• Issue front cover thumbnail

      Volume 96, Issue 6

      December 2017,   pages  865-1059

    • From the editor’s desk

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    • A genetic variant in COL11A1 is functionally associated with lumbar disc herniation in Chinese population

      WENJUN LIU GUISEN SUN LONGSHENG GUO LULU WANG WEIQIANG FAN MINGLEI LANG DAN CHEN XINHAO YI

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      This study aimed to explore whether the genetic variant of COL11A1 is functionally associated with the development of lumbar disc herniation (LDH) in Chinese population. SNP rs1676486 of COL11A1 was genotyped in 647 patients and 532 healthy controls. The differences of genotype and allele distributions between LDH patients and healthy controls were evaluated using the χ2 test. One-way ANOVA test was used to compare the relationship between genotypes and clinical features including tissue expression of COL11A1 and the degree of disc degeneration. Patients were found to have a significantly higher frequency of TT than the controls (10.2% versus 7.3%, P = 0.004). Besides, the frequency of allele T was found to be remarkably higher in the patients than the controls (34.8% versus 28.1%, P < 0.001) with an odds ratio of 1.36 (95% confidential interval=1.14–1.63). Patients with genotype TT were found to have remarkably more severe disc degeneration (P = 0.02). Besides, the expression of COL11A1 in the lumbar disc was significantly lower in the patients with genotype TT than in those with genotype CT or CC (P < 0.001). Moreover, the expression level was inversely correlated with the severity of disc degeneration (P < 0.001). We confirmed that the rs1676486 of COL11A may be functionally associated with LDH in the Chinese population. Extracellular matrix related proteins may play an important role in the pathogenesis of LDH. Our findings shed light on a better understanding of the pathogenesis of LDH, which could be a promising target for a novel treatment modality of LDH.

    • Genetic variability and structure of an isolated population of Ambystoma altamirani, a mole salamander that lives in the mountains of one of the largest urban areas in the world

      ROSA-LAURA HEREDIA-BOBADILLA OCTAVIO MONROY-VILCHIS MARTHA M. ZARCO-GONZÁLEZ DANIEL MARTÍNEZ-GÓMEZ GERMÁN DAVID MENDOZA-MARTÍNEZ ARMANDO SUNNY

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      Amphibians are globally threatened by habitat loss and fragmentation; species within the order Ambystoma are not the exception, as there are 18 species of mole salamanders in México, of which 16 are endemic and all species are under some national or international status of protection. The mole salamander, Ambystoma altamirani is a microendemic species, which is distributed incentral México, within the trans-Mexican volcanic belt, and is one of the most threatened species due to habitat destruction and the introduction of exotic species. Nine microsatellite markers were used to determine the genetic structure, genetic variability, effective population size, presence of bottlenecks and inbreeding coefficient of one population of A. altamirani to generate information which might help to protect and conserve this threatened species. We found two genetic subpopulations with significant level of genetic structure (FST = 0.005) and high levels of genetic variability (Ho = 0.883; He = 0.621); we also found a small population size (Ne = 8.8), the presence of historical (M = 0.486) and recent bottlenecks under IAM and TPM models, with a low, but significantcoefficient of inbreeding (FIS = −0.451). This information will help us to raise conservation strategies of this microendemic mole salamander species.

    • Mutational screening of PKD2 gene in the north Indian polycystic kidney disease patients revealed 28 genetic variations

      SONAM RAJ RANA GOPAL SINGH PARIMAL DAS

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      Polycystic kidney disease (PKD) is a systemic disorder which adds majority of renal patients to end stage renal disease. Autosomal dominant polycystic kidney disease (ADPKD) is more prevalent and leading cause of dialysis and kidney transplant. Linkage analysis revealed some closely linked loci, two of which are identified as PKD1, PKD2 and an unidentified locus to ADPKD. This study was performed using PCR and automated DNA sequencing in 84 cases and 80 controls to test potential candidature of PKD2 as underlying cause of PKD by in silico and statistical analyses. Two associated symptoms, hypertension (19%) and liver cyst (31%) have major contribution to PKD. Gender-based analysis revealed that familial female patients (27%) and familial male patients(33%) are more hypertensive. Liver cyst, the second major contributing symptom presented by large percentage of sporadic males (46%). Genetic screening of all 15 exons of PKD2 revealed eight pathogenic (c.854_854delG, c.915C>A, c.973C>T, c.1050_1050delC, c.1604_1604delT, c.1790T>C, c.2182_2183delAG, c.2224C>T) and eight likely pathogenic (g.11732A>G, c.646T>C, c.1354A>G, g.39212G>C, c.1789C>A, c.1849C>A, c.2164G>T, c.2494A>G)DNA sequence variants. In our study, 27.38% (23/84) cases shown pathogenic / likely pathogenic variants in PKD2 gene. Some regions of PKD2 prone for genetic variation suggested to be linked with disease pathogenesis. This noticeable hot spot regions hold higher frequency (50%) of pathogenic / likely pathogenic genetic variants constituting single nucleotide variants than large deletion and insertion that actually represents only 41.08% of coding sequence ofPKD2. Statistically significant association for IVS3-22AA genotype was observed with PKD, while association of IVS4+62C>T was found insignificant.

