Genetic analysis of case/control data using estimated haplotype frequencies: application to APOE locus variation and Alzheimer's disease

Sister haplotypes and recombination disequilibrium: a new approach to identify associations of haplotypes with complex diseases

Haplotype-based association analysis has several advantages over single-SNP association analysis. However, to date all haplotype-disease associations have not excluded recombination interference among multiple loci and hence some results might be confounded by recombination interference. Association of sister haplotypes with a complex disease, based on recombination disequilibrium (RD) was presented. Sister haplotypes can be determined by translating notation of DNA base haplotypes to notation of genetic genotypes. Sister haplotypes provide haplotype pairs available for haplotype-disease association analysis. After performing RD tests in control and case cohorts, a two-by-two contingency table can be constructed using sister haplotype pair and case-control pair. With this standard two-by-two table, one can perform classical Chi-square test to find statistical haplotype-disease association. Applying this method to a haplotype dataset of Alzheimer disease (AD), association of sister haplotypes containing ApoE3/4 with risk for AD was identified under no RD. Haplotypes within gene IL-13 were not associated with risk for breast cancer in the case of no RD and no association of haplotypes in gene IL-17A with risk for coronary artery disease were detected without RD. The previously reported associations of haplotypes within these genes with risk for these diseases might be due to strong RD and/or inappropriate haplotype pairs.

Association analysis for SNPs of BAAT and COL1A1 genes with cashmere production performance and other production traits in Liaoning cashmere goats

This study aimed to investigate the relationship between the polymorphism of bile acid-CoA: amino acid N-acyltransferase (BAAT) and collagen type I alpha 1 chain (COL1A1) genes and the production performance of Liaoning Cashmere goat (LCG). The potential single nucleotide polymorphisms (SNPs) of LCG were detected by sequence comparison of BAAT and COL1A1 genes and PCR-Seq polymorphism, and the effect of SNPs on production performance was analyzed by SPSS software. The results showed that three SNPs loci were detected in BAAT gene: G7900A, T7967C, C7998T, and one SNP locus T6716C was detected in COL1AL gene. At G7900A locus, the dominant genotype for cashmere performance was GG, and the dominant genotype for body measurement traits and milk production traits was AG. At T7967C locus, the dominant genotype for cashmere performance was TT, and the dominant genotype for body measurement traits and milk production traits was CC. At C7998T locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. At the T6716C locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. H1H1: AACC is the dominant haplotype combination. Therefore, this study will provide a reliable reference for future research on cashmere production performance, body measurement traits, and milk production traits of LCG.

Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges

Human DNA sequencing protocols have revolutionized human biology, biomedical science, and clinical practice, but still have very important limitations. One limitation is that most protocols do not separate or assemble (i.e., "phase") the nucleotide content of each of the maternally and paternally derived chromosomal homologs making up the 22 autosomal pairs and the chromosomal pair making up the pseudo-autosomal region of the sex chromosomes. This has led to a dearth of studies and a consequent underappreciation of many phenomena of fundamental importance to basic and clinical genomic science. We discuss a few protocols for obtaining phase information as well as their limitations, including those that could be used in tumor phasing settings. We then describe a number of biological and clinical phenomena that require phase information. These include phenomena that require precise knowledge of the nucleotide sequence in a chromosomal segment from germline or somatic cells, such as DNA binding events, and insight into unique cis vs. trans-acting functionally impactful variant combinations-for example, variants implicated in a phenotype governed by compound heterozygosity. In addition, we also comment on the need for reliable and consensus-based diploid-context computational workflows for variant identification as well as the need for laboratory-based functional verification strategies for validating cis vs. trans effects of variant combinations. We also briefly describe available resources, example studies, as well as areas of further research, and ultimately argue that the science behind the study of human diploidy, referred to as "diplomics," which will be enabled by nucleotide-level resolution of phased genomes, is a logical next step in the analysis of human genome biology.

Genetic variation in promoter region of the bovine LAP3 gene associated with estimated breeding values of milk production traits and clinical mastitis in dairy cattle

The purpose of this study was to identify genetic variants in the promoter and 5'UTR regions of bovine leucine amino peptidase three (LAP3) gene and analysed their associations with estimated breeding values (EBVs) of milk production traits and clinical mastitis in Sahiwal and Karan Fries cattle. Eleven SNPs were identified within the region under study of the LAP3 gene, including seven promoter variants (rs717156555: C>G, rs720373055: T>C, rs715189731: A>G, rs516876447: A>G, rs461857269: C>T, rs136548163: C>T, and rs720349928: G>A) and four 5'UTR variants (rs717884982: C>T, rs722359733: C>T, rs481631804: C>T and rs462932574: T>G). Out of them, 10 SNPs variants were found in both Sahiwal and Karan Fries cattle, with one SNP variant (rs481631804: C>T) being unique to Karan Fries cattle. Seven of these identified SNPs were chosen for association analyses. Individual SNP based association analysis revealed that two SNPs (rs720373055: T>C and rs720349928: G>A) were significantly associated with EBVs of lactation milk yield (LMY), 305-day milk yield (305dMY), and one significant association of SNP rs722359733: C>T with lactation length (LL) was observed. Haplotype based association analysis indicated that diplotypes are significantly associated with EBVs of LMY, 305dMY, and LL, individuals with H1H3 (CTACGCT/GCGTACG) being linked to higher lactation performance than other diplotypes. Further logistic regression analysis revealed that, animals with diplotype H1H3 was less susceptible to the incidence of clinical mastitis than other cows, as the odds ratio for the non-incidence of clinical mastitis was found to be low. Altogether, variations in the LAP3 gene promoter could be used as a genetic marker, most notably diplotype H1H3, may greatly benefit the simultaneous improvement of mastitis resistance and milk yield traits in dairy cattle. Moreover, bioinformatics analysis predicted that the SNPs rs720373055: T>C, rs715189731:A>G and rs720349928: G>A is located in the core promoter region and in TFBs, play key role in regulation of studied phenotypes.

Non-linear machine learning models incorporating SNPs and PRS improve polygenic prediction in diverse human populations

Polygenic risk scores (PRS) are commonly used to quantify the inherited susceptibility for a trait, yet they fail to account for non-linear and interaction effects between single nucleotide polymorphisms (SNPs). We address this via a machine learning approach, validated in nine complex phenotypes in a multi-ancestry population. We use an ensemble method of SNP selection followed by gradient boosted trees (XGBoost) to allow for non-linearities and interaction effects. We compare our results to the standard, linear PRS model developed using PRSice, LDpred2, and lassosum2. Combining a PRS as a feature in an XGBoost model results in a relative increase in the percentage variance explained compared to the standard linear PRS model by 22% for height, 27% for HDL cholesterol, 43% for body mass index, 50% for sleep duration, 58% for systolic blood pressure, 64% for total cholesterol, 66% for triglycerides, 77% for LDL cholesterol, and 100% for diastolic blood pressure. Multi-ancestry trained models perform similarly to specific racial/ethnic group trained models and are consistently superior to the standard linear PRS models. This work demonstrates an effective method to account for non-linearities and interaction effects in genetics-based prediction models.

