Loss of heterozygosity analyzed by single nucleotide polymorphism array in cancer

Neoplastic progression is generally characterized by the accumulation of multiple genetic alterations including loss of tumor suppression gene function. Loss of heterozygosity （LOH） has been used to identify genomic regions that harbor tumor suppressor genes and to characterize different tumor types, pathological stages and progression. LOH pattern has been detected by allelotyping using restriction fragment length polymorphism, and later by simple sequence length polymorphisms （SSLPs or microsatellite） for 10 years. This paper reviews the detection of LOH by recently developed single nucleotide polymorphism （SNP） arrays （all analyzed by Affymetrix array）; furthermore, its advantage and disadvantage were analyzed in several kinds of cancer.

Breastfeeding and genetic factors in the etiology of inflammatory bowel disease in children

Inflammatory bowel disease is a chronic,debilitating disorder of the gastrointestinal tract.The etiology of inflammatory bowel disease has not been elucidated,but is thought to be multifactorial with both environmental and genetic influences.A large body of research has been conducted to elucidate the etiology of inflammatory bowel disease.This article reviews this literature,emphasizing the studies of breastfeeding and the studies of genetic factors,particularly NOD2 polymorphisms.

The association of lumican polymorphisms and high myopia in a Southern Chinese population

AIM：To investigate the correlation between lumican（LUM）gene and high myopia in a Southern Chinese population.METHODS：The study comprised of 95 high myopia patients with a spherical equivalent≤-6.5 diopters（D）.The control group recruited 95 individuals with a spherical equivalent ranging from-0.5 D to＋0.5 D.Direct sequencing was used to detect the single nucleotide polymorphisms（SNPs）of LUM gene in coding region.Genotype distributions were tested for Hardy-Weinberg disequilibrium.Genotypic and allelic frequencies were analyzed through Chi-square test or Fisher’s exact test.RESULTS：We identified 3 SNPs of the LUM gene：LUM c.32（rs577456426）,LUM c.507（rs17853500）and LUM c.849（rs181915277）.Among the three SNPs,the genotype and allele frequencies of rs17853500 showed a significant difference between patients and control subjects（P〈0.05）.However,there were no significant differences in rs181915277and rs577456426 between the two groups（P〉0.05）.CONCLUSION：LUM c.507 polymorphism may be a risk factor for the pathogenesis of high myopia in the Southern Chinese population.

The norepinephrine transporter gene is associated with the retardation symptoms of major depressive disorder in the Han Chinese population

The norepinephrine transporter plays an important role in the pathophysiology and pharmacological treatment of major depressive disorder. Consequently, the norepinephrine transporter gene is an attractive candidate in major depressive disorder research. In the present study, we evaluated the depression symptoms of subjects with major depressive disorder, who were all from the North of China and of Hart Chinese origin, using the Hamilton Depression Scale. We examined the relationship between two single nucleotide polymorphisms in the norepinephrine transporter, rs2242446 and rs5569, and the retardation symptoms of major depressive disorder using quantitative trait testing with the UNPHASED program, rs5569 was associated with depressed mood, and the GG genotype may be a risk factor for this; rs2242446 was associated with work and interest, and the TT genotype may be a risk factor for loss of interest. Our findings suggest that rs2242446 and rs5569 in the norepinephrine transporter gene are associated with the retardation symptoms of depression in the Hart Chinese population.

DNA methyltransferase 3B promoter polymorphism and its susceptibility to primary hepatocellular carcinoma in the Chinese Han nationality population:A case-control study

