Linkage Disequilibrium Mapping Research Articles

Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm.

Oil palm is the world’s leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits.

Challenges in Rare Variant Association Studies for Complex Kidney Traits: CFHR5 and IgA Nephropathy

With the first successful genome–wide application of linkage disequilibrium mapping in 2005,[1][1] genome–wide association studies (GWASs) have now surpassed their 10th anniversary. GWASs have been applied extensively to dissect contributions of common variants to complex disease, and thousands

Multi-marker linkage disequilibrium mapping of quantitative trait loci.

Single nucleotide polymorphisms (SNPs), the most common genetic markers in genome-wide association studies, are usually in linkage disequilibrium (LD) with each other within a small genomic region. Both single- and two-marker-based LD mapping methods have been developed by taking advantage of the LD structures. In this study, a more general LD mapping framework with an arbitrary number of markers has been developed to further improve LD mapping and its detection power. This method is referred as multi-marker linkage disequilibrium mapping (mmLD). For the parameter estimation, we implemented a two-phase estimation procedure: first, haplotype frequencies were estimated for known markers; then, haplotype frequencies were updated to include the unknown quantitative trait loci based on estimates from the first step. For the hypothesis testing, we proposed a novel sequential likelihood ratio test procedure, which iteratively removed haplotypes with zero frequency and subsequently determined the proper degree of freedom. To compare the proposed mmLD method with other existing mapping methods, e.g. the adjusted single-marker LD mapping and the SKAT_C, we performed extensive simulations under various scenarios. The simulation results demonstrated that the mmLD has the same or higher power than the existing methods, while maintaining the correct type I errors. We further applied the mmLD to a public data set, 'GAW17', to investigate its applicability. The result showed the good performance of mmLD. We concluded that this improved mmLD method will be useful for future genome-wide association studies and genetic association analyses.

Dissection of QTL alleles for blast resistance based on linkage and linkage disequilibrium mapping in japonica rice seedlings

Rice blast is one of the major fungal diseases that badly reduce rice production in China and worldwide. Molecular markers tightly linked to resistant genes can be used for marker-assisted and/or genomic selection. In this study, linkage mapping and association mapping were used to identify the QTLs for the disease index of 7 and 14 days after inoculation (DI7 and DI14) conferring resistance against two highly pathogenic and locally predominant isolates (DB22 and DB77) in japonica rice at the seedling stage. The recombinant inbred line (RIL) population with 114 SSR markers derived from Dongnong 415 (resistant to rice blast) as the male parent and Lijiangxintuanheigu (LTH, susceptible to rice blast) as the female parent was used for linkage mapping. A total of 10 QTLs were identified by the inclusive composite interval mapping method (ICIM), explaining 7.89–33.75 % of the total phenotypic variance. This study was supplemented with association mapping, which was conducted using a panel of 227 japonica rice cultivars released in Northeastern China during the past 50 years with 118 selected SSR markers. A total of 13 significant marker-trait associations (P ≤ 0.01) involving 10 markers were identified using the MLM (Q + K) models in TASSEL 3.0. Among them, 8 of the SSR markers confirmed or narrowed the genomic regions for blast resistance that were reported in linkage studies, including five QTLs identified during the present study. Phenotypic effects of each allele of the 8 stable markers were compared, and 12 resistant alleles were identified. These resistant alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the resistant alleles per QTL (apart from possible epistatic effects). The results should increase our understanding of the genetic basis of blast resistance and facilitate future resistant breeding in rice.

