Molecular analyses of HLA-DRB1, -DPB1, and -DQB1 in Jing ethnic minority of Southwest China

Association between the PINX1 and NAT2 polymorphisms and serum lipid levels

Jing nationality is a relatively conservative and isolated minority in China. Little is known about the association of the PIN2/TERF1-interacting telomerase inhibitor 1 (PINX1) and N-acetyltransferase 2 (NAT2) single nucleotide polymorphisms (SNPs) and serum lipid levels in the Chinese populations. This study aimed to clarify the association of 6 SNPs of the PINX1 and NAT2 and serum lipid levels in two Chinese populations. Genotyping of the SNPs was performed in 1236 Han subjects and 1248 Jing participants. Allelic and genotypic frequencies of these variants (except NAT2 rs1799931) were different between the two ethnic groups. The minor allele carriers had higher triglyceride (TG, rs11776767, rs1495743 and rs1799930), low-density lipoprotein cholesterol (rs6601530) levels and the apolipoprotein (Apo)A1/ApoB ratio (rs1495743) in Han nationality; and higher total cholesterol (rs1961456), TG (rs11776767, rs6601530 and rs1495743) and lower ApoA1 (rs6601530 and rs1799931) levels in Jing minority than the minor allele non-carriers. The SNPs were not statistically independent by the multiple-locus linkage disequilibrium analyses. The integrative haplotypes and gene-by-gene (G × G) interactions on serum lipid traits were also observed in the two populations. Association analysis based on haplotypes and G × G interactions might be powerful than single-locus tests. Differences in serum lipid profiles between the two populations might partially be attributed to these SNPs, their haplotypes and G × G interactions.

Association of the SPTLC3 rs364585 polymorphism and serum lipid profiles in two Chinese ethnic groups

BACKGROUND

Little is known about the association of the single nucleotide polymorphism (SNP) of rs364585 near serine palmitoyl-transferase long-chain base subunit 3 gene (SPTLC3) and serum lipid profiles. The present study was detected the association of the SPTLC3 rs364585 SNP and several environmental factors with serum lipid profiles in the Han and Jing populations.

METHODS

Genotyping of the SPTLC3 rs364585 SNP was performed in 824 unrelated individuals of Han and 783 participants of Jing by polymerase chain reaction and restriction fragment length polymorphism combined with gel electrophoresis, and then confirmed by direct sequencing.

RESULTS

There was no significant difference in either genotypic or allelic frequencies between Han and Jing, or between males and females of the both ethnic groups. The levels of serum low-density lipoprotein cholesterol (LDL-C) and the ratio of apolipoprotein (Apo) A1 to ApoB in Han; and total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and LDL-C in Jing were different between the A allele carriers and the A allele non-carriers (P < 0.05-0.001). Subgroup analysis according to sex showed that the levels of LDL-C in Han males; TC and LDL-C in Jing males; and HDL-C and LDL-C in Jing females were different between the A allele carriers and the A allele non-carriers (P < 0.05-0.001), the A allele carriers had higher LDL-C and TC levels, and lower HDL-C levels than the A allele non-carriers. Serum lipid traits were also associated with several environmental factors in the Han and Jing populations, or in males and females of the both ethnic groups.

CONCLUSIONS

The present study demonstrates the association between the SPTLC3 rs364585 SNP and serum TC, HDL-C and LDL-C levels in our study populations. These associations might have ethnic- and/or sex-specificity.

TRIAL REGISTRATION

Retrospectively registered.

The tip of the "celiac iceberg" in China: a systematic review and meta-analysis

Objective

Until recently, celiac disease was considered to be rare in China. We aimed to estimate its true status.

Methods

By searching the MEDLINE database and four Chinese full-text databases (CNKI, CBM, VIP and WANFANG) (up to August 2012), as well as two HLA allele frequency net databases and the Chinese Statistics Yearbook databases, we systematically reviewed the literature on definite and suspected cases of celiac disease, the predisposing HLA allele frequencies, and on gluten exposure in China. Meta-analysis was performed by analyzing DQ2, DQ8 and DQB1*0201 gene frequencies and heterogeneity in populations from different geographic regions and ethnicities in China.

