Objective To examine the clinical phenotype and genetic deficiencies present in Chinese aniridia families with PAX6 haplotype deficiency.Methods A comprehensive questionnaire and ophthalmological assessments were admi...Objective To examine the clinical phenotype and genetic deficiencies present in Chinese aniridia families with PAX6 haplotype deficiency.Methods A comprehensive questionnaire and ophthalmological assessments were administered to both affected patients and unaffected relatives.The clinical feature analysis included the evaluation of visual acuity,intraocular pressure,slit-lamp anterior segment examination,fundus photography,and spectral domain optical coherence tomography.To identify the mutation responsible for aniridia,targeted next-generation sequencing was used as a beneficial technique.Results A total of 4 mutations were identified,consisting of two novel frameshift mutations(c.314delA,p.K105Sfs*33 and c.838_845dup AACACACC,p.S283Tfs*85),along with two recurring nonsense mutations(c.307C>T,p.R103X and c.619A>T,p.K207*).Complete iris absence,macular foveal hypoplasia,and nystagmus were consistent in these PAX6 haplotype-deficient Chinese aniridia families,while corneal lesions,cataracts,and glaucoma exhibited heterogeneity both among the families and within the same family.Conclusion In our study,two novel PAX6 mutations associated with aniridia were identified in Chinese families,which expanded the phenotypic and genotypic spectrum of PAX6 mutations.We also analyzed the clinical characteristics of PAX6 haplotype deficiency in Chinese aniridia families.展开更多
Background: In Côte d’Ivoire so far, the circulating haplotypes have been inferred on the phenotypic profiling of SCD patients. The impact of the circulating haplotypes on the use of Hydroxyurea has not been ass...Background: In Côte d’Ivoire so far, the circulating haplotypes have been inferred on the phenotypic profiling of SCD patients. The impact of the circulating haplotypes on the use of Hydroxyurea has not been assessed yet. Therefore the objective of this study is to identify in Abidjan the HbS haplotypes that modulate HU treatment responses. Methods: In a cross-sectional descriptive and analytical study, children aged 5 to 15 years with SCD, and carrying the hemoglobin phenotypes SSFA2 and SFA2, were recruited into a HU treatment cohort. Various parameters on the haplotypes and the outcomes of the treatment were analyzed. Results: Thirty nine children with SCD were included. The phenotypic profile of the cohort was 86.6% of SSFA2 and 15.4% of SFA2. Three haplotypes were found, the Benin haplotype, the Senegal haplotype, and an atypical one. The participants belonged to three genotypes, Benin/atypical (64.1%), Benin/Senegal (33.3%) and Senegal/Senegal (2.6%). Overall, HU treatment was successful in all haplotypes with 12 out of 39 patients failing treatment after 12 months in the Benin haplotype group. The association between HU treatment success and the Benin haplotype was found in terms of the decrease in the number of white blood cells and the students missing class. Conclusion: The study revealed that inferring haplotype based on the phenotypic profile could be inaccurate. The proportion of atypical haplotype that were not previously described in Côte d’Ivoire was high. All the haplotypes seemed to be associated with HU treatment success but some patients with Benin haplotype did not respond well.展开更多
The paternally inherited Y chromosome has been widely used in forensics for personal identification, in anthropology and population genetics to understand origin and migration of human populations, and also in medical...The paternally inherited Y chromosome has been widely used in forensics for personal identification, in anthropology and population genetics to understand origin and migration of human populations, and also in medical and clinical studies （Wang and Li, 2013; Wang et al., 2014）. There are two kinds of extremely useful markers in Y chromosome, single nucle- otide polymorphism （SNP） and short tandem repeats （STRs）. With a very low mutation rate on the order of 3.0 x 10-8 mutations/nucleotide/generation （Xue et al., 2009）, SNP markers have been used in constructing a robust phylogeny tree linking all the Y chromosome lineages from world pop- ulations （Karafet et al., 2008）. Those lineages determined by the pattern of SNPs are called haplogroups. That is to say, we have to genotype an appropriate number of SNPs in order to assign a given Y chromosome to a haplogroup. Compared with SNPs, the mutation rates of STR markers are about four to five orders of magnitude higher （Gusmgo et al., 2005; Ballantyne et al., 2010）. Typing STR has advantages of saving time and cost compared with typing SNPs in phylogenetic assignment of a Y chromosome （Wang et al., 2010）. A set of STR values for an individual is called a haplotype. Because of the disparity in mutation rates between SNP and STR, one SNP haplogroup could actually comprise many STR haplotypes （Wang et al., 2010）. It is most interesting that STR variability is clustered more by haplogroups than by populations （Bosch et al., 1999; Behar et al., 2004）, which indicates that STR haplotypes could be used to infer the haplogroup information of a given Y chromosome. There has been increasing interest in this cost- effective strategy for predicting the haplogroup from a given STR haplotype when SNP data are unavailable. For instance, Vadim Urasin＇s YPredictor （http：//predictor.ydna.ru/）, Whit Atheys＇ haplogroup predictor （http：//www.hprg.com/hapest5/） （Athey, 2005, 2006）, and haplogroup classifier of Arizona University （Schlecht et al., 2008） have been widely employed in previous studies for haplogroup prediction （Larmuseau et al., 2010; Bembea et al., 2011; Larmuseau et al., 2012; Tarlykov et al., 2013）.展开更多
The laying quail is a worldwide breed which exhibits high economic value. In our current study, the vas- oactive intestinal peptide receptor-1 （VIPR-1） was selected as the candidate gene for identifying traits of eg...The laying quail is a worldwide breed which exhibits high economic value. In our current study, the vas- oactive intestinal peptide receptor-1 （VIPR-1） was selected as the candidate gene for identifying traits of egg produc- tion. A single nucleotide polymorphism （SNP） detection was performed in 443 individual quails, including 196 quails from the H line, 202 quails from the L line, and 45 wild quails. The SNPs were genotyped using a polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP）. Two mutations （G373T, A313G） were detected in all the tested quail populations. The associated analysis showed that the SNP genotypes of the VIPR-1 gene were sig- nificantly linked with the egg weight of G373T and A313G in 398 quails. The quails with the genotype GG always exhibited the largest egg weight for the two mutations in the H and L lines. Linkage disequilibrium （LD） analysis in- dicated that G373T and A313G loci showed the weakest LD. Seven main diplotypes from the four main reconstructed haplotypes were observed, indicating a significant association of diplotypes with egg weight. Quails with the hlh2 （GGGT） diplotype always exhibited the smallest egg weight and largest egg number at 20 weeks of age. The overall results suggest that the alterations in quails may be linked with potential major loci or genes affecting reproductive traits.展开更多
