Single-nucleotide polymorphisms and haplotype LD analysis of the 29-kb IGF2 region on chromosome 11p15.5 in the Korean population

OBJECTIVE: We investigated sequence variations of the 29-kb insulin-like growth factor 2 (IGF2) region in human chromosome region 11p15.5 in the Korean population. This region consists of IGF2, insulin-like growth factor 2 antisense (IGF2AS), and the insulin gene, all important candidate genes for various diseases, including cancer, obesity, diabetes, and coronary disease. While single nucleotide polymorphisms (SNPs) have been identified for this region and used in association studies, ethnic differences in genetic variation at this site have not been addressed. To date, SNPs for the entire 29-kb region in the Korean population have not been reported. METHODS: We surveyed a population of 108 Koreans for SNPs in the 29-kb IGF2 region. RESULTS: We identified 62 SNPs, consisting of 6 SNPs in the promoter region, 17 in the untranslated region, 19 in introns, and 20 in the intergenic region. We also analyzed linkage disequilibrium (LD) patterns and haplotypes using 36 high-frequency (> 5%)SNPs and found a well-defined LD block spanning about 13 kb that includes 8 kb of the IGF2AS gene, with two hot-spot regions flanking the LD block. CONCLUSION: These SNPs may be useful as genetic markers in disease association studies in the Korean population.     

Candidate-gene screening and association analysis at the autism-susceptibility locus on chromosome 16p: evidence of association at GRIN2A and ABAT

Autism is a highly heritable neurodevelopmental disorder whose underlying genetic causes have yet to be identified. To date, there have been eight genome screens for autism, two of which identified a putative susceptibility locus on chromosome 16p. In the present study, 10 positional candidate genes that map to 16p11-13 were examined for coding variants: A2BP1, ABAT, BFAR, CREBBP, EMP2, GRIN2A, MRTF-B, SSTR5, TBX6, and UBN1. Screening of all coding and regulatory regions by denaturing high-performance liquid chromatography identified seven nonsynonymous changes. Five of these mutations were found to cosegregate with autism, but the mutations are not predicted to have deleterious effects on protein structure and are unlikely to represent significant etiological variants. Selected variants from candidate genes were genotyped in the entire International Molecular Genetics Study of Autism Consortium collection of 239 multiplex families and were tested for association with autism by use of the pedigree disequilibrium test. Additionally, genotype frequencies were compared between 239 unrelated affected individuals and 192 controls. Patterns of linkage disequilibrium were investigated, and the transmission of haplotypes across candidate genes was tested for association. Evidence of single-marker association was found for variants in ABAT, CREBBP, and GRIN2A. Within these genes, 12 single-nucleotide polymorphisms (SNPs) were subsequently genotyped in 91 autism trios (one affected individual and two unaffected parents), and the association was replicated within GRIN2A (Fisher's exact test, P<.0001). Logistic regression analysis of SNP data across GRIN2A and ABAT showed a trend toward haplotypic differences between cases and controls.     

Haplotype diversity in 11 candidate genes across four populations

Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of "tagging" SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.     

Evolutionary signatures of common human cis-regulatory haplotypes

Variation in gene expression may give rise to a significant fraction of inter-individual phenotypic variation. Studies searching for the underlying genetic controls for such variation have been conducted in model organisms and humans in recent years. In our previous effort of assessing conserved underlying haplotype patterns across ethnic populations, we constructed common haplotypes using SNPs having conserved linkage disequilibrium (LD) across ethnic populations. These common haplotypes cluster into a simple evolutionary structure based on their frequencies, defining only up to three conserved clusters termed 'haplotype frameworks'. One intriguing preliminary finding was that a significant portion of reported variants strongly associated with cis-regulation tags these globally conserved haplotype frameworks. Here we expand the investigation by collecting genes showing stringently determined cis-association between genotypes and expression phenotypes from major studies. We conducted phylogenetic analysis of current major haplotypes along with the corresponding haplotypes derived from chimpanzee reference sequences. Our analysis reveals that, for the vast majority of such cis-regulatory genes, the tagging SNPs showing the strongest association also tag the haplotype lineages directly separated from ancestry, inferred from either chimpanzee reference sequences or the allele frequency-derived haplotype frameworks, suggesting that the differentially expressed phenotypes were evolved relatively early in human history. Such evolutionary signatures provide keys for a more effective identification of globally-conserved candidate regulatory haplotypes across human genes in future epidemiologic and pharmacogenetic studies.     

