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Characterization of genetic sequence variation of 58 STR loci in four major population groups

Novroski NMM, King JL, Churchill JD, Seah LH, Budowle B

Forensic Sci Int Genet, 2016 11;25:214-226.
PMID: 27697609 DOI: 10.1016/j.fsigen.2016.09.007

Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X-chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X-chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X-chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X-chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X-chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X-chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data.

Matched MeSH terms: Continental Population Groups/genetics*
Population and performance analyses of four major populations with Illumina's FGx Forensic Genomics System

Churchill JD, Novroski NMM, King JL, Seah LH, Budowle B

Forensic Sci Int Genet, 2017 09;30:81-92.
PMID: 28651097 DOI: 10.1016/j.fsigen.2017.06.004

The MiSeq FGx Forensic Genomics System (Illumina) enables amplification and massively parallel sequencing of 59 STRs, 94 identity informative SNPs, 54 ancestry informative SNPs, and 24 phenotypic informative SNPs. Allele frequency and population statistics data were generated for the 172 SNP loci included in this panel on four major population groups (Chinese, African Americans, US Caucasians, and Southwest Hispanics). Single-locus and combined random match probability values were generated for the identity informative SNPs. The average combined STR and identity informative SNP random match probabilities (assuming independence) across all four populations were 1.75E-67 and 2.30E-71 with length-based and sequence-based STR alleles, respectively. Ancestry and phenotype predictions were obtained using the ForenSeq™ Universal Analysis System (UAS; Illumina) based on the ancestry informative and phenotype informative SNP profiles generated for each sample. Additionally, performance metrics, including profile completeness, read depth, relative locus performance, and allele coverage ratios, were evaluated and detailed for the 725 samples included in this study. While some genetic markers included in this panel performed notably better than others, performance across populations was generally consistent. The performance and population data included in this study support that accurate and reliable profiles were generated and provide valuable background information for laboratories considering internal validation studies and implementation.

Matched MeSH terms: Continental Population Groups/genetics*
The Endurance and Contestations of Colonial Constructions of Race Among Malaysians and Singaporeans

Reddy G, Gleibs IH

Front Psychol, 2019;10:792.
PMID: 31040805 DOI: 10.3389/fpsyg.2019.00792

Psychological literature on race has discussed in depth how racial identities are dialogically constructed and context dependent. However, racial identity construction is often not compared across different socio-political contexts. By researching racial identity construction in three different multicultural countries, Malaysia, Singapore, and the United Kingdom, we examined how three racial identities, Chinese, Malay, and Indian, are constructed among Malaysians and Singaporeans in this qualitative study comprised of 10 focus group discussions (N = 39). We applied Dialogical Analysis to the data. This paper shows that both racial ingroups and outgroups constructed all three racial identities, with ingroups constructing their identities more heterogeneously compared to outgroups. Participants also engaged with colonial constructions of the three racial identities. The geographical locations, and therefore their perceptual contexts, of the participants differed. Yet, colonial constructions of race endured in contemporary identity construction and were contested in the group settings. We conclude that the socio-political context as understood by the context of colonialism and post-coloniality influenced their racial identity constructions. Participants, regardless of differences in geographical location, used similar colonial constructions of Malay, Chinese, and Indian identities to position themselves as well as Others in their group interactions. These findings show that there is value in conceptualising the context beyond that which individuals are immediately presented with, and that psychologists should consider the inclusion of cultural legacies of colonialism in their conceptualisation of the present context.

Matched MeSH terms: Continental Population Groups
Fulltext Mental Health Conceptualization and Resilience Factors in the Kalasha Youth: An Indigenous Ethnic and Religious Minority Community in Pakistan