The standard diagnostic modalities for Prostate Cancer (PC) include serum Prostate-Specific Antigen (PSA) assay, Digital Rectal Examination (DRE), and histological examination of prostate biopsy. They are limited by l...The standard diagnostic modalities for Prostate Cancer (PC) include serum Prostate-Specific Antigen (PSA) assay, Digital Rectal Examination (DRE), and histological examination of prostate biopsy. They are limited by low predictive potential and inability to predict which patients are at risk of developing metastatic disease. The aim of this study is to investigate the exon 4 of the KLK2 gene of subjects for changes in its nucleotide sequences (SNPs) and determine the correlation of these changes with serum PSA in an Igbo population of Nigeria. One hundred male subjects aged 40 years and above, who gave their consent, were used for the study. Their PSA determinations were done using ELISA technique while genetic studies were carried out using real-time PCR. tPSA, fPSA, and % fPSA of the subjects ranged between 0.8% - 18.30%, 0.10% - 1.60% and 0.0% - 0.7% respectively. Of the 100 subjects, 28 subjects had tPSA levels above 4.0 ng/ml with a mean of 7.10 (±3.30) ng/ml. Those with tPSA less than 4 ng/ml had a mean of 1.87 (±0.85) ng/m. 15 subjects showed SNPs with a mean tPSA of 6.87 (±4.82) ng/ml while the remaining 85 subjects without SNPs had a mean of 1.86 (±0.80) ng/ml. Results from direct DNA sequencing showed 11 SNPs. Ten subjects are curated in SNP database while one is uncurated. The Chi-square test showed significant association (p = 0.00) between tPSA levels and SNPs mutation (X<sup>2</sup> = 17.35, p = 0.00). A Kruskal-Wallis test demonstrated that the positional arrangement of the SNP mutations had no effect on PSA-total or free-values (H (10) = 10.92, p = 0.28;H (10) = 10.07, p = 0.38 respectively). Two SNPs: rs6072 and rs74478031 were associated with elevated PSA levels (p < 0.05). Their presence, therefore, has the potential to serve, in conjunction with raised PSA, as biomarkers of prostate cancer in the study population.展开更多
Atlantic blue crabs(Callinectes sapidus)are ecologically and commercially fundamental.Life stages are punctuated with migration.Adults and juveniles live in estuaries and sounds.Larval stages develop in the coastal oc...Atlantic blue crabs(Callinectes sapidus)are ecologically and commercially fundamental.Life stages are punctuated with migration.Adults and juveniles live in estuaries and sounds.Larval stages develop in the coastal ocean.Juvenile and adult crabs occupy habitats from high salinities to fresh water.We determined whether maturing juvenile and adult blue crab habitat use is reflected in mitochondrial cytochrome oxidase 1 haplotypes.High salinity crabs had lower haplotype diversity(0.7260±.03900)compared to spawning crabs(0.9841±.00021)and low salinity crabs(0.94154±.00118).Significant pairwise differences in haplotypes were found between high salinity and spawning crabs(Nm=0.26018,p<0.001),and between high salinity and low salinity crabs(Nm=0.19482,p<0.001)indicating a lack of gene flow.Crabs from high salinity had highly significant genetic differentiation compared to spawning crabs(Fst=0.11830,p<0.001)and low salinity crabs(Fst=0.09689,p<0.001).Results support the hypothesis that genetics influence habitat selection.Crab larvae mix in the coastal ocean but occupy specific habitats upon return to sounds and estuaries.These findings have implications for the management of fisheries.展开更多
BACKGROUND Celiac disease(CD)is a multifactorial disease,but genetic factors play a major role in its etiology.It has been known that human leucocyte antigen(HLA)-DQ2/DQ8 haplotypes are one of the most important predi...BACKGROUND Celiac disease(CD)is a multifactorial disease,but genetic factors play a major role in its etiology.It has been known that human leucocyte antigen(HLA)-DQ2/DQ8 haplotypes are one of the most important predisposing genetic factors.The risk of developing CD in first-degree relatives and especially siblings of celiac patients is quite high because of having the same HLA haplotypes.AIM To evaluate the frequency of CD and the distribution of the HLA-DQ2/DQ8 haplotypes in siblings of celiac patients.METHODS Patients with biopsy-proven CD and their siblings were included in the study;those who did not have HLA genotyping were excluded from the study.All siblings were on a gluten-containing diet.The HLA genotyping,tissue transglutaminase antibody IgA antibody test,and total IgA test were performed in all participants.RESULTS A total of 57 celiac patients and their 112 siblings were included in the study.The mean age of celiac patients and siblings were 10.30±3.87 years and 9.90±6.11 years,respectively.HLA-DQ2/DQ8 alleles were detected in 98.2%of patients with CD and 90.2%of siblings of celiac patients.HLA-DQ genotypes were present in all siblings diagnosed with CD.Tissue transglutaminase antibody IgA test was found to be positive in 16 siblings.CD was diagnosed in 12 siblings(10.7%)by intestinal biopsy.CONCLUSION The prevalence of CD was found to be 10.7%in siblings of celiac patients in our study.One-third of the siblings diagnosed with CD were asymptomatic.We detected HLA-DQ alleles in 98.2%of celiac patients and 100%in siblings diagnosed with CD.In addition,1 of the 2 siblings was diagnosed with CD 1 year later and the other 4 years later.Therefore,we suggest that siblings of celiac patients should be followed up with clinical findings as well as HLA analysis and serological examination.Since the risk of developing CD is much higher in asymptomatic siblings,we recommend that siblings should be screened for CD even if they are asymptomatic.展开更多
AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping wa...AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping was performed for 15 single nucleotide polymorphisms(SNPs)in ITGA1.The associations between gastric cancer and these SNPs and haplotypes were analyzed with multivariate conditional logistic regression models.Multiple testing corrections were carried out following methodology for controlling the false discovery rate.Gene-based association tests were performed using the versatile gene-based association study(VEGAS)method.RESULTS:In the codominant model,the ORs for SNPs rs2432143(1.517;95%CI:1.144-2.011)and rs2447867(1.258;95%CI:1.051-1.505)were statistically significant.In the dominant model,polymorphisms of rs1862610 and rs2447867 were found to be significant risk factors,with ORs of 1.337(95%CI:1.029-1.737)and 1.412(95%CI:1.061-1.881),respectively.In the recessive model,only the rs2432143 polymorphism was significant(OR=1.559,95%CI:1.150-2.114).The C-C type of ITGA1 haplotype block 2 was a significant protective factor against gastric cancer in the both codominant model(OR=0.602,95%CI:0.212-0.709,P=0.021)and the dominant model(OR=0.653,95%CI:0.483-0.884).The ITGA1 gene showed a significant gene-based association with gastric cancer in the VEGAS test.In the dominant model,the A-T type of ITGA1 haplotype block 2 was a significant risk factor(OR=1.341,95%CI:1.034-1.741).SNP rs2447867 might be related to the severity of gastric epithelial injury due to inflammation and,thus,to the risk of developing gastric cancer.CONCLUSION:ITGA1 gene SNPs rs1862610,rs2432143,and rs2447867 and the ITGA1 haplotype block that includes SNPs rs1862610 and rs2432143 were significantly associated with gastric cancer.展开更多