Combining a standard polygenic risk score (PRS) as a feature in a machine learning model increases the percentage variance explained for those traits, helping to account for non-linearities or interaction effects in genetics-based prediction models.

Association analysis of single-nucleotide polymorphism in prolactin and its receptor with productive and body conformation traits in Liaoning cashmere goats

The results of this study showed that the single-nucleotide polymorphism (SNP) sites of the PRL and PRLR genes have a certain association with the milk production performance, body size and cashmere performance of Liaoning cashmere goats (LCGs). Through our designed experiment, the potential SNPs of LCG were detected by sequence alignment, and two SNPs were found on two genes. The CC genotype of the PRL gene is the dominant genotype among the three genotypes. The GG genotype of the PRLR gene is the dominant genotype among the two genotypes. At the same time, the two genotypes also have good performance in cashmere production and body size. Through the screening of haplotype combination, the milk fat rate > 7.6 %, the milk protein rate > 5.6 %, the milk somatic cell number < 1500 × 103 mL-1, the cashmere fineness < 15.75 µm, the chest girth > 105 cm, the chest depth > 33 cm, and the waist height > 67.5 cm are considered as screening indexes for comprehensive production performance of Liaoning cashmere goats. It is concluded that the GCGC type is the dominant haplotype combination. According to our research data, we found that the biological indicators of Liaoning cashmere goat milk are higher than the national standards, so we think it is very significant to study the milk production performance of our experiment. Further research can be done on goat milk production and body conformation traits around PRL gene and PRLR gene.

Association analysis for SNPs of KRT26 and TCHH genes with cashmere production performance, body measurement traits and milk production traits in Liaoning cashmere goats

Cashmere fineness is getting thicker, which is one of the key problems in cashmere breeding, however, there have been no systematic studies on the molecular regulation of cashmere fineness. The aim of this study was to investigate the relationship between KRT26 and TCHH gene polymorphism and production performance in Liaoning cashmere goats (LCG). The potential single nucleotide polymorphisms (SNPs) of LCG were detected by sequence alignment and PCR-Seq polymorphism of KRT26 and TCHH genes and analyzed the effect of SNPs on production performance by SPSS software. Two SNPs sites (A559T and A6839G) of two genes were detected. The AA genotype of KRT26 A559T locus was the dominant genotype. AG and GG at TCHH A6839G locus were the dominant genotypes. AAAA was the dominant haplotype combination. The results showed that KRT26 and TCHH genes were associated with cashmere fineness of LCG, and A559T (AA) and A6839G (GG) genotypes were the preferred marker genotypes for cashmere fineness, which provided more theoretical basis for further research on cashmere fineness.

Identification of polymorphic loci in the deiodinase 2 gene and their associations with head dimensions in geese

Objective

This study was conducted to clone and compare the molecular characteristics of the deiodinase 2 (DIO2) gene between Sichuan White geese and Landes geese, and to analyze the association between polymorphisms of the DIO2 gene and head dimensions in Tianfu meat geese.

Methods

The coding sequence of the DIO2 gene was cloned by polymerase chain reaction (PCR) and vector ligation and aligned by DNAMAN software. A total of 350 Tianfu meat geese were used to genotype the polymorphisms of the DIO2 gene and measure the head dimensions. Association analysis between the polymorphisms of the DIO2 gene and head dimensions was carried out.

Results

An 840-bp coding sequence of the DIO2 gene was obtained and comparison analysis identified four polymorphic loci between Sichuan White geese and Landes geese. Further analysis showed that the dominant alleles for the four polymorphic loci were G, G, A, and T and the frequency of the heterozygous genotype was higher than that of the homozygous genotype in Tianfu meat geese. Compared to that in the population of non-knob geese of Tianfu meat geese, the head dimensions in the population of knob geese were significantly higher except for nostril height. However, in the non-knob geese, beak width 1 (BW1), beak width 2 (BW2), nostril length (NL), cranial width 1 (CW1), and maxillary length (ML) had significant differences among different genotypes or haplotypes/diplotypes.

Conclusion

These results suggested that polymorphisms of the DIO2 gene could be considered molecular markers to select larger heads of geese in the population of non-knob geese.

Polymorphisms of the PRLR Gene and Their Association with Milk Production Traits in Egyptian Buffaloes

Simple Summary

The two non-synonymous g.11685G>A and g.11773T>C SNPs of PRLR(L2) were significantly associated with milk yield, fat%, and protein%, and mRNA and protein levels of PRL and PRLR in milk somatic cells. GT-animals had the best milk performance; however, AC-animals had inferior milk production. Thus, the selection of buffaloes with GT haplotypes may enhance milk performance in Egyptian buffaloes.

Abstract

Prolactin (PRL) and its receptor (PRLR) were considered as potential genetic markers for milk production and quality traits in cattle. However, little information is available regarding PRLR genetic diversity and association studies with milk traits in Egyptian water buffaloes. Therefore, the present study was conducted to search for mutations in PRLR and determine their associations with milk performance in these animals. Exon3 (E3) and E10 of PRLR were screened for polymorphisms using single strand conformation polymorphism (SSCP) and sequencing in 400 buffaloes. The associations between haplotypes and milk production (fat%, protein%, lactose%, and solid%) traits as well as mRNA and protein levels of PRL and PRLR were studied. Two single nucleotide polymorphisms (SNPs) in E10 were detected: g.11685G>A (p.Ala494Thr) and g.11773T>C (p.Val523Aal). The G and T alleles were wild (ancestral) alleles, while the A and C alleles were mutant alleles. These SNPs resulted in four haplotypes; AC, AT, GC, and GT. Buffaloes with wild GT haplotypes showed significantly higher milk yield, fat% and protein%, mRNA and protein levels of PRL and PRLR in milk somatic cells than other animals. Animals carrying mutant AC haplotype had inferior milk traits and lowest levels of associated mRNAs and proteins. With these results, we could conclude that the selection of buffaloes with wild GT haplotypes for g.11685G>A and g.11773T>C SNPs of the PRLR gene might improve the milk production traits of Egyptian water buffaloes.

Efficient verification for outsourced genome-wide association studies

With cloud computing is being widely adopted in conducting genome-wide association studies (GWAS), how to verify the integrity of outsourced GWAS computation remains to be accomplished. Here, we propose two novel algorithms to generate synthetic SNPs that are indistinguishable from real SNPs. The first method creates synthetic SNPs based on the phenotype vector, while the second approach creates synthetic SNPs based on real SNPs that are most similar to the phenotype vector. The time complexity of the first approach and the second approach is Om and Omlogn², respectively, where m is the number of subjects while n is the number of SNPs. Furthermore, through a game theoretic analysis, we demonstrate that it is possible to incentivize honest behavior by the server by coupling appropriate payoffs with randomized verification. We conduct extensive experiments of our proposed methods, and the results show that beyond a formal adversarial model, when only a few synthetic SNPs are generated and mixed into the real data they cannot be distinguished from the real SNPs even by a variety of predictive machine learning models. We demonstrate that the proposed approach can ensure that logistic regression for GWAS can be outsourced in an efficient and trustworthy way.

