Immunochip Analysis Identification of 6 Additional Susceptibility Loci for Crohn's Disease in Koreans.
Inflamm Bowel Dis. 2014 Dec 8;
Authors: Yang SK, Hong M, Choi H, Zhao W, Jung Y, Haritunians T, Ye BD, Kim KJ, Park SH, Lee I, Kim WH, Cheon JH, Kim YH, Jang BI, Kim HS, Choi JH, Koo JS, Lee JH, Jung SA, Shin HD, Kang D, Youn HS, Taylor KD, Rotter JI, Liu J, McGovern DP, Song K
BACKGROUND:: Crohn's disease (CD) is an intractable inflammatory bowel disease of unknown cause. Recent genome-wide association studies of CD in Korean and Japanese populations suggested marginal sharing of susceptibility loci between Caucasian and Asian populations. As the 7 identified loci altogether explain 5.31% of the risk for CD, the objective of this study was to identify additional CD susceptibility loci in the Korean population.
METHODS:: Using the ImmunoChip custom single-nucleotide polymorphism array designed for dense genotyping of 186 loci identified through GWAS, we analyzed 722 individuals with CD and 461 controls for 96,048 SNP markers in the discovery stage, followed by validation in an additional 948 affected individuals and 977 controls.
RESULTS:: We confirmed 6 previously reported loci in whites: GPR35 at 2q37 (rs3749172; P = 5.30 × 10, odds ratio [OR] = 1.45), ZNF365 at 10q21 (rs224143; P = 2.20 × 10, OR = 1.38), ZMIZ1 at 10q22 (rs1250569; P = 3.05 × 10, OR = 1.30), NKX2-3 at 10q24 (rs4409764; P = 7.93 × 10, OR = 1.32), PTPN2 at 18p11 (rs514000; P = 9.00 × 10, OR = 1.33), and USP25 at 21q11 (rs2823256; P = 2.49 × 10, OR = 1.35), bringing the number of known CD loci (including 3 in the HLA) in Koreans to 15. The 6 additional loci increased the total genetic variance for CD risk from 5.31% to 7.27% in Koreans.
CONCLUSIONS:: Although the different genetic backgrounds of CD between Asian and Western countries has been well established for the major susceptibility genes, our findings of overlapping associations offer new insights into the genetic architecture of CD.
PMID: 25489960 [PubMed - as supplied by publisher]
Analysis of Multiple Cytokine Polymorphisms in Individuals with Untreated Deep Carious Lesions Reveals IL1B (rs1143643) as a Susceptibility Factor for Periapical Lesion Development.
J Endod. 2014 Dec 2;
Authors: Dill A, Letra A, Chaves de Souza L, Yadlapati M, Biguetti CC, Garlet GP, Vieira AR, Silva RM
INTRODUCTION: It has been proposed that individual genetic predisposition may contribute to persistent apical periodontitis. Cytokines are associated with levels of inflammation and are involved in caries, pulpal, and periapical tissue destruction. We hypothesized that polymorphisms in cytokine genes may contribute to an individual's increased susceptibility to apical tissue destruction in response to deep carious lesions.
METHODS: Subjects with deep carious lesions with or without periapical lesions (≥3 mm) were recruited at the University of Pittsburgh, Pittsburgh, PA, and the University of Texas at Houston, Houston, TX. Genomic DNA samples of 316 patients were sorted into 2 groups: 136 cases with deep carious lesions and periapical lesions (cases) and 180 cases with deep carious lesions but no periapical lesions (controls). Nine single-nucleotide polymorphisms in IL1B, IL6, TNF, RANK, RANKL, and OPG genes were selected for genotyping. Genotypes were generated by end point analysis using TaqMan chemistry (Invitrogen, Carlsbad, CA) in a real-time polymerase chain reaction instrument. Allele and genotype frequencies were compared among cases and controls using the PLINK program (http://pngu.mgh.harvard.edu/purcell/plink/). Ninety-three human periapical granulomas and 24 healthy periodontal ligament tissues collected postoperatively were used for messenger RNA expression analyses of IL1B.
RESULTS: A single-nucleotide polymorphism in IL1B (rs1143643) showed allelic (P = .02) and genotypic (P = .004) association with cases of deep caries and periapical lesions. We also observed altered transmission of IL1B marker haplotypes (P = .02) in these individuals. IL1B was highly expressed in granulomas (P < .001).
CONCLUSIONS: Variations in IL1B may be associated with periapical lesion formation in individuals with untreated deep carious lesions. Future studies could help predict host susceptibility to developing periapical lesions.
PMID: 25476976 [PubMed - as supplied by publisher]
206 genome-wide associations for reproductive traits in Russian holstein population.