    • Identification of housekeeping genes as references for quantitative real-time RT-PCR analysis in Misgurnus anguillicaudatus

      XIAOHUA XIA WEIRAN HUO RUYAN WAN XIAOPEI XIA QIYAN DU ZHONGJIE CHANG

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      Quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) is a well-known method to quantify gene expression by comparing with the reference genes. Generally, housekeeping genes were set as references, as for their stable expression in varying conditions. Here, we try to evaluate few of such genes to identify suitable housekeeping genes as references for qRT-PCR analysis of gene expression in Misgurnus anguillicaudatus. This study evaluated the expression of four commonly used housekeeping genes, i.e. b-actin (ACTB), elongation factor 1 alpha (EF-1a), glyceraldehyde-3-phosphate (GAPDH) and 18S ribosomal RNA (18S rRNA), in gender difference, effects of tissue type, different developmental stages, chemical treatment of embryos/larvae with commonly used vehicles for administration and agents that represent known environmental toxicant. Rank ordering of expression stability was done using geNorm, NormFinder and BestKeeper algorithms. Results suggested that in the qRTPCR test, in all the experimental conditions, EF-1a could be selected as reference gene when analysing a target gene. For the study of different development stages, ACTB could be a candidate as reference gene. For the studies associated with different gender and tissue types, EF-1a would be better targeted as reference gene. Meanwhile, in toxicant treatment, expression of EF-1a seems to be more stable than others and could be considered as reference gene. This study could provide useful guidelines that can be expected to aid M. anguillicaudatus researchers in their initial choice of housekeeping genes for future studies and enable more accurate normalization of gene expression data.

    • Influence of thiopurine methyltransferase gene polymorphism on Egyptian children with acute lymphoblastic leukaemia

      AZZA A. G. TANTAWY FATMA S. E. EBEID AMIRA A. M. ADLY EMAN EL-GHOROURY MAI MOSTAFA

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      Thiopurine methyltransferase (TPMT) gene polymorphism regulates thiopurine therapeutic efficacy and toxicity. The aim of this study was to determine the influence of TPMT gene polymorphism in Egyptian children with acute lymphoblastic leukaemia (ALL). Sixty-four patients with ALL, T lineage (27%) and pre-B phenotype (73%), who were treated with BFM 90 or CCG 1991 standard risk protocol, and who also experienced myleosuppresion toxicity and required interruption and/or modification of thiopurine chemotherapy were recruited over a year period. Thirty-two patients were on maintenance and another 32 completedtheir chemotherapy. Seventy healthy age-matched and sex-matched children served as controls. They were subjected to clinicalassessment, haematological panel investigations and TPMT gene polymorphism for G238C, G460A and A719G alleles assessment using PCR followed by RFLP analysis.Although none of the studied patients had themutantTPMTvariant alleles,myelosuppression toxicity in the form of different degree of neutropenia was detected in all patients. As a result of myelosuppression toxicity, most ofthe patients needed 6-MP dose modification either once (53.1%), twice (15.6%), or ≥ thrice (25.1%) during their maintenance course and 96.9% of the patients required to stop 6-MP for less than a week (62.5%), up to 2 weeks (28.1%), or > 2 weeks (6.3%). Patients also developed infection who mostly (71%) needed hospitalization. None of the studied G238C, G460A and A719G TPMT variant alleles were detected. Infections and febrile neutropenia were common causes of 6-PM dose modification and interruption.

    • Analysis of two susceptibilitySNPsinHLAregion and evidence of interaction between rs6457617 in HLA-DQB1 and HLA-DRB1*04 locus on Tunisian rheumatoid arthritis

      YOSSER ACHOUR MARIEM BEN HAMAD SOUHIR CHAABANE AHMED REBAI SAMEH MARZOUK NADIA MAHFOUDH ZOUHIR BAHLOUL LEILA KESKES ABDELLATIF MAALEJ