Linkage disequilibrium in wild and cultured populations of Pacific oyster (Crassostrea gigas)

Linkage disequilibrium (LD) can be applied for mapping the actual genes responsible for variation of economically important traits through association mapping. The feasibility and efficacy of association studies are strongly dependent on the extent of LD which determines the number and density of markers in the studied population, as well as the experimental design for an association analysis. In this study, we first characterized the extent of LD in a wild population and a cultured mass-selected line of Pacific oyster (Crassostrea gigas). A total of 88 wild and 96 cultured individuals were selected to assess the level of genome-wide LD with 53 microsatellites, respectively. For syntenic marker pairs, no significant association was observed in the wild population; however, three significant associations occurred in the cultured population, and the significant LD extended up to 12.7 cM, indicating that strong artificial selection is a key force for substantial increase of genome-wide LD in cultured population. The difference of LD between wild and cultured populations showed that association studies in Pacific oyster can be achieved with reasonable marker densities at a relatively low cost by choosing an association mapping population. Furthermore, the frequent occurrence of LD between non-syntenic loci and rare alleles encourages the joint application of linkage analysis and LD mapping when mapping genes in oyster. The information on the linkage disequilibrium in the cultured population is useful for future association mapping in oyster.

Constructing a linkage-linkage disequilibrium map using dominant-segregating markers.

The relationship between linkage disequilibrium (LD) and recombination fraction can be used to infer the pattern of genetic variation and evolutionary process in humans and other systems. We described a computational framework to construct a linkage–LD map from commonly used biallelic, single-nucleotide polymorphism (SNP) markers for outcrossing plants by which the decline of LD is visualized with genetic distance. The framework was derived from an open-pollinated (OP) design composed of plants randomly sampled from a natural population and seeds from each sampled plant, enabling simultaneous estimation of the LD in the natural population and recombination fraction due to allelic co-segregation during meiosis. We modified the framework to infer evolutionary pasts of natural populations using those marker types that are segregating in a dominant manner, given their role in creating and maintaining population genetic diversity. A sophisticated two-level EM algorithm was implemented to estimate and retrieve the missing information of segregation characterized by dominant-segregating markers such as single methylation polymorphisms. The model was applied to study the relationship between linkage and LD for a non-model outcrossing species, a gymnosperm species, Torreya grandis, naturally distributed in mountains of the southeastern China. The linkage–LD map constructed from various types of molecular markers opens a powerful gateway for studying the history of plant evolution.

Combined gating and trafficking defect in Kv11.1 manifests as a malignant long QT syndrome phenotype in a large Danish p.F29L founder family

Background. Congenital long QT syndrome (LQTS) is a hereditary cardiac channelopathy characterized by delayed ventricular repolarization, syncope, torsades de pointes and sudden cardiac death. Thirty-three members of five apparently ‘unrelated’ Danish families carry the KCNH2:c.87C> A; p.F29L founder mutation. Methods and Results. Linkage disequilibrium mapping with microsatellites around KCNH2 enabled us to estimate the age of the founder mutation to be approximately 22 generations, corresponding to around 550 years. Neighbouring-Joining analysis disclosed one early and three later nodes. The median QTc time of the carriers was 490 ms (range: 415–589 ms) and no difference was seen between the different branches of the family. The mutation is malignant with a penetrance of 73%. Ten F29L carriers received implantable defibrillators (ICDs) (median age at implant 20 years), and of those four individuals experienced eight appropriate shocks. Patch-clamp analysis in HEK 293 cells, performed at 34°C disclosed a loss-of-function phenotype with fast deactivation, reduced steady-state inactivation current density and a positive voltage shift in inactivation. Western blotting of HEK 293 cells transfected with KCNH2:WT and KCNH2:c.87C> A revealed a reduced fraction of fully glycosylated hERG:p.F29L suggesting that this mutation results in defective trafficking. Conclusion. The altered channel gating kinetics in combination with defective trafficking of mutated channels is expected to result in reduced repolarizing current density and, thus, a LQTS phenotype.

Genetic variation in the oxytocin receptor gene is associated with a social phenotype in autism spectrum disorders.