Statistically efficient association analysis of quantitative traits with haplotypes and untyped SNPs in family studies

Background

Associations between haplotypes and quantitative traits provide valuable information about the genetic basis of complex human diseases. Haplotypes also provide an effective way to deal with untyped SNPs. Two major challenges arise in haplotype-based association analysis of family data. First, haplotypes may not be inferred with certainty from genotype data. Second, the trait values within a family tend to be correlated because of common genetic and environmental factors.

Results

To address these challenges, we present an efficient likelihood-based approach to analyzing associations of quantitative traits with haplotypes or untyped SNPs. This approach properly accounts for within-family trait correlations and can handle general pedigrees with arbitrary patterns of missing genotypes. We characterize the genetic effects on the quantitative trait by a linear regression model with random effects and develop efficient likelihood-based inference procedures. Extensive simulation studies are conducted to examine the performance of the proposed methods. An application to family data from the Childhood Asthma Management Program Ancillary Genetic Study is provided. A computer program is freely available.

Conclusions

Results from extensive simulation studies show that the proposed methods for testing the haplotype effects on quantitative traits have correct type I error rates and are more powerful than some existing methods.

Association of GHR Polymorphisms with Milk Production in Buffaloes

Simple Summary

The present study reported two missense mutations in the buffalo GHR gene: A novel (c.380G>A) and (c.836T>A) which was described in previous studies. These two single nucleotide polymorphisms (SNPs) were found to be associated with milk yield, fat %, protein %, and 305 day-milk, fat and protein yield, with higher performance for AA haplotype animals. Therefore, selection of buffaloes with AA haplotype would more likely improve milk production traits. Consequently, this would allow breeders to take more precise selection decisions, leading to significantly higher productivity and profitability within the Egyptian buffalo herds.

Abstract

For its role in the mediation of growth hormone (GH) galactopoietic effect, growth hormone receptor (GHR) was considered a functional candidate gene for milk performance in cattle. However, its genetic variation and potential effect have not been investigated in Egyptian buffaloes. This study aimed to screen GHR for polymorphisms and study their associations with milk traits in Egyptian buffaloes. Polymerase chain reaction, single-strand conformation polymorphism, and sequencing were used to identify mutations in 4 exons (E4–E6 and E8) of the GHR gene in 400 Egyptian buffaloes. No polymorphisms were found in E4, while 2 SNPs (c.380G>A/p.Arg127Lys and c.387C>T/p.Gly129) in E5, one silent mutation (c.435A>G/p.Pro145) in E6, and another missense mutation (c.836T>A/p.Phe279Tyr) in E8 were detected. The c.380G>A SNP in the extracellular domain was associated with milk yield, fat %, protein %, and 305-day milk, fat and protein yield, with higher levels in animals carrying the mutant A allele. The c.836T>A SNP in the transmembrane domain was associated with milk yield, fat %, protein %, and 305-day milk, fat and protein yield, with higher milk yield and lower fat %, protein %, fat and protein yield in the mutant A allele-animals. Interestingly, animals with the two mutant AA alleles produced higher milk yield, fat %, protein %, fat and protein yield, accompanied with upregulated expressions of GHR, GH, insulin-like growth factor 1 (IGF1), prolactin (PRL), prolactin receptor (PRLR), β-casein (encoded by CSN2 gene), and diacylglycerol acyltransferase-1 (DGAT1) genes and proteins in milk somatic cells. Therefore, selection of Egyptian buffaloes with mutant AA haplotypes for the novel c.380G>A SNP and the well-known c.836T>A SNP could improve milk yield and quality in buffaloes.

Statistical Method Based on Bayes-Type Empirical Score Test for Assessing Genetic Association with Multilocus Genotype Data

Simultaneous testing of multiple genetic variants for association is widely recognized as a valuable complementary approach to single-marker tests. As such, principal component regression (PCR) has been found to have competitive power. We focus on exploring a robust test for an unknown genetic mode of all SNPs, an unknown Hardy-Weinberg equilibrium (HWE) in a population, and a large number of all SNPs. First, we propose a new global test by means of the use of codominant codes for all markers and PCR. The new global test is built on an empirical Bayes-type score statistic for testing marginal associations with each single marker. The new global test gains power by robustly exploiting the Hardy-Weinberg equilibrium in the control population and effectively using linkage disequilibrium among test markers. The new global test reduces to PCR when the genotype for each marker is coded as the number of minor alleles. This connection lends insight into the power of the new global test relative to PCR and some other popular multimarker test methods. Second, we propose a robust test method based on the new global test and the ordinary PCR test built on a prospective score statistic for testing marginal associations with each single marker when the genotype for each marker is coded as the number of minor alleles by taking the minimum p value of these two tests. Finally, through extensive simulation studies and analysis of the association between pancreatic cancer and some genes of interest, we show that the proposed robust test method has desirable power and can often identify association signals that may be missed by existing methods.

Genetic association of FKBP5 with PTSD in US service members deployed to Iraq and Afghanistan

Post-traumatic stress disorder (PTSD) is a debilitating mental disorder with a prevalence of more than 7% in the US population and 12% in the military. An interaction of childhood trauma with FKBP5 (a glucocorticoid-regulated immunophilin) has been reported to be associated with PTSD in the general population. However, there are few reports on the association of FKBP5 with PTSD, particularly in important high-risk population such as the military. Here, we examined the association between four single-nucleotide polymorphisms (SNPs; rs3800373, rs9296158, rs1360780, rs9470080) covering the FKBP5 gene and probable PTSD in US service members deployed to Iraq and Afghanistan, a high-risk military population (n = 3890) (Hines et al., 2014). We found that probable PTSD subjects were significantly more likely to carry the A-allele of rs3800373, G-allele of rs9296158, C-allele of rs1360780, and C-allele of rs9470080. Furthermore, the four SNPs were in one block of strong pairwise linkage disequilibrium (r = 0.91-0.96). Within the block there were two major haplotypes of CATT and AGCC (rs3800373-rs9296158-rs1360780-rs9470080) that account for 99% of haplotype diversity. The distribution of the AGCC haplotype was significantly higher in probable PTSD subjects compared to non-PTSD (p<.05). The diplotype-based analysis indicated that the AGCC carriers tended to be probable PTSD. In this study, we demonstrated the association between FKBP5 and probable PTSD in US service members deployed to Iraq and Afghanistan, indicating that FKBP5 might be a risk factor for PTSD.

Genetic and regulatory architecture of Alzheimer's disease in the APOE region

INTRODUCTION

Apolipoprotein E (APOE) ε2 and ε4 alleles encoded by rs7412 and rs429358 polymorphisms, respectively, are landmark contra and pro "risk" factors for Alzheimer's disease (AD).

METHODS

We examined differences in linkage disequilibrium (LD) structures between (1) AD-affected and unaffected subjects and (2) older AD-unaffected and younger subjects in the 19q13.3 region harboring rs7412 and rs429358.

