Serogenetic investigations of Tibetans and Himachalis from Himachal Pradesh, India: genetic relationship between Tibetans and certain selected mongoloid populations

Twenty two serogenetic systems were investigated in 115 Tibetans and 128 Himachalis from the state of Himachal Pradesh, northwest India. For eight of the loci (ABO, Rh, MNSs, P, Fy, 6PGD, EsD, and AK) the two populations showed conclusive heterogeneity and their frequency distribution showed that the serogenetic differences between two populations are due to their different racial affiliations. The Tibetans were also analysed for their genetic relationship with certain selected populations from the Cis-Himalayan, far east and south Asian regions. The calculations of the Harpending's kinship matrix R and the genetic distances showed that the Tibetans are closer to the mongoloid populations of the Cis-Himalayan region and the differences in the present day population structure of the mongoloid groups of this region are more likely to be due to differential migration, admixture and racial affiliation although there is a slight possibility of disruptive selection for certain loci such as 6PGD and AK which showed an exceptionally high value of Canning (6PGD*C) and AK*1 genes.     

HMOX2 Functions as a Modifier Gene for High‐Altitude Adaptation in Tibetans

Tibetans are well adapted to high‐altitude environments. Among the adaptive traits in Tibetans, the relatively low hemoglobin level is considered a blunted erythropoietic response to hypoxic challenge. Previously, EPAS1 and EGLN1, the major upstream regulators in the hypoxic pathway, were reportedly involved in the hemoglobin regulation in Tibetans. In this study, we report a downstream gene (HMOX2) involved in heme catabolism, which harbors potentially adaptive variants in Tibetans. We first resequenced the entire genomic region (45.6 kb) of HMOX2 in Tibetans, which confirmed the previously suspected signal of positive selection on HMOX2 in Tibetans. Subsequent association analyses of hemoglobin levels in two independent Tibetan populations (a total of 1,250 individuals) showed a male‐specific association between the HMOX2 variants and hemoglobin levels. Tibetan males with the derived C allele at rs4786504:T>C displayed lower hemoglobin level as compared with the T allele carriers. Furthermore, our in vitro experiments indicated that the C allele of rs4786504 could increase the expression of HMOX2, presumably leading to a more efficient breakdown of heme that may help maintain a relatively low hemoglobin level at high altitude. Collectively, we propose that HMOX2 contributes to high‐altitude adaptation in Tibetans by functioning as a modifier in the regulation of hemoglobin metabolism.     

Identification of single-nucleotide polymorphisms (SNPs) of human N-acetyltransferase genes NAT1, NAT2, AANAT, ARD1, and L1CAM in the Japanese population

By direct sequencing of regions of the human genome containing five genes belonging to the acetyltransferase family, arylamine N-acetyltransferase (NAT1), arylamine N-acetyltransferase (NAT2), arylalkylamine N-acetyltransferase (AANAT), L1 cell adhesion molecule (L1CAM), and the human homolog of Saccharomyces cerevisiae N-acetyltransferase ARD1, we identified 53 single-nucleotide polymorphisms (SNPs) and two insertion/deletion polymorphisms in 48 healthy Japanese volunteers. NAT1 and NAT2 are so-called drug-metabolizing enzymes. In the NAT1 gene we found two SNPs and a 3-bp insertion/deletion polymorphism that corresponded to the NAT1^*3, ^*10, and ^*18A/^*18B alleles reported in other populations. The frequencies of NAT1^* alleles in our Japanese subjects were 52.6% for NAT1^*4, 1.0% for NAT1^*3, 40.6% for NAT1^*10, 2.6% for NAT1^*18A and 3.1% for NAT1^*18B. In the NAT2 gene we found 32 SNPs and a 1-bp insertion/deletion polymorphism; 6 SNPs within the coding region were reported previously and belonged to the slow acetylator group (NAT2^*5, NAT2^*6 and NAT2^*7), and 2 of the 8 SNPs in the 5′ flanking region were reported in the dbSNP of GenBank, but the remaining 24 SNPs and the insertion/deletion polymorphism were novel. The frequencies of NAT2^* alleles in Japanese (51.3% for NAT2^*4, 1.6% for ^*5B, 26.1% for ^*6A, 2.2% for ^*6B, 1.2% for ^*7A, 10.1% for ^*7B, 7.4% for ^*12A, and 1.1% for ^*13) were significantly different from those reported in Caucasian populations. In the AANAT gene we found 4 novel SNPs: 2 in the 5′ flanking region, 1 in exon 4, and 1 in intron 3. In the two genes belonging to the N-terminal N-acetyltransferase family, we identified 9 SNPs, 7 of them novel, for ARD1, and six novel SNPs for L1CAM. Variations at these loci may contribute to an understanding of the way in which different genotypes may affect the activities of human N-acetyltransferases, especially as regards the therapeutic efficacy of certain drugs and antibiotics. Received: February 9, 2001 / Accepted: February 19, 2001     