Oxytocin regulates social behavior in animal models. Research supports an association between genetic variation in the oxytocin receptor gene (OXTR) and autism spectrum disorders (ASD). In this study, we examine the association between the OXTR gene and a specific social phenotype within ASD. This genotype-phenotype investigation may provide insight into how OXTR conveys risk for social impairment. The current study investigated 10 SNPS in the OXTR gene that have been previously shown to be associated with ASD. We examine the association of these SNPs with both a social phenotype and a repetitive behavior phenotype comprised of behaviors commonly impaired in ASD in the Simons simplex collection (SSC). Using a large sample to examine the association between OXTR and ASD (n = range: 485-1002), we find evidence to support a relation between two OXTR SNPs and the examined social phenotype among children diagnosed with ASD. Greater impairment on the social responsiveness scale standardized total score and on several subdomains was observed among individuals with one or more copies of the minor frequency allele in both rs7632287 and rs237884. Linkage disequilibrium (LD) mapping suggests that these two SNPs are in LD within and overlapping the 3' untranslated region (3'-UTR) of the OXTR gene. These two SNPs were also associated with greater impairment on the repetitive behavior scale. Results of this study indicate that social impairment and repetitive behaviors in ASD are associated with genomic variation in the 3'UTR of the OXTR gene. These variants may be linked to an allele that alters stability of the mRNA message although further work is necessary to test this hypothesis.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations.

BackgroundAn understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution.ResultsWe compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure.ConclusionsWGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1854-0) contains supplementary material, which is available to authorized users.

Inferring the evolutionary history of outcrossing populations through computing a multiallelic linkage–linkage disequilibrium map

Summary Linkage disequilibrium (LD), the non‐random association of alleles at different loci, has been used as an important parameter to study the genetic diversity and evolutionary history of natural populations. A joint analysis of LD with the linkage of the same marker pair has proven to gain more insight into the genetic signature of population diversification than LD analysis alone. We develop a unifying framework for simultaneously estimating the linkage and LD across pairs of multiallelic markers. The framework has particular power to construct the LD map from any markers with an arbitrary number of alleles per locus. We provide an efficient strategy to manipulate disequilibrium parameters whose number increases exponentially with the number of alleles. The model was tested through extensive simulation studies and validated by analysing a real marker data set from a population genetic research project of euphrates poplar, a desert tree, distributed in the north‐western China. For widespread undomesticated natural populations, compared with biallelic markers, multiallelic markers with a high level of polymorphism are more powerful to study their genetic structure and organization of an outcrossing population. The model developed will potentially have an immediate implication for population and evolutionary genetic studies.

Genetic structure, linkage disequilibrium and association mapping of salt tolerance in japonica rice germplasm at the seedling stage

Soil salinity is a major constraint to rice production. Understanding the genetic basis of salt tolerance is crucial for the improvement of salt tolerance through breeding. Previous quantitative trait locus (QTL) studies for salt tolerance were mainly derived from bi-parental segregating populations and relatively little is known about the results from natural populations. Understanding the genetic diversity, population structure and linkage disequilibrium (LD) in an association panel can effectively avoid spurious associations in association mapping. In this study, 341 japonica rice (Oryza sativa L. subsp. japonica) accessions worldwide were genotyped with 160 simple sequence repeat (SSR) markers to identify marker-trait associations with salt tolerance at the seedling stage. Salt tolerance was evaluated by survival days of seedlings and shoot K+/Na+ ratio. A total of 872 alleles ranging from 2 to 9 per locus were identified from all collections. Population structure analysis identified three main subpopulations for the accessions. Of the SSR pairs in these accessions, 40.05 % marker pairs showed significant LD (P < 0.01). The LD level for linked markers is significantly higher than that for unlinked markers, and LD level was elevated when the panel was classified into subpopulations. The LD decayed to the background at approximately 20–50 cM within the total panel and each subpopulation. A total of ten marker loci associated with salt tolerance were identified using MLM (Q + K) models in TASSEL 3.0. Among which nine marker loci confirmed or narrowed the genomic region reported to harbor QTLs for salt tolerance by linkage mapping in previous reports, and four salt tolerance-related genes were located in the QTL regions in the present study. According to phenotypic effects for alleles of the detected QTLs, favorable alleles were mined. These favorable alleles could be used to design parental combinations and the expected results would be obtained by pyramiding or substituting the favorable alleles per QTL (apart from possible epistatic effects). Our results demonstrate that association mapping can complement and enhance previous QTL information for marker-assisted selection and breeding by design.