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      Previous genomewide association studies (GWAS) and meta-analyses have enumerated several genes/loci in major histocompatibility complex region, which are consistently associated with rheumatoid arthritis (RA) in different ethnic populations. Given the genetic heterogeneity of the disease, it is necessary to replicate these susceptibility loci in other populations. In this case, weinvestigate the analysis of two SNPs, rs13192471 and rs6457617, from the human leukocyte antigen (HLA) region with the risk of RA in Tunisian population. These SNPs were previously identified to have a strong RA association signal in several GWAS studies. A case–control sample composed of 142 RA patients and 123 healthy controls was analysed. Genotyping of rs13192471 and rs6457617was carried out using real-time PCR methods by Taq Man allelic discrimination assay. A trend of significant association was found in rs6457617 TT genotype with susceptibility to RA (P = 0.04, p pc = 0.08, OR = 1.73). Moreover, using multivariable analysis, the combination of rs6457617*TT–HLA-DRB1*04 ⁺ increased risk of RA (OR = 2.38), which suggest a gene–gene interaction event between rs6457617 located within the HLA-DQB1 and HLA-DRB1. Additionally, haplotypic analysis highlighted a significant association of rs6457617*T–HLA-DRB1*04 ⁺ haplotype with susceptibility to RA (P = 0.018, pc = 0.036, OR = 1.72). An evidence of association was shown subsequently in antiCCP ⁺ subgroup with rs6457617 both in T allele and TT genotype (P = 0.01, pc = 0.03, OR = 1.66 and P = 0.008, pc = 0.024, OR = 1.28, respectively). However, no association was shown for rs13192471 polymorphism with susceptibility and severity to RA. This study suggests the involvement of rs6457617 locus as risk variant for susceptibility/severity to RA in Tunisian population. Secondly, it highlights the gene–gene interaction between HLA-DQB1 and HLA-DRB1.

    • Neuro-fuzzy model of homocysteine metabolism

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      In view of well-documented association of hyperhomocysteinaemia with a wide spectrum of diseases and higher incidence of vitamin deficiencies in Indians, we proposed a mathematical model to forecast the role of demographic and geneticvariables in influencing homocysteine metabolism and investigated the influence of life style modulations in controlling homocysteine levels. Total plasma homocysteine levels were measured in fasting samples using reverse phase HPLC. Multiple linear regression (MLR) and neuro-fuzzy models were developed. The MLR model explained 64% variability in homocysteine, while the neurofuzzymodel showed higher accuracy in predicting homocysteine with a mean absolute error of 0.00002 μmol/L. Methylene tetrahydrofolate reductase (MTHFR) C677T, 5-methyltetrahydrofolate homocysteine methyltransferase (MTR) A2756G and 5-methyltetrahydrofolate homocysteine methyltransferase reductase (MTRR) A66G were shown to be positively associatiated with homocysteine, while nonvegetarian diet, serine hydroxymethyltransferase 1 (SHMT1) C1420T and TYMS 5'-UTR 28 bp tandem repeat exhibited negative association with homocysteine. The protective role of SHMT1 C1420T was attributed to more H-bonding interactions in the mutant modelled compared to the wild type, as shown through in silico analysis. To conclude, polymorphisms in genes regulating remethylation of homocysteine strongly influence homocysteine levels. The restoration of one-carbon homeostasis by SHMT1 C1420T or increased flux of folate towards remethylation due to TYMS 5'-UTR 28 bp tandem repeat or nonvegetariandiet can lower homocysteine levels.

    • Glutathione S-transferase P1 gene polymorphisms and susceptibility to coronary artery disease in a subgroup of north Indian population

      M. A. BHAT G. GANDHI

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      The present study aimed to investigate the association of g.313A>G and g.341C>T polymorphisms of GSTP1 with coronary artery disease (CAD) in a subgroup of north Indian population. In the present case–control study, CAD patients (n = 200) and age-matched, sex-matched and ethnicity-matched healthy controls (n = 200) were genotyped for polymorphisms in GSTP1 using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Genotype distribution of g.313A>G and g.341C>T polymorphisms of GSTP1 gene was significantly different between cases and controls (P = 0.005 and 0.024, respectively). Binary logistic regression analysis showed significant association of A/G (odds ratio (OR): 1.6, 95% CI: 1.08–2.49, P = 0.020) and G/G (OR: 3.1, 95% CI: 1.41–6.71, P = 0.005) genotypes of GSTP1 g.313A>G, and C/T (OR: 5.8, 95% CI: 1.26–26.34, P = 0.024) genotype of GSTP1 g.341C>T with CAD. The A/G and G/G genotypes of g.313A>G and C/T genotype of g.341C>T conferred 6.5-fold increased risk for CAD (OR: 6.5, 95% CI: 1.37–31.27, P = 0.018).Moreover, the recessive model of GSTP1 g.313A>G is the best fit inheritance model to predict the susceptible gene effect (OR: 2.3, 95% CI: 1.11–4.92, P = 0.020). In conclusion, statisticallysignificant associations of GSTP1 g.313A>G (A/G, G/G) and g.341C>T (C/T) genotypes with CAD were observed.