AIM： To investigate the correlation between C/T single nucleotide polymorphism （SNP） in the promoter of the DNA methyltransferase 3B （D/VMT3B） gene and risk for development and progression of primary hepatocellular carcinoma （HCC）. METHODS： One hundred case subjects were selected consecutively from Tongji Hospital （Wuhan, China）. from March to November 2006. They did not receive radiotherapy or chemotherapy for newly diagnosed and histopathologically confirmed HCC. One hundred and forty control subjects having no history of cancerous or genetic diseases were healthy volunteers to Wuhan Blood Center in the same period. Frequency was matched for sex, age, alcohol consumption and cigarette smoking status of the case subjects. C/T polymorphism of the DNMT3B promoter was analyzed using polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP） and sequencing analysis. The association between genotypes of DNMT3B and clinicopathological parameters among cases was also studied. RESULTS： The CC genotype HCC patients and controls. was not detected in both In control subjects, the frequency of TT and CT genotypes was 99.3% and 0.7% respectively, and that of T and C alleles was 99.6% and 0.4% respectively. The frequency of CT genotype was higher in HCC （3.0%）. The frequency of T and C alleles was 98.5% and 1.5% respectively. However, the genotype and allelotype distribution in HCC patients was not significantly different from that in controls. CONCLUSION： C/T polymorphism is not associated with the increased risk of HCC. DNMT3B genetic polymorphism is variable in different races, ethnic groups or geographic areas. Further study is needed to clarify the role of DNMT3B SNP in the development of HCCamong other populations.

Distribution Characteristics and Linkage Disequilibrium of TIM4 Promoter Polymorphisms in Asthma Patients of Chinese Han Population

To investigate the distribution characteristics and linkage disequilibrium of T cell immunoglobulin domain and mucin domain protein 4 （TIM4） promoter polymorphisms in asthma patients of Chinese Han population, the promoter region of TIM4 was re-sequenced by PCR-sequencing, and linkage disequilibrium was analyzed by SHEsis software. Four single nucleotide polymor- phisms （SNPs） in the promoter region of TIM4 were detected, including two new SNPs （at positions -1609, -153） and two reported SNPs （rs6874202, rs6882076）. The frequency distribution of rs6882076 was different among different races （P〈0.05）. In addition, linkage disequilibrium among the SNPs of the promoter region of TIM4 was found and GGTG was the predominant haplotype. There were four SNPs in the promoter region of TIM4 in asthma patients of Chinese Han population, which were in linkage disequilibrium.

Inherited susceptibility for aggressive prostate cancer

Whether or not there is inherited basis for prostate cancer aggressiveness is not clear, but advances in DNA analysis should provide an answer to this question in the very near future.

On-chip detection of a single nucleotide polymorphism without polymerase amplification

A nanoparticle-assembled photonic crystal （PC） array was used to detect single nucleotide polymorphism （SNP）. The assay platform with PC nanostructure enhanced the fluorescent signal from nanoparticle-hybridized DNA complexes due to phase matching of excitation and emission. Nanoparticles coupled with probe DNA were trapped into nanowells in an array by using an electrophoretic particle entrapment system. The PC/DNA assay platform was able to identify a 1 base pair （bp） difference in synthesized nucleotide sequences that mimicked the mutation seen in a feline model of human autosomal dominant polycystic kidney disease （PKD） with a sensitivity of 0.9 fg/mL （50 aM）-sensitivity, which corresponds to 30 oligos/array. The reliability of the PC/DNA assay platform to detect SNP in a real sample was demonstrated by using genomic DNA （gDNA） extracted from the urine and blood of two PKD-wild type and three PKD positive cats. The standard curves for PKD positive （PKD＋） and negative （PKD-） DNA were created using two feline-urine samples. An additional three urine samples were analyzed in a similar fashion and showed satisfactory agreement with the standard curve, confirming the presence of the mutation in affected urine. The limit of detection （LOD） was 0.005 ng/mL which corresponds to 6 fg per array for gDNA in urine and blood. The PC system demonstrated the ability to detect a number of genome equivalents for the PKD SNP that was very similar to the results reported with real time polymerase chain reaction （PCR）. The favorable comparison with quantitative PCR suggests that the PC technology may find application well beyond the detection of the PKD SNP, into areas where a simple, cheap and portable nucleic acid analvsis is desirable.