Blood pressure variation among Tibetans at different altitudes

Background: Age-related increase in blood pressure (BP) throughout adulthood have been commonly observed in industrialized and developing populations which is generally not observed in traditional populations. Based on studies in the Andes, Tien Shan, Pamir and US highlands, BP values are generally lower in high- than low-altitude populations. At present, Tibetans are residing at different altitudes in India and little is known about BP variation for this population.

Aims: This study reports BP variation among Tibetans in India in view of the hypothesis of age-related increase and of lower BP at high altitude.

Subjects and methods: BP, height, weight, triceps skinfold thickness (SFT), mid-upper arm circumference (MUAC), and haemoglobin and haematocrit level were obtained from 1091 individuals (508 males, 583 females) at four different settlements, one being at high altitude (Choglamsar, Leh; altitude: 3521?m) and three at low altitudes (Bylakuppe, Chandragiri and Delhi; altitude: less than 1000?m), which were pooled. Comparison between altitudes was carried out separately for the two sexes and for the two age groups: children and adolescents 10–19 years of age; and adults 20 years and above. Those independent variables that could significantly explain the variance in systolic blood pressure (SBP) and diastolic blood pressure (DBP) in stepwise regression were controlled for while comparing high and low altitudes using analysis of covariance (ANCOVA).

Results: The three low-altitude samples showed similar values for adult BP after controlling for age and other BP correlates. Age was highly correlated to adult BP for both males and females after adjusting for anthropometric and haematological variables. A similar analysis for children and adolescents showed lower BP values at high altitude.

Conclusion: Lower BP values among Tibetan children and adolescents at high altitude suggest that altitude affects BP as previously hypothesized, but only in youth. Similar BP in adults at low and high altitudes may reflect the effects of other variables on BP. Measures of adiposity (SFT, BMI and MUAC) have a significant effect on BP. Increase in BP with adult age is observed in Tibetans, which is similar to the pattern observed among populations undergoing modernization.     

Gene order and localization of enzyme loci on the short arm of chromosome 1

Analysis of hybrids containing different rearrangements involving human chromosome 1 suggests that GDH and ENO1 are distal to PGD , and that all 3 loci are distal to 1p36.13. Evidence is presented indicating that FUCA and AK 2 are in 1p34.     

Association of diffuse panbronchiolitis with microsatellite polymorphism of the human interleukin 8 (IL-8) gene

Diffuse panbronchiolitis (DPB) is a distinctive chronic inflammatory lung disease predominantly found in Asian populations. Although its etiology is unknown, DPB is considered to be a multifactorial disease of whose susceptibility is determined by genetic predisposition unique to Asians. We and others have previously reported that the B^*5401 allele of the human leukocyte antigen (HLA)-B gene or a closely linked gene in the HLA region on 6p21.3 is one of the major genetic factors in susceptibility to this disease . However, the association with B^*5401 is not absolute and the contribution of other genetic or environmental factors should also be considered. Here, four candidate genes that are postulated to play a role in the pathophysiology of DPB, namely, RON-kinase, CYP3A4, motilin, and interleukin (IL)-8, were chosen, and association studies between microsatellite markers at these loci and DPB were conducted. We demonstrated the presence of a specific allele at the IL-8 locus was associated with the disease (c2 = 9.13; P = 0.0025; corrected P [Pc] < 0.05). Although further studies are needed to examine whether neutrophil accumulation in the airways of patients with DPB is controlled by a possible genetic variation of IL-8 or other chemokine genes located in the region 4q12-q13, our data suggest that genes other than those of the HLA system may also contribute to a genetic predisposition to DPB. Received: October 27, 1998 / Accepted: January 5, 1999     

