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Genetic polymorphisms of TP53-binding protein 1 (TP53BP1) gene and association with breast cancer risk

Naidu R, Har YC, Taib NA

APMIS, 2011 Jul;119(7):460-7.
PMID: 21635553 DOI: 10.1111/j.1600-0463.2011.02753.x

In the present study, we evaluated the association between the TP53BP1 Glu353Asp and T-885G polymorphisms and breast cancer risk as well as with the clinicopathological characteristics of the patients. Genotyping of these polymorphisms was performed on 387 breast cancer patients and 252 normal and healthy women who had no history of any malignancy using PCR-RFLP method in a hospital-based Malaysian population. Breast cancer risk was not observed among women who were heterozygous (OR(adj) = 0.887; 95% CI, 0.632-1.245) or homozygous (OR(adj) = 1.083; 95% CI, 0.595-1.969) for Asp allele, and those carriers of Asp allele (OR(adj) = 0.979; 95% CI, 0.771-1.243). Similarly, women who were TG heterozygotes (OR(adj) = 1.181; 95% CI, 0.842-1.658) or GG homozygotes (OR(adj) = 1.362; 95% CI, 0.746-2.486) and carriers of G allele (OR(adj) = 1.147; 95% CI, 0.903-1.458) were not associated with increased risk of breast cancer. Asp allele genotype was significantly associated with ER negativity (p = 0.0015) and poorly differentiated tumours (p = 0.008), but G allele genotype was not associated with the clinicopathological characteristics. In conclusion, Glu353Asp and T-885G polymorphic variants might not have an influence on breast cancer risk, thus might not be potential candidates for cancer susceptibility. Glu353Asp variant might be associated with tumour aggressiveness as defined by its association with ER negativity and poorly differentiated tumours.

Matched MeSH terms: Gene Frequency
Dermatoglyphic patterns in schizophrenic patients

Varma SL, Chary TV, Singh S, Azhar MZ, Dharap AS

Acta Psychiatr Scand, 1995 Mar;91(3):213-5.
PMID: 7625199

Schizophrenics (n = 250) and normal controls (n = 90) were studied to investigate and compare their dermatoglyphic patterns. Their fingerprint patterns were studied. The frequency of arches in the patient and control groups was similar. The frequency of loops in the control group was higher than in the patient group, and the trend was consistent in all the digits. The whorls in the patient group showed an increase over the control group in all the digits, although this finding was not statistically significant.

Matched MeSH terms: Gene Frequency/genetics
Human leucocyte antigen determinants of susceptibility to Barrett's oesophagus in Asians--a preliminary study

Rajendra S, Ackroyd R, Murad S, Mohan C, Ho JJ, Goh KL, et al.

Aliment Pharmacol Ther, 2005 Jun 1;21(11):1377-83.
PMID: 15932368

Characteristic immune profiles have been demonstrated in gastro-oesophageal reflux disease. However, the genetic basis of gastro-oesophageal reflux disease remains unclear.

Matched MeSH terms: Gene Frequency
Semai Senoi fertility and population dynamics: Two-census method

Fix AG

Am J Hum Biol, 1989;1(4):463-469.
PMID: 28514113 DOI: 10.1002/ajhb.1310010409

The fertility and parameters of population growth of the Semai Senoi of Malaysia are studied by using a two-census method based on nonstable population theory. Semai fertility is shown to be moderately high; female completed fertility is 7.42 children and the crude birth rate is greater than 0.050. Previous estimates of Semai mortality rates are also moderately high but are insufficient to balance birth; thus, the overall rate of growth is presently nearly 2%. Compared with an earlier description of the pre-1969 Semai population, fertility has increased markedly leading to a nearly threefold increase in the annual growth rate.

