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2+0 CYP21A2 deletion carrier—a limitation of the genetic testing and counseling:A case report

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World Journal of Clinical Cases 2021年第23期9卷 6789-6797页

作者： Na Xi Xiao Song Xue-Yan Wang Sheng-Fang Qin Guan-Nan He Ling-Ling Sun Xi-Min Chen Department of Medical genetics and Prenatal Diagnosis Sichuan Provincial Hospital for Women and ChildrenChengdu 610045Sichuan ProvinceChina Department of Ultrasound Sichuan Provincial Hospital for Women and ChildrenChengdu 610045Sichuan ProvinceChina

BACKGROUND CYP21A2 gene mutations may all cause reduction or loss of 21-hydroxylase activity,leading to development of congenital adrenal hyperplasia(CAH)with different clinical *** families with CAH children,genetic testing of the parents and genetic counseling are recommended to assess the risk of *** SUMMARY We report a case of CAH with a high suspicion before *** risk of the child suffering from CAH during the pregnancy had been underestimated due to the deviation of genetic counseling and genetic testing *** report confirmed a CYP21A2 homozygous deletion in this case,CYP21A2 heterozygous deletion in the mother,and a rare 2+0 CYP21A2 deletion in the *** It is important to analyze the distribution of CYP21A2 gene in the two alleles of parents of children with CAH.

关键词： CYP21A2 gene mutations Congenital adrenal hyperplasia Pregnancy genetic counseling genetic testing Pathogenic point mutations Alleles

Role of genetic testing in cardiomyopathies:Αprimer for cardiologists

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维普期刊数据库

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World Journal of Cardiology 2022年第1期14卷 29-39页

作者： Georgia Vogiatzi George Lazaros Evangelos Oikonomou Emilia Lazarou Emmanouil Vavuranakis Dimitris Tousoulis The Third Department of Cardiology Sotiria HospitalAthens 11527Greece The First Department of Cardiology Hippokration HospitalAthens 11526Greece The First Department of Cardiology Hippokration HospitalMedical School of National and Kapodistrian University of AthensAthens 11527Greece

Recent advances in cardiovascular genetics have transformed genetic testing into a valuable part of management of families with inherited *** novel mutations have been identified,understanding when to consider genetic testing has emerged as an important consideration in the management of these *** genetic testing has a paramount importance in the risk stratification of family members,in the prognosis of probands at higher risk of a serious phenotype expression,and finally in the identification of new mutations,all of which are discussed in this *** indications for each type of cardiomyopathy are described,along with the limitations of genetic ***,the importance of public sharing of variants in large data sets is *** ultimate aim of this review is to present key messages about the genetic testing process in order to minimize potential harms and provide suggestions to specialized clinicians who act as a part of a multidisciplinary team in order to offer the best care to families with inherited cardiomyopathies.

关键词： Cardiomyopathy genetic counselling genetic testing Variant Hereditary

Implications of genetic testing and informed consent before and after genetic testing in individuals with cancer

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维普期刊数据库

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World Journal of Clinical Oncology 2024年第8期15卷 975-981页

作者： Priyanka Kumar David J Benjamin Sourat Darabi Goetz Kloecker Arash Rezazadeh Kalebasty Department of Hematology and Medical Oncology Harbor-UCLA Medical CenterTorranceCA 90502United States Department of Medical Oncology Hoag Family Cancer InstituteNewport BeachCA 92663United States Department of Precision Medicine Hoag Family Cancer InstituteNewport BeachCA 92663United States Department of Hematology and Medical Oncology University of LouisvilleLouisvilleKY 40202United States Department of Hematology and Medical Oncology University of California-IrvineOrangeCA 92868United States

Recent advancements in next generation sequencing have allowed for genetic information become more readily available in the clinical setting for those affected by cancer and by treating *** the lack of access to geneticists,medical oncologists and other treating physicians have begun ordering and interpreting genetic tests for individuals with cancer through the process of"mainstreaming".While this process has allowed for quicker access to genetic tests,the process of"mainstreaming"has also brought several challenges including the dissemination of variants of unknown significance results,ordering of appropriate tests,and accurate interpretation of genetic results with appropriate followup testing and *** this editorial,we seek to explore the process of informed consent of individuals before obtaining genetic testing and offer potential solutions to optimize the informed consent process including categorization of results as well as a layered consent model.

关键词： genetic testing Informed consent genetic counseling Next generation sequencing Mainstreaming Layered consent

Progresses in genetic testing in congenital heart disease

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维普期刊数据库

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医学+（英文） 2024年第2期1卷 64-77页

作者： Han Gao Ying Liu Wei Sheng Weinian Shou Guoying Huang Children's Hospital of Fudan University Shanghai 201102China Shanghai Key Laboratory of Birth Defects Shanghai 201102China Research Unit of Early Intervention of genetically Related Childhood Cardiovascular Diseases Chinese Academy of Medical SciencesShanghai 201102China Herman B Wells Center for Pediatric Research Department of PediatricsIndiana University School of MedicineIndianapolisIN 46202USA

Congenital heart disease(CHD)encompasses a range of structural malformations affecting the heart and major blood vessels present at *** genetic under-pinnings of CHD have long been recognized as pivotal,facilitated by a deeper mo-lecular understanding of *** genetic variants,including single nucleotide variations,structural variations,and chromosomal abnormalities,have been identified in association with both syndromic and non-syndromic *** ge-netic technologies evolve and improve,the application of genetic testing in CHD patients promises to yield valuable insights for both clinical practice and basic *** the advancement of cohort studies,genomic data on these variations can be robustly collected and classified according to their pathogenicity,thereby en-hancing our understanding of CHD *** tools have been developed to interpret variants identified in both coding and non-coding regions through genetic testing,providing substantial reference points for clinical decision-making in CHD *** integration of genetic testing stands to benefit CHD management across various fronts,including diagnosis,prognosis prediction,and recurrence risk estimation.A thorough understanding of the genetic investigations and clinical practices related to CHD genetics is essential for the advanced application of genetic testing in CHD *** leveraging this knowledge,healthcare professionals can effectively incorporate genetic testing into the broader framework of CHD care,ul-timately improving patient outcomes and advancing our understanding of these complex conditions.