AIM： To determine the distribution and frequencies of the genotypes and haplotypes of the genes encoding for the glucocorticoid receptor （GR）, the tumor necrosis factor （TNF）-α and the interleukin （IL）-10 in c...AIM： To determine the distribution and frequencies of the genotypes and haplotypes of the genes encoding for the glucocorticoid receptor （GR）, the tumor necrosis factor （TNF）-α and the interleukin （IL）-10 in childhood Crohn＇s disease （CD） and to assess the impact of the corresponding DNA variants on clinical and disease phenotypes.METHODS： Ten variants in GR, TNF-a and IL-10 were genotyped in 113 childhood CD cases and 95 healthy subjects, both of French-Canadian origin.RESULTS： For the GR polymorphisms （R23K and N363S） and IL-10 variants in the 5＇flanking region （-1082 G 〉 A, -819 T 〉 C and -592 A 〉 C）, no difference was observed in allele and genotype frequencies between CD patients and controls. At the haplotype level, we found three IL-10 haplotypes previously described in Caucasians （GCC, ACC and ATA） and three novel haplotypes only present in IBD patients. When we analyzed the haplotype distribution with the anatomical location of the disease, the GCC haplotype was associated with the colonic and the ACC haplotype with the terminal ileum location, respectively. The genotyping of five polymorphisms in the promoter region of the TNF-α gene （-1031 T 〉 C, -863 A 〉 C, -857 T 〉 C, -308 A 〉 G and -238 A 〉 G） revealed a significant overrepresentation of homozygous -1031 CC among CD patients （OR = 9.9） and an association with the colonic location. For TNF-α, eleven haplotypes were inferred, including two frequent ones, TCCGG and CACGG, which were significantly observed more frequently in controls and cases, respectively.CONCLUSION： This is one of the first studies investigating the association between haplotype structure and disease location in a CD pediatric cohort. Our results will help to increase our understanding of the genetic determinants of childhood CD.展开更多
The present study was aimed to analyze the frequencies of human leukocyte antigen （HLA）-A, -B, and -DRB1 alleles and A-B-DRBI, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples...The present study was aimed to analyze the frequencies of human leukocyte antigen （HLA）-A, -B, and -DRB1 alleles and A-B-DRBI, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples were typed in the HLA-A,-B, and -DRB1 loci using the polymerase chain reaction-reverse sequence spe- cific oligonucleotide probe （PCR-rSSOP） method and HLA polymorphisms were analyzed. A total of 18 HLA-A, 31 HLA-B, and 13 HLA-DRB1 alleles were found in the Guizhou population. The first two frequent alleles in the HLA-A, -B, and -DRB1 loci were A＊1 1（30.72%） and A＊02（30.65%）, B＊40（16.27%） and B＊46（16.27%）, and DRBl＊09（15.91%） and DRBl＊15（13.51%）, respectively. The most common haplotype was A＊02-B＊46- DRBl＊09（5.59%） in A-B-DRB1, A＊02-B＊46（I 1.73%） in A-B, B＊46-DRBl＊09（7.49%） in B-DRB1, and A＊02- DRBl＊09（8.08%） in A-DRB1. Some baplotypes with strong linkage disequilibrium （LD） were found not only in the common haplotypes, such as A＊33-B＊58, B＊30-DRB1＊07, and B＊33-DRB1＊03, but also in the rare haplotypes, such as A＊01-B＊37, B＊37-DRB1＊10, and A＊01-DRB1＊10. Guizhou inhabitants shared some characteristics of the Southern Chinese population but also had their own unique features. Overall, HLA polymorphism in Guizhou population was more consistent with that of Chengdu population than that of other populations in China.展开更多
The associations of polymorphic Alu insertions （POALINs） with major histocompatibility complex （MHC） class I genes enable us to better identify origins and evolution of MHC class I region haplotypes in different p...The associations of polymorphic Alu insertions （POALINs） with major histocompatibility complex （MHC） class I genes enable us to better identify origins and evolution of MHC class I region haplotypes in different populations. For further studying origins and evolution of MHC class I region haplotypes in Han and Jinuo populations in Yunnan Province, we investigated frequencies of five POALINs, their associations with HLA-A and -B, the three-loci POALINs haplotype frequencies and HLA/POALIN four-loci haplotype frequencies within the alpha block of MHC class I region. We found that a strong positive association between AluHG and HLA-A＊02 is in Jinuo, but not in Yunnan Han. These results suggest that MHC class I region haplotypes of the two studied populations might derive from different progenitor haplotypes and MHC I-POALINs are informative genetic markers for investigating origins and evolution of MHC class I region haplotypes in different populations.展开更多
Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and-B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing...Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and-B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing for HLA-A and-B loci was performed using the polymerase chain reaction-sequence-based typing (PCR-SBT) method on 114 randomly selected healthy individuals of the Yi population. The allelic frequencies of HLA-A and-B loci were calculated by direct counting and HLA-A-B haplotypes were estimated using the expectation maximization algorithm. Results: A total of 17 HLA-A and 38 HLA-B alleles were found in the Yi population. The most frequent alleles were A2402 (32.46%), A1101 (26.32%), and A0203 (10.09%) at the HLA-A locus and B4601 (12.28%), B1525 (10.09%), B4001 (8.77%), and B3802 (7.89%) at the HLA-B locus. The predominant HLA-A-B haplotypes were A2402-B1525 (7.86%) and A0203-B3802 (5.64%), followed by A1101-B4001 (4.69%). Phylogenetic analysis indicates that the Yi population in the Honghe, Yunnan Province of China basically belongs to groups of southeastern Asian origin, but shares some characteristics with northeastern Asian groups. Conclusion: The present study may add to the understanding of HLA polymorphism in the Yi ethnic group that was poorly defined previously, and provide useful information for bone marrow transplantation, anthropological research, and forensic sciences as well as for disease-association studies.展开更多
More than 3 years have passed since the outbreak of COVID-19 and yet, the origin of the causal virus SARS-CoV-2 remains unknown. We examined the evolutionary trajectory of SARS-CoV-2 by analyzing non-redundant genome ...More than 3 years have passed since the outbreak of COVID-19 and yet, the origin of the causal virus SARS-CoV-2 remains unknown. We examined the evolutionary trajectory of SARS-CoV-2 by analyzing non-redundant genome sets classified based on six closely linked mutations. The results indicated that SARS-CoV-2 emerged in February 2019 or earlier and evolved into three main haplotypes (GL, DS, and DL) before May 2019, which then continued to evolve in parallel. The dominant haplotype GL had spread worldwide in the summer (May to July) of 2019 and then evolved into virulent strains in December 2019 that triggered the global pandemic, whereas haplotypes DL and DS arrived in China in October 2019 and caused the epidemic in China in December 2019. Therefore, haplotype GL neither originated in China nor from the viral strains that caused the epidemic in China. Accordingly, considering data solely from China would be inadequate to reveal the mysterious origin of SARS-CoV-2, emphasizing the necessity of global cooperation.展开更多
Peroxisome proliferator-activated receptor g（PPARg） is an important regulator of chicken preadipocyte proliferation and differentiation.In this study,polymorphisms were detected by DNA sequencing,PCR-RFLP and some o...Peroxisome proliferator-activated receptor g（PPARg） is an important regulator of chicken preadipocyte proliferation and differentiation.In this study,polymorphisms were detected by DNA sequencing,PCR-RFLP and some other methods and three polymorphisms（g.-1784_-1768del17,c.-1241GA and c.-75GA） were found in the 5＇ flanking region of PPARg gene.Growth and body composition traits were measured in the 8th-10th generation populations of the Northeast Agricultural University broiler lines were divergently selected for abdominal fat content.Polymorphisms among individuals were screened in the above populations.The haplotype-based association analysis on growth and body composition traits was carried out.The association analysis showed that haplotypes based on three polymorphisms at 5＇ flanking region of PPARg gene were significantly associated with abdominal fat weight（AFW）,abdominal fat percentage（AFP,AFW/BW7）,liver weight（LW）,liver weight percentage（LFP,LW/BW7）,shank length（ShL）,femur weight（FeW）,keel length（KeL）,and metatarsus circle（MeC）（P0.05） and suggestive significantly associated with pectoralis major weight（PMaW）,pectoralis minor weight（PMiW）,pectoralis minor weight percentage（PMiWP,PMiW/BW7）,and metatarsus length（MeL）（P0.2）.The least square analysis showed that the birds with BGA haplotype had significantly higher AFW and AFP than the birds with other haplotypes（P0.05）.The birds with AAG haplotype had significantly higher LW and LW/BW than the birds with other haplotypes（P0.05）.The birds with AAG haplotype had significantly higher PMiW and PMiW/BW than the birds with other haplotypes（P0.05）.The birds with AAG haplotype had significantly higher ShL,FeW,MeL,MeC and KeL than the birds with AGG haplotypes（P0.05）.The results in this study revealed that QTL affecting fatness traits may exist in 5＇ flanking region of PPARg gene in chickens and PPARg gene might be one of the genes having important influences on the growth and bone traits in chickens.展开更多