Multiple Linkage Disequilibrium Mapping Methods to Validate Additive Quantitative Trait Loci in Korean Native Cattle (Hanwoo).

The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a BayesCπ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

Genetic fine‐mapping and gene identification of adiposity traits in outbred rats

Obesity and overweight are major risk factors for multiple diseases including cardiovascular disease and type 2 diabetes. Genetic factors are known to contribute significantly to obesity and related traits with heritability ranging from 50‐80%. Human genome‐wide association studies have identified over 50 genes for traits related to adiposity. These genes, however, explain less than 10% of the heritable variance. Heterogeneous stock (HS) rats are outbred from eight inbred strains and allow genetic fine‐mapping to only a few Megabases. The goal of the current study was to use HS rats to fine‐map adiposity traits genome‐wide and identify underlying candidate genes. We measured body weight, body mass index and visceral adiposity in 1090 male HS rats and genotyped all rats using the Affymetrix 10K SNP array. Linkage disequilibrium mapping by mixed model regression was used to identify significant loci. We identified one or more significant loci for all traits, with an average confidence interval of only 2.2 Mb. Using expression data and founder sequence, we identified potential candidate genes within several loci, including those that have previously been identified in human genome‐wide association studies. Protein modeling was used to support a causal role for some of the genes. These results demonstrate the power of HS rats for fine‐mapping metabolic traits and rapidly identifying candidate genes.Supported by NIH R01 DK‐088975 and the Individualized Medicine Institute at MCW.

Constructing a Genome-Wide LD Map of Wild A. gambiae Using Next-Generation Sequencing.

Anopheles gambiae is the major malaria vector in Africa. Examining the molecular basis of A. gambiae traits requires knowledge of both genetic variation and genome-wide linkage disequilibrium (LD) map of wild A. gambiae populations from malaria-endemic areas. We sequenced the genomes of nine wild A. gambiae mosquitoes individually using next-generation sequencing technologies and detected 2,219,815 common single nucleotide polymorphisms (SNPs), 88% of which are novel. SNPs are not evenly distributed across A. gambiae chromosomes. The low SNP-frequency regions overlay heterochromatin and chromosome inversion domains, consistent with the lower recombinant rates at these regions. Nearly one million SNPs that were genotyped correctly in all individual mosquitoes with 99.6% confidence were extracted from these high-throughput sequencing data. Based on these SNP genotypes, we constructed a genome-wide LD map for wild A. gambiae from malaria-endemic areas in Kenya and made it available through a public Website. The average size of LD blocks is less than 40 bp, and several large LD blocks were also discovered clustered around the para gene, which is consistent with the effect of insecticide selective sweeps. The SNPs and the LD map will be valuable resources for scientific communities to dissect the A. gambiae genome.

Comparative mapping and discovery of segregation distortion and linkage disequilibrium across the known fragrance chromosomal regions in a rice F2 population

Segregation distortion analysis in plant breeding is highly important because deviation factors are occasionally serious barriers for introgression of genes of interest into cultivated species. Also, the identification of major QTLs by high linkage disequilibrium is highly useful for breeders in order for crop improvement programs and the further fine mapping of particular genes. Consequently, simultaneous consideration of segregation distortion and linkage disequilibrium leads to developing fertile hybrids and normal inheritance of agronomically favorable genes. Hence, the goal of this study was to investigate genomic regions known to contain fragrance quantitative trait loci (QTLs) in terms of segregation distortion and linkage disequilibrium pattern, and to seek for a possible relationship between them using codominant markers on chromosomes 3, 4, and 8 in a set containing 189 F2 progenies. For the first time, we discovered the presence and extent of segregation distortion and linkage disequilibrium across the fragrance chromosomal areas of rice. The high frequency of skewed allelic segregations in the chromosomes 3 and 4 supports reports of possible gametic selection (ga) and hybrid sterility (S) genes. Finally, the highest linkage disequilibrium values, the lowest recombination frequency, and the shortest distances were observed in the chromosomal regions without segregation distortion. High linkage disequilibrium correlations between markers at short distances may show that such markers can maintain high linkage disequilibrium with linked QTLs and are influential for both MAS and QTL mapping analysis. Moreover, an indirect relationship between segregation distortion and linkage disequilibrium was detected, and thus linkage disequilibrium maps were introduced as useful diagnostic tools for segregation distortion.