Matched MeSH terms: Gene Frequency
Genetic factors and malaria in the Temuan

Baer A, Lie-Injo LE, Welch QB, Lewis AN

Am J Hum Genet, 1976 Mar;28(2):179-88.
PMID: 817597

The jungle habitat of the Temuan aborigines harbors a variety of infectious diseases, the most notable being malaria. Our study of 15 genetic systems in the Temuan revealed substantial polymorphism and within-population genetic diversity. The polymorphisms for Hb beta, G6PD, and El are of interest in regard to genetic adaptation to malaria. Among the polymorphisms investigated we conclude that G6PD deficiency and elliptocytosis are likely to have malaria-resistant effects as evidenced by their low association with malarial parasitemia or their higher frequency in adults than in children. These findings suggest that the malarial habitat of the Temuans is livable in the long range sense for them because of the cluster of malaria-resistant alleles in their gene pool (G6PD)-, El, and possibly, but not tested here because of its low frequency, Hb beta E). The same condition probably holds for the Semai, the nearest aborigine neighbors of the Temuan (although the Semai have not been tested for malarial parasitemia and for these polymorphisms simultaneously), since the Semai have substantial Hb betaE, G6PD-, and El. The Temuan have a cultural identity system of rituals, beliefs, and certain aspects of language which effectively isolates them genetically from Malays and other nonaborigines. This system hinders the dilution of the malaria-resistant alleles of the Temuan gene pool with the malaria-susceptible alleles of the nonaborigine gene pools.

Matched MeSH terms: Gene Frequency*
Erythrocyte and leukocyte phosphoglucomutase in Chinese

Lie-Injo Luan Eng, Lopez CG, Poey-Oey Hoey Giok

Am J Hum Genet, 1968 Mar;20(2):101-6.
PMID: 5643177
Matched MeSH terms: Gene Frequency
Genetic markers of an aboriginal Taiwanese population

Chen KH, Cann H, Chen TC, Van West B, Cavalli-Sforza L

Am. J. Phys. Anthropol., 1985 Mar;66(3):327-37.
PMID: 3857010

A group of Taiwan aborigines, the Toroko, was typed for 21 classical genetic loci. This is part of an ongoing program aimed at a comprehensive study of Taiwan aborigines. In this first paper a short summary of historical, archeological, and anthropological data in the literature is made, and results of the present survey are compared with older results from other aborigine tribes. An analysis of other neighboring populations from southeast Asia has also been carried out in order to give a preliminary answer to the question of origin of Taiwanese aborigines. Fifteen populations were studied for 13 loci by tree analysis, principal components, and isolation by distance. Tree analysis and principal component analysis gave results in fairly good agreement and indicate three major population clusters: a northeast cluster (Ainu, Korea, Japan, and Ryukyu); a southeast cluster (south China, Thailand, Vietnam, Philippines, Taiwan, and Toroko); and a third cluster including Malaya and Borneo. The positions of Polynesia, Micronesia, and Melanesia are somewhat peripheral. Analysis of the tree shows some potential cases of convergence, perhaps owing to admixture, and of divergence. The analysis of isolation by distance shows that geographic propinquity is a reasonably good predictor of general similarity in this area.

Matched MeSH terms: Gene Frequency
Distribution of red cell phosphoglucomutase-1 subtypes in several Mongoloid populations of East Asia

Saha N

Am. J. Phys. Anthropol., 1988 Sep;77(1):91-6.
PMID: 2973240

The distribution of red cell phosphoglucomutase (PGM) subtypes was determined by starch-gel electrophoresis and isoelectric focusing in a group of 2,484 unrelated individuals from ten Mongoloid populations of East Asia. The sample comprised 998 Chinese from various localities--Singapore, 325; Malaysia, 270; Taiwan, 276; Hong Kong, 67; Fouzhou, 60--as well as 342 Koreans; 252 Filipinos; 529 Thais; 336 Malays, and 27 Indonesians. Altogether 15 phenotypes controlled by four common and five rare alleles at the PGM1 locus were observed in these populations. The frequency of the most frequent allele (PGM1+) varied from 0.56 to 0.74, with the highest frequency observed in the Singapore Chinese and the lowest in the Malays. Within the Chinese from different localities a significant degree of heterogeneity was observed at the PGM1 locus. The rare allele (PGM17)6 was observed only among the Chinese, Thais, and Malays, while the PGM1 was lacking in the Filipinos. A new allele with ahigh pI (6.5) was observed in a low frequency in all the populations but the Malays.