Haplotype variation of Green Revolution gene Rht-D1 during wheat domestication and improvement

Green Revolution made a substantial contribution to wheat yields worldwide in the 196os and 197os. It is of great importance to analyze the haplotype variation of Rht-D1, the Green Revolution gene, during wheat （Triticum aestivum L.） domestication and breeding to understand its evolution and function in wheat breeding history. In this study, the Rht-D1 and its flanking regions were sequenced and single nucleotide polymorphisms were detected based on a panel of 45 accessions of Aegilops tauschii, 51 accessions of landraces and 8o accessions of commercial varieties. Genetic diversity in the wild accessions was much higher than that in the varieties and higher than that reported previously. Seven haplotypes （Hapl I to Hapl VII） of Rht-D1 were identified and their evolutionary relationships were proposed. In addition to the well-known Green Revolution allele Rht-Dlb, Hapl Vii （an allele Rht-Dlk） was identified in early breeding varieties, whichreduced plant height by 16%. The results suggested that Rht-Dlk had been used in breeding before the Green Revolution and made a great contribution to wheat production worldwide. Based on the breeding history and molecular evidence, we proposed that the wheat Green Revolution in China and International Maize and Wheat Improvement Center （CIMMYT） occurred independently.

Variant rs2237892 of KCNQ1 Is Potentially Associated with Hypertension and Macrovascular Complications in Type 2 Diabetes Mellitus in A Chinese Han Population

KCNQ1 has been identified as a susceptibility gene of type 2 diabetes mellitus （T2DM） in Asian populations through genome-wide association studies. However, studies on the association between gene polymorphism of KCNQ1 and T2DM complications remain unclear. To further ana- lyze the association between different alleles at the single nncleotide polymorphism （SNP） rs2237892 within KCNQ1 and TD2M and its complications, we conducted a case-control study in a Chinese Han population. The C allele of rs2237892 variant contributed to susceptibility to T2DM （odds ratio [OR], 1.45; 95% confidence interval [CI], 1.20 1.75）. Genotypes CT （OR, 1.97; 95% CI, 1.24-3.15） and CC （OR, 2.49; 95% CI, 1.57-3.95） were associated with an increased risk of T2DM. Multivariate regression analysis was performed with adjustment of age, gender, and body mass index. We found that systolic blood pressure （P = 0.015）, prevalence of hypertension （P = 0.037）, and risk of maerovascnlar disease （OR, 2.10; CI, 1.00-4.45） were significantly higher in subjects with the CC genotype than in the combined population with genotype either CT or TT. Therefore, our data support that KCNQ1 might contribute to the higher incidence of patients with T2DM carrying the risk allele C population. is associated with an increased risk for T2DM and hypertension and macrovascular complications in though it needs further to be confirmed in a larger

NanoHDA： A nanoparticle-assisted isothermal amplification technique for genotyping assays

Isothermal methods, such as helicase-dependent amplification （HDA）, have an advantage over polymerase chain reaction for DNA amplification owing to their ease of operation. Here, we developed a new HDA method that is nanoparticle-assisted, termed nanoHDA. This method uses gold nanoparticles （AuNPs） to improve the sensitivity and specificity of the isothermal method. In HDA, the denaturation of DNA templates is mediated by helicases, but this method is limited by the low denaturation efficiency of helicases. In this report, AuNPs with preferential affinity for single-stranded DNA （ssDNA） were utilized to improve the denaturation efficiency of helicases. The same affinity property of nanoparticles can also enhance specificity by suppressing primer-dimer formation. This nanoHDA method was employed to genotype the KRAS gene in genomic DNA samples from colorectal cancer patients, as achieved by the hybridization of nanoHDA amplicons using the NanoBioArray chip.

Identification of SNPs involved in regulating a novel alternative transcript of P450 CYP6ER1 in the brown planthopper

Cytochrome P450-mediated metabolic resistance is one of the major mecha- nisms involved in insecticide resistance. Although the up-regulation of cytochrome P450 plays a vital role in insecticide metabolism, the molecular basis for the transcriptional regulation of cytochrome P450 remains largely unknown. The P450 gene CYP6ERI, has been reported to confer imidacloprid resistance to the brown planthopper, Nilaparvata lugens. Here, we identified a novel alternative transcript of CYP6ER1 （transcript A2） that had different expression patterns between resistant and susceptible populations, and was more stable after insecticide induction. The promoter of this transcript was sequenced and multiple single nucleotide polymorphisms （SNPs） were detected in individuals from susceptible and resistant field-collected populations. Resistant alleles of four SNPs were found to significantly enhance the promoter activity of the CYP6ER1 transcript A2. Elec- trophoretic mobility shift assays （EMSAs） revealed that these SNPs might regulate the binding of transcription factors to the promoter. Our findings provide novel evidence re- garding the transcriptional regulation of a metabolic resistance-related gene and may be useful to understand the resistance mechanism ofN. lugens in the field.