Genetic polymorphisms of orosomucoid and alpha-2-HS-glycoprotein in Thai,Sri Lankan and Paraguayan populations

The genetic polymorphism of orosomucoid (ORM) and alpha-2-HS-glycoprotein (AHSG) were studied in Thai, Sri Lankan and Paraguayan populations using isoelectric focusing. Gene frequencies in these populations were compared with those in other populations. Four new ORM variants were detected:ORM1 ^* 15 in Thai,ORM1 ^* 16 in Paraguayan,ORM2 ^* 21 andORM2 ^* 22 in Sri Lankan.     

Hemoglobin levels in Tibet: different effect of age and gender for Tibetans vs Han

Tibetans form a population which has resided on the Qinghai–Tibetan plateau for thousands of years, and are reported to have less hemoglobin than Han Chinese lowlanders who have migrated to the plateau. However, for various altitudes, detailed comparisons of hemoglobin in the two ethnic groups has not been reported. We investigated the hypothesis that the effects of altitude, age, and gender on hemoglobin concentration would differ between Han and Tibetan residents of the plateau. Hematological parameters for both genders were determined in healthy Tibetan adults (n=3,000) and children (n=332), and healthy Han Chinese adults (n=2,612) and children (n=275), aged 5–60 years living at four different altitudes (mean altitude of 2,664, 3,813, 4,525, and 5,200 m). Hemoglobin values increased with altitude for all ages in both ethnic groups and in both genders. The gain in hemoglobin with altitude had the rank order: Han males > Han females > Tibetan males and females. Even before puberty, Han children had more hemoglobin than Tibetan children. An effect of age on hemoglobin was seen at the time of puberty in men, but not in women. A positive correlation was found between hemoglobin concentration and age in adult Han males and females, but not in Tibetan males, and only at the higher altitudes, in Tibetan females. In both Tibetans and Hans, males had higher hemoglobin values than females at each altitude, but the gender differences increased with altitude in Han, whereas it either decreased or did not change in Tibetans. Examination of hemoglobin levels by histogram showed non-Gaussian distributions: Tibetan men and women had skewing to higher values, whereas Han men and women had skewing in the opposite direction. We conclude that increasing age and the effect of gender in Tibetans are associated with different hemoglobin responses to altitude than in Han, and we speculate that genetic influences may be involved.     

Nucleotide Sequence Analyses of Human Complement 6 (C6) Gene Suggest Balancing Selection

The sixth complement component (C6) has a common charge polymorphism, C6A and C6B, with similar gene frequencies in all major populations. In addition, C6B₂ is also found in Japanese populations at a frequency of about 6%. Sequence analyses of the coding region of three human and ape C6 alleles indicated four nonsynonymous and three synonymous changes in C6*B₂ relative to C6*A, suggesting that a recombination event occurred between C6*B₂ and C6*A to give rise to C6*B. Sequence variation in a 3.86 kb region encompassing exon 3, where the causal base change of the common C6 polymorphism is found, indicated that several single nucleotide polymorphisms (SNPs) were in extensive linkage disequilibrium (LD), with little differentiation among populations. Sliding window estimates of two test statistics for neutrality revealed significant values in a subregion where the replacement coding polymorphism resides, in all three human populations. These results raise the possibility that the two common C6 alleles in human populationsw are maintained by balancing selection.     

