HapMap filter 1.0: a tool to preprocess the HapMap genotypic data for association studies

The International HapMap Project provides a resource of genotypic data on single nucleotide polymorphisms (SNPs), which can be used in various association studies to identify the genetic determinants for phenotypic variations. Prior to the association studies, the HapMap dataset should be preprocessed in order to reduce the computation time and control the multiple testing problem. The less informative SNPs including those with very low genotyping rate and SNPs with rare minor allele frequencies to some extent in one or more population are removed. Some research designs only use SNPs in a subset of HapMap cell lines. Although the HapMap website and other association software packages have provided some basic tools for optimizing these datasets, a fast and user-friendly program to generate the output for filtered genotypic data would be beneficial for association studies. Here, we present a flexible, straight-forward bioinformatics program that can be useful in preparing the HapMap genotypic data for association studies by specifying cell lines and two common filtering criteria: minor allele frequencies and genotyping rate. The software was developed for Microsoft Windows and written in C++. AVAILABILITY: The Windows executable and source code in Microsoft Visual C++ are available at Google Code (http://hapmap-filter-v1.googlecode.com/) or upon request. Their distribution is subject to GNU General Public License v3.     

Navigating the HapMap

With the availability of the HapMap--a resource which describes common patterns of linkage disequilibrium (LD) in four different human population samples, we now have a powerful tool to help dissect the role of genetic variation in the biology of the genome. HapMap is entirely complimentary to the human genome map and so it is particularly fitting that it should be viewed in a full genomic context. However, characterization of high resolution LD across the genome can be a challenging task, owing in part to the sheer volume of data and the inherent dimensionality that its analysis entails. However, a number of tools are now available to make this task easier for researchers. This review will examine tools for viewing and analysing haplotype and LD data, enabling a number of tasks; including identification of optimal sets of haplotype tagging single nucleotide polymorphisms (SNPs); drawing links between associated SNPs and putative causal alleles; or simply viewing LD and haplotypes across a gene or region of interest. The data generated by the HapMap also has other important applications, informing, for example, on the demographic history and evidence of selection in human populations and on previously undetected regulatory relationships and gene networks. All of these properties make the HapMap no less an important resource than the human genome sequence itself and so this makes it essential viewing for all in the field of human biology.     

Constructing an initial map of transmission distortion based on high density HapMap SNPs across the human autosomes

Transmission distortion （TD） is a significant departure from Mendelian predictions of genes or chromosomes to offspring. While many biological processes have been implicated, there is still much to be understood about TD in humans. Here we present our findings from a genome-wide scan for evidence of TD using haplotype data of 60 trio families from the International HapMap Project. Fisher＇s exact test was applied to assess the extent of TD in 629,958 SNPs across the autosomes. Based on the empirical distribution of PFisher and further permutation tests, we identified 1,205 outlier loci and 224 candidate genes with TD. Using the PANTHER gene ontology database, we found 19 categories of biological processes with an enrichment of candidate genes. In particular, the “protein phosphorylation” category contained the largest number of candidates in both HapMap samples. Further analysis uncovered an intriguing non-synonymous change in PPPIR12B, a gene related to protein phosphorylation, which appears to influence the allele transmission from male parents in the YRI （Yoruba from Ibadan, Nigeria） population. Our findings also indicate an ethnicity-related property of TD signatures in HapMap samples and provide new clues for our understanding of TD in humans.     

The effect of cell synchronization upon the detection of T and B lymphoid cell receptors on two continuous lymphoid cell lines