Choudhry FR, Khan TM, Park MS, Golden KJ

Front Public Health, 2018;6:187.
PMID: 30065918 DOI: 10.3389/fpubh.2018.00187

The Kalasha are a religious, ethnic, and linguistic minority community in Pakistan. They are indigenous people living in remote valleys of the Hindu Kush Mountains in northern Pakistan, neighboring Afghanistan. The Kalasha are pastoral, as well as agricultural people to some extent, although they are increasingly facing pressures from globalization and social change, which may be influencing youth and community development. Their traditional world view dichotomizes and emphasizes on the division of the pure (Onjeshta) and the impure (Pragata). There remains a scarcity of literature on mental health and resilience of indigenous communities in South Asia and Pakistan generally, and the polytheistic Kalasha community specifically. Thus, the current study was conducted with the aim to explore the cultural protective factors (resilience) of the Kalasha youth (adolescents and emerging adults) and to explore their perceived etiological understandings and preferred interventions for mental health support systems. The theoretical framework of Bronfenbrenner's (1, 2) ecological systems model was used. Interpretative Phenomenological Analysis (IPA) was conducted, considering the advantage of its idiographic approach and the "double hermeneutic" analytic process. This methodology was consistent with the aim to understand and make sense of mental health and resilience from the Kalasha indigenous perspective. A total of 12 in-depth interviews were conducted with adolescents and emerging adults (5 males, 7 females), along with ethnographic observations. The analysis revealed 3 superordinate themes of mental health perceptions and interventions, each with more specific emergent themes: (1) Psychological Resilience/Cultural Protective Factors Buffering Against Mental Health Problems (Intra-Communal Bonding & Sharing; Kalasha Festivals & Traditions; Purity Concept; Behavioral Practice of Happiness and Cognitive Patterns); (2) Perceived Causes of Mental Health Issues (Biological & Psychosocial; Supernatural & Spiritual; Environmental); and (3) Preferred Interventions [Shamanic Treatment; Ta'awiz (Amulets); Communal Sharing & Problem Solving; Medical Treatment; Herbal Methods]. The overall findings point to the need for developing culturally-sensitive and indigenous measures and therapeutic interventions. The findings highlighted the Kalasha cultural practices which may promote resilience. The findings also call for indigenous sources of knowledge to be considered when collaboratively designing public health programs.

Matched MeSH terms: Population Groups
Fulltext Epidemiology of Helicobacter pylori infection and public health implications

Goh KL, Chan WK, Shiota S, Yamaoka Y

Helicobacter, 2011 Sep;16 Suppl 1:1-9.
PMID: 21896079 DOI: 10.1111/j.1523-5378.2011.00874.x

This review summarizes studies on the epidemiology and public health implications of Helicobacter pylori published in peer-reviewed journals from April 2010 through March 2011. Prevalence rates vary widely between different geographical regions and ethnic groups. An interesting study from the USA identified the degree of African ancestry as an independent predictor of H. pylori infection. Two studies have demonstrated early childhood as the period of transmission of infection and identified an infected sibling as an important risk factor. An oral-oral route of spread has been substantiated with several studies showing the presence of H. pylori in the oral cavity. Studies have shown the presence of H. pylori in drinking water and the role of poor living conditions and sanitation in H. pylori infection, supporting an oral-fecal route of spread. Screening for H. pylori as a gastric cancer pre-screening strategy has been described in Japan, and the importance of H. pylori eradication as a gastric cancer-prevention strategy has now been further emphasized in Japanese guidelines. Two studies have shown a decrease in the burden of dyspepsia and peptic ulcer disease with H. pylori eradication.

Matched MeSH terms: Continental Population Groups
Non-alcoholic fatty liver disease in a young multiracial Asian population: a worrying ethnic predilection in Malay and Indian males

Chan WK, Bahar N, Razlan H, Vijayananthan A, Sithaneshwar P, Goh KL

Hepatol Int, 2014 Jan;8(1):121-7.
PMID: 26202413 DOI: 10.1007/s12072-013-9510-8

PURPOSE: Previous studies on multiracial Malaysian populations found inordinately high prevalence of NAFLD among Malays and Indians. Whether the prevalence of NAFLD is different among young adults of different ethnic origins is not known. We aimed to determine racial differences in NAFLD in a young multiracial Malaysian population and associated factors.
METHODS: This was a cross-sectional study on medical students from the University of Malaya. Diagnosis of NAFLD was by transabdominal ultrasonography and following exclusion of significant alcohol intake and other causes of chronic liver disease.
RESULTS: Data of 469 subjects were analyzed (mean age 23.2 ± 2.4 years, 40.3 % male). The racial distribution was: Chinese 53.9 %, Malay 30.5 % and Indian 15.6 %. The overall prevalence of NAFLD was 7.9 %. Subjects with NAFLD were older, had greater BMI and WC, higher SBP and DBP, higher FBS, serum TG and LDL levels, and lower serum HDL level. The prevalence of NAFLD was higher among males compared to females (17.9 % vs. 3.3 %, p

Matched MeSH terms: Continental Population Groups
[Descriptive epidemiology of urolithiasis]