CYP2D6 polymorphism screening in a selected population of Spain (La Alpujarra): No effect of geographical isolation

Background: There is growing interest in theCYP2D6 gene because of its key role in the metabolism of numerous commonly used drugs.

Aim: We compared the frequency of the most frequent nullCYP2D6 alleles (CYP2D6*3,CYP2D6*4,CYP2D6*5,CYP2D6*6,CYP2D6*7 andCYP2D6*8) between individuals from the Spanish population and from La Alpujarra.

Subjects and methods: The present study comprises Spanish cohort (n = 185) and from La Alpujarra (n = 104). The latter is a small mountainous region of Spain that shows a remarkable degree of geographical and cultural isolation. We genotyped six polymorphisms in the coding region of theCYP2D6 gene, i.e. five single nucleotide polymorphisms (SNP) (CYP2D6*3,CYP2D6*4,CYP2D6*6,CYP2D6*7 andCYP2D6*8) and one deletion (CYP2D6*5).

Results: No significant differences were observed between groups in allelic and genotype distributions of the aforementioned variants. The total frequency of functional alleles was comparable between the two groups (79% and 81.3% in controls and La Alpujarra, respectively).

Conclusion: Despite demographic and cultural isolation in La Alpujarra, the distribution ofCYP2D6 polymorphisms in habitants of this area is similar to that reported in the rest of Spain. At present, there seems to be little allele heterogeneity inCYP2D6 amongst different European populations (e.g. amongst different Spanish populations) that have shown diversity in other loci.     

Studies on temperature-sensitive mutants of Chinese hamster ovary cells affected in DNA synthesis

DNA synthesis in two mutants of Chinese hamster overy cells,ts 13A andts 15C, which were temperature sensitive for growth, was found to be shut off rapidly at the nonpermissive temperature. The mutants did not complement each other and thets lesion was not located on the X chromosome. Both isolates were found to be considerably more sensitive to the alkylating agents, ethylmethanesulfonate (EMS) and methylmethanesulfonate (MMS), as compared to the parental cells, but showed normal sensitivity to UV irradiation. The mutants also showed interesting differences in their response to EMS-induced mutation frequencies at the ouabain-resistant and thioguanine-resistant loci. At high survival (50%) the frequencies of mutations at these genetic loci were markedly low in thets mutants as compared to the parental cells. Ints ^* revertants isolated from the mutants, thets phenotype and the increased sensitivity to EMS and MMS were affected simultaneously, indicating that both these characteristics resulted from a single genetic lesion.     

The red cell 6-phosphogluconate dehydrogenase polymorphism in certain Southern African populations; with the first report of a new phenotype

• 1 Studies have been carried out on the 6-phosphogluconate dehydrogenase polymorphism in over 3400 Southern Africans representing 34 distinct populations. The two commonest variant alleles, PGD^Cand PGD^R, attain their highest known frequencies in the subcontinent.
• 2 It has been shown that while the very high frequency of PGD^Cfound by previous workers in the Xhosa does not extend to the other South African Negro populations, the Dama of South West Africa have a frequency of PGD^Rhigh enough to be polymorphic. It is suggested that certain other populations possessing the PGD^Rallele may have obtained it from the Dama via the slave trade from Angola.
• 3 A new electrophoretic variant of GPG^D, has been found in a member of the Kuanyama division of the Ambo peoples of South West Africa and has been named 6PGD Oshakati and the allele determining its synthesis PGD^S.

     

Birth weight among Tibetans at different altitudes in India: Are Tibetans better protected from IUGR?

We report the variation in birth weight among the Tibetans at different altitudes in India to test the hypothesis of greater protection from intrauterine growth retardation (IUGR) among Tibetan compared with other high-altitude native populations. We found that the birth weight of Tibetans at Leh (3521 m, high altitude) is quite similar to what has been reported previously for Tibetans at similar altitudes and is significantly higher than the low-altitude native populations living at similar altitudes. Tibetan birth weights are greater than those of other ethnic groups, both at high and low altitudes. Compared with Tibetans at high altitude (Leh, India; 3521 m), Tibetans at low altitudes (Bylakuppe, India; 800 m and Chandragiri, India; 970 m) have heavier birth weights. This finding is similar to what has been observed previously for other high-altitude native populations. Greater protection from IUGR is not observed for Tibetans compared with other high-altitude native populations as was reported previously. Genetic potential for birth weight is seemingly manifested only at low altitude.     

