Single nucleotide polymorphisms and disease gene mapping

Single nucleotide polymorphisms are the most important and basic form of variation in the genome, and they are responsible for genetic effects that produce susceptibility to most autoimmune diseases. The rapid development of databases containing very large numbers of single nucleotide polymorphisms, and the characterization of haplotypes and patterns of linkage disequilibrium throughout the genome, provide a unique opportunity to advance association strategies in common disease rapidly over the next few years. Only the careful use of these strategies and a clear understanding of their statistical limits will allow novel genetic determinants for many of the common autoimmune diseases to be determined.     

Single nucleotide polymorphisms in caprine calpastatin gene

The calpains and calpastatin (CAST) make up a major cytosolic proteolytic system, the calpain-calpastatin system, found in mammalian tissues. The relative levels of the components of the calpain-calpastatin system determine the extent of meat tenderization during postmortem storage. Calpastatin (CAST) is a protein inhibitor of the ubiquitous calcium-dependent proteases, μ-calpain, and m-calpain. Polymorphisms in the bovine, ovine and pig CAST gene have been associated with meat tenderness but little is known about how caprine CAST gene may affect goat meat quality traits. In this study we selected different parts of the CAST gene: (1) that have been previously reported to be polymorphic, intron 5 and 12 and 3’UTR; (2) first time explored (exon 3, 7 and 8 and part of intron 7 and 8) to investigate polymorphic status of caprine CAST gene. Using comparative sequencing ten novel SNPs located in exon 3 and intron 5, 7 and 8 were identified. Previously reported SNPs in intron 5, 3’UTR and intron 12 were absent. Sequence analysis revealed a non synonymous amino acid variation in exon 3, which would result in Lys/Arg substitution in the corresponding protein sequence. Considerable variation was detected in intronic regions. Twenty-four InDel were also recognized in intronic regions (15) and 3’UTR (9). All the sequences shared high homology with published bovine and ovine sequences. Three PCR-RFLP loci have been established for further analyzing genetic polymorphism in indigenous goats.     

Single nucleotide polymorphisms in the equine transferrin gene

Single nucleotide polymorphisms (SNPs) in exons 13, 15 and 16 of equine transferrin for common, rare and mutant variants were investigated. Compared with previous work a further 13 SNPs have been identified, allowing for the two previously identified clades to be subdivided into 11 groups. A combination of one or more of eight SNPs can be used to classify the equine variants into these 11 groups, since most are co-inherited. Putative sites of glycosylation in exons 13 and 16 showed no polymorphism, suggesting that presence or absence of sugar moieties does not lead to electrophoretic variation between the variants. Using the 26 SNPs currently identified in transferrin it is still not possible to differentiate variants F1 from F2, or D from H2, which represent 75% of the variants occurring in Thoroughbred equine population. This suggests that further SNPs exist in equine transferrin. The significance of the high level of variation in exon 15 is discussed.     

The role of functional single nucleotide polymorphisms of the human glucocorticoid receptor gene NR3C1 in Polish patients with bronchial asthma

N363S and ER22/23EK polymorphisms observed within glucocorticoid receptor gene (NR3C1) may play an important role in the development of bronchial asthma. NR3C1 gene is associated with an altered sensitivity to GCs. The aim of the research project was to study the correlation between this NR3C1 gene polymorphisms and occurrence of asthma in the population of Polish asthmatics. Peripheral blood was obtained from 207 healthy volunteers and 221 asthma patients. Genotyping was carried out with PCR-RFLP method. In the groups of patients with uncontrolled moderate asthma and uncontrolled severe disease, the genotype distribution for the investigated polymorphisms was as follows: N363S-AA, AG, GG occurring with 0.881/0.073/0.046 frequency and ER22/23EK-GG, GA, AA occurring with 0.963/0.037/0.000 frequency. Chi-square analysis revealed a significantly different (P < 0.05) distribution between cases and controls for the N363S polymorphisms. The N363S polymorphism of NR3C1 gene is significantly associated with bronchial asthma, susceptibility to the development of moderate to severe form of uncontrolled bronchial asthma.     

Single nucleotide polymorphisms in the human E-cadherin gene

We report four DNA variants in the gene coding for the cell adhesion molecule E-cadherin. The polymorphisms affect codons 115, 133, 582 and the 3-noncoding region.     