Matched MeSH terms: Gene Frequency*
Kin groups and trait groups: population structure and epidemic disease selection

Fix AG

Am. J. Phys. Anthropol., 1984 Oct;65(2):201-12.
PMID: 6507610

A Monte Carlo simulation based on the population structure of a small-scale human population, the Semai Senoi of Malaysia, has been developed to study the combined effects of group, kin, and individual selection. The population structure resembles D.S. Wilson's structured deme model in that local breeding populations (Semai settlements) are subdivided into trait groups (hamlets) that may be kin-structured and are not themselves demes. Additionally, settlement breeding populations are connected by two-dimensional stepping-stone migration approaching 30% per generation. Group and kin-structured group selection occur among hamlets the survivors of which then disperse to breed within the settlement population. Genetic drift is modeled by the process of hamlet formation; individual selection as a deterministic process, and stepping-stone migration as either random or kin-structured migrant groups. The mechanism for group selection is epidemics of infectious disease that can wipe out small hamlets particularly if most adults become sick and social life collapses. Genetic resistance to a disease is an individual attribute; however, hamlet groups with several resistant adults are less likely to disintegrate and experience high social mortality. A specific human gene, hemoglobin E, which confers resistance to malaria, is studied as an example of the process. The results of the simulations show that high genetic variance among hamlet groups may be generated by moderate degrees of kin-structuring. This strong microdifferentiation provides the potential for group selection. The effect of group selection in this case is rapid increase in gene frequencies among the total set of populations. In fact, group selection in concert with individual selection produced a faster rate of gene frequency increase among a set of 25 populations than the rate within a single unstructured population subject to deterministic individual selection. Such rapid evolution with plausible rates of extinction, individual selection, and migration and a population structure realistic in its general form, has implications for specific human polymorphisms such as hemoglobin variants and for the more general problem of the tempo of evolution as well.

Matched MeSH terms: Gene Frequency
Genetic differentiation of water buffalo (Bubalus bubalis) populations in China, Nepal and south-east Asia: inferences on the region of domestication of the swamp buffalo

Zhang Y, Vankan D, Zhang Y, Barker JS

Anim. Genet., 2011 Aug;42(4):366-77.
PMID: 21749419 DOI: 10.1111/j.1365-2052.2010.02166.x

Data from three published studies of genetic variation at 18 microsatellite loci in water buffalo populations in China (18 swamp type, two river type), Nepal (one wild, one domestic river, one hybrid) and south-east Asia (eight swamp, three river) were combined so as to gain a broader understanding of genetic relationships among the populations and their demographic history. Mean numbers of alleles and expected heterozygosities were significantly different among populations. Estimates of θ (a measure of population differentiation) were significant among the swamp populations for all loci and among the river populations for most loci. Differentiation among the Chinese swamp populations (which was due primarily to just one population) was much less than among the south-east Asian. The Nepal wild animals, phenotypically swamp type but genetically like river type, are significantly different from all the domestic river populations and presumably represent the ancestral Bubalus arnee (possibly with some river-type introgression). Relationships among the swamp populations (D(A) genetic distances, principal component analysis and structure analyses) show the south-east Asian populations separated into two groups by the Chinese populations. Given these relationships and the patterns of genetic variability, we postulate that the swamp buffalo was domesticated in the region of the far south of China, northern Thailand and Indochina. Following domestication, it spread south through peninsular Malaysia to Sumatra, Java and Sulawesi, and north through China, and then to Taiwan, the Philippines and Borneo.

Matched MeSH terms: Gene Frequency
Influence of the Angiotensin II type I receptor gene 1166A > C polymorphism on BP and aortic pulse wave velocity among Malays