RESULTS

AD is associated with sex-nonspecific heterogeneous patterns of decreased and increased LD of rs7412 and rs429358, respectively, with other polymorphisms from five genes in this region in AD-affected subjects. The LD patterns in older AD-unaffected subjects resembled those in younger individuals. Polarization of the ε4- and ε2 allele-related heterogeneous LD clusters differentiated cell types and implicated specific tissues in AD pathogenesis.

DISCUSSION

Protection and predisposition to AD is characterized by an interplay of rs7412 and rs429358, with multiple polymorphisms in the 19q13.3 region in a tissue-specific manner, which is not driven by common evolutionary forces.

Insights into the Potential Role of Mercury in Alzheimer's Disease

Mercury (Hg), which is a non-essential element, is considered a highly toxic pollutant for biological systems even when present at trace levels. Elevated Hg exposure with the growing release of atmospheric pollutant Hg and rising accumulations of mono-methylmercury (highly neurotoxic) in seafood products have increased its toxic potential for humans. This review aims to highlight the potential relationship between Hg exposure and Alzheimer's disease (AD), based on the existing literature in the field. Recent reports have hypothesized that Hg exposure could increase the potential risk of developing AD. Also, AD is known as a complex neurological disorder with increased amounts of both extracellular neuritic plaques and intracellular neurofibrillary tangles, which may also be related to lifestyle and genetic variables. Research reports on AD and relationships between Hg and AD indicate that neurotransmitters such as serotonin, acetylcholine, dopamine, norepinephrine, and glutamate are dysregulated in patients with AD. Many researchers have suggested that AD patients should be evaluated for Hg exposure and toxicity. Some authors suggest further exploration of the Hg concentrations in AD patients. Dysfunctional signaling pathways in AD and Hg exposure appear to be interlinked with some driving factors such as arachidonic acid, homocysteine, dehydroepiandrosterone (DHEA) sulfate, hydrogen peroxide, glucosamine glycans, glutathione, acetyl-L carnitine, melatonin, and HDL. This evidence suggests the need for a better understanding of the relationship between AD and Hg exposure, and potential mechanisms underlying the effects of Hg exposure on regional brain functions. Also, further studies evaluating brain functions are needed to explore the long-term effects of subclinical and untreated Hg toxicity on the brain function of AD patients.

A Robust Reduced Rank Graph Regression Method for Neuroimaging Genetic Analysis

To characterize associations between genetic and neuroimaging data, a variety of analytic methods have been proposed in neuroimaging genetic studies. These methods have achieved promising performance by taking into account inherent correlation in either the neuroimaging data or the genetic data alone. In this study, we propose a novel robust reduced rank graph regression based method in a linear regression framework by considering correlations inherent in neuroimaging data and genetic data jointly. Particularly, we model the association analysis problem in a reduced rank regression framework with the genetic data as a feature matrix and the neuroimaging data as a response matrix by jointly considering correlations among the neuroimaging data as well as correlations between the genetic data and the neuroimaging data. A new graph representation of genetic data is adopted to exploit their inherent correlations, in addition to robust loss functions for both the regression and the data representation tasks, and a square-root-operator applied to the robust loss functions for achieving adaptive sample weighting. The resulting optimization problem is solved using an iterative optimization method whose convergence has been theoretically proved. Experimental results on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset have demonstrated that our method could achieve competitive performance in terms of regression performance between brain structural measures and the Single Nucleotide Polymorphisms (SNPs), compared with state-of-the-art alternative methods.

Effect of complement component 5 polymorphisms on mastitis resistance in Egyptian buffalo and cattle

Mastitis is one of the costliest diseases affecting the world's dairy industry. The important contribution of complement Component 5 (C5) to phagocytosis, which plays a major role in the defence of the bovine mammary gland against infection, makes this component of innate immunity a potential contributor in defending udder against mastitis. The objectives of this study were to sequence and analyse the whole coding region of the C5 gene in Egyptian buffalo and cattle, to detect any nucleotide variations (polymorphisms) and to investigate their associations with milk somatic cell score (SCS) as an indicator of mastitis in dairy animals. We sequenced a buffalo C5 cDNA fragment of 5336 bp (KP221293) and a cattle C5 cDNA fragment of 5303 bp (KP221294), which included the whole coding region and 3-UTR. Buffalo and cattle C5 cDNA shared sequence identity of 99%. The predicted complement C5 proteins consist of 1677 amino acid residues in both animals, one amino acid less than in humans and three amino acids more than in mouse C5 protein. Comparing cDNA sequences of different animals revealed nine novel SNPs in buffalo and seven SNPs in cattle, with two of them being novel. The association analysis revealed that five SNPs in buffalo are highly associated with SCS; indicating the contribution of complement C5 variants in buffalo mastitis resistance. No significant associations were detected between C5 variants and SCS in cattle. This is the first report about C5 variants in buffalo and its association with SCS.

Genetic variants of fatty acid elongase 6 in Chinese Holstein cow

In the dairy industry, genetic variants have contributed to the improvement of milk production traits. Fatty acid elongase 6 (ELOVL6), which elongates saturated fatty acids (SFAs) and monounsaturated fatty acids (MUFAs), plays a distinct role in the balance of long-chain fatty acids composition in animals. ELOVL6 catalyzes the elongation of palmitic acids (C16:0) which is the most common saturated fatty acid found in animals and also an essential precursor to synthesize other long-chain fatty acids. However, the genetic variant research of bovine ELOVL6 on milk quality traits is still unknown. Therefore, our study aimed to detect the single nucleotide polymorphism (SNPs) of bovine ELOVL6 and explored the relationship between SNPs and milk quality traits including milk yield, fat content, protein content and somatic cell score. In this study, three SNPs, including SNP1 (g16379651A>G), SNP2 (g16458976A>G) and SNP3 (g16511290A>G), have been identified in intron 3 and 3'UTR regions of ELOVL6 in Chinese Holstein (CH) cows. Besides, the results of genetic diversity analysis, linkage disequilibrium and haplotype analysis indicated that these SNPs presented moderate polymorphisms which reflected relatively high genetic diversity. No strong linkage among these SNPs were detected in sampled population of cows. Moreover, the results of correlation analyses demonstrated that these SNPs of bovine ELOVL6 were significantly related to milk yield (P < 0.05). The SNP1 was also correlated with somatic cell score, whereas the SNP3 was associated with fat content. The 21 combined genotypes (diplotypes) were highly significantly correlated (P < 0.01) with milk yield. These results revealed that the genetic variants of bovine ELOVL6 influenced the milk production of CH cows. Hence, the three SNPs could be regarded as molecular markers in marker-assisted selection (MAS) of the dairy cow breeding.