PPARA, RXRA, NR1I2 and NR1I3 gene polymorphisms and lipid and lipoprotein levels in a Southern Brazilian population

Cardiovascular disease is the main cause of death worldwide, and dyslipidemia is an important multifactorial risk factor. Considering the involvement of nuclear receptors in metabolic pathways, and that some of the receptors act in lipid metabolism and homeostasis, the aim of the present study was to investigate the influence of genetic variations in RXRA, PPARA, NR1I2, and NR1I3 on lipid and lipoprotein levels. Five polymorphisms in the aforementioned genes were genotyped in 622 Brazilians of European descent by PCR-RFLP or TaqMan genotyping assays. In general, carriers of the A insertion of RXRA rs11381416 polymorphism showed higher levels of triglyceride (TG; 1.80 ± 1.20 vs. 1.52 ± 1.20 mmol/L; P = 0.020). Moreover, sexual dimorphic association was found (gender*NR1I3 rs2501873 genotype interaction P < 0.001), males with NR1I3 rs2501873 G/G genotype had lower TG levels (ANCOVA, P = 0.009). Our results suggest that polymorphisms in the RXRA and NR1I3 genes influence lipid profile in a Southern Brazilian population. However, these general and gender association require confirmation in subsequent studies.     

中国北方汉族人群sTnT基因单核苷酸多态性分析

目的：研究中国北方汉族人群sTnT基因的单核苷酸多态性（SNP）,观察其在北方汉族人群中的分布。方法：用PCR-RFLP的方法对204名中国北方汉族人群sTnT基因的SNP进行分析,确定其等位基因频率。结果：美国国立生物技术信息中心报告的外显子11上的27916722 A／C未在本项研究人群中检测到。27930097 C／G和的27920978 C／F的等位基因频率与美国国立生物技术信息中心（NCBI）报道均有显著性差异。结论：sTnT基因SNP分布具有种族差异性。     

汉族人群中22个HLA-Cw等位基因全长序列单核苷酸多态性分析

为探讨HLA-Cw (Human leukocyte antigen-Cw)基因全长序列分子遗传多态性, 文章对28个HLA-Cw基因型已知的汉族个体样本, 采用长距离PCR技术和高保真性的Pfu酶, 扩增HLA-Cw基因全长序列4.5 kb, 进行分子克隆和单倍体测序。采用群体遗传学研究方法分析了HLA-Cw等位基因全长序列中各亚区的单核苷酸多态性。结果表明: 在28个样本中共检测出22种等位基因, 序列均已提交GenBank和国际IMGT/HLA数据库并获得了认可; 其中Cw*0706、Cw*030301、Cw*140201的全长序列为首次报道, 尤其是Cw*0706内含子序列的获得, 能够重新设计对该等位基因测序分型的引物, 避免测序分型中可能对这一等位基因的漏检。将28个样本的56条单倍体序列用Clustal软件进行序列排比, 输入到DnaSP4.0进行多态性分析, 共发现244个SNPs, 10处插入/缺失多态性。对HLA-Cw等位基因各亚区多态性的分析, 发现第4内含子及以前并没有受到关注的第5外显子受到平衡选择的作用, 在进化中受到了选择压力, 预示着它们在免疫系统的进化过程中可能扮演着重要的角色。     

Single nucleotide polymorphisms of myostatin gene in Chinese domestic horses

The myostatin gene (MSTN) is a genetic determinant of skeletal muscle growth. Single nucleotide polymorphisms (SNP) in MSTN are of importance due to their strong associations with horse racing performances. In this study, we screened the SNPs in MSTN gene in 514 horses from 15 Chinese horse breeds. Six SNPs (g.26 T > C, g.156 T > C, g.587A > G, g.598C > T, g.1485C > T, g.2115A > G) in MSTN gene were detected by sequencing and genotyped using PCR-RFLP method. The g.587A > G and g.598C > T residing in the 5′UTR region were novel SNPs identified by this study. The g.2115A > G which have previously been associated with racing performances were present in Chinese horse breeds, providing valuable genetic information for evaluating the potential racing performances in Chinese domestic breeds. The six SNPs together defined thirteen haplotypes, demonstrating abundant haplotype diversities in Chinese horses. Most of the haplotypes were shared among different breeds with no haplotype restricted to a specific region or a single horse breed. AMOVA analysis indicated that most of the genetic variance was attributable to differences among individuals without any significant contribution by the four geographical groups. This study will provide fundamental and instrumental genetic information for evaluating the potential racing performances of Chinese horse breeds.     