Results

At present, the number of reported celiac disease cases is extremely low in China. The frequencies of the HLA-DQ2.5 and HLA-DQ8 haplotypes were 3.4% (95% confidence interval 1.3–5.5%) and 2.1% (0.1–4.1%), respectively. HLA-DQ2 and HLA-DQ8 antigen frequencies were 18.4% (15.0–21.7%) and 8.0% (4.5–11.4%), respectively. The frequency of the DQB1*0201 allele was 10.5% (9.3–11.6%) and it was more common in the northern Chinese than in the southern Chinese populations. The chance of being exposed to gluten is rapidly increasing all over China nowadays.

Conclusion

The data on HLA haplotyping, in conjunction with increasing wheat consumption, strongly suggests that the occurrence of celiac disease is more common in China than currently reported. Coordinated measures by the Chinese government, medical and agricultural research institutions, and food industries, would be justified to create more awareness about celiac disease and to prevent it becoming a medical and societal burden.

Anthropological analysis of Koreans using HLA class II diversity among East Asians

Human leukocyte antigens (HLAs) are useful markers for anthropological investigations because the allele and haplotype distributions at these loci vary widely among ethnic groups. HLA frequencies in Koreans, however, have not previously been analyzed on a phylogenetic basis. We determined the allele frequencies of four HLA class II (HLA-DRB1, -DQA1, -DQB1, and -DPB1) loci in 149 unrelated Korean individuals using a sequence-based typing method. A total of 29 HLA-DRB1, 17 HLA-DQA1, 16 HLA-DQB1, and 15 HLA-DPB1 alleles were identified. The most common allele at each locus was DRB1*0901, DQA1*0102, DQB1*0301, and DPB1*0501, respectively. Four-locus allelic association analysis showed the existence of 25 DRB1-DQA1-DQB1-DPB1 haplotypes with a frequency greater than 0.010. A dataset comprising ethnicity-specific information from published literature and the dbMHC database, as well as the allele frequencies determined in this study, was subjected to phylogenetic analysis. The analysis showed that Koreans are most closely related to Japanese and Han Chinese from Shandong province. Correspondence analyses showed that the current Korean population is located in a position intermediate between the northern and southern East Asian groups, supporting the theory of a bi- and/or multidirectional route of migration of early Korean settlers. This report can be used for anthropological studies, and may also be of use in the International Hematopoietic Stem Cell Sharing program.

Polymorphism of HLA-DRB1, -DQB1 and -DPB1 genes in Bai ethnic group in southwestern China

In this work, polymorphism of human leukocyte antigen (HLA)-DRB1, -DQB1 and -DPB1 genes was detected using polymerase chain reaction-sequence-based typing method in 128 healthy unrelated volunteers from the Bai ethnic group of Yunnan province of southwest China. Among all the 28 alleles detected for the DRB1 gene, the most common allele was DRB1*120201 with a frequency of 16.41%, followed by DRB1*090102, DRB1*080302, DRB1*1404, DRB1*150101, DRB1*140101 and DRB1*160201, with frequencies of 10.16%, 9.77%, 9.38%, 8.98%, 8.59% and 8.21%, respectively. Among 19 DQB1 alleles detected, the most frequent allele was DQB1*030101/0309 (35.94%), followed by DQB1*050201 (11.33%), DQB1*060101/060103 (10.54%) and DQB1*0401 (10.16%). For the DPB1 locus, the most common alleles were DPB1*0501 (42.19%), DPB1*1301 (13.28%), DPB1*020102 (10.93%) and DPB1*040101 (9.77%). The comparison of HLA class II allele frequencies of Bais with those of other Chinese populations suggested that the Bai ethnic group belonged to the southern group of Chinese.

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.