An Association Study of CASQ1 Gene Polymorphisms and Heat Stroke

Although molecular mechanisms of heat stroke under physiological and pathological conditions have not yet been elucidated, a novel disease-associated gene encoding a calcium-binding protein, calsequestrin-1 （CASQ1）, was suggested relevant based on results from a transgenic murine model. Here, we show the association between single nucleotide polymorphisms （SNPs） of CASQ1 and physiological parameters for heat stroke from a study involving 150 patients. Pooled DNA from heat stroke patients were subjected to sequencing and 3 SNPs were identified. Genotypes were assigned for all patients according to g. 175A 〉 G, one SNP which leads to a nonsynonymous sub- stitution （N59D） in the first exon of human CASQ1 gene. We analyzed the genotypic data with a linear model based on significance scores between SNP （175A 〉 G） and heat stroke parameters. As a result, we found a significant association between SNP A175G and heat stroke （P ~ 0.05）. Further bioinformatics analysis of the 1-Mb flanking sequence revealed the presence of two genes that encode DDB1 and CUL4 associated factor 8 （DCAF8）, and peroxisomal biogenesis factor 19 （PEX19）, respectively, which might be functionally related to CASQ1. Our results showed that the blood calcium of patients with allele D increased significantly, compared to patients with allele N （P 〈 0.05）, which may result from the decreased calcium in muscle, suggesting that N59D in CASQ1 might account for the dysfunction of CASQ1 in calcium regulation during heat stroke.

Enhanced destabilization of mismatched DNA using gold nanoparticles offers specificity without compromising sensitivity for nucleic acid analyses

Here, we report a method that uses gold nanoparticles （AuNPs） to enhance the specificity of DNA hybridization without reducing its detection sensitivity. The conventional stringent wash method utilizes high-temperatureflow-salt conditions to enhance the specificity of DNA hybridization-based assays. This method creates a destabilizing environment for base pairing that affects specific and nonspecific duplexes. Therefore, specificity is achieved at the expense of signal intensity or sensitivity. However, in the proposed wash method, AuNPs predominantly destabilize nonspecific duplexes, offering specificity without compromising sensitivity. This AuNP wash technique has proven to be effective in detecting single nucleotide polymorphisms （SNPs） in genomic samples even at room temperature in a CD-like NanoBioArray （CD-NBA） chip. This method is also robust with sequence variation and is compatible with multiplex DNA analyses on microarrays. Thus, the AuNP wash method could potentially be useful for improving the accuracy of DNA hybridization results.

Association of Genetic Polymorphisms of Anti-Müllerian Hormone (AMH) and Its Type II Receptor with Ovarian Hyperstimulation Syndrome

Objective To explore the association of genetic polymorphisms in the genes encoding the anti-Miillerian hormone （AMH） and its type H receptor （AMHRII） with ovarian hyperstimulation syndrome （OHSS）. Methods Using polymerase chain reaction （PCR） and DNA sequencing techniques, the exons of AMH and AMHRII were analyzed in 27 OHSS patients （OHSS group） and 22 non-OHSS patients （control group） who were applied controlled ovarian hyper- stimulation （COH）. Single nucleotide polymorphisms （SNPs） were also analyzed. Results SNPs G〉 T at position 146 of AMH exon 1 and G〉 A at position 134 of AMH exon 2 showed significant differences between the OHSS group and control group （P〈0.05）. SNP G〉 T at position 303 of AMH exon 1 showed no significant difference between the OHSS group and control group （P〉0.05）. No SNP was detected from the AMHR H exons 1 to 11 in either groups. Conclusion Genetic polymorphisms in the AMH gene may be a cause of ovarian hypersensitivity to exogenous hormone stimulation and the development of OHSS.