Single nucleotide polymorphisms of the MCHR1 gene do not affect metabolism in humans

Melanin concentrating hormone receptor-1 (MCHR1) is a centrally and peripherally expressed receptor that regulates energy expenditure and appetite. Single nucleotide polymorphisms (SNPs) of the MCHR1 gene have been previously associated with obesity, but the results are inconsistent among different populations. This study was performed to determine whether SNPs of MCHR1 affect glucose and energy metabolism. We screened six SNPs of MCHR1 in a cross-sectional study of 217 middle-age, non-diabetic Finnish subjects who were offspring of type 2 diabetic patients. Insulin secretion was evaluated by an intravenous glucose tolerance test and insulin sensitivity and energy metabolism by the hyperinsulinemic euglycemic clamp and indirect calorimetry. SNPs of MCHR1 were not associated with BMI, waist circumference, subcutaneous or intra-abdominal fat area, glucose tolerance, first-phase insulin release, insulin sensitivity, or energy metabolism. One SNP, which was in >0.50 linkage disequilibrium with the other five SNPs, was also screened in 1455 unrelated Finnish middle-age subjects in a population-based study. No differences in BMI, waist circumference, or glucose or insulin levels in an oral glucose tolerance test among the genotypes were found. In conclusion, SNPs of MCHR1 did not have effects on metabolic variables in humans.     

Single nucleotide polymorphisms in an intron of the ovine calpastatin gene

Calpastatin is the specific inhibitor of the ubiquitous calcium-dependent proteases mu-calpain and m-calpain. Enzyme assay data from sheep and cattle inversely correlates post-mortem muscle calpastatin levels with ultimate meat tenderness. Genetic markers of meat quality may therefore be found linked to the calpastatin gene (CAST). A three-allele system detected by polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) has been observed in the ovine CAST. The three allele amplimers have been fully nucleotide sequenced and their differences in terms of single nucleotide polymorphism (SNPs) in the intron region of the amplimer are reported and compared to a consensus sequence of the orthologous region of the cattle CAST. A PCR-RFLP for more rapid CAST genotyping of all three ovine alleles was also developed.     

Single nucleotide polymorphisms (SNPs) in human lactoferrin gene.

The lactoferrin protein possesses antimicrobial and antiviral activities. It is also involved in the modulation of the immune response. In a normal healthy individual, lactoferrin plays a role in the front-line host defense against infection and in immune and inflammatory responses. Whether genomic variations, such as single nucleotide polymorphisms (SNPs), have an effect on the structure and function of lactoferrin protein and whether these variations contribute to the different susceptibility of individuals in response to environmental insults are interesting health-related issues. In this study, the lactoferrin gene was resequenced as part of the Environmental Genome Project of the National Institute of Environmental Health Sciences, which operates within the National Institutes of Health. Ninety-one healthy donors of different ethnicities were used to establish common SNPs in the exons of the lactoferrin gene in the general population. The data will serve as a basis from which study the association of lactoferrin polymorphism and disease.     

Single nucleotide polymorphisms in chicken lmbr1 gene were associated with chicken growth and carcass traits

Lmbr1 is the key candidate gene controlling vertebrate limb development, but its effects on animal growth and carcass traits have never been reported. In this experiment, lmbr1 was taken as the candi-date gene affecting chicken growth and carcass traits. T/C and G/A mutations located in exon 16 and one A/C mutation located in intron 5 of chicken lmbr1 were detected from Silky, White Plymouth Rock broilers and their F2 crossing chickens by PCR-SSCP and sequencing methods. The analysis of vari-ance (ANOVA) results suggests that T/C polymorphism of exon 16 had significant association with eviscerated yield rate (EYR), gizzard rate (GR), shank and claw rate (SCR) and shank girth (SG); A/C polymorphism of intron 5 was significantly associated with SCR, liver rate and head-neck weight (HNW), while both sites had no significant association with other growth and carcass traits. These results demonstrate that lmbr1 gene could be a genetic locus or linked to a major gene significantly affecting these growth and carcass traits in chicken.     

Interaction between CRHR1 and BDNF genes increases the risk of recurrent major depressive disorder in Chinese population

Background

An important etiological hypothesis about depression is stress has neurotoxic effects that damage the hippocampal cells. Corticotropin-releasing hormone (CRH) regulates brain-derived neurotrophic factor (BDNF) expression through influencing cAMP and Ca2+ signaling pathways during the course. The aim of this study is to examine the single and combined effects of CRH receptor 1 (CRHR1) and BDNF genes in recurrent major depressive disorder (MDD).