CREB1 functional polymorphisms modulating promoter transcriptional activity are associated with type 2 diabetes mellitus risk in Chinese population

The cAMP responsive element binding protein 1 (CREB1) is a ubiquitous transcription factor that contributes to the regulation of gluconeogenesis. The mechanisms of the CREB1 function remain largely unknown. In this study, we aimed to explore genetic variations in CREB1 promoter region and determine whether these loci affect transcriptional activity and risk on type 2 diabetes (T2D). Three polymorphisms were identified and designated as MU₁, MU₂ and MU₃, respectively. Genotypic distribution analysis revealed that MU₁ genotypes presented similar distribution between T2D and healthy controls (P > 0.05), while the MU₂ and MU₃ showed significant differences (P < 0.05). Haplotypic blocks of the three loci were constructed, and H1-TGA, H2-TTT and H3-ATT had higher frequencies in T2D patients than those in controls. Association studies revealed that the three loci significantly affected plasma glucose, glycated hemoglobin and insulin secretion. Disequilibrium analysis identified that the MU₂ and MU₃ variants were strongly linked in T2D (r² = 0.348, D' = 1.0). Further analysis indicated that MU₂ (TT vs GG, OR = 2.38, 95%CI = 1.19-4.77, P = 0.01) and MU₃ (AA vs TT, OR = 1.16, 95%CI = 1.19-4.77, P = 0.04) were significantly associated with T2D in dominant genotypes. Luciferase assay showed that T-A haplotype from the highly linked MU₂ and MU₃ exhibited maximal promoter activity, which was consistent with the correlation results. We concluded that the TT genotype of MU₂ and the AA genotype of MU₃ could be used as molecular markers for evaluating the risk on T2D.

The effect of the SNP g.18475 A>G in the 3'UTR of NCF4 on mastitis susceptibility in dairy cattle

Neutrophil cytosolic factor 4 (NCF4) is a member of the nicotinamide adenine dinucleotide phosphate oxidase subunit. This protein functions as an essential factor in the host defense against the progression of bacterial infection. To explore the variability of the NCF4 gene and the susceptibility of cows to mastitis, NCF4 functional single nucleotide polymorphism (SNP) of the 3' untranslated region (3'UTR) and its targeted microRNA (miRNA) were identified. One SNP g.18475 A>G in the 3'UTR of NCF4 was found within the binding seed region of bta-miR-2426. We constructed two recombinant pMIR-REPORT™ vectors with the A or G allele in the g.18475 locus and transiently co-transfected the vectors in human embryo kidney 293T (HEK 293T) cells, along with bta-miR-2426 mimics. A luciferase assay indicated that this SNP affects the binding of NCF4 and bta-miR-2426. In addition, the association analysis results showed that cows with the GG genotype in SNP g.18475 A>G had a relatively lower SCS value than cows with the AA genotype. Finally, quantitative real-time PCR (RT-qPCR) results showed that the cows with genotype GG had a relatively higher expression of NCF4 mRNA compared to the cows with genotype AA. NCF4 expression was regulated by the miRNA-mRNA interaction mechanism, and an important role for NCF4 in mastitis susceptibility in dairy cow was suggested.

ITPR3 gene haplotype is associated with cervical squamous cell carcinoma risk in Taiwanese women

Host immunogenetic background plays an important role in human papillomavirus (HPV) infection and cervical cancer development. Inositol 1,4,5-triphosphate receptor type 3 (ITPR3) is essential for both immune activation and cancer pathogenesis. We aim to investigate if ITPR3 genetic polymorphisms are associated with the risk of cervical cancer in Taiwanese women. ITPR3 rs3748079 A/G and rs2229634 C/T polymorphisms were genotyped in a hospital-based study of 462 women with cervical squamous cell carcinoma (CSCC) and 921 age-matched healthy control women. The presence and genotypes of HPV in CSCC was determined. No significant association of individual ITPR3 variants were found among controls, CSCC, and HPV-16 positive CSCC. However, we found a significant association of haplotype AT between CSCC and controls (OR = 2.28, 95% CI 1.31-3.97, P = 2.83 × 10-3) and the OR increased further in CSCC patients infected with HPV-16 (OR = 2.89, 95% CI 1.55-5.37, P = 4.54 × 10-4). The linkage disequilibrium analysis demonstrated that ITPR3 association with CSCC was independent of HLA-DRB1 alleles. In conclusion, these findings suggest that AT haplotype in the ITPR3 gene may serve as a potential marker for genetic susceptibility to CSCC.

Novel Muscle-Specific Genes TCAP, TNNI1, and FHL1 in Cattle: SNVs, Linkage Disequilibrium, Combined Genotypes, Association Analysis of Growth Performance, and Carcass Quality Traits and Expression Studies

TCAP, TNNI1, and FHL1 regulate muscle growth and development. In this study, four single nucleotide variants (SNVs) were discovered in almost all of the exon and intron regions of the TCAP, TNNI1, and FHL1 genes using DNA pooled sequencing, polymerase chain reaction (PCR)-RFLP, and forced-PCR-RFLP methods in 576 cattle. Four SNVs were significantly associated with the growth performance and carcass quality traits of the cattle. In addition, the haplotype, haplotype frequency, and linkage disequilibrium coefficient of three sequence variants were also evaluated in the cattle population. Haplotype analysis demonstrated that eight haplotypes were present in the Qinchuan cattle population and no haplotypes were present in the Chinese Holstein population; haplotype 1 had the highest frequency in the Qinchuan (42.7%) population. Statistical analyses of 12 combined genotypes indicated that some were significantly associated with the growth performance and carcass quality traits of the Qinchuan cattle population. Moreover, the quantitative real-time polymerase chain reaction results demonstrated that the bovine TCAP, TNNI1, and FHL1 genes were exclusively expressed in muscle tissue. These data support the high potentials of the TCAP, TNNI1, and FHL1 as marker genes to improve the growth performance and carcass quality traits of Qinchuan cattle or other animals selection programs.

Effects of GnRHR polymorphisms on sperm quality in Chinese water buffalo

Gonadotropin-releasing hormone receptor (GnRHR) plays a critical physiological role in animal reproduction and is a potential marker for improving sperm quality. In the present study, eight SNPs (g.539T>C, g.640A>G, g.655T>C, g.707T>C, g.812A>G, g.18951A>T g.16867T>C and g.18953Indel GGCAAAGTAA) were detected in the GnRHR gene from one-hundred-sixty-five water buffalo by direct sequencing and identification of overlapping peaks. All SNPs were associated significantly with the ejaculate volume and two genes (g.655T>C and g.707T>C) were correlated with sperm abnormalities. Furthermore, three haplotypes (H1:TAI, H2:CT-, and H3:TT-) were identified by linkage disequilibrium analysis and were composed of four combined genotypes. Notably, buffalo with the combined genotypes H1H2 and H1H3 had the higher ejaculate volume compared to the other combined genotypes. Among the eight SNPs and four combined genotypes, the deletion of GGCAAAGTAA at position 18953bp in GnRHR was associated significantly with a higher ejaculate volume. Moreover, the GGCAAAGTAA deletion may lead to the miR8661 binding failure and subsequent changes in GnRHR gene expression. In the present study, we demonstrate that there is a significant association between SNPs in the GnRHR gene and the sperm ejaculate volume of Chinese water buffalo. To the best of our knowledge, this study is the first to address the association between the SNPs in the GnRHR gene and the sperm quality of Chinese buffalo.