Genetics of sputum gene expression in chronic obstructive pulmonary disease

Previous expression quantitative trait loci (eQTL) studies have performed genetic association studies for gene expression, but most of these studies examined lymphoblastoid cell lines from non-diseased individuals. We examined the genetics of gene expression in a relevant disease tissue from chronic obstructive pulmonary disease (COPD) patients to identify functional effects of known susceptibility genes and to find novel disease genes. By combining gene expression profiling on induced sputum samples from 131 COPD cases from the ECLIPSE Study with genomewide single nucleotide polymorphism (SNP) data, we found 4315 significant cis-eQTL SNP-probe set associations (3309 unique SNPs). The 3309 SNPs were tested for association with COPD in a genomewide association study (GWAS) dataset, which included 2940 COPD cases and 1380 controls. Adjusting for 3309 tests (p<1.5e-5), the two SNPs which were significantly associated with COPD were located in two separate genes in a known COPD locus on chromosome 15: CHRNA5 and IREB2. Detailed analysis of chromosome 15 demonstrated additional eQTLs for IREB2 mapping to that gene. eQTL SNPs for CHRNA5 mapped to multiple linkage disequilibrium (LD) bins. The eQTLs for IREB2 and CHRNA5 were not in LD. Seventy-four additional eQTL SNPs were associated with COPD at p<0.01. These were genotyped in two COPD populations, finding replicated associations with a SNP in PSORS1C1, in the HLA-C region on chromosome 6. Integrative analysis of GWAS and gene expression data from relevant tissue from diseased subjects has located potential functional variants in two known COPD genes and has identified a novel COPD susceptibility locus.     

Bayesian logistic regression using a perfect phylogeny

Haplotype data capture the genetic variation among individuals in a population and among populations. An understanding of this variation and the ancestral history of haplotypes is important in genetic association studies of complex disease. We introduce a method for detecting associations between disease and haplotypes in a candidate gene region or candidate block with little or no recombination. A perfect phylogeny demonstrates the evolutionary relationship between single-nucleotide polymorphisms (SNPs) in the haplotype blocks. Our approach extends the logic regression technique of Ruczinski and others (2003) to a Bayesian framework, and constrains the model space to that of a perfect phylogeny. Environmental factors, as well as their interactions with SNPs, may be incorporated into the regression framework. We demonstrate our method on simulated data from a coalescent model, as well as data from a candidate gene study of sarcoidosis.     

SNP identification, linkage disequilibrium, and haplotype analysis for a 200-kb genomic region in a Korean population

Understanding patterns of linkage disequilibrium (LD) across genomes may facilitate association mapping studies to localize genetic variants influencing complex diseases, a recognition that led to the International Haplotype Mapping Project (HapMap). Divergent patterns of haplotype frequency and LD across global populations require that the HapMap database be supplemented with haplotype and LD data from additional populations. We conducted a pilot study of the LD and haplotype structure of a genomic region in a Korean population. A total of 165 SNPs were identified in a 200-kb region of 22q13.2 by direct sequencing. Unphased genotype data were generated for 76 SNPs in 90 unrelated Korean individuals. LD, haplotype diversity, and recombination rates were assessed in this region and compared with the HapMap database. The pattern of LD and haplotype frequencies of Korean samples showed a high degree of similarity with Japanese data. There was a strong correlation between high LD and low recombination frequency in this region. We found considerable similarities in local LD patterns between three Asian populations (Han Chinese, Japanese, and Korean) and the CEPH population. Haplotype frequencies were, however, significantly different between them. Our results should further the understanding of distinctive Korean genomic features and assist in designing appropriate association studies.     