Our previous studies have demonstrated that ceruloplasmin （CP） dysmetabolism is correlated with Parkinson＇s disease （PD）. However, the causes of decreased serum CP levels in PD patients remain to be clarified. Th...Our previous studies have demonstrated that ceruloplasmin （CP） dysmetabolism is correlated with Parkinson＇s disease （PD）. However, the causes of decreased serum CP levels in PD patients remain to be clarified. This study aimed to explore the potential association between genetic variants of the CP gene and PD. Clinical features, serum CP levels, and the CP gene （both promoter and coding regions） were analyzed in 60 PD patients and 50 controls. A luciferase reporter system was used to investigate the function of promoter single-nucleotide polymorphisms （SNPs）. High-density comparative genomic hybridization microarrays were also used to detect large-scale copy-number variations in CP and an additional 47 genes involved in PD and/or copper/ iron metabolism. The frequencies of eight SNPs （one intronic SNP and seven promoter SNPs of the CP gene） and their haplotypes were significantly different between PD patients, especially those with lowered serum CP levels, and controls. However, the luciferase reporter system revealed no significant effect of the risk haplotype on promoter activity of the CP gene. Neither these SNPs nor their haplotypes were correlated with the Hoehn and Yahr staging of PD. The results of this study suggest that common genetic variants of CP are associated with PD and further investigation is needed to explore their functions in PD.展开更多
Background: The role of human multidrug resistance gene (MDR1) SNPs in the interindividual variability of imatinib mesylate (IM) response has received considerable attention. We aimed to study the association between ...Background: The role of human multidrug resistance gene (MDR1) SNPs in the interindividual variability of imatinib mesylate (IM) response has received considerable attention. We aimed to study the association between SNPs of the MDR1 gene (C1236T, G2677T/A, C3435T) and IM response in chronic myeloid leukemia (CML) patients. Method: A retrospective case-control study was conducted on 48 patients with CML undergoing IM therapy. All patients were genotyped using PCR-RFLP method. Results: The genotype and allele frequencies of C1236T and C3435T were not significantly different between CML patients responders and non-responders to IM (p > 0.05). The frequencies of 2677T allele and 2677TT genotype were significantly increased in CML patients IM responders which as compared with IM non-responders (50% vs 26.9%, p = 0.013 and 27.3% vs 3.8%, p = 0.029 respectively). Whereas the 2677AA genotype and CAC haplotype were found only in CML patients IM non-responders (15.4%). Conclusion: Pretreatment genotyping of G2677A/T appears to be useful for predicting IM resistance, which may allow the best choice of drug treatment for CML patients.展开更多
The tooth extraction is a routine surgical procedure in the dental treatment where the healing process results in a saddle-shaped residual ridge in the edentulous jaw. There are substantial differences among individua...The tooth extraction is a routine surgical procedure in the dental treatment where the healing process results in a saddle-shaped residual ridge in the edentulous jaw. There are substantial differences among individuals in the end result. In some cases, there is excessive bone atrophy, which complicates the dental restorative treatment. The alveolar ridge receives the mechanical load continuously from the periodontal ligament connected to the teeth and it diminishes dramatically as a consequence of dental extraction;thus it is believed the continuing pattern of the alveolar bone resorption is related to this change. The reduced partial pressure of oxygen is the most prominent event from the reduced mechanical load. Vascular Endothelial Growth Factor (VEGF), regulated by HIF-1, reported close association with angiogenesis and bone turn over, where partial oxygen pressure has changed. Therefore the genetic association between Single Nucleotide Polymorphsim (SNP) of VEGF gene and RRR was investigated. 120 subjects (70.93 ± 9.28 years) which were treated at Dental clinic of Yonsei University with edentulous mandible were recruited. Mandibular bone height was measured following the protocol of the American College of Prosthodontists. Three variants, rs1570360, rs25648, and rs3025039 in VEGF from previous study, were used as tag-SNPs and genotyping for the study. Student’s t-test and ANOVA were used for statistical analysis. There was a notable association with rs1570360 (P = 0.051) in dominant group and haplotype A-C-C showed a statistically significant association with RRR in dominant group (P = 0.042). Results of this study may be useful in developing novel genetic diagnostic tests and identifying Koreans susceptible to developing severe RRR after dental extraction.展开更多
Twenty two haplotypes were generated from a pool of 60 unrelated Saudi β thalassemia major patients using previously described restriction sites in the β globin gene. Linkage disequilibrium analysis of the polymorph...Twenty two haplotypes were generated from a pool of 60 unrelated Saudi β thalassemia major patients using previously described restriction sites in the β globin gene. Linkage disequilibrium analysis of the polymorphic sites was also conducted, a few identified haplotypes were novel while the remainder was previously reported, haplotype1222212 was the most frequent haplotype in the study group and a strong linkage disequilibrium between two polymorphic restriction sites in these β thalassemia patients was uncovered.展开更多
文摘Objective To examine the clinical phenotype and genetic deficiencies present in Chinese aniridia families with PAX6 haplotype deficiency.Methods A comprehensive questionnaire and ophthalmological assessments were administered to both affected patients and unaffected relatives.The clinical feature analysis included the evaluation of visual acuity,intraocular pressure,slit-lamp anterior segment examination,fundus photography,and spectral domain optical coherence tomography.To identify the mutation responsible for aniridia,targeted next-generation sequencing was used as a beneficial technique.Results A total of 4 mutations were identified,consisting of two novel frameshift mutations(c.314delA,p.K105Sfs*33 and c.838_845dup AACACACC,p.S283Tfs*85),along with two recurring nonsense mutations(c.307C>T,p.R103X and c.619A>T,p.K207*).Complete iris absence,macular foveal hypoplasia,and nystagmus were consistent in these PAX6 haplotype-deficient Chinese aniridia families,while corneal lesions,cataracts,and glaucoma exhibited heterogeneity both among the families and within the same family.Conclusion In our study,two novel PAX6 mutations associated with aniridia were identified in Chinese families,which expanded the phenotypic and genotypic spectrum of PAX6 mutations.We also analyzed the clinical characteristics of PAX6 haplotype deficiency in Chinese aniridia families.