Kodama H, Ohno Y

Hinyokika Kiyo, 1989 Jun;35(6):923-34.
PMID: 2678977

In this paper, urolithiasis is remarked from the standpoint of descriptive epidemiology, which examines the frequency distribution of a given disease in a population in terms of time, place and personal characteristics with an aim of identifying risk factors or some clues to the etiology. Some descriptive epidemiological features of urolithiasis are summarized. Prevalence rate is around 4% (4-15% in males and 4-8% in females), and incidence rate varies from area to area: 53.2 per 100,000 population in 1975 in Japan, 364 in 1976 in Malaysia, and 540 in 1979 in West Germany. Prevalence and/or incidence rates have, in general, increased in the developed countries since World War II and in the developing countries as well, where upward trends are quite analogous to the trends observed in the nineteenth century in Europe. Recurrence rate, which is much higher in males than in females, ranges from 31% to 75%, depending on the follow-up periods. In the industrialized countries, upper urinary (renal and ureteral) stones account for more than 90% of total stones, which are ordinarily calcium complexes in composition. More common in the developing countries are lower urinary (bladder and urethral) stones, frequently composed of magnesium ammonium phosphate, which indicates a close association with urinary tract infections. Variations in frequency are evident by season and by region within a country. Age and sex differentials in urinary stone formers are substantial: more common in males 30-40 years old in the industrialized countries and in children under 10 years old in the developing countries. Racial differentials are also noted; blacks appear to suffer less frequently than whites. Stone formers experience more frequent episodes of stone formation in their family members, particularly father and brothers, than non-stone formers. These findings on racial differentials and family preponderance suggest the possible relevance of genetic factors in stone formation. Stone formers are more likely to be occupationally sedentary and socially affluent. This observation and differentials by age and sex suggest the probable relevance of lifestyle and environmental factors in stone formation. Epidemiological factors incriminated for stone formation will be discussed in a separate paper.

Matched MeSH terms: Continental Population Groups
Fulltext Population genetic study among the Orange Asli (Semai Senoi) of Malaysia: Malayan aborigines

Saha N, Mak JW, Tay JS, Liu Y, Tan JA, Low PS, et al.

Hum Biol, 1995 Feb;67(1):37-57.
PMID: 7721278

A population genetic study was undertaken to provide gene frequency data on the additional blood genetic markers in the Semai and to estimate the genetic relations between the Semai and their neighboring and linguistically related populations by genetic distance and principal components analyses. Altogether 10 polymorphic and 7 monomorphic blood genetic markers (plasma proteins and red cell enzymes) were studied in a group of 349 Senoi Semai from 11 aboriginal settlements (villages) in the Pahang State of western Malaysia. Both the red cell glucose-6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase (PGD) loci reveal the presence of polymorphic frequencies of a nondeficient slow allele at the G6PD locus and a fast allele at the PGD locus. The Semai are characterized by high prevalences of ahaptoglobinemia and G6PD deficiency, high frequencies of HP*1, HB*E, RH*R1, ACP*C, GLO1*1, PGM1*2+, and GC*1F and corresponding low frequencies of ABO*A, HbCoSp, HB*B0, TF*D, CHI, and GC*2. Genetic distance analyses by both cluster and principal components models were performed between the Semai and 14 other populations (Malay; Javanese; Khmer; Veddah; Tamils of Malaysia, Sri Lanka, and India; Sinhalese; Oraon; Toda and Irula of India; Chinese; Japanese; Koreans) on the basis of 30 alleles at 7 polymorphic loci. A more detailed analysis using 53 alleles at 13 polymorphic loci with 10 populations was carried out. Both analyses give genetic evidence of a close relationship between the Semai and the Khmer of Cambodia. Furthermore, the Semai are more closely related to the Javanese than to their close neighbors--the Malay, Chinese, and Tamil Indians. There is no evidence for close genetic relationship between the Semai and the Veddah or other Indian tribes. The evidence fits well with the linguistic relationship of the Semai with the Mon-Khmer branch of the Austro-Asiatic language family.

Matched MeSH terms: Continental Population Groups
Changing sex ratio of mortality in the Semai Senoi, 1969-1987