    • Genetic analysis of 55 northern Vietnamese patients with Wilson disease: seven novel mutations in ATP7B

      LE ANH TUAN PHAM TRONG TUE NGUYEN HOANG BICH NGA LE DAT QUOC TRAN CAM TU HO THINH HUY TRAN VAN THANH TA THE HUNG BUI VAN KHANH TRAN

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      Wilson disease (WD) is an autosomal recessive disorder of copper metabolism. The gene responsible for WD was discovered in 1993 and is located on chromosome 13 at 13q14.3. It encodes a copper-specific transporting P-type ATPase. Early diagnosis can improve treatment outcome and decrease the rate of disability or even mortality.We used Sanger sequencing to identify mutation hot spots in 55 northern Vietnamese with a clinical diagnosis of WD. Mutations were screened and detected by direct DNA sequencing. A total of 26 different ATP7B gene mutations were identified, including seven novel mutations (five nonsense and two missense mutations). The most frequent mutations were p.Ser105Ter (24.55%), p.Arg778Leu (5.45%) and p.Thr850Ile (4.55%). Mutation detection rate in exon 2 was 34.55% and ranked first, followed by exon 8 with 16.36%, and exon 18 with 10.91% each, thus, exons 2, 8 and 18 are the mutation hot spots for northern VietnameseWD patients. These findings were different from previousstudies in Asia. Our research established a suitable strategy for ATP7B gene testing in northern Vietnamese WD patients.

    • Identification and association of novel lncRNA pouMU1 gene mutations with chicken performance traits

      TUANHUI REN YANTING ZHOU YU ZHOU WEIHUA TIAN ZHENZHEN GU SONG ZHAO YADI CHEN RUILI HAN XIAOJUN LIU XIANGTAO KANG ZHUANJIAN LI

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      The biological functions of long noncoding RNAs (lncRNAs), which play an important role in regulating development and gene expression, may be affected by variations in lncRNA gene loci or associated genomic sequences. However, the functions of many lncRNAs remain unknown. To analyse correlations between mutations in pouMU1 with chicken growth and carcass traits, 860 chickens from a Gushi×Anka F2 resource population and 96 Lushi, Xichuan, Changshun and recessive white chickens were used to evaluate the genetic effect of the pouMU1 gene. We performed quantitative real-time polymerase chain reaction (qRT-PCR) to analyse the relative expression levels of pouMU1 in nine different tissues and stages of development. pouMU1 expression was highest in pectoralis and leg muscles, whereas no expression was observed in the heart, liver and abdominal fat. Using direct sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods, two novel sequence mutations(g.1198A>G and g.1238-1239del/insGA) were detected in the pouMU1 gene. SPSS software was used for statistical analysis in association studies. Based on the association data, the presence of both variants was significantly associated with leg muscle fibre width and leg muscle fibre roundness (P < 0.05) and highly associated with leg muscle fibre girth and body weight at 0 week of age (P < 0.01). These data suggest that pouMU1 might participate in regulating chicken muscle development and growth, and the findings offer new insight into the functions of sequence mutations in lncRNAs.

    • Marker-assisted pyramiding of Thinopyrum-derived leaf rust resistance genes Lr19 and Lr24 in bread wheat variety HD2733

      MONA SINGH N. MALLICK S. CHAND P. KUMARI J. B. SHARMA M. SIVASAMY P. JAYAPRAKASH K. V. PRABHU S. K. JHA VINOD

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      This study was undertaken to pyramid two effective leaf rust resistance genes (Lr19 and Lr24) derived from Thinopyrum (syn. Agropyron), in the susceptible, but agronomically superior wheat cultivar HD2733 using marker-assisted selection. In the year 2001, HD2733 was released for irrigated timely sown conditions of the north eastern plains zone (NEPZ) of India became susceptibleto leaf rust, a major disease of the region. Background selection helped in developing near-isogenic lines (NILs) of HD2733 with Lr19 and Lr24 with 97.27 and 98.94%, respectively, of genomic similarity with the parent cultivar, after two backcrossing and one generation of selfing.NILs were intercrossed to combine the genes Lr19 and Lr24. The combination of these two genes in the cultivarHD2733 is expected to provide durable leaf rust resistance in farmers’ fields.