HLA class II similarities in Iranian Kurds and Azeris

The genetic relationship between Kurds and Azeris of Iran was investigated based on human leukocyte antigen (HLA) class II profiles. HLA typing was performed using polymerase chain reaction/restriction fragment-length polymorphism (PCR/RFLP) and PCR/sequence-specific primer (PCR/SSP) methods in 100 Kurds and 100 Azeris. DRB1*1103/04, DQA1*0501 and DQB1*0301 were the most common alleles and DRB1*1103/04-DQA1*0501-DQB1*0301 was the most frequent haplotype in both populations. No significant difference was observed in HLA class II allele distribution between these populations except for DQB1*0503 which showed a higher frequency in Kurds. Neighbor-joining tree based on Nei's genetic distances and correspondence analysis according to DRB1, DQA1 and DQB1 allele frequencies showed a strong genetic tie between Kurds and Azeris of Iran. The results of amova revealed no significant difference between these populations and other major ethnic groups of Iran. No close genetic relationship was observed between Azeris of Iran and the people of Turkey or Central Asians. According to the current results, present-day Kurds and Azeris of Iran seem to belong to a common genetic pool.

Sequencing-based analysis of the HLA-DPB1 polymorphism in Nu ethnic group of south-west China

In the present study, DNA typing for HLA-DPB1 was performed using polymerase chain reaction-sequencing-based typing method in 72 randomly selected Nu ethnic individuals inhabiting the Yunnan province of south-west China. Among the 12 detected DPB1 alleles, the most frequent was DPB1*1301, with the percentage of 20.83%, followed by DPB1*0501 (19.44%), DPB1*040101 (16.67%) and DPB1*2801 (9.72%). The allele DPB1*1501 was found for the first time in the Chinese population. Neighbour-joining showed that the Nu ethnic minority belonged to East Asian cluster and was most closely related to Lisu, being consistent with the historical records. In addition, the results obtained in this study will also provide useful information on organ transplantation, forensic investigations and disease association studies.

HLA class II gene polymorphism in Parsees and Zoroastrians of Iran

Extensive polymorphism of the HLA genes in different ethnic groups has been used as an invaluable tool for anthropological studies. In this study, HLA-DRB1, DQA1 and DQB1 allele frequencies and haplotypes were determined in 72 Parsees and 65 Zoroastrians living in Iran. The predominant DRB1 allele was *1103 = 4 in Parsees and *0701 in Zoroastrians. DQA1*0501 was the most common alleles in both spopulations. The most frequent DQB1 allele was *0301 in Parsees and *0201 in Zoroastrians. DRB1*1103 = 4-DQA1*0501-DQB1*0301 and DRB1*0701-DQA1*0201-DQB1*0201 were the most prevalent haplotypes in Parsees and Zoroastrians, respectively. Significant deviation from Hardy-Weinberg equilibrium was observed in DQA1 and DQB1 loci of Zoroastrians. The former locus also departed from neutrality due to balancing selection. All pairs of the studied loci in this study showed significant linkage disequilibrium. Analysis of molecular variance indicated that the main variation was confined to individuals within the studied populations. Neighbour-joining tree based on Nei's genetic distances according to DRB1 and DQB1 allele frequencies showed that Parsees and Zoroastrians of Iran were located in the same cluster of the phylogenetic tree. Furthermore, Zoroastrians of Iran and Pakistan are very close to each other. This study will serve as a reference for further anthropological studies when the HLA profile of all ethnic groups of Iran is investigated.

Polymorphism of HLA class II genes in Miao and Yao nationalities of Southwest China

In the present study, the polymorphism of human leucocyte antigen class II genes was investigated by the sequence-based typing method in two Chinese populations: the Miaos (n = 85) from Guizhou province and the Yaos (n = 66) from Yunnan province. These two populations exhibited certain similarity in their allelic distributions. Among 24 DRB1 alleles detected, DRB1*150101, DRB1*140101, DRB1*160201 and DRB1*090102 in Miao and DRB1*120201, DRB1*140101, DRB1*150101 and DRB1*090102 in Yao were highly predominant. Sixteen DQB1 alleles in total were found in these two populations among which DQB1*050201, DQB1*060101/060103 and DQB1*030101/0309 in both Miao and Yao and DQB1*050301 in Yao were commonly observed. In the 13 DPB1 alleles detected, the most frequent allele was DPB1*0501 in Miao and Yao followed by DPB1*02 and DPB1*1301. Frequent comparisons with other Chinese populations suggested the southern Chinese feature for both the Miao and Yao nationalities.