Summary In the present study, the effect of the cell synchronization on the detection of T and B cell surface markers of two continuous lines of lymphoid cells (FL-74 and CT45-S) was examined. Suspension cultures were synchronized by deprivation of isoleucine and surface markers were quantitated by T rosette formation with guinea pig erythrocytes (E) and B rosette formation with an erythrocyte-antibody-complement (EAC) complex. After 24 hr, cells were resuspended in complete culture medium. Virtually 100% of FL-74 cells expressed the T cell marker at time 0, with a progressive decline to 80% at saturation density. A bell-shaped curve for expression of the EAC marker on CT45-S cells was seen with maximum expression in the logarithmic phase of the growth cycle. Spent culture medium was examined for the presence of free soluble receptor. Preincubation of E and EAC in appropriate old medium resulted in 42% inhibition of E rosettes and 42% inhibition of EAC rosettes with FL-74 and CT45-S cells, respectively. Thus quantitation of lymphocyte subpopulations as B, T or null cells with these cellular markers may be influenced by the age of the cell examined, phase of the cell cycle and the amount of free receptor present in the surrounding medium. This research was supported in part by contract NO1 CP 5-3571 with the Virus Cancer Program of the NCI, NIH, PHS grant no. 2 RO1 A1-09022-07, Allergy and Infectious Diseases NIH, PHS and The State of Ohio Canine Research Funds.     

MHC-dependent mate choice in humans: why genomic patterns from the HapMap European American dataset support the hypothesis

The role of the major histocompatibility complex (MHC) in mate choice in humans is controversial. Nowadays, the availability of genetic variation data at genomic scales allows for a careful assessment of this question. In 2008, Chaix et al. reported evidence for MHC-dependent mate choice among European American spouses from the HapMap 2 dataset. Recently, Derti et al. suggested that this observation was not robust. Furthermore, when Derti et al. applied similar analyses to the HapMap 3 European American samples, they did not see a significant effect. Although some of the points raised by Derti et al. are relevant, we disagree with the reported absence of evidence for MHC-dependent mate choice within the HapMap samples. More precisely, we show here that the MHC dissimilarity among HapMap 3 European American spouses is still extreme in comparison to the rest of the genome, even after multiple testing correction. This finding supports the hypothesis of MHC-dependent mate choice in some human populations.     

Genome-Wide Variation of Cytosine Modifications Between European and African Populations and the Implications for Complex Traits

Elucidating cytosine modification differences between human populations can enhance our understanding of ethnic specificity in complex traits. In this study, cytosine modification levels in 133 HapMap lymphoblastoid cell lines derived from individuals of European or African ancestry were profiled using the Illumina HumanMethylation450 BeadChip. Approximately 13% of the analyzed CpG sites showed differential modification between the two populations at a false discovery rate of 1%. The CpG sites with greater modification levels in European descent were enriched in the proximal regulatory regions, while those greater in African descent were biased toward gene bodies. More than half of the detected population-specific cytosine modifications could be explained primarily by local genetic variation. In addition, a substantial proportion of local modification quantitative trait loci exhibited population-specific effects, suggesting that genetic epistasis and/or genotype × environment interactions could be common. Distinct correlations were observed between gene expression levels and cytosine modifications in proximal regions and gene bodies, suggesting epigenetic regulation of interindividual expression variation. Furthermore, quantitative trait loci associated with population-specific modifications can be colocalized with expression quantitative trait loci and single nucleotide polymorphisms previously identified for complex traits with known racial disparities. Our findings revealed abundant population-specific cytosine modifications and the underlying genetic basis, as well as the relatively independent contribution of genetic and epigenetic variations to population differences in gene expression.     

非综合征耳聋大家系永生细胞系的建立及几种EB病毒转化外周血淋巴细胞建系方法的探讨

永久保存珍贵的家系材料,是对该家系进行深入研究的基础,为此采用EB病毒（Epstein-Barr virus,EBV）转化淋巴细胞的方法对中国江苏淮阴地区非综合征耳聋大家系行建系工作。该家系患者呈典型的母系遗传特征,且研究发现患者中均具有线粒体DNA 12s RNA A1555G突变,是迄今世界上最大的非综合征耳聋家系之一,在该家系的建系过程中 使用了4种不同的方法。建系结果分别为：微量全血法1株,冻存全血法1株,冻存白细胞法14株及环孢霉素A（CyA）法36株,共计52株。本文就建系工作及这四种转化方法作一简单探讨。     

47例染色体异常患者永生淋巴细胞株的建立

采用4种不同的血细胞/EB病毒（Epstein-Barr Virus,EBV）比率系列转染冻存血方法建立永生淋巴细胞株,建株成功率达97.87%,并成功地对47例染色体异常患者建立了永生淋巴细胞株,为今后不断进行的深入研究奠定了基础。     