Fix AG

Hum Biol, 1991 Apr;63(2):211-20.
PMID: 2019414

An excess of male over female deaths is characteristic of modern national populations, whereas in some high-mortality societies female mortality exceeds that of males. Among the Semai Senoi, a Malaysian Orang Asli ("aboriginal") population, women experienced higher mortality than males in the decades before 1969. This differential occurred in all age classes older than 15 years so that the sex ratio progressively increased with age. A recent (1987) restudy of the Semai population found that sex-specific differential mortality is much reduced. A comparison of the 1969 and 1987 life tables shows a sharp shift in the sex ratios of mortality for the post-15-year-old age classes (the geometric means of age classes 15-44 were 0.768 in 1969 and 0.997 in 1987) so that male and female expectations of further life at age 15 are now nearly identical. In contrast to the best-known cases of high female mortality (mostly in South Asia), Semai sex differential mortality does not include the childhood ages. The Semai have traditionally been relatively sexually egalitarian, and sex bias in care has not occurred. Analysis of sex-specific causes of death for the pre-1969 population suggests that maternal mortality is the major cause of the excess female deaths. The reduced number of maternal deaths seems largely due to better health care, particularly the availability of hospital services. Interestingly, the reduction in female mortality has occurred simultaneously with increased fertility, and overall mortality has continued at relatively high levels (eO less than 36). Thus, rather than forming a component of a unitary demographic transition, declining sex differences in mortality can be accounted for by a specific factor, better maternal care.

Matched MeSH terms: Continental Population Groups
Genotype associations among seven apolipoprotein B polymorphisms in a population of Orang Asli of western Malaysia

Gajra B, Candlish JK, Heng CK, Mak JW, Saha N

Hum Biol, 1997 Oct;69(5):629-40.
PMID: 9299883

Associations among seven apolipoprotein B (APOB) gene polymorphisms [C-T promoter site; Leu-Ala-Leu signal peptide (SP) insertion/deletion; AG C,G site at codon 71; AG A1,D site at codon 591; XbaI site at codon 2488; AG H,I site at codon 3611; and AG T,Z site at codon 4154] were investigated in 195 members of an Orang Asli (aborigine) population from western Malaysia. Frequencies of the rare alleles for all these polymorphisms turned out to be low when compared with European but not Asian populations. The AG H,I site was not polymorphic. The highly polymorphic sites are in linkage disequilibrium among themselves, as shown by their delta values: SP 24,27 and AG C,G, 0.68; SP 24,27 and AG A1,D, 0.71; XbaI and AG C,G, 0.64; XbaI and AG A1,D, 0.57; SP 24,27 and XbaI, 0.48; and AG C,G and AG A1,D, 0.68. Ten unequivocal haplotypes on the basis of six sites (excluding the promoter polymorphism) were observed, and they represent 80% of the sample. The frequency of haplotype SP27,G,A1,X-,I,T, defined by the common homozygotes at all the sites for the APOB gene was 0.7, compared with 0.22 in Europeans. The ancestral haplotype SP27,G,D,X-,I,T was present at low frequency (0.01) in both the Orang Asli and Europeans. A cladogram constructed on the basis of haplotypes in the Orang Asli shows two different lines of evolution and that other haplotypes evolved by subsequent mutations on the ancestral haplotype.

Matched MeSH terms: Continental Population Groups
The population genomic landscape of human genetic structure, admixture history and local adaptation in Peninsular Malaysia

Deng L, Hoh BP, Lu D, Fu R, Phipps ME, Li S, et al.

Hum Genet, 2014 Sep;133(9):1169-85.
PMID: 24916469 DOI: 10.1007/s00439-014-1459-8

Peninsular Malaysia is a strategic region which might have played an important role in the initial peopling and subsequent human migrations in Asia. However, the genetic diversity and history of human populations--especially indigenous populations--inhabiting this area remain poorly understood. Here, we conducted a genome-wide study using over 900,000 single nucleotide polymorphisms (SNPs) in four major Malaysian ethnic groups (MEGs; Malay, Proto-Malay, Senoi and Negrito), and made comparisons of 17 world-wide populations. Our data revealed that Peninsular Malaysia has greater genetic diversity corresponding to its role as a contact zone of both early and recent human migrations in Asia. However, each single Orang Asli (indigenous) group was less diverse with a smaller effective population size (N(e)) than a European or an East Asian population, indicating a substantial isolation of some duration for these groups. All four MEGs were genetically more similar to Asian populations than to other continental groups, and the divergence time between MEGs and East Asian populations (12,000--6,000 years ago) was also much shorter than that between East Asians and Europeans. Thus, Malaysian Orang Asli groups, despite their significantly different features, may share a common origin with the other Asian groups. Nevertheless, we identified traces of recent gene flow from non-Asians to MEGs. Finally, natural selection signatures were detected in a batch of genes associated with immune response, human height, skin pigmentation, hair and facial morphology and blood pressure in MEGs. Notable examples include SYN3 which is associated with human height in all Orang Asli groups, a height-related gene (PNPT1) and two blood pressure-related genes (CDH13 and PAX5) in Negritos. We conclude that a long isolation period, subsequent gene flow and local adaptations have jointly shaped the genetic architectures of MEGs, and this study provides insight into the peopling and human migration history in Southeast Asia.