    • Genetic diversity, phylogeographic structure and effect of selection at the mitochondrial hypervariable region of Nigerian chicken populations

      ABDULHAKEEM B AJIBIKE OLUWAGBEMIGA O ADELEYE BABATUNDE M ILORI DAMILOLA A OSINBOWALE OMOLOLA A ADENIYI SAMUEL O. DUROSARO ADEYINKA J. SANDA OLUWAFUNMILAYO A. ADEBAMBO AYOTUNDE O. ADEBAMBO

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      In this study, the maternal genetic diversity, phylogenetic relationship and effect of natural selection on indigenous chickens from Nigeria were assessed. A total of 397-bp fragment of the mitochondrial DNA (mtDNA) D-loop region of 171 indigenous chickens from four populations of Nigeria and four commercial egg line strains (two Anak titan, one Giriraja and one Yaffa) as out-groups were analysed. Thirty-one haplotypes (28 from Nigerian chickens and three from commercial strains) and 34 polymorphic sites were identified. The mean haplotypic and nucleotide diversity were found to be 0.39 ± 0.05 and 0.02 ± 0.02, respectively. Majority of Nigerian chicken haplotypes observed were grouped into haplogroup D which originated from Indian subcontinent, suggesting a single maternal lineage. Genetic variation within and between populations accounted for 97.30 and 2.70%of the total genetic variation, respectively, which is in agreement with a recent and maternal founding effect. High number (4) of negatively selected sites observed based on single likelihood ancestral counting (SLAC) model indicated that the sampled Nigerian chicken populations were undergoing purifying selection. This study concluded that there was relatively high genetic diversity and differentiation, thus, this information will probably paveway for further evaluation studies, preservation and improvement of Nigerian chickens as genetic resources towards ensuring food security.

    • The connexin 46 mutant (V44M) impairs gap junction function causing congenital cataract

      LIJUAN CHEN DONGMEI SU SIJIA LI LINA GUAN CUIGE SHI DIANJUN LI SHANSHAN HU XU MA

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      Connexin 46 (Cx46) is important for gap junction channels formation which plays crucial role in the preservation of lens homeostasis and transparency. Previously, we have identified a missense mutation (p.V44M) of Cx46 in a congenital cataractfamily. This study aims at dissecting the potential pathogenesis of the causative mutant of cataract. Plasmids carrying wild-type (wt) and mutant (V44M) of Cx46 were constructed and expressed in Hela cells respectively.Western blotting and fluorescence microscopy were applied to analyse the expression and subcellular localization of recombinant proteins, respectively. Scrape loading dye transferexperiment was performed to detect the transfer capability of gap junction channels among cells expressed V44Mmutant. The results demonstrated that in transfected Hela cells, both wt-Cx46 and Cx46 V44M were localized abundantly in the plasma membrane. No significant difference was found between the protein expressions of the two types of Cx46. The fluorescent localization assay revealedthe plaque formation, significantly reduced in the cells expressing Cx46 V44M. Immunoblotting analysis demonstrated that formation of Triton X-100 insoluble complex decreased obviously in mutant Cx46. Additionally, the scrape-loading dye-transfer experiment showed a lower dye diffusion distance of Cx46 V44M cells, which indicates that the gap junction intercellular communication activitywas aberrant. Human Cx46 V44M mutant causing cataracts result in abnormally decreased formation of gap junction plaques and impaired gap junction channel function.

    • Mapping of Id locus for dermal shank melanin in a Chinese indigenous chicken breed

      JIGUO XU SHUDAI LIN XINFENG GAO QINGHUA NIE

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      The dermal shank pigmentation, one of the defining traits of chicken breeds, is caused by an abnormal deposition of melanin in the dermis of the shank. The abnormal deposition is controlled by the sex-linked inhibitor of dermal melanin (Id). In this study, we aim to locate the gene responsible for the dermal shank pigmentation in chickens by an association analysis and a differential expression analysis. Based on our results, 72 single-nucleotide polymorphisms (SNPs) located in Z chromosome (chrZ): 71–73 Mb (galGal3) were selected to further explore their relationships with the dermal shank pigmentation in pure lines of 96 Gushi hens and 96 Gushi hens with a yellow shank skin colour. The results of the association analysis showed that the SNPs located in chrZ: 72.58–72.99 Mb (galGal3) (chrZ: 79.02–79.44 Mb (galGal4)) are significantly associated with the dermal shank pigmentation. Based on the results of our previous studies and the present association analysis, the zinc-finger protein 608 (ZNF608), GRAM domain containing 3 (GRAMD3), aldehyde dehydrogenase 7 family member A1 (ALDH7A1), fem-1 homologue C (FEM1C), beta-1,4-galactosyltransferase 1 (B4GALT1) and versican (VCAN) genes were selected for the differential expression analysis. The gene expression profiles showed that the expression ofGRAMD3gene in the dermis tissues of the shank was significantly (P = 0.010738 < 0.05) higher in 350-day-old Gushi chickens characterized by the dermal shank pigmentation than in one-day-old Gushi chickens. The dermal shank pigmentation was not present in the one-day-old Gushi chickens. Additionally, the results of the association analysis and the expression analysis showed that GRAMD3 could be the most likely candidate gene for the Id locus. However, we did not detect a mutation, i.e. significantly associated with this trait within GRAMD3. Therefore, we concluded that the variations located in the flanking region of GRAMD3 led to the abnormal expression of GRAMD3, which requires further study.