Functional analysis of HapMap SNPs

Genome-wide association studies (GWAS) have successfully identified many genetic variants associated with complex diseases and traits. However, functional consequence of genetic variants studied in GWAS is not yet fully investigated, which would hinder the application of GWAS. We therefore performed a systematic functional analysis of HapMap SNPs, which have been most commonly used as the reference panel for GWAS. Our study highlights several characteristics of HapMap SNPs and identifies subsets of genetic variants with interesting functional implication. The results show that HapMap SNPs have good coverage within RefSeq genes, especially within known disease-related genes. On the other hand, only a small percentage of SNPs are non-synonymous SNPs while many SNPs are actually located at gene deserts. Moreover, many functionally important variants are not yet still interrogated. A redesigned SNP reference panel with additional functionally important variants would be useful to identify disease-causal variants in the future genome-wide studies.     

FstSNP-HapMap3: a database of SNPs with high population differentiation for HapMap3

The International HapMap Project has recently made available genotypes and frequency data for phase 3 (NCBI build 36, dbSNPb129) of the HapMap providing an enriched genotype dataset for approximately 1.6 million single nucleotide polymorphisms (SNPs) from 1,115 individuals with ancestry from parts of Africa, Asia, Europe, North America and Mexico. In the present study, we aim to facilitate pharmacogenetics studies by providing a database of SNPs with high population differentiation through a genomewide test on allele frequency variation among 11 HapMap3 samples. Common SNPs with minor allele frequency greater than 5¢ from each of 11 HapMap3 samples were included in the present analysis. The population differentiation is measured in terms of fixation index (Fst), and the SNPs with Fst values over 0.5 were defined as highly differentiated SNPs. Our tests were carried out between all pairs of the 11 HapMap3 samples or among subgroups with the same continental ancestries. Altogether we carried out 64 genomewide Fst tests and identified 28,215 highly differentiated SNPs for 49 different combinations of HapMap3 samples in the current database.     

Biocontrol of Ascochyta blight by Azospirillum sp. depending on the degree of resistance of chickpea genotypes

Throughout arable land that was devoted to chickpea (Cicer arietinum L. (Family: Leguminosae) production, Ascochyta blight (Ascochyta rabiei (Pass.) L. (Order: Sphaeriales; Family: Mycosphaerellaceae) is a widespread disease that would lead to significant loss of chickpea yield. This study's purpose was to explain the responses of a resistant chickpea cultivar (ICC 12004) and a susceptible cultivar (Bivanij) in terms of disease resistance, disease symptoms appearance and expression pattern of two defence‐related genes (DEF0442 and Snakin2) after the Azospirillum brasilense seeds inoculation. In this research, the Snakin2 gene expression was affected by Azospirillum inoculation. The gene expression has been enhanced in plants inoculated with Azospirillum in both cultivars in comparison with non‐inoculated plants, but this change in ICC 12004 and Bivanij were significant and non‐significant, respectively. Although, Azospirillum would up regulate the DEF0422 gene expression in ICC 12004, but it would down regulate the expression of this gene in Bivanij. A. brasilense inoculation decreased the A. rabiei disease severity, regardless of the chickpea cultivar. Bivanij still could be classified as susceptible, even if treated with A. brasilense.     

已建株鼻咽癌细胞的PLUNC基因启动子区序列多态性分析

目的检测人类标准鼻咽癌细胞中是否存在已知的PLUNC基因启动子-437bp-＋87bp区域的单核苷酸多态性（SNP）。以便进一步探索SNP与鼻咽癌的关系。方法采用PCR产物直接测序的方法,对7株体外培养的鼻咽癌细胞基因组DNA的PLUNC基因启动子区进行序列分析。结果发现7株PLUNC基因的启动子区皆存在已知的3个SNP位点（1888、2128和N2）和未知一个突变位点（N1）,其测观杂合度分别为85．7％、100％、100％和28．6％。其中3个已知SNP位点在筛查的细胞株中均存在T-C的突变,而且SUNE-1鼻咽癌细胞株的1888位点基因型为突变纯合子CC型。结论体外培养的标准鼻咽癌细胞株中存在已知的3个SNP位点（1888、2128和N2）的突变现象,且突变率为100％;1888位点鼻咽癌易患型（CC型）已在体外稳定建株;首次发现启动子-195bp区域N1突变位点。     