Reprod Fertil Dev. 2014 Dec;27(1):194
Authors: Kramarenko AS, Lopukchov AA, Gladyr EA, Singina GN, Ermilov AN, Yanchukov IN, Brem G, Zinovieva NA
Reproductive health is an important trait in selection of dairy cattle. A genome-wide association study (GWAS) is a powerful tool for annotating phenotypic effects on the genome and to get knowledge of genes and chromosomal regions associated with reproductive performance (Cole et al. 2011). Combining GWAS and genetic profiling of embryos before implantation enables to develop new strategies to select elite breeding genotypes before transfer (Humblot et al. 2010; Ponsart et al. 2013). The aim of the current study was to evaluate the association between single nucleotide polymorphisms (SNP) and estimated breeding values (EBV) for reproductive traits [interval to insemination (EBVII) and interval between calving (EBVIC)] for Russian Holstein cattle and to evaluate the effect of the biopsy procedure on the viability of bovine embryos produced in vitro as a basis for pre-implantation genetic diagnosis (PGD). Ninty-six progeny-tested sires of artificial insemination station Moscowskoe were selected based on the reliability for EBVII and EBVIC. Estimations of breeding values of sires were performed by best linear unbiased prediction (BLUP) mixed model equations. DNA was extracted from sire semen samples. SNP genotyping was performed using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA, USA) containing 54609 SNPs. Quality control information was carried out in PLINK (v. 1.07; Purcell et al. 2007 Am. J. Hum. Genet. 81). Based on the quality control information, 41442 SNPs were selected for subsequent GWAS. We have identified 3270 SNPs having significant effect (P<0.05) on studied traits. The most significant associations with EBVII were found for SNPs Hapmap38548-BTA-97184 and ARS-BFGL-BAC-11821 with coefficient of determination (R(2)) of 0.2189 and 0.1937, and P-values 2.27×10(-6) and 1.01×10(-6), respectively. The most significant effect on EBVIC was detected for SNPs ARS-BFGL-NGS-59769 and ARS-BFGL-NGS-38020 with coefficient of determination (R(2)) of 0.236 and 0.2421, and P-values 1.49×10(-8) and 7.24×10(-8), respectively. The highest number of significant associations was found on BTA5, BTA12, BTA19, and BTA14. Bovine embryos were produced in vitro using a standard procedure. Six to 8 cell biopsies were carried out at Day 6.5 after fertilization. The viability of biopsied embryos was evaluated comparing the hatching rates to non-manipulated embryos. The study of embryos viability after biopsy showed that the hatching rate of biopsied embryos (the number of hatched embryos from the number of embryos in stages of late morula and early blastocyte) was 48% comparing to 67% for non-manipulated embryos. Embryo biopsy is not dramatically decreasing embryo viability. Combining our results of association studies, performed on Russian Holstein population, and technique of embryo biopsy will provide us a powerful tool for selection progress.
PMID: 25472255 [PubMed - in process]
307 maturation rate and gene expression analysis of goat oocytes selected by follicle size and brilliant cresyl blue staining.
Reprod Fertil Dev. 2014 Dec;27(1):242
Authors: Yang M, Hu S, Cox L, Regouski M, Rutigliano H, Isom C, Polejaeva I
Oocyte quality plays a critical role in determining the success of embryo development. Studies on cattle and goats indicate that oocytes derived from large follicles (LFO) have greater developmental competence than those derived from small follicles (SFO). Brilliant cresyl blue (BCB) staining determines the activity of glucose-6-phosphate dehydrogenase and is a commonly used noninvasive marker of oocyte competence. Studies in pigs, goats, cows, mice, and dogs showed that the maturation and blastocyst developmental rate of BCB+ oocytes is significantly higher than BCB- oocytes. The aim of this study was to evaluate the maturation rate of goat oocytes selected based on follicular size and BCB staining and compare their relative patterns of gene expression. Maturation rate and gene expression profile were expected to be different in these oocyte groups. Cumulus-oocyte complexes were recovered from abattoir-derived ovaries using a slicing technique. Eleven rounds of oocyte maturation and 4 rounds of BCB staining were carried out. During each replicate, oocytes from large (≥3mm) and small (<3mm) follicles were collected separately from the same group of ovaries. Oocyte maturation rates were 54.3±5.4% for LFO (n=378) and only 33.5±3.7% for SFO (n=981; P<0.01). The BCB+ (n=223) oocytes yielded a significantly higher maturation rate than the BCB- (n=194) oocytes (56.1±1.8 v. 20.6±3.8%, respectively; P<0.001). Gene expression analysis was conducted on individual MII oocytes (21 oocytes per group). Specific target amplification was performed on a single oocyte directly by using the CellsDirect One-Step qRT-PCR Kit (Invitrogen). Quantitative real-time PCR was then performed using the 48.48 BioMark platform from Fluidigm. Forty two genes were selected from the following categories: growth factors, transcription factors, metabolism, pluripotency, cell cycle, apoptosis, and oocyte-specific genes. Relative expression values were calculated using the ΔΔCT (fold change) method and analysed by ANOVA. The significance was assigned at P<0.05. The relative expression of CCNA2, CDK2, CCNB1, POU5F1, SOX2, EGF, FGF2, GDF9, ZP3, BCL2, GJA1, DDR1, PFKFB3, IGF2R, and GRB10 was significantly greater (P<0.05) in both LFO and BCB+ oocytes compared to SFO and BCB- oocytes, respectively. The proapoptotic gene BAX, the ACSL3 gene involved in fatty acid oxidation, and the growth factor IGF1 were expressed significantly higher (P<0.05) in SFO compared to LFO. By investigating these differentially expressed transcripts, we will better understand pathways involved in oocyte developmental competence and potentially use them as markers of oocyte quality. We expect that the ability to select oocytes of better quality based on BCB staining will improve outcomes of IVF and SCNT.
PMID: 25472355 [PubMed - in process]