    • Genetic variants influencing lipid levels and risk of dyslipidemia in Chinese population

      HUAICHAO LUO XUEPING ZHANG PING SHUAI YUANYING MIAO ZIMENG YE YING LIN

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      Recently, several human genetic and genomewide association studies (GWAS) have discovered many genetic loci that are associated with the concentration of the blood lipids. To confirm the reported loci in Chinese population, we conducted a cross section study to analyse the association of 25 reported SNPs, genotyped by the ABI SNaPshot method, with the blood levels of total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglycerides (TG) in 1900 individuals by multivariate analysis. Logistic regression was applied to assess the association of the genetic loci withthe risk of different types of dyslipidemia. Our study has convincingly identified that 12 of 25 studied SNPs were strongly associated with one or more blood lipid parameters (TC, LDL, HDL and TG). Among the 12 associated SNPs, 10 significantly influence the risk of one or more types of dyslipidemia.We firstly found four SNPs (rs12654264 in HMGCR; rs2479409 in PCSK9; rs16996148 inCILP2, PBX4; rs4420638 in APOE-C1-C4-C2) robustly and independently associate with four types of dyslipidemia (MHL, mixed hyperlipidemia; IHTC, isolated hypercholesterolemia; ILH, isolated low HDL-C; IHTG, isolated hypertriglyceridemia). Our results suggest that genetic susceptibility is different on the same candidate locus for the different populations. Meanwhile, most of thereported genetic variants strongly influence one or more plasma lipid levels and the risk of dyslipidemia in Chinese population.

    • Association of lactase 13910 C/T polymorphism with bone mineral density and fracture risk: a meta-analysis

      YOUGEN WU YINGHUA LI YUNQING CUI YUNJIAO ZHOU QINGQING QIAN YANG HONG

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      Anumber of studies have investigated the association of lactase (LCT,C/T-13910) gene polymorphismwith bonemineral density (BMD) and fracture risk, but previous results were inconclusive. In this study, a meta-analysis was performed to quantifythe association of LCT (C/T-13910) polymorphism with BMD and fracture risk. Eligible publications were searched in the PubMed, Web of Science, Embase databases, Google Scholar, Yahoo and Baidu. Pooled weighed mean difference (WMD) or odds ratio (OR) with their 95% confidence interval (CI) were calculated using a fixed-effects or random-effects model. A total of nine articles with8871 subjects were investigated in the presentmeta-analysis. Overall, the TT/TC genotypes of LCT 13910 C/T polymorphism showed significantly higher BMD than those with the CC genotype at femur neck (FN) (WMD = 0.011 g/cm2, 95% CI = 0.004–0.018, P = 0.003). Besides, LCT 13910 C/T polymorphism may decrease the risk of any site fractures (for TT versus TC+CC, OR = 0.813, 95% CI = 0.704–0.938, P = 0.005; for T allele versus C allele, OR = 0.885, 95% CI = 0.792–0.989, P = 0.032). However, there was no significant association of LCT 13910 C/T polymorphism with BMD at lumbar spine and risk of vertebral fractures under all genetic contrast models (all P values were >0.05). The meta-analysis suggests that there are significant effects of LCT 13910 C/T polymorphism on BMD and fracture risk. Large-scale studies with different ethnic populations will be needed to further investigate the possible race-specific effect of LCT 13910 C/T polymorphism on BMD and fracture risk

    • Ellis–van Creveld syndrome and profound deafness resulted by sequence variants in theEVC/EVC2 and TMC1genes

      MUHAMMAD UMAIR HEIDE SEIDEL ISHTIAQ AHMED ASMAT ULLAH TOBIAS B. HAACK BADER ALHADDAD ABID JAN AFZAL RAFIQUE TIM M. STROM FAROOQ AHMAD THOMAS MEITINGER WASIM AHMAD

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      Ellis–van Creveld syndrome is an autosomal recessive skeletal dysplasia primarily characterized by the features such as disproportionate dwarfism, short ribs, short limbs, dysplastic nails, cardiovascular malformations, post-axial polydactyly (PAP)(bilateral) of hands and feet. EVC/EVC2 located in head-to-head arrangement on chromosome 4p16 are the causative genes for EvC syndrome. In the study, we present two families, A and B, with Pakistani and Republic of Kosovo origin, respectively. They showed features of EvC syndrome and were clinically and genetically characterized. In family A, the affected members showed anadditional feature of profound deafness. The whole exome sequencing (WES) in this family revealed two homozygous variants in EVC2 (c.30dupC; p.Thr11Hisfs*45) and TMC1 (c.1696-1G>A) genes. In family B, WES revealed novel compound heterozygous variants (p.Ser307Pro, c.2894+3A>G) in the EVC gene. This study reports first case of variants in the genes causing EvC syndromeand profound deafness in the same family.