Genetic variants at the EGLN1 locus associated with high‐altitude adaptation in Tibetans are absent or found at low frequency in highland Andeans

EGLN1 encodes the hypoxia‐inducible factor (HIF) pathway prolyl hydroxylase 2 (PHD2) that serves as an oxygen‐sensitive regulator of HIF activity. The EGLN1 locus exhibits a signature of positive selection in Tibetan and Andean populations and is associated with hemoglobin concentration in Tibetans. Recent reports provide evidence for functional roles of protein‐coding variants within the first exon of EGLN1 (rs186996510, rs12097901) that are linked to an adaptive signal in Tibetans, yet whether these same variants are present and contribute to adaptation in Andean highlanders is unknown. We determined the frequencies of these adaptive Tibetan alleles in Quechua Andeans resident at high altitude (4,350 m) in addition to individuals of Nepali ancestry resident at sea level. The rs186996510 C (minor) allele previously found at high frequency in Tibetans is absent in Andean (G: 100%) and rare among Nepali (C: 11.8%, G: 88.2%) cohorts. The minor G allele of rs12097901 is found at similarly low frequencies in Andeans (G: 12.7%, C: 87.3%) and Nepalis (G: 23.5%, C: 76.5%) compared to Tibetans. These results suggest that adaptation involving EGLN1 in Andeans involves different mechanisms than those described in Tibetans. The precise Andean adaptive variants remain to be determined.     

IgH (μ-switch and γ-1) region restriction fragment length polymorphism in human narcolepsy

Predisposition to narcolepsy involves genetic factors both in humans and in a canine model of the disorder. In humans, narcolepsy is strongly associated with HLA DR15 and DQB1^*0602. In Dobermans and Labradors, narcolepsy is transmitted as a single autosomal recessive gene with full penetrance (canarc-1). Canine narcolepsy is not linked with DLA, the canine equivalent of HLA, but cosegregates with a DNA segment with high homology with the immunoglobulin heavy-chain (IgH) switch-like region (S). To determine if the IgH locus is involved in genetic predisposition to human narcolepsy, restriction fragment length polymorphisms specific for the IgM and IgG cluster within this locus were studied in sporadic cases of the disease, as well as in five families with two or more affected individuals. Comparisons were made between control populations and both familial and sporadic cases and for patients with and without HLA-DR15 and DQB1^*0602. RFLP analysis at the S and-1 loci, which cover over 200 kb of 14q32.3, indicates that there is no evidence for any association between the IgH region and human narcolepsy.     

Microgeographic and temporal genetic variation in populations of the bluetongue virus vector Culicoides variipennis (Diptera: Ceratopogonidae).

Seven Colorado populations of the bluetongue virus vector Culicoides varipennis (Coquillett) were analyzed for genetic variation at 19-21 isozyme loci. Permanent populations, which overwinter as larvae, showed little temporal genetic change at 19 loci. PGD and MDH showed seasonal changes in gene frequencies, attributable to selection at two permanent populations. Two temporary populations showed low heterozygosity compared with permanent populations. Independent estimates of gene flow, calculated using FST and the private allele method, were Nm* = 2.15 and 6.95, respectively. Colorado C. variipennis permanent populations showed high levels of gene flow which prevented significant genetic differentiation due to genetic drift. Temporary populations showed significant gene frequency differences from nearby permanent populations due to the "founder effect" associated with chance colonization.     