文摘Background: In Côte d’Ivoire so far, the circulating haplotypes have been inferred on the phenotypic profiling of SCD patients. The impact of the circulating haplotypes on the use of Hydroxyurea has not been assessed yet. Therefore the objective of this study is to identify in Abidjan the HbS haplotypes that modulate HU treatment responses. Methods: In a cross-sectional descriptive and analytical study, children aged 5 to 15 years with SCD, and carrying the hemoglobin phenotypes SSFA2 and SFA2, were recruited into a HU treatment cohort. Various parameters on the haplotypes and the outcomes of the treatment were analyzed. Results: Thirty nine children with SCD were included. The phenotypic profile of the cohort was 86.6% of SSFA2 and 15.4% of SFA2. Three haplotypes were found, the Benin haplotype, the Senegal haplotype, and an atypical one. The participants belonged to three genotypes, Benin/atypical (64.1%), Benin/Senegal (33.3%) and Senegal/Senegal (2.6%). Overall, HU treatment was successful in all haplotypes with 12 out of 39 patients failing treatment after 12 months in the Benin haplotype group. The association between HU treatment success and the Benin haplotype was found in terms of the decrease in the number of white blood cells and the students missing class. Conclusion: The study revealed that inferring haplotype based on the phenotypic profile could be inaccurate. The proportion of atypical haplotype that were not previously described in Côte d’Ivoire was high. All the haplotypes seemed to be associated with HU treatment success but some patients with Benin haplotype did not respond well.
基金supported by the National Excellent Youth Science Foundation of China(No.31222030)the National Natural Science Foundation of China(No.91131002)+3 种基金the Shanghai Rising-Star Program(No.12QA1400300)the China Ministry of Education Scientific Research Major Project(Nos. 311016 and 113022A)the MOE University Doctoral Research Supervisor's Funds(No.20120071110021)the Shanghai Professional Development Funding(No.2010001)
文摘The paternally inherited Y chromosome has been widely used in forensics for personal identification, in anthropology and population genetics to understand origin and migration of human populations, and also in medical and clinical studies （Wang and Li, 2013; Wang et al., 2014）. There are two kinds of extremely useful markers in Y chromosome, single nucle- otide polymorphism （SNP） and short tandem repeats （STRs）. With a very low mutation rate on the order of 3.0 x 10-8 mutations/nucleotide/generation （Xue et al., 2009）, SNP markers have been used in constructing a robust phylogeny tree linking all the Y chromosome lineages from world pop- ulations （Karafet et al., 2008）. Those lineages determined by the pattern of SNPs are called haplogroups. That is to say, we have to genotype an appropriate number of SNPs in order to assign a given Y chromosome to a haplogroup. Compared with SNPs, the mutation rates of STR markers are about four to five orders of magnitude higher （Gusmgo et al., 2005; Ballantyne et al., 2010）. Typing STR has advantages of saving time and cost compared with typing SNPs in phylogenetic assignment of a Y chromosome （Wang et al., 2010）. A set of STR values for an individual is called a haplotype. Because of the disparity in mutation rates between SNP and STR, one SNP haplogroup could actually comprise many STR haplotypes （Wang et al., 2010）. It is most interesting that STR variability is clustered more by haplogroups than by populations （Bosch et al., 1999; Behar et al., 2004）, which indicates that STR haplotypes could be used to infer the haplogroup information of a given Y chromosome. There has been increasing interest in this cost- effective strategy for predicting the haplogroup from a given STR haplotype when SNP data are unavailable. For instance, Vadim Urasin＇s YPredictor （http：//predictor.ydna.ru/）, Whit Atheys＇ haplogroup predictor （http：//www.hprg.com/hapest5/） （Athey, 2005, 2006）, and haplogroup classifier of Arizona University （Schlecht et al., 2008） have been widely employed in previous studies for haplogroup prediction （Larmuseau et al., 2010; Bembea et al., 2011; Larmuseau et al., 2012; Tarlykov et al., 2013）.
基金supported by the Open Project of Hubei Key Laboratory of Animal Embryo and Molecular Breeding(No.2015ZD146),China
文摘The laying quail is a worldwide breed which exhibits high economic value. In our current study, the vas- oactive intestinal peptide receptor-1 （VIPR-1） was selected as the candidate gene for identifying traits of egg produc- tion. A single nucleotide polymorphism （SNP） detection was performed in 443 individual quails, including 196 quails from the H line, 202 quails from the L line, and 45 wild quails. The SNPs were genotyped using a polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP）. Two mutations （G373T, A313G） were detected in all the tested quail populations. The associated analysis showed that the SNP genotypes of the VIPR-1 gene were sig- nificantly linked with the egg weight of G373T and A313G in 398 quails. The quails with the genotype GG always exhibited the largest egg weight for the two mutations in the H and L lines. Linkage disequilibrium （LD） analysis in- dicated that G373T and A313G loci showed the weakest LD. Seven main diplotypes from the four main reconstructed haplotypes were observed, indicating a significant association of diplotypes with egg weight. Quails with the hlh2 （GGGT） diplotype always exhibited the smallest egg weight and largest egg number at 20 weeks of age. The overall results suggest that the alterations in quails may be linked with potential major loci or genes affecting reproductive traits.
