of EA haplotypes were found in SEA only and 5% were found in CSA only, indicating that SEA was a major geographic source of EA populations.

Expanding the phenotypic spectrum of acro-cardio-facial syndrome (ACFS): Exclusion of P63 mutation

Acro-cardio-facial syndrome (ACFS) is a rare autosomal recessive congenital malformation syndrome; consistent features include ectrodactyly, cleft lip/palate with minor facial anomalies, genital abnormalities, mental retardation, and growth retardation. Five cases have been reported. We report on a new patient with ACFS syndrome. In addition to the characteristic features of ACFS, the reported patient also has mild scoliosis, hemivertebrae and subclinical hyperthyroidism. These additional features may expand the phenotypic spectrum of the syndrome.

Genetic variation in Northern Thailand Hill Tribes: origins and relationships with social structure and linguistic differences

Background

Ethnic minorities in Northern Thailand, often referred to as Hill Tribes, are considered an ideal model to study the different genetic impact of sex-specific migration rates expected in matrilocal (women remain in their natal villages after the marriage and men move to their wife's village) and patrilocal societies (the opposite is true). Previous studies identified such differences, but little is known about the possible interaction with another cultural factor that may potentially affect genetic diversity, i.e. linguistic differences. In addition, Hill Tribes started to migrate to Thailand in the last centuries from different Northern areas, but the history of these migrations, the level of genetic legacy with their places of origin, and the possible confounding effects related to this migration history in the patterns of genetic diversity, have not been analysed yet. Using both original and published data on the Hill Tribes and several other Asian populations, we focused on all these aspects.

Results

Genetic variation within population at mtDNA is lower in matrilocal, compared to patrilocal, tribes. The opposite is true for Y-chromosome microsatellites within the Sino-Tibetan linguistic family, but Hmong-Mien speaking patrilocal groups have a genetic diversity very similar to the matrilocal samples. Population divergence ranges between 5% and 14% at mtDNA sequences, and between 5% and 36% at Y- chromosomes STRs, and follows the sex-specific differences expected in patrilocal and matrilocal tribes. On the average, about 2 men and 14 women, and 4 men and 4 women, are exchanged in patrilocal and matrilocal tribes every generation, respectively. Most of the Hill Tribes in Thailand seem to preserve a genetic legacy with their likely geographic origin, with children adoption probably affecting this pattern in one tribe.

Conclusion

Overall, the sex specific genetic signature of different postmarital habits of residence in the Hill Tribes is robust. However, specific perturbations related to linguistic differences, population specific traits, and the complex migratory history of these groups, can be identified. Additional studies in different populations are needed, especially to obtain more precise estimates of the migration parameters.