The characteristics of motor activity in ISIAH rats in an open field test are controlled by genes on chromosomes 2 and 16

Quantitative Trait Locus (QTL) analysis was used to identify the loci of polygenic characteristics in a study of the genetic determination of the behavior of rats with inherited stress-induced arterial hypertension (ISIAH rats). Analysis was performed using males of two populations of F₂ hybrids (ISIAH × WAG) of different ages: 3–4 (n = 106) and six months (n = 130). Chromosomes 2 and 16 in the young population of F₂ rats showed significant associations between two characteristics of behavior in ISIAH rats and genetic loci: a) the rats' motor activity at the periphery of the open field area with loci in the regions of markers D2Rat157-D2Rat88 (LOD score 4.83; p = 0.000058) and D16Rat32 (LOD score 3.71; p = 0.00023). Together, these two loci accounted for 42.9% of the trait variability; b) the rats' motor activity during the first minute of the open field test and loci in the region of the marker D16Rat58 (LOD score 3.78; p = 0.00028). Results obtained by QTL analysis demonstrated a relationship between the genetic control of these traits and the animals' age. Translated from Zhurnal Vysshei Nervnoi Deyatel'nosti imeni I. P. Pavlova, Vol. 57, No. 6, pp. 692–701, November–December, 2007.     

Responses of Han Migrants Compared to Tibetans at High Altitude

While many studies have compared Tibetans and low‐altitude born Han living at high altitude, few have carefully controlled the chronological age at which lowlanders migrated, the length of time they had lived at high altitude, their nutrition, and their socio‐economic status. This has produced an array of results that frequently do not support the hypothesis that Tibetans and Han show fundamental differences in their response to hypoxia. Unlike the situation in the Andes, only one study has tested the developmental adaptation hypothesis on the Qinghai‐Tibetan plateau. This study shows that Tibetans and Han of the same age, who were born and raised in the same towns at the same altitudes, show considerable overlap in the individual distribution of [Hb], SaO₂ and lung volumes. These results indicate that second‐generation Han make substantial developmental adjustments to hypoxia that are not reflected in studies of first‐generation migrants. Thus, there is a great need for further developmental studies to determine whether and/or how Han and Tibetan responses to hypoxia diverge, as well as for studies exploring whether Han and Tibetans who show similar responses also share genetic adaptations. Am. J. Hum. Biol. 25:169–178, 2013. © 2013 Wiley Periodicals, Inc.     

Genome-wide Association with C-Reactive Protein Levels in CLHNS: Evidence for the CRP and HNF1A Loci and their Interaction with Exposure to a Pathogenic Environment

Recent genome-wide association studies have related several genetic loci, including C-reactive protein (CRP), hepatocyte nuclear factor 1 homeobox (HNF1A), and genetic variations in the leptin receptor (LEPR), to circulating CRP levels in populations of European ancestry. The genetic effects in other populations and across varying levels of exposure to a pathogenic environment, an important environmental factor associated with CRP, remain to be determined. We tested 2,073,674 single-nucleotide polymorphisms (SNPs) for association with plasma CRP (limited to ≤10 mg/L) in 1,709 unrelated Filipino women from the Cebu Longitudinal Health and Nutrition Survey. The strongest evidence of association was observed with variants at CRP (rs876537, P = 1.4 × 10⁻⁹) and HNF1A (rs7305618, P = 1.0 × 10⁻⁸). Among other previously reported CRP-associated loci, the apolipoprotein E ε4 haplotype was associated with decreased CRP level (P = 7.1 × 10⁻⁴), and modest association was observed with LEPR (rs1892534, P = 0.076), with direction of effects consistent with previous studies. The strongest signal at a locus not previously reported mapped to a gene desert region on chromosome 6q16.1 (rs1408282, P = 2.9 × 10⁻⁶). Finally, we observed nominal evidence of interaction with exposure to a pathogenic environment for top main effect SNPs at HNF1A (rs7305618, P = 0.031), LEPR (rs1892535, P = 0.030) and 6q16.1 (rs1408282, P = 0.046). Our findings demonstrate convincing evidence that genetic variants in CRP and HNF1A contribute to plasma CRP in Filipino women and provide the first evidence that exposure to a pathogenic environment may modify the genetic influence at the HNF1A, LEPR, and 6q16.1 loci on plasma CRP level.