nm23-H1基因转染L9981肺癌细胞前后基因表达谱的变化

应用基因芯片检测L9981细胞转染nm23-H1基因前后细胞基因表达谱的改变.提取L9981细胞转染nm23-H1基因前后细胞的总RNA,纯化为mRNA后再转录为cDNA.cDNA经限制性内切酶Sau3AI消化后,cDNA片段分别用cy3和cy5标记,与定制的包含14000个基因芯片杂交.杂交结果经扫描和软件分析,nm23-H1基因转染L9981细胞后发现1156(8.26%,1156/14000)个基因表达上调,而642(4.59%,642/14000)个基因表达下调.涉及基因包括信号传导、癌基因与抑癌基因、转移相关基因、细胞周期与凋亡、细胞外基质与细胞骨架相关基因,以及细胞因子和转录因子等.nm23-H1基因是通过对转移相关基因的调节来发挥其抑制肺癌细胞株L9981侵袭和转移作用的.     

Association of single nucleotide polymorphism in melatonin receptor 1A gene with egg production traits in Yangzhou geese

In the present study the melatonin receptor 1A gene (MTNR1A) was proposed to be a candidate gene for egg production in Yangzhou geese. A total of 210 goose blood samples were collected to investigate the association of the MTNR1A gene with the number of eggs produced. Using a direct sequencing method, a single nucleotide polymorphism (SNP; g.177G>C) was detected in the 5? regulatory region of the MTNR1A gene (Genbank ss1985399687). Two alleles (G and C) and three genotypes were identified. Association analysis results showed that the g.177G>C SNP significantly affected the level of egg production within a 34‐week egg‐laying period (P < 0.05). Furthermore, the geese with the GG genotype produced significantly more eggs compared to the geese with the CC genotype. Quantitative real‐time PCR analysis showed that the MTNR1A gene was highly expressed in small intestine, granulosa cell and ovary compared to other examined tissues. In addition, the mRNA expression level of MTNR1A in ovary indicated that significantly higher expression levels were recorded for geese with the GG genotype compared to those with the CC genotype. Moreover, a luciferase reporter assay showed that the CC genotype had significantly lower promoter activity than did GG. These results suggest that the identified SNP in the MTNR1A gene may influence the number of eggs produced and mRNA expression levels in Yangzhou geese and could be considered as a useful molecular marker in goose selection and improvement, especially for egg production.     

The effect of a c.-8G>T polymorphism on the expression of cytochrome b5A and boar taint in pigs

The level of cytochrome b5A ( CYB5A ) in pig testis is correlated with boar taint from androstenone and an AF016388:c.-8G>T polymorphism in CYB5A has been linked with low androstenone levels in the fat of pigs. In this study, we developed a polymerase chain reaction-based assay to genotype 1242 boars from eight lines for the c.-8G>T SNP. The c.-8T allele was found in all eight lines at a frequency ranging from 1.8% to 20.3% with an overall frequency of 8.6%. Significant deviations from Hardy–Weinberg equilibrium were found in the Hampshire, Landrace and Yorkshire breeds. The homozygous mutant c.-8TT occurred infrequently and was not found in some lines, but was consistently associated with low androstenone levels in fat. Both CYB5A mRNA and CYB5A protein levels were decreased in the c.-8TT genotype in a subset of Yorkshire boars, suggesting that low levels of CYB5A protein in the c.-8TT mutant were not due to inefficient translation of CYB5A mRNA. There were significant but modest marker effects on fat androstenone levels in Landrace, Yorkshire and a Large White/Duroc cross and fat skatole in Duroc and Sire Line breeds. There was no effect of CYB5A genotype on bulbourethral gland length, suggesting that this SNP will not affect reproductive traits. We conclude that the c.-8G>T SNP in the CYB5A gene has a significant but modest effect on boar taint in male pigs and could be useful in some breeds as part of a panel of SNP markers in a marker-assisted selection programme to produce low boar taint pigs.