文摘The standard diagnostic modalities for Prostate Cancer (PC) include serum Prostate-Specific Antigen (PSA) assay, Digital Rectal Examination (DRE), and histological examination of prostate biopsy. They are limited by low predictive potential and inability to predict which patients are at risk of developing metastatic disease. The aim of this study is to investigate the exon 4 of the KLK2 gene of subjects for changes in its nucleotide sequences (SNPs) and determine the correlation of these changes with serum PSA in an Igbo population of Nigeria. One hundred male subjects aged 40 years and above, who gave their consent, were used for the study. Their PSA determinations were done using ELISA technique while genetic studies were carried out using real-time PCR. tPSA, fPSA, and % fPSA of the subjects ranged between 0.8% - 18.30%, 0.10% - 1.60% and 0.0% - 0.7% respectively. Of the 100 subjects, 28 subjects had tPSA levels above 4.0 ng/ml with a mean of 7.10 (±3.30) ng/ml. Those with tPSA less than 4 ng/ml had a mean of 1.87 (±0.85) ng/m. 15 subjects showed SNPs with a mean tPSA of 6.87 (±4.82) ng/ml while the remaining 85 subjects without SNPs had a mean of 1.86 (±0.80) ng/ml. Results from direct DNA sequencing showed 11 SNPs. Ten subjects are curated in SNP database while one is uncurated. The Chi-square test showed significant association (p = 0.00) between tPSA levels and SNPs mutation (X<sup>2</sup> = 17.35, p = 0.00). A Kruskal-Wallis test demonstrated that the positional arrangement of the SNP mutations had no effect on PSA-total or free-values (H (10) = 10.92, p = 0.28;H (10) = 10.07, p = 0.38 respectively). Two SNPs: rs6072 and rs74478031 were associated with elevated PSA levels (p < 0.05). Their presence, therefore, has the potential to serve, in conjunction with raised PSA, as biomarkers of prostate cancer in the study population.
文摘Atlantic blue crabs(Callinectes sapidus)are ecologically and commercially fundamental.Life stages are punctuated with migration.Adults and juveniles live in estuaries and sounds.Larval stages develop in the coastal ocean.Juvenile and adult crabs occupy habitats from high salinities to fresh water.We determined whether maturing juvenile and adult blue crab habitat use is reflected in mitochondrial cytochrome oxidase 1 haplotypes.High salinity crabs had lower haplotype diversity(0.7260±.03900)compared to spawning crabs(0.9841±.00021)and low salinity crabs(0.94154±.00118).Significant pairwise differences in haplotypes were found between high salinity and spawning crabs(Nm=0.26018,p<0.001),and between high salinity and low salinity crabs(Nm=0.19482,p<0.001)indicating a lack of gene flow.Crabs from high salinity had highly significant genetic differentiation compared to spawning crabs(Fst=0.11830,p<0.001)and low salinity crabs(Fst=0.09689,p<0.001).Results support the hypothesis that genetics influence habitat selection.Crab larvae mix in the coastal ocean but occupy specific habitats upon return to sounds and estuaries.These findings have implications for the management of fisheries.
文摘BACKGROUND Celiac disease(CD)is a multifactorial disease,but genetic factors play a major role in its etiology.It has been known that human leucocyte antigen(HLA)-DQ2/DQ8 haplotypes are one of the most important predisposing genetic factors.The risk of developing CD in first-degree relatives and especially siblings of celiac patients is quite high because of having the same HLA haplotypes.AIM To evaluate the frequency of CD and the distribution of the HLA-DQ2/DQ8 haplotypes in siblings of celiac patients.METHODS Patients with biopsy-proven CD and their siblings were included in the study;those who did not have HLA genotyping were excluded from the study.All siblings were on a gluten-containing diet.The HLA genotyping,tissue transglutaminase antibody IgA antibody test,and total IgA test were performed in all participants.RESULTS A total of 57 celiac patients and their 112 siblings were included in the study.The mean age of celiac patients and siblings were 10.30±3.87 years and 9.90±6.11 years,respectively.HLA-DQ2/DQ8 alleles were detected in 98.2%of patients with CD and 90.2%of siblings of celiac patients.HLA-DQ genotypes were present in all siblings diagnosed with CD.Tissue transglutaminase antibody IgA test was found to be positive in 16 siblings.CD was diagnosed in 12 siblings(10.7%)by intestinal biopsy.CONCLUSION The prevalence of CD was found to be 10.7%in siblings of celiac patients in our study.One-third of the siblings diagnosed with CD were asymptomatic.We detected HLA-DQ alleles in 98.2%of celiac patients and 100%in siblings diagnosed with CD.In addition,1 of the 2 siblings was diagnosed with CD 1 year later and the other 4 years later.Therefore,we suggest that siblings of celiac patients should be followed up with clinical findings as well as HLA analysis and serological examination.Since the risk of developing CD is much higher in asymptomatic siblings,we recommend that siblings should be screened for CD even if they are asymptomatic.
基金Supported by The National R and D Program for Cancer ControlMinistry of Health and Welfare+1 种基金South KoreaNo.1120330
文摘AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping was performed for 15 single nucleotide polymorphisms(SNPs)in ITGA1.The associations between gastric cancer and these SNPs and haplotypes were analyzed with multivariate conditional logistic regression models.Multiple testing corrections were carried out following methodology for controlling the false discovery rate.Gene-based association tests were performed using the versatile gene-based association study(VEGAS)method.RESULTS:In the codominant model,the ORs for SNPs rs2432143(1.517;95%CI:1.144-2.011)and rs2447867(1.258;95%CI:1.051-1.505)were statistically significant.In the dominant model,polymorphisms of rs1862610 and rs2447867 were found to be significant risk factors,with ORs of 1.337(95%CI:1.029-1.737)and 1.412(95%CI:1.061-1.881),respectively.In the recessive model,only the rs2432143 polymorphism was significant(OR=1.559,95%CI:1.150-2.114).The C-C type of ITGA1 haplotype block 2 was a significant protective factor against gastric cancer in the both codominant model(OR=0.602,95%CI:0.212-0.709,P=0.021)and the dominant model(OR=0.653,95%CI:0.483-0.884).The ITGA1 gene showed a significant gene-based association with gastric cancer in the VEGAS test.In the dominant model,the A-T type of ITGA1 haplotype block 2 was a significant risk factor(OR=1.341,95%CI:1.034-1.741).SNP rs2447867 might be related to the severity of gastric epithelial injury due to inflammation and,thus,to the risk of developing gastric cancer.CONCLUSION:ITGA1 gene SNPs rs1862610,rs2432143,and rs2447867 and the ITGA1 haplotype block that includes SNPs rs1862610 and rs2432143 were significantly associated with gastric cancer.