Rehman A, Rasool AH, Naing L, Roshan TM, Rahman AR

Ann. Hum. Genet., 2007 Jan;71(Pt 1):86-95.
PMID: 17227479

Angiotensin II type 1 receptor (AGT1R) gene 1166A > C polymorphism has been shown to be associated with essential hypertension and aortic stiffness as measured by carotid femoral pulse wave velocity (PWV). This study was carried out to investigate the association of the 1166A > C polymorphism with blood pressure (BP) and PWV among Malay hypertensive and normotensive subjects. Two hundred and one hypertensive subjects without evidence of cardiovascular (CV) complications and 201 age- and sex-matched normotensive subjects were studied in a cross-sectional design. Blood pressures (BP) and PWV were measured, and 1166A > C genotype was determined by polymerase chain reaction followed by restriction enzyme digestion. The 1166C allele frequency was 7.96% and 7.73% among Malay hypertensive and normotensive subjects, respectively. There was no association of the 1166A > C polymorphism with BP in the hypertensive, normotensive or overall Malay populations. PWV was significantly higher among 1166C allele carriers as compared to non-carriers (10.52 +/- 1.82 vs. 10.15 +/- 1.80, p = 0.040) in the overall population, but not in the hypertensive and normotensive populations separately. In conclusion, the frequency of 1166C polymorphism is similar among Malay hypertensive and normotensive subjects. This polymorphism has no association with BP but may have an influence on PWV in Malays, which needs further investigation.

Matched MeSH terms: Gene Frequency
The effects of three factor VII polymorphisms on factor VII coagulant levels in healthy Singaporean Chinese, Malay and Indian newborns

Quek SC, Low PS, Saha N, Heng CK

Ann. Hum. Genet., 2006 Nov;70(Pt 6):951-7.
PMID: 17044869

Factor VII (FVII) is an independent risk factor for coronary artery disease. Three polymorphisms of the factor VII gene (F7) were studied in a group of healthy newborns comprising 561 Chinese, 398 Malays and 226 Asian Indians from Singapore. The allele frequencies of 3 polymorphisms (R353Q, Promoter 0/10bp Del/Ins and Intron 7) in the FVII gene were ascertained through genotyping by polymerase chain reaction and restriction digestion of amplified fragments. In Chinese the minor allele frequencies are Q: 0.04, Ins: 0.03, R7: 0.44; Malays, Q: 0.06, Ins: 0.10, R7: 0.41; and Indians, Q: 0.25, Ins: 0.23, R7: 0.43. Strong linkage disequilibrium (Delta > 0.7) is observed between the 0/10 bp and the R353Q sites in all ethnic groups. We conclude that: (i) the prevalence of the minor Q and Ins alleles of the R353Q and 0/10 bp polymorphisms are significantly higher in the Indian newborns than the Chinese and Malays; (ii) the Q allele is significantly associated (p = 0.01) with a lower plasma FVII coagulant level in the Indian and Malay neonates; and this polymorphism explains up to 3.8% of the variance in FVII coagulant levels; (iii) there is no significant difference in allele frequencies of the three polymorphisms between neonates with and without family histories of CAD.

Matched MeSH terms: Gene Frequency
The association of mitochondrial DNA 5178 C > a polymorphism with plasma lipid levels among three ethnic groups

Lal S, Madhavan M, Heng CK

Ann. Hum. Genet., 2005 Nov;69(Pt 6):639-44.
PMID: 16266403

Mitochondria are eukaryotic cytoplasmic organelles responsible for oxidative phosphorylation. The C to A nucleotide transversion in the NADH dehydrogenase subunit 2 (MT-ND2) coding region of mitochondrial DNA has been reported to be associated with plasma lipid levels, adult onset diseases and longevity. We have examined the role of this polymorphism in relation to plasma lipid levels and age in a total of 713 healthy individuals belonging to 3 ethnic groups in Singapore. The frequency of the A allele was significantly higher (p < 0.05) among the Chinese (0.15) in comparison to the Malays (0.05) and Indians (0.02). No significant difference in the frequency of the allele was observed between healthy and coronary artery disease subjects, and between age-stratified subjects. We found that the polymorphism is significantly associated in an ethnic- and gender-specific manner with plasma apoB levels in the Chinese males (p < 0.05). This is the first epidemiological report of the mt5178 C > A polymorphism and its association with plasma lipid levels in Asian populations outside Japan.

Matched MeSH terms: Gene Frequency
Apolipoprotein E (APOE) allele distribution in the world. Is APOE*4 a 'thrifty' allele?