Methodology/Principal Finding

The sample consists of 181 patients with recurrent MDD and 186 healthy controls. Whether genetic variations interaction between CRHR1 and BDNF genes might be associated with increased susceptibility to recurrent MDD was studied by using a gene-based association analysis of single-nucleotide polymorphisms (SNPs). CRHR1 gene (rs1876828, rs242939 and rs242941) and BDNF gene (rs6265) were identified in the samples of patients diagnosed with recurrent MDD and matched controls. Allelic association between CRHR1 rs242939 and recurrent MDD was found in our sample (allelic: p = 0.018, genotypic: p = 0.022) with an Odds Ratio 0.454 (95% CI 0.266–0.775). A global test of these four haplotypes showed a significant difference between recurrent MDD group and control group (chi-2 = 13.117, df = 3, P = 0.016. Furthermore, BDNF and CRHR1 interactions were found in the significant 2-locus, gene–gene interaction models (p = 0.05) using a generalized multifactor dimensionality reduction (GMDR) method.

Conclusion

Our results suggest that an interaction between CRHR1 and BDNF genes constitutes susceptibility to recurrent MDD.     

Maternal prenatal depressive symptoms predict infant NR3C1 1F and BDNF IV DNA methylation

Prenatal maternal psychological distress increases risk for adverse infant outcomes. However, the biological mechanisms underlying this association remain unclear. Prenatal stress can impact fetal epigenetic regulation that could underlie changes in infant stress responses. It has been suggested that maternal glucocorticoids may mediate this epigenetic effect. We examined this hypothesis by determining the impact of maternal cortisol and depressive symptoms during pregnancy on infant NR3C1 and BDNF DNA methylation. Fifty-seven pregnant women were recruited during the second or third trimester. Participants self-reported depressive symptoms and salivary cortisol samples were collected diurnally and in response to a stressor. Buccal swabs for DNA extraction and DNA methylation analysis were collected from each infant at 2 months of age, and mothers were assessed for postnatal depressive symptoms. Prenatal depressive symptoms significantly predicted increased NR3C1 1F DNA methylation in male infants (β = 2.147, P = 0.044). Prenatal depressive symptoms also significantly predicted decreased BDNF IV DNA methylation in both male and female infants (β = −3.244, P = 0.013). No measure of maternal cortisol during pregnancy predicted infant NR3C1 1F or BDNF promoter IV DNA methylation. Our findings highlight the susceptibility of males to changes in NR3C1 DNA methylation and present novel evidence for altered BDNF IV DNA methylation in response to maternal depression during pregnancy. The lack of association between maternal cortisol and infant DNA methylation suggests that effects of maternal depression may not be mediated directly by glucocorticoids. Future studies should consider other potential mediating mechanisms in the link between maternal mood and infant outcomes.     

Single nucleotide polymorphisms in theRET gene and their correlations with Hirschsprung disease phenotype

Hirschsprung disease (HSCR) is a congenital, heterogeneous disorder, characterized by the absence of intestinal ganglion cells. Recent advances show that the RET gene is a major locus involved in the pathogenesis of HSCR. The aim of this study was to analyse if the HSCR phenotype in the Polish population is associated with the presence of polymorphisms in exons 2, 3, 7, 11, 13, 14 and 15 of the RET gene. Molecular results were compared with clinical and long-term follow-up data in 70 Polish patients with HSCR (84.3% with a short segment and 15.7% with a long segment of aganglionic gut). Single-nucleotide polymorphisms were analysed by using the minisequencing SNaPshot multiplex method. The 135G>A polymorphism in RET exon 2 was overrepresented in HSCR patients, compared with a healthy control group. Moreover, the 135G>A variant was shown to be associated with the severe HSCR phenotype. Two other polymorphisms, 2071G>A in exon 11 and 2712C>G in exon 15, were underrepresented in the patients. The results confirm that these RET polymorphisms play a role in the aetiology of HSCR.     

黑柄炭角菌的单核苷酸多态性研究

以SNPs作为分子标记,对黑柄炭角菌的生活史和遗传多样性进行研究。基于黑柄炭角菌的基因组文库,在两个菌株（X-WC和X-LY）的34个片段（19,680bp）中共发现193个SNPs,SNP发生率为0.981%。193个SNPs位点都有两个可变的核苷酸,其中132个转换,61个颠换,转换与颠换比率为2.16。此外,对两个菌株序列进行比较,发现了41个插入/缺失位点。从34个片段中选择4个片段,分别比较菌株内的SNPs情况。X-WC的菌株内SNP发生率为每个核苷酸1.308%（30/2293）,X-LY的菌     

Single nucleotide polymorphisms and recombination rate in humans

Levels of heterozygosity for single nucleotide polymorphisms vary by more than one order of magnitude in different regions of the human genome. Regional differences in the rate of recombination explain a substantial fraction of the variation in levels of nucleotide polymorphism, consistent with the widespread action of natural selection at the molecular level.