基金Supported by Crohn’s and Colitis Foundation of Canada and Valorisation Recherche Quebec
文摘AIM： To determine the distribution and frequencies of the genotypes and haplotypes of the genes encoding for the glucocorticoid receptor （GR）, the tumor necrosis factor （TNF）-α and the interleukin （IL）-10 in childhood Crohn＇s disease （CD） and to assess the impact of the corresponding DNA variants on clinical and disease phenotypes.METHODS： Ten variants in GR, TNF-a and IL-10 were genotyped in 113 childhood CD cases and 95 healthy subjects, both of French-Canadian origin.RESULTS： For the GR polymorphisms （R23K and N363S） and IL-10 variants in the 5＇flanking region （-1082 G 〉 A, -819 T 〉 C and -592 A 〉 C）, no difference was observed in allele and genotype frequencies between CD patients and controls. At the haplotype level, we found three IL-10 haplotypes previously described in Caucasians （GCC, ACC and ATA） and three novel haplotypes only present in IBD patients. When we analyzed the haplotype distribution with the anatomical location of the disease, the GCC haplotype was associated with the colonic and the ACC haplotype with the terminal ileum location, respectively. The genotyping of five polymorphisms in the promoter region of the TNF-α gene （-1031 T 〉 C, -863 A 〉 C, -857 T 〉 C, -308 A 〉 G and -238 A 〉 G） revealed a significant overrepresentation of homozygous -1031 CC among CD patients （OR = 9.9） and an association with the colonic location. For TNF-α, eleven haplotypes were inferred, including two frequent ones, TCCGG and CACGG, which were significantly observed more frequently in controls and cases, respectively.CONCLUSION： This is one of the first studies investigating the association between haplotype structure and disease location in a CD pediatric cohort. Our results will help to increase our understanding of the genetic determinants of childhood CD.
基金supported by the Chinese Marrow Donor Program(CMDP),CMDP Guizhou Registry
文摘The present study was aimed to analyze the frequencies of human leukocyte antigen （HLA）-A, -B, and -DRB1 alleles and A-B-DRBI, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples were typed in the HLA-A,-B, and -DRB1 loci using the polymerase chain reaction-reverse sequence spe- cific oligonucleotide probe （PCR-rSSOP） method and HLA polymorphisms were analyzed. A total of 18 HLA-A, 31 HLA-B, and 13 HLA-DRB1 alleles were found in the Guizhou population. The first two frequent alleles in the HLA-A, -B, and -DRB1 loci were A＊1 1（30.72%） and A＊02（30.65%）, B＊40（16.27%） and B＊46（16.27%）, and DRBl＊09（15.91%） and DRBl＊15（13.51%）, respectively. The most common haplotype was A＊02-B＊46- DRBl＊09（5.59%） in A-B-DRB1, A＊02-B＊46（I 1.73%） in A-B, B＊46-DRBl＊09（7.49%） in B-DRB1, and A＊02- DRBl＊09（8.08%） in A-DRB1. Some baplotypes with strong linkage disequilibrium （LD） were found not only in the common haplotypes, such as A＊33-B＊58, B＊30-DRB1＊07, and B＊33-DRB1＊03, but also in the rare haplotypes, such as A＊01-B＊37, B＊37-DRB1＊10, and A＊01-DRB1＊10. Guizhou inhabitants shared some characteristics of the Southern Chinese population but also had their own unique features. Overall, HLA polymorphism in Guizhou population was more consistent with that of Chengdu population than that of other populations in China.
文摘The associations of polymorphic Alu insertions （POALINs） with major histocompatibility complex （MHC） class I genes enable us to better identify origins and evolution of MHC class I region haplotypes in different populations. For further studying origins and evolution of MHC class I region haplotypes in Han and Jinuo populations in Yunnan Province, we investigated frequencies of five POALINs, their associations with HLA-A and -B, the three-loci POALINs haplotype frequencies and HLA/POALIN four-loci haplotype frequencies within the alpha block of MHC class I region. We found that a strong positive association between AluHG and HLA-A＊02 is in Jinuo, but not in Yunnan Han. These results suggest that MHC class I region haplotypes of the two studied populations might derive from different progenitor haplotypes and MHC I-POALINs are informative genetic markers for investigating origins and evolution of MHC class I region haplotypes in different populations.
基金Project supported by the National Natural Science Foundation of China (Nos. 30700470 and 30871348)the Shaan’xi Provincial Science and Technology Research and Development Project Fund (No. 2008K09-02), China
文摘Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and-B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing for HLA-A and-B loci was performed using the polymerase chain reaction-sequence-based typing (PCR-SBT) method on 114 randomly selected healthy individuals of the Yi population. The allelic frequencies of HLA-A and-B loci were calculated by direct counting and HLA-A-B haplotypes were estimated using the expectation maximization algorithm. Results: A total of 17 HLA-A and 38 HLA-B alleles were found in the Yi population. The most frequent alleles were A2402 (32.46%), A1101 (26.32%), and A0203 (10.09%) at the HLA-A locus and B4601 (12.28%), B1525 (10.09%), B4001 (8.77%), and B3802 (7.89%) at the HLA-B locus. The predominant HLA-A-B haplotypes were A2402-B1525 (7.86%) and A0203-B3802 (5.64%), followed by A1101-B4001 (4.69%). Phylogenetic analysis indicates that the Yi population in the Honghe, Yunnan Province of China basically belongs to groups of southeastern Asian origin, but shares some characteristics with northeastern Asian groups. Conclusion: The present study may add to the understanding of HLA polymorphism in the Yi ethnic group that was poorly defined previously, and provide useful information for bone marrow transplantation, anthropological research, and forensic sciences as well as for disease-association studies.
基金supported by grants from the National Key R&D Program of China and the Central Public-interest Scientific Institution Basal Research Fund to J.Z.(1630052020022)by the Project of Science and Technology Department of Sichuan Provincial of China to L.Y.(2019JDJQ0035).
文摘More than 3 years have passed since the outbreak of COVID-19 and yet, the origin of the causal virus SARS-CoV-2 remains unknown. We examined the evolutionary trajectory of SARS-CoV-2 by analyzing non-redundant genome sets classified based on six closely linked mutations. The results indicated that SARS-CoV-2 emerged in February 2019 or earlier and evolved into three main haplotypes (GL, DS, and DL) before May 2019, which then continued to evolve in parallel. The dominant haplotype GL had spread worldwide in the summer (May to July) of 2019 and then evolved into virulent strains in December 2019 that triggered the global pandemic, whereas haplotypes DL and DS arrived in China in October 2019 and caused the epidemic in China in December 2019. Therefore, haplotype GL neither originated in China nor from the viral strains that caused the epidemic in China. Accordingly, considering data solely from China would be inadequate to reveal the mysterious origin of SARS-CoV-2, emphasizing the necessity of global cooperation.