Simultaneous estimation of the locations and effects of multiple disease loci in case-control studies.

The genetic basis of complex diseases often involves multiple causative loci. Under such a disease etiology, assuming one disease locus in linkage disequilibrium mapping is likely to induce bias and lead to efficiency loss in disease locus estimation. An approach is needed for simultaneously localizing multiple functional loci within the same region. However, due to the increasing number of parameters accompanying disease loci, these estimates can be computationally infeasible. To circumvent this problem, we propose to estimate the main and two-adjacent-locus joint effects and a nuisance parameter at the disease loci separately through a linear approximation. Estimates of the genetic effects are entered into a generalized estimating equation to estimate disease loci, and the procedure is conducted iteratively until convergence. The proposed method provides estimates and confidence intervals (CIs) for the disease loci, the genetic main effects, and the joint effects of two adjacent disease loci, with the CIs for the disease loci providing useful regions for further fine-mapping. We apply the proposed approach to a data example of case-control studies. Results of the simulations and data example suggest that the developed method performs well in terms of bias, variance, and coverage probability under scenarios with up to three disease loci.

Follow-up to genome-wide linkage and admixture mapping studies implicates components of the extracellular matrix in susceptibility to and size of uterine fibroids

To conduct a follow-up association mapping to independent genome-wide linkage and admixture mapping studies of uterine leiomyoma. Case-control, cross-sectional study. Not applicable. A total of 1,045 premenopausal North American participants in the National Institute of Environmental Health Sciences Uterine Fibroid Study. None. We genotyped 2,772 single-nucleotide polymorphisms from candidate genes located in peaks of linkage (2q37, 3p21, 5p13, 10p11, 11p15, 12q14, and 17q25) or admixture linkage disequilibrium (2q37, 4p16.1, and 10q26) mapping and reported to have regulated expression in uterine fibroids. We report significant associations of variant members of the collagen gene family with risk and tumor size, including missense variants in COL6A3 and COL13A, with replications in African American and European American study groups. Furthermore, the cell-matrix Rho GTPase-encoding ARHGAP26 gene, and MAN1C1, a gene encoding a Golgi mannosidase involved in the maturation of procollagens, emerged as new candidate uterine leiomyoma genes affecting both risk and tumor size. Our data converge onto a possible model of uterine leiomyoma pathogenesis resulting from altered regulation, maintenance, and/or renewal of the extracellular matrix.

Linkage disequilibrium and haplotype block structure in a composite beef cattle breed.

BackgroundThe development of linkage disequilibrium (LD) maps and the characterization of haplotype block structure at the population level are useful parameters for guiding genome wide association (GWA) studies, and for understanding the nature of non-linear association between phenotypes and genes. The elucidation of haplotype block structure can reduce the information of several single nucleotide polymorphisms (SNP) into the information of a haplotype block, reducing the number of SNPs in a coherent way for consideration in GWA and genomic selection studies.ResultsThe maximum average LD, measured by r2 varied between 0.33 to 0.40 at a distance of < 2.5 kb, and the minimum average values of r2 varied between 0.05 to 0.07 at distances ranging from 400 to 500 kb, clearly showing that the average r2 reduced with the increase in SNP pair distances. The persistence of LD phase showed higher values at shorter genomic distances, decreasing with the increase in physical distance, varying from 0.96 at a distance of < 2.5 kb to 0.66 at a distance from 400 to 500 kb. A total of 78% of all SNPs were clustered into haplotype blocks, covering 1,57 Mb of the total autosomal genome size.ConclusionsThis study presented the first high density linkage disequilibrium map and haplotype block structure for a composite beef cattle population, and indicates that the high density SNP panel over 700 k can be used for genomic selection implementation and GWA studies for Canchim beef cattle.