HLA-A, -B, and -DRB1 polymorphism defined by sequence-based typing of the Han population in Northern China

DNA typing for human leukocyte antigen (HLA)-A, -B and -DRB1 was performed using polymerase chain reaction-sequence-based typing method on 618 randomly selected healthy individuals of the Han population in Northern China. Allele frequencies and haplotypes were statistically analyzed. A total of 84 HLA-A alleles, 143 B alleles, and 122 DRB1 alleles were detected, and 853 A-B-DRB1 haplotypes, 473 A-B haplotypes, and 551 B-DRB1 haplotypes were statistically inferred. Statistical analysis of three-locus haplotypes showed that A*0207-B*4601-DRB1*0901 (3.06%) was the most predominant. Gene frequencies and haplotypic associations within HLA-A, -B, and -DRB1 loci were determined at a high-resolution (four digit) allelic level and should provide useful information in anthropology, bone marrow donor registry, legal medicine, and disease association studies.

Polymorphism of human leukocyte antigen-DRB1, -DQB1, and -DPB1 genes of Shandong Han population in China

In the present study, polymerase chain reaction-sequence-based typing (PCR-SBT) was used to analyze human leukocyte antigen (HLA)-DRB1, -DQB1, and -DPB1 alleles of 98 unrelated healthy Shandong Han individuals. A total of 60 alleles, in which 28 in DRB1, 15 in DQB1 and 17 in DPB1 were found. Among the 28 detected DRB1 alleles, DRB1*150101, DRB1*070101, DRB1*090102, DRB1*120201, and DRB1*080302 were commonly observed, with frequencies of 16.3%, 11.2%, 10.2%, 8.2%, and 5.6%, respectively. The most predominant DQB1 allele was DQB1*030101/0309 with the frequency of 20.4%, followed by DQB1*0201/0202 (14.8%), DQB1*0602 (14.3%), DQB1*030302 (12.2%), and DQB1*060101/060103 (10.7%). Of the 17 detected DPB1 alleles, DPB1*0501 was the most frequent allele with the frequency of 37.2%. DPB1*020102 (18.4%), DPB1*040101 (11.2%), DPB1*0402 (7.1%), and DPB1*1701 (6.6%) were also very frequent alleles. A total of 53 estimated DRB1-DQB1 two-locus haplotypes were observed in Shandong Han population, of which DRB1*150101-DQB1*0602 was the most predominant, followed by DRB1*090102-DQB1*030302, DRB1*070101-DQB1*0201/0202 DRB1*120201-DQB1*030101/0309, and DRB1*080302- DQB1*060101/060103. The distribution of the HLA class II alleles and haplotypes frequencies as well as the dendrogram showed that the Shandong Han population belongs to the northern group of Chinese. The data have implications for anthropological studies and disease associations.

HLA-DPA1 promoter haplotypes are differently distributed in southern Chinese ethnic groups

DPA1 gene is one of the human leukocyte antigen (HLA) class II genes and its promoter is highly polymorphic. From comparative studies among five southern Chinese populations, Jing, Li, Bai, Lahu, and Meizhou Han, we describe their single-nucleotide polymorphism (SNP)/haplotype frequency data of HLA-DPA1 gene promoter in this study. Within the 760-bp promoter region, we have identified 21 SNPs and nine possible haplotypes. Pair-wise comparisons show similar frequencies distribution of the HLA-DPA1 promoter haplotypes among Jing, Li, and Bai, whereas all pair-wise comparisons involved with Lahu or Meizhou Han and other ethnic groups show remarkable difference. The differences in frequencies of HLA-DPA1 promoter alleles may reveal different ethnic origins and demographic histories of the five populations. Our study may help distinguishing each of these populations by sequence variations of HLA-DPA1 promoter, which may be served as functional molecular markers for clinical and immunological studies involving the DPA1 locus.