Corbo RM, Scacchi R

Ann. Hum. Genet., 1999 Jul;63(Pt 4):301-10.
PMID: 10738542

Apolipoprotein E (APOE = gene, apoE = protein) plays a central role in plasma lipoprotein metabolism and in lipid transport within tissues. The APOE shows a genetic polymorphism determined by three common alleles, APOE*2, APOE*3, APOE*4 and the product of the three alleles differs in several functional properties. APOE is involved in the development of certain pathological conditions. In particular, the APOE*4 allele is a risk factor for susceptibility to coronary artery disease (CAD) and Alzheimer's Disease (AD). In the present study we analyzed the APOE allele distribution in the world. The APOE*3 is the most frequent in all the human groups, especially in populations with a long-established agricultural economy like those of the Mediterranean basin (0.849-0.898). The frequency of APOE*4, the ancestral allele, remains higher in populations like Pygmies (0.407) and Khoi San (0.370), aborigines of Malaysia (0.240) and Australia (0.260), Papuans (0.368), some Native Americans (0.280), and Lapps (0.310) where an economy of foraging still exists, or food supply is (or was until the recent past) scarce and sporadically available. The APOE*2 frequency fluctuates with no apparent trend (0.145-0.02) and is absent in Native Americans. We suggest that the APOE*4, based on some functional properties it has and on its distribution among human populations, could be identified as a 'thrifty' allele. The exposure of APOE*4 to the contemporary environmental conditions (Western diet, longer lifespans) could have rendered it a susceptibility allele for CAD and AD. The absence of the association of APOE*4 with CAD and AD in Sub-Saharan Africans, and its presence in African Americans, seems to confirm this hypothesis.

Matched MeSH terms: Gene Frequency
The role of kin-structured migration in genetic microdifferentiation

Fix AG

Ann. Hum. Genet., 1978 Jan;41(3):329-39.
PMID: 626477

Most current models of human population structure view migration solely as a deterministic force reducing the variance in gene frequencies among the local colonies of a subdivided population. By an empirical example and through simulation experiments, it is shown that migration structured along kinship lines (by analogy to the lineal or 'kinship' effect) does not always reduce the variances of gene frequencies arising through intergenerational random genetic drift. Thus populations experiencing high rates of migration may not be genetically homogenous.

Matched MeSH terms: Gene Frequency
Fulltext Diagnostic Utility of Human Leukocyte Antigen B*15:02 Screening in Severe Carbamazepine Hypersensitivity Syndrome

Moutaouakkil Y, Adouani B, Cherrah Y, Lamsaouri J, Bousliman Y

Ann Indian Acad Neurol, 2019 10 25;22(4):377-383.
PMID: 31736555 DOI: 10.4103/aian.AIAN_492_18

Background: Despite many studies suggesting an association between human leukocyte antigen (HLA)-B*15:02 and carbamazepine (CBZ)-induced severe cutaneous adverse drug reactions essentially toxic epidermal necrolysis (TEN) and Stevens-Johnson syndrome (SJS), the evidence of association in different populations and the degree of association remain uncertain.
Materials and Methods: The primary analysis was based on population control studies. Data were pooled by means of a random-effects model, and sensitivity, specificity, positive and negative likelihood ratios (LR+ and LR-), diagnostic odds ratios (DOR), and areas under the summary receiver operating characteristic curve (AUC) were calculated.
Results: In 23 population control studies, HLA-B*15:02 was measured in 373 patients with CBZ-induced TEN/SJS and 3452 patients without CBZ-induced TEN/SJS. The pooled sensitivity, specificity, LR+, LR-, DOR, and AUC were 0.67 (95% confidence interval [CI] = 0.63-0.72), 0.98 (95% CI = 0.98-0.99), 19.73 (95% CI = 10.54-36.92), 0.34 (95% CI = 0.23-0.49), 71.38 (95% CI = 34.89-146.05), and 0.96 (95% CI = 0.92-0.98), respectively. Subgroup analyses for Han Chinese, Thai, and Malaysian populations yielded similar findings. Specifically, racial/ethnic subgroup analyses revealed similar findings with respect to DOR for Han Chinese (99.28; 95% CI = 22.20-443.88), Thai (61.01; 95% CI = 23.05-161.44), and Malaysian (30; 95% CI = 7.08-126.68) populations, which are similar to the pooled DOR for the relationship between the HLA-B*15:02 allele and CBZ-induced TEN/SJS across all populations (71.38; 95% CI = 34.89-146.05).
Conclusions: The present study reveals that CBZ is the leading cause of TEN/SJS in many countries. Screening of HLA-B*15:02 may help patients to prevent the occurrence of CBZ-induced TEN/SJS, especially in populations with a higher (≥5%) risk allele frequency.