Identification of Four SNPs in LHB Gene and Their Associations with Sperm Qualities of Chinese Buffaloes

Luteinizing hormone beta polypeptide (LHB) gene has been considered important for sexual behavior and has associations with sperm quality. In this study, four SNPs (g.276 T>C, g.377A>C, g.401T>C, and g.412A>G) were detected in the LHB gene of 165 water buffaloes by direct sequencing and identification of overlap peaks, each of which was associated with at least one sperm quality trait of ejaculate volume, sperm concentration, post-thaw sperm motilities, and sperm abnormalities by chi-square analysis. Among them, g.276 T>C was associated with ejaculate volume (F = 2.857, p < 0.05), sperm concentration (F = 2.052, p < 0.05), and post-thaw sperm motilities (F = 3.480, p < 0.05); g.377A>C was related to ejaculate volume (F = 4.178, p < 0.05), g.401T>C had a marker effect on sperm abnormalities (F = 3.332, p < 0.05), g.412A>G was associated with sperm concentration (F = 3.579, p < 0.05), and sperm abnormalities (F = 3.408, p < 0.05). Furthermore, four haplotypes (H1: ACG, H2: CCG, H3: CTA, H4: CCA) were generated by linkage disequilibrium analysis, which composed seven genotypes. Among them, the buffaloes with combined genotype H2H2 had the higher ejaculate volume and the individuals with the combined haplotypes H1H4 had higher sperm concentration. In summary, our study showed that there was a significant association between SNPs of LHB gene and Chinese water buffalo sperm quality traits. To the best of our knowledge, this is the first report addressing the associations between the SNPs in the LHB gene and the sperm qualities of Chinese buffaloes.

Genetic Variants in the STMN1 Transcriptional Regulatory Region Affect Promoter Activity and Fear Behavior in English Springer Spaniels

Stathmin 1 (STMN1) is a neuronal growth-associated protein that is involved in microtubule dynamics and plays an important role in synaptic outgrowth and plasticity. Given that STMN1 affects fear behavior, we hypothesized that genetic variations in the STMN1 transcriptional regulatory region affect gene transcription activity and control fear behavior. In this study, two single nucleotide polymorphisms (SNPs), g. -327 A>G and g. -125 C>T, were identified in 317 English Springer Spaniels. A bioinformatics analysis revealed that both were loci located in the canine STMN1 putative promoter region and affected transcription factor binding. A statistical analysis revealed that the TT genotype at g.-125 C>T produced a significantly greater fear level than that of the CC genotype (P < 0.05). Furthermore, the H4H4 (GTGT) haplotype combination was significantly associated with canine fear behavior (P < 0.01). Using serially truncated constructs of the STMN1 promoters and the luciferase reporter, we found that a 395 bp (−312 nt to +83 nt) fragment constituted the core promoter region. The luciferase assay also revealed that the H4 (GT) haplotype promoter had higher activity than that of other haplotypes. Overall, our results suggest that the two SNPs in the canine STMN1 promoter region could affect canine fear behavior by altering STMN1 transcriptional activity.

Simultaneous inference of haplotypes and alleles at a causal gene

We present a methodology which jointly infers haplotypes and the causal alleles at a gene influencing a given trait. Often in human genetic studies, the available data consists of genotypes (series of genetic markers along the chromosomes) and a phenotype. However, for many genetic analyses, one needs haplotypes instead of genotypes. Our methodology is not only able to estimate haplotypes conditionally on the disease status, but is also able to infer the alleles at the unknown disease locus. Some applications of our methodology are in genetic mapping and in genetic counseling.

Detecting associations of rare variants with common diseases: collapsing or haplotyping?

In recent years, a myriad of new statistical methods have been proposed for detecting associations of rare single-nucleotide variants (SNVs) with common diseases. These methods can be generally classified as 'collapsing' or 'haplotyping' based. The former is the predominant class, composed of most of the rare variant association methods proposed to date. However, recent works have suggested that haplotyping-based methods may offer advantages and can even be more powerful than collapsing methods in certain situations. In this article, we review and compare collapsing- versus haplotyping-based methods/software in terms of both power and type I error. For collapsing methods, we consider three approaches: Combined Multivariate and Collapsing, Sequence Kernel Association Test and Family-Based Association Test (FBAT): the first two are population based and are among the most popular; the last test is family based, a modification from the popular FBAT to accommodate rare SNVs. For haplotyping-based methods, we include Logistic Bayesian Lasso (LBL) for population data and family-based LBL (famLBL) for family (trio) data. These two methods are selected, as they can be used to test association for specific rare and common haplotypes. Our results show that haplotype methods can be more powerful than collapsing methods if there are interacting SNVs leading to larger haplotype effects. Even if only common SNVs are genotyped, haplotype methods can still detect specific rare haplotypes that tag rare causal SNVs. As expected, family-based methods are robust, whereas population-based methods are susceptible, to population substructure. However, the population-based haplotype approach appears to have smaller inflation of type I error than its collapsing counterparts.

Tetra-primer ARMS-PCR identifies the novel genetic variations of bovine HNF-4α gene associating with growth traits

Hepatocyte nuclear factor-4α (HNF-4α), a member of the hepatocyte nuclear factor family, plays an important role in regulating the expression of genes involved in the development, differentiation and normal function of liver and pancreatic β cells, as well as the maintenance of glucose homeostasis. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) is a new method offering fast detection and extreme simplicity at a negligible cost for SNP genotyping. In this paper, we characterize the polymorphisms of the bovine HNF-4α gene in three Chinese indigenous cattle breeds (n=660). Six novel SNPs were identified including 1 mutation in the coding region and others in introns. The statistical analyses indicated that 4 SNPs (g.T53729C, g.A53861G, g.A65188C and g.T65444C) affected growth traits markedly (P<0.05) in Qinchuan cattle (2 years after birth). Besides, haplotypes involving these 4 SNP sites in the bovine HNF-4α gene were identified and their effects on growth traits were also analyzed. The results showed that haplotypes 2, 7, 9 and 11 were predominant and accounted for 73.2%, 59.6%, and 67.1% in Qinchuan, Nanyang and Jiaxian cattle breeds, respectively. Hap9 (TAAT) was extremely predominant in all test populations, which suggested that individuals with Hap9 were more adapted to the environment. Furthermore, 4 combined haplotypes were constructed to guarantee the reliability of analysis results in Qinchuan cattle. There were also significant differences in body length (P<0.05). These findings will benefit for the application of DNA marker related to the growth traits on marker-assisted selection (MAS), and improve the performance of beef cattle.

Association of a novel SNP in exon 10 of the IGF2 gene with growth traits in Egyptian water buffalo (Bubalus bubalis)

Insulin-like growth factor 2 (IGF2) plays an important role in muscle growth and it might be used as a marker for the growth traits selection strategies in farm animals. The objectives of this study were to detect polymorphisms in exon 10 of IGF2 and to determine associations between these polymorphisms and growth traits in Egyptian water buffalo. PCR-single-strand conformation polymorphism (SSCP) and DNA sequencing methods were used to detect any prospective polymorphism. A novel single nucleotide polymorphism (SNP), C287A, was detected. It was a non-synonymous mutation and led to replacement of glutamine (Q) amino acid (aa) by histidine (H) aa. Three different SSCP patterns were observed: AA, AC, and CC, with frequencies of 0.540, 0.325, and 0.135, respectively. Association analyses revealed that the AA individuals had a higher average daily gain (ADG) than other individuals (CC and AC) from birth to 9 months of age. We conclude that the AA genotype in C287A SNP in the exon 10 of the IGF2 gene is associated with the ADG during the age from birth to 9 months and could be used as a potential genetic marker for selection of growth traits in Egyptian buffalo.