    • A novel contiguous deletion involving NDP, MAOBand EFHC2gene in a patient with familial Norrie disease: bilateral blindness and leucocoria without other deficits

      BEI JIA LIPING HUANG YAOYU CHEN SIPING LIU CUIHUA CHEN KE XIONG LANLIN SONG YULAI ZHOU XINPING YANG MEI ZHONG

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      Contiguous microdeletions of the Norrie disease pseudoglioma (NDP) region on chromosome Xp11.3 have been widely confirmed as contributing to the typical clinical features of Norrie disease (ND). However, the precise relation between genotype and phenotype could vary. The contiguous deletion of NDP and its neighbouring genes, MAOA/B and EFHC2, reportedly leads to syndromic clinical features such as microcephaly, intellectual disability, and epilepsy. Herewe report a novel contiguous microdeletion of theNDPregion containing theMAOBandEFHC2genes,which causes eye defects but no cognitive disability.We detected a deletion of 494.6 kb atXp11.3 in both the proband and carrier mother. This deletionwas then used as the molecularmarker in prenatal diagnosis for two subsequent pregnancies. The deletion was absent in one of the foetuses, who remain without any abnormalities at 2 years of age. The proband shows the typical ocular clinical features of ND including bilateral retinal detachment, microphthalmia, atrophic irides, corneal opacification, and cataracts, but no symptoms of microcephaly, intellectual disability, and epilepsy. This familial study demonstrates that a deficiency in one of two MAO genes may not lead to psychomotor delay, and deletion of EFHC2 may not cause epilepsy. Our observations provide new information on the genotype–phenotype relations of MAOA/B and EFHC2 genes involved in the contiguous deletions of ND

    • A novel missense mutation of ADAR1gene in a Chinese family leading to dyschromatosis symmetrica hereditaria and literature review

      SHUAI-MEI LIU MENG-XIA NI MING-CHAO ZHANG PEI-RAN ZHU QIU-YU WU WEI-JUN JIANG JING ZHANG WEI-WEI LI XIN-YI XIA

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      Dyschromatosis symmetrica hereditaria (DSH) is a rare autosomal dominant pigmentary genodermatosis, which is characterized by a mixture of hyperpigmented and hypopigmented macules on the dorsal of the hands and feet, and on the face presented like freckle. Identification of RNA-specific adenosine deaminase 1 (ADAR1) gene results in DSH. This study was mainlyto explore the pathogenic mutation of ADAR1 gene and provide genetics counselling and prenatal diagnostic testing for childbearing individuals.Mutational analysis of ADAR1 gene was performed by polymerase chain reaction (PCR) and electrophoretic separation of PCR products by 1.5% agarose gel electrophoresis. The coding exons and intron/exon flanking regions followed by bidirectionalsequencing was performed on all participants. In this study, we found that a 28 year-old male patient harbouring a deleterious substitution of Leu1052Pro in the ADAR1 gene in a typical DSH family. His mother suffered from the DSH also owns the same mutation. This mutation, however, is not identified in the unaffected members in this family and those 200 normal controls. In summary, this new mutation Leu1052Pro reported here is pathogenic and detrimental for DSH. Our finding not only enriches mutation database and contributes to dissecting further the correlation between mutation position and phenotypical features ofDSH, but also provides genetics counselling and prenatal diagnostic testing for childbearing couple.

    • Dominance effects estimation of TLR4and CACNA2D1genes for health and production traits using logistic regression

      MASOUMEH BAGHERI AZADEH ZAHMATKESH

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      Knowledge of nonadditive variance and genetic effects can be helpful in explaining the total genetic variation formost of the traits. The objective of this study was to estimate dominance effects of several single-nucleotide polymorphism (SNP) genotypes for the production traits and clinical mastitis residual (CMR), in Holstein dairy cattle in a case–control study. Records of 305 days lactation were obtained for production traits and CMR. Animals were selected based on extreme values for CMR from mixed model analyses. Samples were genotyped for four SNP-single genotypes and their associations with production traits (breeding values forprotein and fat yield, and protein and fat percentage) were estimated by applying logistic regression analyses. Calculation of contrast between both homozygous and heterozygous genotypes permitted to estimate dominance effects, which ranged from −0.49 to 0.35 standard deviation units for the production traits and clinical mastitis (CM), respectively. Results showed that the dominance effectsmay be important in contribution of total genetic effects for production traits and CM. Therefore, evaluation of animals based on additive variance alone and disregarding nonadditive effects may lead to failure in selection programmes and exactly estimating the genetic variation. The method that we used would help breeders in accurately estimation of genotypic values in a new genomicselection scenario including dominance effects