Matched MeSH terms: Population Groups/ethnology; Population Groups/genetics*
Effects of the apolipoprotein(a) size polymorphism on the lipoprotein(a) concentration in 7 ethnic groups

Sandholzer C, Hallman DM, Saha N, Sigurdsson G, Lackner C, Császár A, et al.

Hum Genet, 1991 Apr;86(6):607-14.
PMID: 2026424

Apolipoprotein(a) [apo(a)] exhibits a genetic size polymorphism explaining about 40% of the variability in lipoprotein(a) [Lp(a)] concentration in Tyroleans. Lp(a) concentrations and apo(a) phenotypes were determined in 7 ethnic groups (Tyrolean, Icelandic, Hungarian, Malay, Chinese, Indian, Black Sudanese) and the effects of the apo(a) size polymorphism on Lp(a) levels were estimated in each group. Average Lp(a) concentrations were highly significantly different among these populations, with the Chinese (7.0 mg/dl) having the lowest and the Sudanese (46 mg/dl) the highest levels. Apo(a) phenotype and derived apo(a) allele frequencies were also significantly different among the populations. Apo(a) isoform effects on Lp(a) levels were not significantly different among populations. Lp(a) levels were however roughly twice as high in the same phenotypes in the Indians, and several times as high in the Sudanese, compared with Caucasians. The size variation of apo(a) explains from 0.77 (Malays) to only 0.19 (Sudanese) of the total variability in Lp(a) levels. Together these data show (I) that there is considerable heterogeneity of the Lp(a) polymorphism among populations, (II) that differences in apo(a) allele frequencies alone do not explain the differences in Lp(a) levels among populations and (III) that in some populations, e.g. Sudanese Blacks, Lp(a) levels are mainly determined by factors that are different from the apo(a) size polymorphism.

Matched MeSH terms: Continental Population Groups/genetics*
Gc subtyping in Malaysians and in Indonesians from north Sumatra

Tan SG, Gan YY, Asuan K, Abdullah F

Hum Genet, 1981;59(1):75-6.
PMID: 10819027

Malays, Chinese and Indians from peninsular Malaysia; Ibans and Bidayuh from Sarawak state, Northern Borneo; and Bataks, Minangkabau and Javanese from North Sumatra, Indonesia, were subtyped for Gc (group-specific component) by polyacrylamide gel isoelectric focusing. All eight populations investigated were found to be polymorphic for three common alleles, Gc1F, Gc1S and Gc2.

Matched MeSH terms: Continental Population Groups/genetics*
Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia

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.

Matched MeSH terms: Population Groups/genetics*
Effect of apolipoprotein E variants on plasma lipids and apolipoproteins in the Orang Asli ('aborigines') of Malaysia

Gajra B, Candlish JK, Saha N, Mak JW, Tay JS

Hum. Hered., 1994 Jul-Aug;44(4):209-13.
PMID: 8056432

Members of the Semai group of Orang Asli ('aborigines') in peninsular Malaysia were examined for apolipoprotein E (apo E) variants in relation to plasma total cholesterol (TC), high density lipoprotein cholesterol, low density lipoprotein cholesterol (LDLC), triglycerides (TG), apolipoprotein AI and apolipoprotein B (apo B). The e2 and e4 alleles were found to be higher than in most other groups as reported. The sample as a whole was normotriglyceridaemic (mean plasma TG, 1.5 mmol/l) and very markedly hypocholesterolaemic (mean plasma TC 1.7 mmol/l). The distribution of apo E variants was not related to any of the plasma lipids or apolipoprotein fractions using results from all subjects, but if a distinctly hypertriglyceridaemic sub-section was omitted (TG > 1.7 mmol/l) then apo E variants were determinants of plasma TC, LDLC, and apo B concentrations, the lower values of these being associated with the 2-2 and 2-3 genotypes, and the higher with 3-4, and 4-4.