P.1.a.003 Epigenetic regulation at the FKBP5 genetic locus by age and depressive phenotypes: implications for age-related disease

were excluded from this study. One hundred and nineteen voluntary controls were recruited from the personnel and medical students of the Yeouido St. Mary’s Hospital. Before blood sample collection, a semi-structured interview was performed to determine whether the control subjects had current psychiatric problems, or had history of psychiatric or neurological illness. All subjects were biologically unrelated and were native Koreans residing in the Republic of Korea. Genomic DNA was extracted from blood by standard methods and quantified. The high-throughput genotyping method using pyrosequencer (Biotage AB, Uppsala, Sweden) was used for genytyping four single nucleotide polymorphisms (rs2306987, rs2306990, rs2637777 and rs2304865) within the FAT gene, which were selected based on public database (National Center for Biotechnology Information, dbSNP, http://www.ncbi.nlm.nih.gov/SNP) and data from previous studies. Haploview 4.2 was used to generate a linkage disequilibrium (LD) map and to test for Hardy–Weinberg equilibrium (HWE). Association for single markers and clinical variables were performed using the chi-square, t-test and the analysis of variance. Test for associations using multimarker haplotypes were performed using the statistics software ‘R’ (http://www.R-project.org), package ‘haplo.stat’. Results: Significant association at the rs273777 with schizophrenia was observed; however, rs2306987, rs2306990, and rs2304865 were not associated with schizophrenia. Haplotype analyses revealed that the haplotype A/T/T/G was associated with a significantly protective effect. Sliding window analysis (rs2637777 G/T and rs2304865 G/C) revealed the more common T/G haplotype, included in the A/T/T/G protective combination, showed a small protective effect, in particular the effect was due to the rs273777 T variant (minor allele). Conclusion: The present finding suggests that FAT polymorphism may play a putative role in the susceptibility to schizophrenia in the Korean population. Further studies using a larger number of subjects should be performed to determine whether the FAT gene polymorphism may be truly involved in the development of schizophrenia.

Targeted next-generation sequencing and fine linkage disequilibrium mapping reveals association of PNPLA3 and PARVB with the severity of nonalcoholic fatty liver disease

The genomic regions containing PNPLA3, SAMM50 and PARVB are susceptibility loci for the development and progression of nonalcoholic fatty liver disease (NAFLD). In order to search for all common variations in this region, we amplified the genomic DNA of 28 NAFLD patients by long-range PCR, covering the entire susceptibility region and sequenced the DNA using indexed multiplex next-generation sequencing. We found 329 variations, including four novel variations. Fine mapping of variations including insertion/deletions was performed for 540 NAFLD patients (488 with nonalcoholic steatohepatitis (NASH) and 52 with simple steatosis) and 1012 control subjects. HaploView analysis showed that linkage disequilibrium (LD) block 1 and 2 occurred in PNPLA3, block 3 in SAMM50 and block 4 in PARVB. Variations in LD blocks 1-4 were significantly associated with NAFLD as compared with control subjects (P<1 × 10(-8)). Variations in LD block 2 were significantly associated with the NAFLD activity score (NAS), aspartate aminotransferase and alanine aminotransferase. Variations in LD block 1 were significantly associated with the fibrosis stage. The strongest associations were observed for variations in LD block 4, with NASH as compared with simple steatosis (P=7.1 × 10(-6)) and NAS (P=3.4 × 10(-6)). Our results suggested that variations, including insertion/deletions, in PARVB, as well as those in PNPLA3, are important in the progression of NAFLD.