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Re-evaluating data quality of dog mitochondrial,Y chromosomal,and autosomal SNPs genotyped by SNP array

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Zoological Research 2016年第6期37卷 356-360页

作者： Newton O.OTECKO Min-Sheng PENG He-Chuan YANG Ya-Ping ZHANG Guo-Dong WANG State Key Laboratory of Genetic Resources and Evolution Yunnan Key Laboratory of Molecular Biology of Domestic AnimalsGermplasm Bank of Wild SpeciesKunming Institute of ZoologyChinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences State Key Laboratory for Conservation and Utilization of Bio-Resources Yunnan University

Quality deficiencies in single nucleotide polymorphism （SNP） analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was -43.8%, with 980 （18.1%）individuals completely missing mitochondrial SNP genotyping （missingness rate=l）. In males, the genotype missingness rate was -28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping （locus missingness rate=0）, whereas 5.9% of autosomal SNPs had a locus missingness rate=l. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.

关键词： SNP array Dog Mitochondrial Ychromosomal autosomal

A novel mutation in FBN1 gene in autosomal dominant Marfan syndrome and macular degeneration in a Chinese consanguineous family

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International Journal of Ophthalmology(English edition) 2019年第5期12卷 725-730页

作者： Ping-Bo Ouyang Yuan Zhao Ying-Qian Peng Lu-Si Zhang Jian Cao Yun Li Department of Ophthalmology the Second Xiangya Hospital of Central South University Hunan Clinical Research Center of Ophthalmic Disease Department of Cardiovascular Surgery the Second Xiangya Hospital of Central South University

AIM: To report a novel mutation in FBN1 gene in a Chinese consanguineous family with common Marfan syndrome(MFS) phenotype and an unusual bilateral macular degeneration. METHODS: Ophthalmic, cardiovascular and systemic examinations were performed, and genomic DNA extracted from all living family members. The 24-32 exon mutations of FBN1 gene were screened by Sanger Sequencing in all family members and 100 unrelated healthy Chinese individuals. RESULTS: In the four-generation family, classic MFS phenotypes were observed in all 5 patients, 2 of them had peculiar phenotype of bilateral macular degeneration. Mutation screening in FBN1 identified a heterozygous missense mutation(c.3932 A>G, p.Y1311 C) with co-segregation. This mutation was found with the MFS phenotypes in all 5 patients but not in unaffected members or unrelated controls. CONCLUSION: A Chinese consanguineous MFS family with uncommon bilateral macular degeneration and an unreported c.3932 A>G mutation in FBN1 was identified. Our finding expands the FBN1 mutation spectrum and its possible role in the pathogenesis of Marfan syndrome.

关键词： Marfan syndrome fibrillin-1 autosomal dominant heterozygous mutation

Deciphering the pathogenicity of COL4A4 heterozygous splicing mutations and the genotypephenotype correlation in autosomal dominant Alport syndrome

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中国医学文摘:内科学分册(英文版) 2023年第2期40卷 114-115页

作者：戴选彤 Renal Div Dept Intern MedXinhua HospShanghai Jiaotong Univ Med SchShanghai 200092

Objective Through the investigation of the pathogenicity of COL4A4 heterozygous splicing mutations and the genotype-phenotype correlation in autosomal dominant Alport syndrome(ADAS),to better understand the impact of COL4A4 heterozygous splicing mutations on *** The study was a case series *** from 5 ADAS families with COL4A4 heterozygous splicing mutations detected by whole exome sequencing were recruited by three hospitals.

关键词： ADAS COL autosomal

Acute abdomen and ascites as presenting features of autosomal dominant polycystic kidney disease

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World Journal of Hepatology 2012年第12期4卷 394-398页

作者： Sanjay Chaudhary Qi Qian Division of Nephrology and Hypertension Department of MedicineMayo Clinic College of MedicineRochesterMN 55905United States

We describe a patient with sudden onset of abdominal pain and ascites,leading to the diagnosis of autosomal dominant polycystic kidney disease(ADPKD).Her presentation was consistent with acute liver cyst rupture as the cause of her acute illness.A review of literature on polycystic liver disease in patients with ADPKD and current management strategies are *** case alerts physicians that ADPKD could occasionally present as an acute abdomen;cyst rupture related to ADPKD may be considered in the differential diagnoses of acute abdomen.