Characterisation of the genetic effects of the ADFP gene and its association with production traits in dairy goats

Adipose differentiation-related protein (ADFP) is important for regulation of lipid metabolism and insulin secretion in beta-cells. In this study, we investigated polymorphisms within the caprine ADFP gene and determined its relationship with production traits. As there was no sequence information available for the caprine ADFP gene, we generated DNA sequence data and examined the genomic organisation. The caprine ADFP gene is organised into 7 exons and 6 introns that span approximately 8.7 kbp and is transcribed into mRNA containing 1,353 bp of sequence coding for a protein of 450 amino acids. The protein sequences showed substantial similarity (71-99%) to orthologues from cattle, human and mouse. We identified polymorphisms in the sequences using DNA sequencing, PCR-RFLP and forced PCR-RFLP methods. Seven single nucleotide polymorphisms (SNPs) were identified using samples from 4 different goat populations consisting of 1408 healthy and unrelated individuals. Six haplotypes involving the 7 SNPs from the caprine ADFP gene were identified and their effects on production traits were analysed. Haplotype 6 had the highest haplotype frequency and was highly significantly associated with chest circumference and milk yield in the analysed populations. The results of this study suggest that the ADFP gene is a strong candidate gene affecting production traits and may be used for marker-assisted selection and management in Chinese dairy goat breeding programmes.

Association of a vascular endothelial growth factor polymorphism with the development of bronchopulmonary dysplasia in Japanese premature newborns

Our objective was to correlate vascular endothelial growth factor (VEGF) genetic polymorphisms with the risk of bronchopulmonary dysplasia (BPD) development in premature newborns. Fifty-five newborns with BPD (BPD: median gestational age [GA]: 27 weeks, birthweight [BW]: 786 g) and 42 newborns without BPD (non-BPD: median GA: 29 weeks, BW: 1,165 g), who were born at <32 weeks gestational age and were admitted to Kobe University Hospital, were included. BPD was defined as oxygen dependency at 36 weeks postmenstrual age. Genomic DNA was extracted from the umbilical cord, cord blood, or buccal mucosa. Six VEGF genotypes (-1498T > C, -1154G > A, -634C > G, -7C > T, 936C > T, and 1612G > A) were determined by DNA sequencing. Clinical characteristics, and allele and genotype frequencies of VEGF in the BPD and non-BPD groups were analyzed. G allele frequencies in -634C > G of the BPD group were significantly higher than in the non-BPD group (66.4% vs. 50%, P = 0.02). -634C > G genotype distributions differed significantly between the BPD and non-BPD groups (BPD: CC 7%/CG 53%/GG 40%; non-BPD: CC 24%/CG 52%/GG 24%; P = 0.04). Multivariate logistic regression showed that duration of ventilation, VEGF-634G > C G alleles, and male gender were independent risk factors for BPD. In conclusion, polymorphism VEGF -634C > G may influence the risk of BPD.

Study on genetic variations of PPARα gene and its effects on thermal tolerance in Chinese Holstein

Peroxisome proliferator-activated receptor alpha (PPARα) regulates responses to chemical or physical stress in part by altering expression of genes involved in proteome maintenance. In this research, polymerase chain reaction (PCR) technique was used to amplify 766 and 589 bp fragments of intron 3 and 7 of PPARα gene in Chinese Holstein (n = 771). Sequencing results showed that three novel single nucleotide polymorphisms (SNPs) were identified at position 44087 (G/A), 65550 (G/A), and 65676(G/A) in the PPARα gene. PCR-restriction fragment length polymorphism technology was used to genotype the three SNPs. Association analysis showed that cows with H1H8 (P < 0.05), H2H8 (P < 0.01), H5H7 (P < 0.05), H5H8 (P < 0.05), and H8H8 (P < 0.05) haplotype combinations had lower potassium content in erythrocytes than those with H2H6 haplotype combination. Cows with H1H8, and H8H8 haplotype combinations had lower decrease rate of milk yield than those with H2H6 and H6H8 haplotype combinations (P < 0.05). Cows with H2H8 and H8H8 haplotype combinations had lower rectal temperature than those with H5H8 and H7H7 haplotype combinations (P < 0.05). In conclusion, H8H8 haplotype combination may be advantageous for heat resistance traits in Chinese Holstein cattle.

SNP and haplotype analysis reveal IGF2 variants associated with growth traits in Chinese Qinchuan cattle

Insulin-like growth factor 2 (IGF2) is a potent cell growth and differentiation factor and is implicated in mammals' growth and development. The objective of this study was to evaluate the effects of the mutations in the bovine IGF2 with growth traits in Chinese Qinchuan cattle. Four single nucleotide polymorphisms (SNPs) were detected of the bovine IGF2 by DNA pool sequencing and forced polymerase chain reaction-restriction fragment length polymorphism (forced PCR-RFLP) methods. We also investigated haplotype structure and linkage disequilibrium (LD) coefficients for four SNPs in 817 individuals representing two main cattle breeds from China. The result of haplotype analysis showed eight different haplotypes and 27 combined genotypes within the study population. The statistical analyses indicated that the four SNPs, combined genotypes and haplotypes are associated with the withers height, body length, chest breadth, chest depth and body weight in Qinchuan cattle population (P < 0.05 or <0.01). The mutant-type variants and mutant haplotype (Hap 8: ATGG; likely to be the beneficial QTN allele) was superior for growth traits; the heterozygote diplotype was associated with higher growth traits compared to wild-type homozygote. Our results provide evidence that polymorphisms in the IGF2 gene are associated with growth traits, and may be used for marker-assisted selection in beef cattle breeding program.

Nonparametric tests of associations with disease based on U-statistics

In case-control studies, association analysis was designed to test whether genetic variants were associated with human diseases. To evaluate the association, analysing one genetic marker at a time suffered from weak power, because of the correction for multiple testing and possibly small genetic effects. An alternative strategy was to test simultaneous effects of multiple markers, which was believed to be more powerful. However, when the number of markers under investigation was large, they would be subjected to weak power as well, because of the greater degrees of freedom. To conquer these limitations in case-control studies, we proposed a novel method that could test joint association of several loci (i.e. haplotype), with only a single degree of freedom. In this research, we developed a nonparametric approach, which was based on U-statistics. We also introduced a new kernel for U-statistic, which could combine the haplotype structure information, and was expected to enhance the power. Simulations indicated that our proposed approach offered merits in identifying the associations between diseases and haplotypes. Application of our method to a study of candidate genes for internalising disorder illustrated its virtue in utility and interpretation, and provided an excellent result in detecting the associations.