基金supported by the National 863 Program of China(2006A A10A120)the National 973 Program of China (2006CB102105)the Natural Science Foundation Key Project of Heilongjiang Province,China (ZJN0604-01)
文摘Peroxisome proliferator-activated receptor g（PPARg） is an important regulator of chicken preadipocyte proliferation and differentiation.In this study,polymorphisms were detected by DNA sequencing,PCR-RFLP and some other methods and three polymorphisms（g.-1784_-1768del17,c.-1241GA and c.-75GA） were found in the 5＇ flanking region of PPARg gene.Growth and body composition traits were measured in the 8th-10th generation populations of the Northeast Agricultural University broiler lines were divergently selected for abdominal fat content.Polymorphisms among individuals were screened in the above populations.The haplotype-based association analysis on growth and body composition traits was carried out.The association analysis showed that haplotypes based on three polymorphisms at 5＇ flanking region of PPARg gene were significantly associated with abdominal fat weight（AFW）,abdominal fat percentage（AFP,AFW/BW7）,liver weight（LW）,liver weight percentage（LFP,LW/BW7）,shank length（ShL）,femur weight（FeW）,keel length（KeL）,and metatarsus circle（MeC）（P0.05） and suggestive significantly associated with pectoralis major weight（PMaW）,pectoralis minor weight（PMiW）,pectoralis minor weight percentage（PMiWP,PMiW/BW7）,and metatarsus length（MeL）（P0.2）.The least square analysis showed that the birds with BGA haplotype had significantly higher AFW and AFP than the birds with other haplotypes（P0.05）.The birds with AAG haplotype had significantly higher LW and LW/BW than the birds with other haplotypes（P0.05）.The birds with AAG haplotype had significantly higher PMiW and PMiW/BW than the birds with other haplotypes（P0.05）.The birds with AAG haplotype had significantly higher ShL,FeW,MeL,MeC and KeL than the birds with AGG haplotypes（P0.05）.The results in this study revealed that QTL affecting fatness traits may exist in 5＇ flanking region of PPARg gene in chickens and PPARg gene might be one of the genes having important influences on the growth and bone traits in chickens.
基金supported by the National Natural Science Foundation of China (81200973)the National Basic Research Development Program of China (2011CBA00400)an Independent Scientific Research Project of Fudan University (20520133484)
文摘Our previous studies have demonstrated that ceruloplasmin （CP） dysmetabolism is correlated with Parkinson＇s disease （PD）. However, the causes of decreased serum CP levels in PD patients remain to be clarified. This study aimed to explore the potential association between genetic variants of the CP gene and PD. Clinical features, serum CP levels, and the CP gene （both promoter and coding regions） were analyzed in 60 PD patients and 50 controls. A luciferase reporter system was used to investigate the function of promoter single-nucleotide polymorphisms （SNPs）. High-density comparative genomic hybridization microarrays were also used to detect large-scale copy-number variations in CP and an additional 47 genes involved in PD and/or copper/ iron metabolism. The frequencies of eight SNPs （one intronic SNP and seven promoter SNPs of the CP gene） and their haplotypes were significantly different between PD patients, especially those with lowered serum CP levels, and controls. However, the luciferase reporter system revealed no significant effect of the risk haplotype on promoter activity of the CP gene. Neither these SNPs nor their haplotypes were correlated with the Hoehn and Yahr staging of PD. The results of this study suggest that common genetic variants of CP are associated with PD and further investigation is needed to explore their functions in PD.
文摘Background: The role of human multidrug resistance gene (MDR1) SNPs in the interindividual variability of imatinib mesylate (IM) response has received considerable attention. We aimed to study the association between SNPs of the MDR1 gene (C1236T, G2677T/A, C3435T) and IM response in chronic myeloid leukemia (CML) patients. Method: A retrospective case-control study was conducted on 48 patients with CML undergoing IM therapy. All patients were genotyped using PCR-RFLP method. Results: The genotype and allele frequencies of C1236T and C3435T were not significantly different between CML patients responders and non-responders to IM (p > 0.05). The frequencies of 2677T allele and 2677TT genotype were significantly increased in CML patients IM responders which as compared with IM non-responders (50% vs 26.9%, p = 0.013 and 27.3% vs 3.8%, p = 0.029 respectively). Whereas the 2677AA genotype and CAC haplotype were found only in CML patients IM non-responders (15.4%). Conclusion: Pretreatment genotyping of G2677A/T appears to be useful for predicting IM resistance, which may allow the best choice of drug treatment for CML patients.
文摘The tooth extraction is a routine surgical procedure in the dental treatment where the healing process results in a saddle-shaped residual ridge in the edentulous jaw. There are substantial differences among individuals in the end result. In some cases, there is excessive bone atrophy, which complicates the dental restorative treatment. The alveolar ridge receives the mechanical load continuously from the periodontal ligament connected to the teeth and it diminishes dramatically as a consequence of dental extraction;thus it is believed the continuing pattern of the alveolar bone resorption is related to this change. The reduced partial pressure of oxygen is the most prominent event from the reduced mechanical load. Vascular Endothelial Growth Factor (VEGF), regulated by HIF-1, reported close association with angiogenesis and bone turn over, where partial oxygen pressure has changed. Therefore the genetic association between Single Nucleotide Polymorphsim (SNP) of VEGF gene and RRR was investigated. 120 subjects (70.93 ± 9.28 years) which were treated at Dental clinic of Yonsei University with edentulous mandible were recruited. Mandibular bone height was measured following the protocol of the American College of Prosthodontists. Three variants, rs1570360, rs25648, and rs3025039 in VEGF from previous study, were used as tag-SNPs and genotyping for the study. Student’s t-test and ANOVA were used for statistical analysis. There was a notable association with rs1570360 (P = 0.051) in dominant group and haplotype A-C-C showed a statistically significant association with RRR in dominant group (P = 0.042). Results of this study may be useful in developing novel genetic diagnostic tests and identifying Koreans susceptible to developing severe RRR after dental extraction.
文摘Twenty two haplotypes were generated from a pool of 60 unrelated Saudi β thalassemia major patients using previously described restriction sites in the β globin gene. Linkage disequilibrium analysis of the polymorphic sites was also conducted, a few identified haplotypes were novel while the remainder was previously reported, haplotype1222212 was the most frequent haplotype in the study group and a strong linkage disequilibrium between two polymorphic restriction sites in these β thalassemia patients was uncovered.