关键词： autosomal dominant polycystic kidney disease Acute abdominal pain Ascites Polycystic liver disease

Unique interstitial miRNA signature drives fibrosis in a murine model of autosomal dominant polycystic kidney disease

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World Journal of Nephrology 2018年第5期7卷 108-116页

作者： Ameya Patil William E Sweeney Jr Cynthia G Pan Ellis D Avner Children’s Research Institute Children’s’Hospital Health System of Wisconsin and the Medical College of WisconsinMilwaukeeWI 53226United States

AIM To delineate changes in miRNA expression localized to the peri-cystic local microenvironment(PLM) in an orthologous mouse model of autosomal dominant polycystic kidney disease(ADPKD)(mcwPkd1^(nl/nl)).METHODS We profiled miRNA expression in the whole kidney and laser captured microdissection(LCM) samples from PLM in mcwPkd1^(nl/nl)kidneys with Qiagen miScript 384 HC miRNA PCR arrays. The three times points used are:(1) post-natal(PN) day 21, before the development of trichrome-positive areas;(2) PN28, the earliest sign of trichrome staining; and(3) PN42 following the development of progressive fibrosis. PN21 served as appropriate controls and as the reference time point for comparison of miRNA expression *** LCM samples revealed three temporally upregulated miRNAs [2 to 2.75-fold at PN28 and 2.5 to 4-fold(P ≤ 0.05) at PN42] and four temporally downregulated miRNAs [2 to 2.75 fold at PN28 and 2.75 to 5-fold(P ≤ 0.05) at PN42]. Expression of twenty-six miRNAs showed no change until PN42 [six decreased(2.25 to 3.5-fold)(P ≤ 0.05) and 20 increased(2 to 4-fold)(P ≤ 0.05)]. Many critical miRNA changes seen in the LCM samples from PLM were not seen in the contralateral whole *** Precise sampling with LCM identifies miRNA changes that occur with the initiation and progression of renal interstitial fibrosis(RIF). Identification of the target proteins regulated by these miRNAs will provide new insight into the process of fibrosis and identify unique therapeutic targets to prevent or slow the development and progression of RIF in ADPKD.

关键词： Inflammation End-stage renal disease Cysts autosomal dominant poly cystic kidney disease miRNA Renal interstitial fibrosis

Investigation of Four Genes Responsible for autosomal Recessive Congenital Cataract and Highly Expressed in the Brain in Four Unrelated Tunisian Families

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Open Journal of Ophthalmology 2012年第3期2卷 64-70页

作者： Manèl Chograni Myriam Chaabouni Faouzi Maazoul Habiba Chaabouni Bouhamed Charles Nicolle hospital Congenital and Hereditary Disorders Department Tunis Tunisia University Tunis Elmanar Faculté de Médecine de Tunis Laboratoire Génétique Humaine Tunis Tunisia

Purpose: To identify the causative gene for phenotypes associating autosomal recessive congenital cataract, mental retardation and congenital cataract, mental retardation and microcephaly in four unrelated Tunisian families. Methods: Four genes (EPHA2, GALK1, GCNT2, and CRYBB1) were selected based on expression in human brain and their known or putative function. Linkage analyses were performed for the four genes in multiple affected and unaffected families’ members and results were explored by the GeneMapper ID v3.2 software. Results: No linkage was identified for the four studied genes in the four families. Affected members of each family did not share common haplotypes in corresponding candidate regions containing selected gene. Conclusion: Although the four studied genes were reported responsible for autosomal recessive congenital cataract and highly expressed in the human brain, we report no linkage for EPHA2, GALK1, GCNT2, and CRYBB1 genes in four families with congenital cataract, mental retardation and congenital cataract, mental retardation and microcephaly.

关键词： Congenital Cataract Mental Retardation Microcephaly autosomal Recessive Association Linkage Study

The Association between autosomal Dominant Polycystic Kidney Disease and Renal Cell Carcinoma

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Open Journal of Urology 2015年第6期5卷 84-90页

作者： Chase C. Hansen Michael Derrick Irfan Warriach James Thomas Cammack James Thomas Cammack Werner de Riese School of Medicine Texas Tech University Health Sciences Center Lubbock USA Department of Pathology Texas Tech University Health Sciences Center Lubbock USA Department of Urology Texas Tech University Health Sciences Center Lubbock USA

Objectives: The relationship between autosomal dominant polycystic kidney disease (ADPKD) and renal cell carcinoma (RCC) is investigated to determine a link that would guide management due to elevated RCC risk. Current literature is inconclusive on this topic. Methods: This study is a retrospective chart review of patients having undergone nephrectomy. Those with pathology and history consistent with ADPKD were reviewed for presence of RCC. Results: The review at this institution revealed RCC in 18% of ADPKD patients who underwent nephrectomy. These rates are significantly higher than those found in the general population, and even greater than those would be expected in patients suffering end-stage renal disease (ESRD). Conclusions: Due to the increased prevalence of RCC in ADPKD, clinicians managing patients with ADPKD should maintain a high index of suspicion. Our data suggest a link between ADPKD and RCC, most likely at the genetic level. In light of this, we feel that further genetic research is needed to potentially discover the link between these two disease processes.