Expression, SNV identification, linkage disequilibrium, and combined genotype association analysis of the muscle-specific gene CSRP3 in Chinese cattle

The cysteine and glycine-rich protein 3 (CSRP3) plays an important role in the myofiber differentiation. Here, we identified five SNVs in all exon and intron regions of the CSRP3 gene using DNA sequencing, PCR-RFLP and forced-PCR-RFLP methods in 554 cattle. Four of the five SNVs were significantly associated with growth performance and carcass traits of the cattle. In addition, we evaluated haplotype frequency and linkage disequilibrium coefficient of five sequence variants. The result of haplotype analysis demonstrated 28 haplotypes present in Qinchuan and two haplotypes in Chinese Holstein. Only haplotypes 1 and 8 were being shared by two populations, haplotype 14 had the highest haplotype frequency in Qinchuan (17.4%) and haplotype 8 had the highest haplotype frequency in Chinese Holstein (94.4%). Statistical analyses of combined genotypes indicated that some combined genotypes were significantly or highly significantly associated with growth and carcass traits in the Qinchuan cattle population. qPCR analyses also showed that bovine CSRP3 gene was exclusively expressed in longissimus dorsi muscle and heart tissues. The data support the high potential of the CSRP3 as a marker gene for the improvement of growth performance and carcass traits in selection programs.

An application and empirical comparison of statistical analysis methods for associating rare variants to a complex phenotype

The contribution of collections of rare sequence variations (or 'variants') to phenotypic expression has begun to receive considerable attention within the biomedical research community. However, the best way to capture the effects of rare variants in relevant statistical analysis models is an open question. In this paper we describe the application of a number of statistical methods for testing associations between rare variants in two genes to obesity. We consider the relative merits of the different methods as well as important implementation details, such as the leveraging of genomic annotations and determining p-values.

Haplotype combination of polymorphisms in the ADIPOQ gene promoter is associated with growth traits in Qinchuan cattle

Adiponectin modulates lipid and glucose metabolism in adipose tissues and is also related to bone metabolism. Polymorphisms in the ADIPOQ gene likely have an impact on growth traits in cattle. In this study, we examined the relationship between ADIPOQ polymorphisms and body measurement parameters in Chinese beef cattle. First, we sequenced ADIPOQ and 1.2 kb of DNA upstream of its promoter, and we found 14 polymorphisms. With the luciferase reporter assay, we showed that the two polymorphisms SNP PR_-135 A>G and PR_-68 G>C, which are located in the core region of promoter, influence promoter activity of ADIPOQ. Second, we identified three haplotypes involved in these two polymorphic sites: A (A-135/C-68), B (A-135/G-68), and C (G-135/G-68). Haplotypes B and C are major haplotypes in five Chinese populations of cattle (Qinchuan, Nanyang, Jiaxian, Hazakh, and Chinese Holstein). We studied the effects of these three haplotypes on body measurements, gene expression, and promoter activity, and we found that the genotypes are associated with body measurement parameters in Qinchuan cattle. Individuals with genotype BC (AG/GG) had significantly higher body height and heart girth than others, and this result may be interpreted by the following two observations. The promoter activity with haplotype B (A/G) is significantly higher than those with A (A/C) and C (G/G) in driving reporter gene transcription; the ADIPOQ mRNA level in cattle with genotype BC (AG/GG) is relatively lower than that in cattle with genotype BB (AA/GG).

The effect of haplotype variation in the bovine PAX6 gene

The transcription factor paired box 6 gene (PAX6) plays a key role during the early development of various organs. In this study, three single nucleotide polymorphisms (SNPs) have been identified in the introns 2, 8 and 11 of the bovine PAX6 gene. 8 haplotypes and 13 diplotypes were revealed and the linkage disequilibrium (LD) was assessed in 817 cows representing four main cattle breeds from China (Nanyang, NY; Qinchuan, QC; Jiaxian, JX; Chinese Holstein, CH). The LD analysis revealed that the additional three SNPs were not in strong LD, the wild haplotype (Hap 1: CTT) and mutant haplotype (Hap 8: TCC) have a frequency of 9.36, 35.61, 18.32, 57.15 % and 15.60, 14.19, 0.83, 0 % in the four cattle populations. The statistical analyses indicated that the SNP2 and 3 are associated with the body weight at birth, 6 and 12 months in NY and JX cattle population (P < 0.01 or P < 0.05); and significant association was detected between 19 (NY) or 13 (JX) diplotype (combined genotypes) and body weight at different ages (birth, 6 and 12 months). Our results provide evidence that some polymorphisms in PAX6 are associated with growth traits at some ages, and may be used as candidates for marker-assisted selection in beef cattle breeding program.

Quantitative assessment of the association between XPG Asp1104His polymorphism and bladder cancer risk

Published data regarding the association between XPG Asp1104His polymorphism and bladder cancer risk remained controversial. This meta-analysis of literatures was performed to draw a more precise estimation of the relationship. We systematically searched PubMed, Embase, and Web of Science with a time limit of June 22, 2013. Summary odds ratios (ORs) with 95 % CIs were used to assess the strength of the association between XPG Asp1104His polymorphism and bladder cancer risk using random effects model. A total of eight case-control studies including 2,613 cases and 2,934 controls were included for analysis. Overall, no significant association was found between XPG Asp1104His polymorphism and bladder cancer susceptibility for CC vs. GG (OR = 1.12, 95 % CI = 0.74-1.69), GC vs. GG (OR = 1.12, 95 % CI = 0.86-1.46), the dominant model CC + GC vs. GG (OR = 1.08, 95 % CI = 0.85-1.38), and the recessive model CC vs. GC + GG (OR = 0.92, 95 % CI = 0.66-1.29). In the subgroup analysis, no significant associations were found in either Asian or non-Asian population. This meta-analysis suggested that XPG Asp1104His polymorphism was not associated with bladder cancer risk.

Functional polymorphisms of matrix metalloproteinase-9 and survival in patients with locoregionally advanced nasopharyngeal carcinoma treated with chemoradiotherapy

To investigate the prognostic role of major matrix metalloproteinase (MMP) gene polymorphisms in patients with locoregionally advanced nasopharyngeal carcinoma (NPC) treated with chemoradiotherapy. Four hundred twenty-one consecutive NPC patients were prospectively recruited. Two hundred patients were randomly selected as the training cohort, and the remaining 221 patients were the validation cohort. Twelve polymorphisms in the MMP-1, 2, 3, 7, 8, and 9 genes were genotyped by ligase detection reaction-PCR. MMP-9 rs2250889 PR/RR (HR = 2.287, 95% CI 1.400-3.735) and rs17576 RQ/QQ (HR = 2.347, 95% CI 1.431-3.849) genotypes were significantly related with increased death risk in the training cohort. Analysis of the validation cohort confirmed these results (rs2250889: HR = 2.231, 95% CI 1.281-3.886; rs17576: HR = 2.987, 95% CI 1.674-5.330). Multivariate analysis showed that rs17576 (HR = 2.284, 95% CI 1.123-4.643, P = 0.023) was still an independent prognostic factor. The MMP-9 rs17576 is a novel independent prognostic marker in patients with locoregionally advanced NPC treated with chemoradiotherapy.