Matched MeSH terms: Continental Population Groups
Lactic dehydrogenase variants in different racial groups in Malaysia

Lie-Injo LE, Lopez CG, Ganesan J

Hum. Hered., 1973;23(5):487-91.
PMID: 4799059
Matched MeSH terms: Continental Population Groups
Electrophoretic variants of 6-phosphogluconate dehydrogenase (6PGD) and phosphohexose isomerase (PHI) in different racial groups in Malaysia

Eng LI, Welch QB

Hum. Hered., 1972;22(4):338-43.
PMID: 4647199
Matched MeSH terms: Continental Population Groups
Distribution of HLA-A, -B and -DRB1 alleles in the Kensiu and Semai Orang Asli sub-groups in Peninsular Malaysia

Tasnim AR, Allia S, Edinur HA, Panneerchelvam S, Zafarina Z, Norazmi MN

Hum Immunol, 2016 Aug;77(8):618-619.
PMID: 27296326 DOI: 10.1016/j.humimm.2016.06.009

The earliest settlers in Peninsular Malaysia are the Orang Asli population, namely Semang, Senoi and Proto Malays. In the present study, we typed the HLA-A, -B and -DRB1 loci of the Kensiu and Semai Orang Asli sub-groups. Sequence-based HLA typing was performed on 59 individuals from two Orang Asli sub-groups. A total of 11, 18 and 14 HLA-A, -B and -DRB1 alleles were identified, respectively. These data are available in the Allele Frequencies Net Database under the population name "Malaysia Kedah Kensiu" and "Malaysia Pahang Semai".

Matched MeSH terms: Population Groups
Distribution of cytokine gene polymorphisms in six Orang Asli subgroups in Peninsular Malaysia

Norhalifah HK, Syafawati WU, Che Mat NF, Chambers GK, Edinur HA

Hum Immunol, 2016 Apr;77(4):338-9.
PMID: 26820937 DOI: 10.1016/j.humimm.2016.01.015

Cytokines are involved in immune responses and the pathogenesis of various diseases. Allelic variations within the genes coding for various ∼30kDa cytokine protein/glycoproteins have been reported for many populations and have been the subjects of many ancestry and health analyses. In this study, we typed 22 single nucleotide polymorphisms (SNPs) in 13 cytokine genes of 165 Orang Asli individuals by using sequence specific primer-polymerase chain reaction (SSP-PCR) assay. The volunteers came from all across the Peninsular of Malaysia and belong to six Orang Asli subgroups; Batek, Kensiu, Lanoh, Che Wong, Semai and Orang Kanaq. Here we report our general findings and original genotype data and their associated analyses (Hardy-Weinberg proportions, estimation of allele and haplotype frequencies) can be found in the supplementary files and will be held at Allele Frequency Net Database (AFND).

Matched MeSH terms: Population Groups
Fulltext Combined protein- and nucleic acid-level effects of rs1143679 (R77H), a lupus-predisposing variant within ITGAM

Maiti AK, Kim-Howard X, Motghare P, Pradhan V, Chua KH, Sun C, et al.

Hum Mol Genet, 2014 Aug 1;23(15):4161-76.
PMID: 24608226 DOI: 10.1093/hmg/ddu106

Integrin alpha M (ITGAM; CD11b) is a component of the macrophage-1 antigen complex, which mediates leukocyte adhesion, migration and phagocytosis as part of the immune system. We previously identified a missense polymorphism, rs1143679 (R77H), strongly associated with systemic lupus erythematosus (SLE). However, the molecular mechanisms of this variant are incompletely understood. A meta-analysis of published and novel data on 28 439 individuals with European, African, Hispanic and Asian ancestries reinforces genetic association between rs1143679 and SLE [Pmeta = 3.60 × 10(-90), odds ratio (OR) = 1.76]. Since rs1143679 is in the most active region of chromatin regulation and transcription factor binding in ITGAM, we quantitated ITGAM RNA and surface protein levels in monocytes from patients with each rs1143679 genotype. We observed that transcript levels significantly decreased for the risk allele ('A') relative to the non-risk allele ('G'), in a dose-dependent fashion: ('AA' < 'AG' < 'GG'). CD11b protein levels in patients' monocytes were directly correlated with RNA levels. Strikingly, heterozygous individuals express much lower (average 10- to 15-fold reduction) amounts of the 'A' transcript than 'G' transcript. We found that the non-risk sequence surrounding rs1143679 exhibits transcriptional enhancer activity in vivo and binds to Ku70/80, NFKB1 and EBF1 in vitro, functions that are significantly reduced with the risk allele. Mutant CD11b protein shows significantly reduced binding to fibrinogen and vitronectin, relative to non-risk, both in purified protein and in cellular models. This two-pronged contribution (nucleic acid- and protein-level) of the rs1143679 risk allele to decreasing ITGAM activity provides insight into the molecular mechanisms of its potent association with SLE.

Matched MeSH terms: Continental Population Groups

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