关键词： autosomal Dominant Polycystic Kidney Chronic Kidney Failure Genetic Variation Nephrectomy Renal Cell Carcinoma

An autosomal STR Profile of Napoléon the First

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Open Journal of Genetics 2014年第4期4卷 292-299页

作者： Gérard Lucotte Alexandra Bouin Wilkinson Institute of Molecular Anthropology Paris France

Objective: We report the results of nuclear DNA analyses of Napoléon the First (Napoléon Bonaparte;1769-1821). Design: His genomic DNA was extracted from dandruff adherent to his hair, coming from a lock of his hair dating from the year of 1811. Results: We obtained the complete STR (short tandem repeats) profile of Napoléon, based on fifteen autosomal loci. On this profile, ten loci (D8S1179, D21S11, D7S820, D3S1358, TH01, D16S539, D2S1338, vWa, D18S51 and FGA) are heterozygous;the most frequent alleles in Caucasians are present for only seven (allele 8 for TPOX and allele 11 for D5S818, allele 13 for D8S1179, allele 10 for D7S820, allele 9.3 for THO1, allele 12 for D16S539 and allele 24 for FGA) of the homozygous and heterozygous loci. Conclusions: So the discriminating power of this sort of genetic profile is elevated, permitting useful comparisons to other STR profiles in the future. Finally, an analysis of fifteen Y chromosomal STRs from the dandruff of this lock of hair confirms allele values of Napoléon already obtained or deduced for the corresponding loci in previous determinations.

关键词： Napoléon the First Hair Dandruff Genomic DNA autosomal STR Profile

A Prospective Study on Clinical Profile of autosomal Dominant Polycystic Kidney Disease (ADPKD) in Jammu for a Period of 1 Year

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Open Journal of Nephrology 2012年第4期2卷 123-135页

作者： Ashwani Kumar Zaffar kawoosa Sajad Hamid Surendar Kumar Bali Mymoona Akhter Shahnawaz Hamid Department of Medicine Government Medical College Chandigarh India Department of Medicine Government Medical College Srinagar India Department of Medicine SKIMS Medical College Srinagar India Government Medical College Jammu India Sher-i-Kashmir Institute of Medical Sciences KashmirIndia SKIMS Medical College Srinagar India

The Present Study was conducted in department of Medicine, Govt. Medical College, jammu, Where a total of 41 patients—29 males and 12 females—fulfilled the inclusion criteria of ADPKD, were gathered during the period of 1 year starting from Nov. 2011 to Oct. 2012. All the patients were subjected to a detailed history, clinical examination and laboratory investigations. X-ray chest (PA view), ECG and ultrasound of abdomen for kidneys, liver and spleen were done. Intravenous pyelogram and CT scan of abdomen was done when a definitive diagnosis of (ADPKD) could not be made on abdominal ultrasound. Echocardiography was done to evaluate cardiac murmurs and associated mitral valve prolapse, based on standard criteria. Male to female patients with ADPKD was 2.42:1. Maximum 17 (41.5%) patients of both gender were seen in 30 - 40 years age group, Family history of ADPKD was present in 18 (43.9%) patients;Hypertension, alone or in combination with renal failure, was present in 65.8% patients;Hypertension alone was present in 19 (46.3%) patients;8 (19.5%) patients with hypertension had renal failure;Low back pain was present in 24 (58.5%) and abdominal pain in 22 (53.7%) patients;15 (36.6%) patients presented with at least one episode of gross haematuria;Headache was experienced by 18 (43.9%) patients. On clinical examination, 24 (58.5%) were found to have palpable kidney and 10 (24.4%) had palpable liver. Spleen was palpable in 1 (2.4%) patient, Murmur of mitral valve prolapse was found in 2 (4.9%) Patients;3 (7.3%) patients having left ventricular hypertrophy;mean Hb was 11.2 g/dL. The liver cysts were found in 24.4% of the patients;Out of 10 (24.4%) patients with hepatic cyst involvement, 1 patient each was found to have evidence of portal hypertension and evidence of hepatic cyst infection. In the present study, hypertension was most common presentation of this disease. So, control of hypertension is very important to prevent progression of this disease. Patients who are d

关键词： autosomal Dominant Polycystic Kidney Disease Ronic Kidney Disease End-Stage Renal Disease