Molecular evolution and functional characterisation of haplotypes of an important rubber biosynthesis gene in Hevea brasiliensis

Hydroxy‐methylglutaryl coenzyme‐A synthase (HMGS) is a rate‐limiting enzyme in the cytoplasmic isoprenoid biosynthesis pathway leading to natural rubber production in Hevea brasiliensis (rubber). Analysis of the structural variants of this gene is imperative to understand their functional significance in rubber biosynthesis so that they can be properly utilised for ongoing crop improvement programmes in Hevea. We report here allele richness and diversity of the HMGS gene in selected popular rubber clones. Haplotypes consisting of single nucleotide polymorphisms (SNPs) from the coding and non‐coding regions with a high degree of heterozygosity were identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor to the generation of allelic diversity, rather than point mutations. The evolutionarily conserved nature of some SNPs was identified by comparative DNA sequence analysis of HMGS orthologues from diverse taxa, demonstrating the molecular evolution of rubber biosynthesis genes in general. In silico three‐dimensional structural studies highlighting the structural positioning of non‐synonymous SNPs from different HMGS haplotypes revealed that the ligand‐binding site on the enzyme remains impervious to the reported sequence variations. In contrast, gene expression results indicated the possibility of association between specific haplotypes and HMGS expression in Hevea clones, which may have a downstream impact up to the level of rubber production. Moreover, haplotype diversity of the HMGS gene and its putative association with gene expression can be the basis for further genetic association studies in rubber. Furthermore, the data also show the role of SNPs in the evolution of candidate genes coding for functional traits in plants.     

Large-scale identification and characterization of genetic variants in asthma candidate genes

Asthma is a chronic inflammatory disorder of the airways, and a number of genetic loci are associated with the disease. Candidate gene association studies have been regarded as effective tools to study complex traits. Knowledge of the sequence variation and structure of the candidate genes is required for association studies. Thus, we investigated the genetic variants of 32 asthma candidate genes selected by colocalization of positional and functional candidate genes. We screened all exons and promoter regions of those genes using 12 healthy individuals and 12 asthma patients and identified a total of 418 single nucleotide polymorphisms (SNPs), including 270 known SNPs and 148 novel SNPs. Levels of nucleotide diversity varied from gene to gene (0.72×10⁻⁴–14.53×10⁻⁴), but the average nucleotide diversity between coding SNPs (cSNPs) and noncoding SNPs was roughly equivalent (4.63×10⁻⁴ vs 4.69×10⁻⁴). However, nucleotide diversity of cSNPs was strongly correlated to codon degeneracy. Nucleotide diversity was much higher at fourfold degenerate sites than at nondegenerate sites (9.42×10⁻⁴ vs 3.14×10⁻⁴). Gene-based haplotype analysis of asthma-associated genes in this study revealed that common haplotypes (frequency >5%) represented 90.5% of chromosomes, and they could be uniquely identified with five or fewer haplotype-tagging SNPs per gene. Therefore, our results may have important implications for the selection of asthma candidate genes and SNP markers for comprehensive association studies using large sample populations.     

Ethnic differences in the linkage disequilibrium and distribution of single-nucleotide polymorphisms in 35 candidate genes for cardiovascular diseases

Single-nucleotide polymorphisms (SNPs) are commonly used to study genetics for common diseases and predict pharmacological response. The selection of likely informative SNPs in association studies depends on their allele frequencies and on the linkage disequilibrium (LD) between SNPs, both of which may show interethnic differences. Among three populations consisting of 207 Chinese, 858 French, and 395 Spanish, we compared the allele frequency distributions of 64 intragenic SNPs of 35 candidate genes for cardiovascular diseases. Twenty-eight of these SNPs from 12 genes were also examined for intragenic LD. About 20% of SNPs were restricted to Europeans, being monomorphic in Chinese, among them mostly nonsynonymous coding SNPs and noncoding SNPs. Only 1.6% of SNPs were specific in Chinese, commensurate with the detection of these SNPs almost exclusively in Caucasians. Similarly, these SNPs were more often rare (<0.1 minor allele frequency) in Chinese (44.3%) than in Europeans (31.1%). The variant allele frequencies and intermarker LDs in terms of D' and Delta(2) were highly correlated between French and Spanish populations (r = 0.98-0.99, p < 0.001). However, only moderate correlations of allele frequencies and D' were found between the Chinese and the European populations (r = 0.7 and 0.3, respectively) despite a high correlation of Delta(2) values (r = 0.8). These results suggest that ethnic considerations are important in the selection of SNPs for association studies of candidate genes, as this may affect the power of the study as well as the likelihood of asking relevant questions and getting medically meaningful answers.     