    • Illumina-based de novo transcriptome sequencing and analysis of Chinese forest musk deer

      ZHONGXIAN XU HANG JIE BINLONG CHEN UMA GAUR NAN WU JIAN GAO PINMING LI GUIJUN ZHAO DEJUN ZENG MINGYAO YANG DIYAN LI

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      The Chinese forest musk deer (Moschus berezovskii Flerov) is an endangered artiodactyl mammal. The musk secreted by sexually mature males is highly valued for alleged pharmaceutical properties and perfume manufacturing. However, the genomic and transcriptomic resources of musk deer remain deficiently represented and poorly understood. Next-generation sequencing technique is an efficient method for generating an enormous amount of sequence data that can represent a large number of genes and theirexpression levels. In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI nonredundant protein (Nr) database; 31,039 unigenes were assignedto 61 GO terms, and 11,782 to 332 KEGG pathways. Additionally, 592 and 2282 differentially expressed genes were found to be specifically expressed in the heart and musk gland, respectively. The abundant transcriptomic data generated in the present report will provide a comprehensive sequence resource for Chinese forest musk deer as well as lay down a foundation which will help inaccelerating genetic and functional genomics research in this species.

    • Genome-based exome sequencing analysis identifies GYG1, DIS3L and DDRGK1 are associated with myocardial infarction in Koreans

      JI-YOUNG LEE SANGHOON MOON YUN KYOUNG KIM SANG-HAK LEE BOK-SOO LEE MIN-YOUNG PARK JEONG EUY PARK YANGSOO JANG BOK-GHEE HAN

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      Myocardial infarction (MI) is a complex disease caused by combination of genetic and environmental factors. Although genome-wide association studies (GWAS) identified more than 46 risk loci which are associated with coronary artery disease and MI, most of the genetic variability inMI still remains undefined. Here, we screened the susceptibility loci for MI using exome sequencing and validated candidate variants in replication sets. We identified that three genes (GYG1, DIS3L and DDRGK1) were associated with MI at the discovery and replication stages. Further research will be required to determine the functional association of thesegenes with MI risk, and these associations have to be confirmed in other ethnic populations

    • Venous thromboembolism associated with protein S deficiency due to Arg451∗ mutation in PROS1 gene: a case report and a literature review

      EWA WYPASEK MAREK KARPINSKI MARTINE ALHENC-GELAS ANETTA UNDAS

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      Protein S (PS) is a vitamin K-dependent glycoprotein which plays an important role in the regulation of blood coagulation. PS deficiency has been found in 1.5–7% of thrombophilic patients. Here, we report the first Polish case with PS deficiency caused by the p.Arg451* in the PROS1 gene detected in a 21-year-old man with trauma-induced venous thromboembolism. To our knowledge,we provided the review of all the available data on this mutation (a total of 56 cases). The proband, his mother and his sister were screened for thrombophilia. To elucidate genetic background of PS deficiency, all PROS1 genes were subjected to direct sequencing. The free PS levels were 35% in the proband, 21% in the proband’s mother and 28% in the proband’s sister and their PS total levels were 37.1, 47.5 and 55.1%, respectively. Type I PS deficiency was diagnosed. In all patients, genetic analysis revealed the presence ofheterozygous nonsense mutation (c.1351C>T; p.Arg451*) located in exon 12 of PROS1 gene. This mutation interrupts the reading frame by premature termination codon at position 451 and may lead to the production of truncated protein. The present case combined with the review of the literature suggests that p.Arg451* in the PROS1 gene mainly leads to clinically evident thrombosisfollowing trauma, surgery or serious comorbidities especially malignancy.

    • Drosophila pallidosa : whether a separate species or a light form of D. ananassae

      B. N. SINGH ROSHNI SINGH

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      Drosophila pallidosa belongs to the D. ananassae complex, which includes a total of 10 species. Earlier D. pallidosa was known as light form of D. ananassae but later it was described as a new species, sibling of D. ananassae. Both these terms, light form and sibling species were used by Futch. This makes the taxonomic status of D. pallidosa confusing. In this review we have tried tounderstand the actual status of this sibling species pair. Considering the similarities and dissimilarities, we suggest that D. pallidosa does not have the full status of a species, rather it is in the process of speciation, statu-nascendi. Our suggestion is strengthened by the fact that male genitalia are identical in both the cases and they lack postmating reproductive isolation since hybrids between them are normal and fully fertile.

© 2017 Indian Academy of Sciences, Bengaluru.