Matched MeSH terms: Gene Frequency
Population data of six Alu insertions in indigenous groups from Sabah, Malaysia

Kee BP, Chua KH, Lee PC, Lian LH

Ann Hum Biol, 2012 Nov-Dec;39(6):505-10.
PMID: 22989108 DOI: 10.3109/03014460.2012.719548

The present study is the first to report the genetic relatedness of indigenous populations of Sabah, Malaysia, using a set of Indel markers (HS4.32, TPA25, APO, PV92, B65 and HS3.23). The primary aim was to assess the genetic relationships among these populations and with populations from other parts of the world by examining the distribution of these markers.

Matched MeSH terms: Gene Frequency
Study of the CTLA-4 gene polymorphisms in systemic lupus erythematosus (SLE) samples from Malaysia

Chua KH, Puah SM, Chew CH, Tan SY, Lian LH

Ann Hum Biol, 2010 Apr;37(2):274-80.
PMID: 19951233 DOI: 10.3109/03014460903325185

In this study, we investigated the polymorphisms of the exon 1 (+49A/G), promoter sites (-1722T/C, -1661A/G, -318C/T), and 3'-untranslated region (3'-UTR) (+6230 A/G) of the CTLA-4 gene in systemic lupus erythematosus (SLE) affected patients. Polymerase chain reaction-restriction fragment length polymorphism was used to determine genotypes of these five markers in 130 SLE patients and 130 healthy controls. Of the five tested polymorphisms, there was no statistical significant difference between the genotypic and allelic frequencies of patients with SLE and controls. Hence, we propose that the CTLA-4 gene does not play a major role in the genetic susceptibility to the development of SLE in the Malaysian population.

Matched MeSH terms: Gene Frequency
Population genetics of coagulation factor XIIIB in three ethnic groups of Singapore

Saha N, Tay JS, Low PS, Basair JB

Ann Hum Biol, 1992 5 1;19(3):277-83.
PMID: 1616285

The distribution of plasma coagulation factor XXIIB polymorphism was determined by PAG isoelectric focusing and immunoblotting in a group of 670 subjects comprising 375 Chinese, 110 Malays and 185 Indians. The frequencies of FXIIIB*1, FXIIIB*2, and FXIIIB*3 were found to be 0.27, 0.03 and 0.70 in the Chinese; 0.33, 0.05 and 0.64 in the Malays and 0.58, 0.08 and 0.33 in the Indians. The phenotypic distribution of FXIIIB alleles was at Hardy-Weinberg equilibrium in all three populations. A two-dimensional principal-components analysis on the basis of three common alleles at the FXIIIB locus among 19 populations, so far studied, clearly differentiates the Negroid, Mongoloid and Caucasoid populations into three major groups with the exception of Amerindians (Minnesota) and US Blacks showing some Caucasoid influence.

Matched MeSH terms: Gene Frequency
Alpha 1-protease inhibitor (PI) subtypes in seven populations of east Asia

Saha N

Ann Hum Biol, 1990 5 1;17(3):229-34.
PMID: 2337328

The distribution of serum alpha 1-protease inhibitor (PI) or alpha 1-antitrypsin (alpha 1AT) subtypes was determined by thin-layer isoelectric focusing in a group of 1233 individuals from six Mongoloid populations of East Asia and Dravidian Indians. The sample comprised 385 Chinese from Singapore and 151 Chinese from the Fujien province; 126 Malays; 243 Filipinos; 112 Thais; 56 Koreans and 160 Dravidian Indians. The frequency of PiM1 ranged from 0.65 in the Thais to 0.81 in the Fujien Chinese. The highest frequency of PiM2 was found in the Dravidian Indians (0.28) followed by the Thais (0.25). The frequency of PiM3 was found to vary from 0.03 to 0.07 in these populations. A low frequency of PiF (0.01 to 0.02) and PiS (0.01 to 0.04) was also observed in the Mongoloid populations but absent in the Indians. The PiZ allele was completely absent in all these populations. The phenotypic distribution of PI subtypes was at Hardy-Weinburg equilibrium in all the populations.

Matched MeSH terms: Gene Frequency*

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