Association mapping of morphological traits in wild and captive zebra finches: reliable within,but not between populations

Identifying causal genetic variants underlying heritable phenotypic variation is a long‐standing goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole‐genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild‐caught zebra finches. Then, we validated the most promising SNP–phenotype associations (n = 25 SNPs) in 5228 birds from four populations. Genotype–phenotype associations were generally weak in the wild population, where linkage disequilibrium (LD) spans only short genomic distances. In contrast, in captive populations, where LD blocks are large, apparent SNP effects on morphological traits (i.e. associations) were highly repeatable with independent data from the same population. Most of those SNPs also showed significant associations with the same trait in other captive populations, but the direction and magnitude of these effects varied among populations. This suggests that the tested SNPs are not the causal QTN but rather physically linked to them, and that LD between SNPs and causal variants differs between populations due to founder effects. While the identification of QTN remains challenging in nonmodel organisms, we illustrate that it is indeed possible to confirm the location and magnitude of QTL in a population with stable linkage between markers and causal variants.     

Genetic variation in the odorant receptor OR2J3 is associated with the ability to detect the "grassy" smelling odor, cis-3-hexen-1-ol

The ability to detect many odors varies among individuals; however, the contribution of genotype to this variation has been assessed for relatively few compounds. We have identified a genetic basis for the ability to detect the flavor compound cis-3-hexen-1-ol. This compound is typically described as "green grassy" or the smell of "cut grass," with variation in the ability to detect it linked to single nucleotide polymorphisms (SNPs) in a region on human chromosome 6 containing 25 odorant receptor genes. We have sequenced the coding regions of all 25 receptors across an ethnically mixed population of 52 individuals and identified 147 sequence variants. We tested these for association with cis-3-hexen-1-ol detection thresholds and found 3 strongly associated SNPs, including one found in a functional odorant receptor (rs28757581 in OR2J3). In vitro assays of 13 odorant receptors from the region identified 3 receptors that could respond to cis-3-hexen-1-ol, including OR2J3. This gene contained 5 predicted haplotypes across the 52 individuals. We tested all 5 haplotypes in vitro and several amino acid substitutions on their own, such as rs28757581 (T113A). Two amino acid substitutions, T113A and R226Q, impaired the ability of OR2J3 to respond to cis-3-hexen-1-ol, and together these two substitutions effectively abolished the response to the compound. The haplotype of OR2J3 containing both T113A and R226Q explains 26.4% of the variation in cis-3-hexen-1-ol detection in our study cohort. Further research is required to examine whether OR2J3 haplotypes explain variation in perceived flavor experience and the consumption of foods containing cis-3-hexen-1-ol.     

Implications of inter-population linkage disequilibrium patterns on the approach to a disease association study in the human MHC class III

There is presently much interest in utilizing patterns of linkage disequilibrium (LD) to further genetic association studies. This is particularly pertinent in the class III region of the human major histocompatibility complex (MHC), which has been extensively studied as a disease susceptibility locus in a number of ethnic groups. To date, however, few studies of LD in the MHC have considered non-Caucasian populations. With the advent of large-scale haplotyping of the human genome, the question of utilizing LD patterns across populations has come to the fore. We have previously used LD mapping to direct an MHC class III association study in a UK Caucasian population. As an extension of this, we sought to determine to what extent the pattern of LD observed in that study could be used to conduct a similar study in a West African Gambian population. We found that broad patterns of LD were similar in the two populations, resulting in similar candidate region delineations, but at a higher resolution, marker-specific patterns of LD and population-dependent allele frequencies confounded the choice of regional tagging SNPs. Our results have implications for the applicability of large-scale haplotype maps such as the HapMap to complex regions like the MHC.Electronic Supplementary Material Supplementary material is available for this article at .     

Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium

Common genetic polymorphisms may explain a portion of the heritable risk for common diseases. Within candidate genes, the number of common polymorphisms is finite, but direct assay of all existing common polymorphism is inefficient, because genotypes at many of these sites are strongly correlated. Thus, it is not necessary to assay all common variants if the patterns of allelic association between common variants can be described. We have developed an algorithm to select the maximally informative set of common single-nucleotide polymorphisms (tagSNPs) to assay in candidate-gene association studies, such that all known common polymorphisms either are directly assayed or exceed a threshold level of association with a tagSNP. The algorithm is based on the r(2) linkage disequilibrium (LD) statistic, because r(2) is directly related to statistical power to detect disease associations with unassayed sites. We show that, at a relatively stringent r(2) threshold (r2>0.8), the LD-selected tagSNPs resolve >80% of all haplotypes across a set of 100 candidate genes, regardless of recombination, and tag specific haplotypes and clades of related haplotypes in nonrecombinant regions. Thus, if the patterns of common variation are described for a candidate gene, analysis of the tagSNP set can comprehensively interrogate for main effects from common functional variation. We demonstrate that, although common variation tends to be shared between populations, tagSNPs should be selected separately for populations with different ancestries.     

Global Analysis of ATM Polymorphism Reveals Significant Functional Constraint

ATM, the gene that is mutated in ataxia-telangiectasia, is associated with cerebellar degeneration, abnormal proliferation of small blood vessels, and cancer. These clinically important manifestations have stimulated interest in defining the sequence variation in the ATM gene. Therefore, we undertook a comprehensive survey of sequence variation in ATM in diverse human populations. The protein-encoding exons of the gene (9,168 bp) and the adjacent intron and untranslated sequences (14,661 bp) were analyzed in 93 individuals from seven major human populations. In addition, the coding sequence was analyzed in one chimpanzee, one gorilla, one orangutan, and one Old World monkey. In human ATM, 88 variant sites were discovered by denaturing high-performance liquid chromatography, which is 96%-100% sensitive for detection of DNA sequence variation. ATM was compared to 14 other autosomal genes for nucleotide diversity. The noncoding regions of ATM had diversity values comparable to other genes, but the coding regions had very low diversity, especially in the last 29% of the protein sequence. A test of the neutral evolution hypothesis, through use of the Hudson/Kreitman/Aguadé statistic, revealed that this region of the human ATM gene was significantly constrained relative to that of the orangutan, the Old World monkey, and the mouse, but not relative to that of the chimpanzee or the gorilla. ATM displayed extensive linkage disequilibrium, consistent with suppression of meiotic recombination at this locus. Seven haplotypes were defined. Two haplotypes accounted for 82% of all chromosomes analyzed in all major populations; two others carrying the same D126E missense polymorphism accounted for 33% of chromosomes in Africa but were never observed outside of Africa. The high frequency of this polymorphism may be due either to a population expansion within Africa or to selective pressure.     

Haplotypes within genes of β-chemokines in 17q11 are associated with multiple sclerosis: a second phase study

We previously defined haplotypes of single nucleotide polymorphisms (SNP) with possible relevance to multiple sclerosis (MS) in 2 CC chemokine ligand (CCL) clusters in chromosome 17q11. The 17q11 region was also identified as a susceptibility locus by a meta-analysis of linkage studies. To confirm and refine the previous finding in a second, high resolution SNP scan in a new set of families. We genotyped 232 SNPs in 1369 individuals in 361 MS families. Transmission of marker alleles and haplotypes from unaffected parents to affected offspring was tested by using the pedigree disequilibrium test, the TRANSMIT 2.5 program, and the family and haplotype based association tests. Distribution of linkage disequilibrium (LD) was assessed by ldmax. In consensus with observations in the first scan, the present study identified haplotypes within CCL3 and CCL15 in the telomeric CCL cluster. There was also an overlap in the findings in the centromeric CCL cluster. Strong and extensive LD was detected both within the centromeric and telomeric CCL gene clusters. The present study replicates our previous findings and further suggests the existence of MS associated haplotypes within genes of CCL3 and CCL15. Haplotypes of interest are also present within the centromeric gene cluster (including CCL2, CCL7, CCL11, CCL8, and CCL13), but extensive LD prevents further refinement of these haplotypes by using the methods applied. Sequencing of the identified chromosomal segments and their flanking regions will be necessary to define specific variants with direct relevance to MS pathogenesis.     

Linkage disequilibrium and allele-frequency distributions for 114 single-nucleotide polymorphisms in five populations

Single-nucleotide polymorphisms (SNPs) may be extremely important for deciphering the impact of genetic variation on complex human diseases. The ultimate value of SNPs for linkage and association mapping studies depends in part on the distribution of SNP allele frequencies and intermarker linkage disequilibrium (LD) across populations. Limited information is available about these distributions on a genomewide scale, particularly for LD. Using 114 SNPs from 33 genes, we compared these distributions in five American populations (727 individuals) of African, European, Chinese, Hispanic, and Japanese descent. The allele frequencies were highly correlated across populations but differed by >20% for at least one pair of populations in 35% of SNPs. The correlation in LD was high for some pairs of populations but not for others (e.g., Chinese American or Japanese American vs. any other population). Regardless of population, average minor-allele frequencies were significantly higher for SNPs in noncoding regions (20%-25%) than for SNPs in coding regions (12%-16%). Interestingly, we found that intermarker LD may be strongest with pairs of SNPs in which both markers are nonconservative substitutions, compared to pairs of SNPs where at least one marker is a conservative substitution. These results suggest that population differences and marker location within the gene may be important factors in the selection of SNPs for use in the study of complex disease with linkage or association mapping methods.     

Improved power by use of a weighted score test for linkage disequilibrium mapping

Association studies offer an exciting approach to finding underlying genetic variants of complex human diseases. However, identification of genetic variants still includes difficult challenges, and it is important to develop powerful new statistical methods. Currently, association methods may depend on single-locus analysis--that is, analysis of the association of one locus, which is typically a single-nucleotide polymorphism (SNP), at a time--or on multilocus analysis, in which multiple SNPs are used to allow extraction of maximum information about linkage disequilibrium (LD). It has been shown that single-locus analysis may have low power because a single SNP often has limited LD information. Multilocus analysis, which is more informative, can be performed on the basis of either haplotypes or genotypes. It may lose power because of the often large number of degrees of freedom involved. The ideal method must make full use of important information from multiple loci but avoid increasing the degrees of freedom. Therefore, we propose a method to capture information from multiple SNPs but with the use of fewer degrees of freedom. When a set of SNPs in a block are correlated because of LD, we might expect that the genotype variation among the different phenotypic groups would extend across all the SNPs, and this information could be compressed into the low-frequency components of a Fourier transform. Therefore, we develop a test based on weighted Fourier transformation coefficients, with more weight given to the low-frequency components. Our simulation results demonstrate the validity and substantially higher power of the proposed method compared with other common methods. This method provides an additional tool to existing methods for identification of causative genetic variants underlying complex diseases.     

Family-Based Association Study of Pulmonary Function in a Population in Northeast Asia

The spirometric measurement of pulmonary function by measuring the forced expiratory volume in one second (FEV₁) is a heritable trait that reflects the physiological condition of the lung and airways. Genome-wide linkage and association studies have identified a number of genes and genetic loci associated with pulmonary function. However, limited numbers of studies have been reported for Asian populations. In this study, we aimed to investigate genetic evidence of pulmonary function in a population in northeast Asia. We conducted a family-based association test with 706 GENDISCAN study participants from 72 Mongolian families to determine candidate genetic determinants of pulmonary function. For the replication, we chose seven candidate single nucleotide polymorphisms (SNPs) from the 5 loci, and tested 1062 SNPs for association with FEV₁ from 2,729 subjects of the Korea Healthy Twin study. We identified TMEM132C as a potential candidate gene at 12q24.3, which is a previously reported locus of asthma and spirometric indices. We also found two adjacent candidate genes (UNC93A and TTLL2) in the 6q27 region, which has been previously identified as a pulmonary function locus in the Framingham cohort study. Our findings suggest that novel candidate genes (TMEM132C, UNC93A and TTLL2) in two different regions are associated with pulmonary function in a population in northeast Asia.