关键词： Congenital heart disease genetic testing genetics Clinical practice

JAX-CNV:A Whole-genome Sequencing-based Algorithm for Copy Number Detection at Clinical Grade Level

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1197-1206页

作者： Wan-Ping Lee Qihui Zhu Xiaofei Yang Silvia Liu Eliza Cerveira Mallory Ryan Adam Mil-Homens Lauren Bellfy Kai Ye Charles Lee Chengsheng Zhang Precision Medicine Center The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061China The Jackson Laboratory for Genomic Medicine FarmingtonCT 06032USA School of Cyber Science and Engineering Xi’an Jiaotong UniversityXi’an 710049China Department of Pathology and Laboratory Medicine Perelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPA 19104USA School of Computer Science and Technology Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China MOE Key Lab for Intelligent Networks&Networks Security Faculty of Electronic and Information EngineeringXi’an Jiaotong UniversityXi’an 710049China Department of Life Sciences Ewha Womans UniversitySeoul 03760South Korea

We aimed to develop a whole-genome sequencing(WGS)-based copy number variant(CNV)calling algorithm with the potential of replacing chromosomal microarray assay(CMA)for clinical ***-CNV is thus developed for CNV detection from WGS *** performance of this CNV calling algorithm was evaluated in a blinded manner on 31 samples and compared to the 112 CNVs reported by clinically validated CMAs for these 31 *** result showed that JAX-CNV recalled 100%of these ***,JAX-CNV identified an average of 30 CNVs per individual,representing an approximately seven-fold increase compared to calls of clinically validated *** validation of 24 randomly selected CNVs showed one false positive,i.e.,a false discovery rate(FDR)of 4.17%.A robustness test on lowercoverage data revealed a 100%sensitivity for CNVs larger than 300 kb(the current threshold for College of American Pathologists)down to 10×*** CNVs larger than 50 kb,sensitivities were 100%for coverages deeper than 20×,97%for 15×,and 95%for 10×.We developed a WGS-based CNV pipeline,including this newly developed CNV caller JAX-CNV,and found it capable of detecting CMA-reported CNVs at a sensitivity of 100%with about a FDR of 4%.We propose that JAX-CNV could be further examined in a multi-institutional study to justify the transition of first-tier genetic testing from CMAs to ***-CNV is available at https://***/TheJacksonLaboratory/JAX-CNV.

关键词： Copy number variant Chromosomal microarray assay Whole-genome sequencing JAX-CNV genetic testing

genetic association of urokinase-type plasminogen activator gene rs2227564 site polymorphism with sporadic Alzheimer's disease in the Han Chinese population

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Neural Regeneration Research 2012年第30期7卷 2377-2383页

作者： Xuelian Ji Longfei Jia Jianping Jia Li Qi Department of Neurology Inner Mongolia People's Hospital Huhhot 010017 Inner Mongolia Autonomous Region China Department of Neurology Xuanwu Hospital Capital Medical University Beijing 100053 China Inner Mongolia Corps Hospital Chinese People's Armed Police Forces Huhhot 010040 Inner Mongolia Autonomous Region China

A missense C/T polymorphism in exon 6 （the NCBI rslD is rs2227564） of the urokinase-type plasminogen activator gene has been identified as a possible hot spot for Alzheimer＇s disease risk. The present study analyzed urokinase-type plasminogen gene polymorphisms of rs2227564 with sporadic Alzheimer＇s disease by PCR-restriction fragment length polymorphism. Results showed that CC, CT and TT genotype distribution frequencies had significant differences between sporadic Aizheimer＇s disease patients and healthy controls, in-depth analysis of the association between urokinase-type plasminogen gene rs2227564 polymorphisms and sporadic Alzheimer＇s disease indicated that people with the C-positive genotype CC ＋ CT were at a higher risk for developing sporadic Alzheimer＇s disease. These results support the contribution of the polymorphisms of rs2227564 in the urokinase-type plasminogen gene to the pathogenesis of sporadicAIzheimer＇s disease in the Han Chinese population.

关键词： Alzheimer's disease urokinase plasminogen activator polymorphism genetic testing Han Chinesepopulation neural regeneration

genetic variation and selection of introduced provenances of Siberian Pine(Pinus sibirica) in frigid regions of the Greater Xing'an Range,Northeast China

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Journal of Forestry Research 2014年第3期25卷 549-556页

作者： Xiyang Zhao Cheng Wang Shuchun Li Wei Hou Shiqing Zhang Guijie Han Deng Pan Ping Wang Yufei Cheng Guifeng Liu State Key Laboratory of Tree genetics and Breeding (Northeast Forestry University) Northeast Forestry University Tree Seedling Management Station Forestry Department of Jilin Province Department of Preventive Medicine Stony Brook University Forestry Bureau of Xinlin Agricultural Bureau of Taobei District

Siberian Pine （Pinus sibirica） is an ecologically and eco-nomically important species in pristine forests throughout northern Rus-sia. Four provenances of P. sibirica were introduced from Mongolia and Russia to the Greater Xing’an Range （the Daxing’anling）, northeast China in 1993. The aim of this research was to study genetic variation and selection of the introduced four Pinus sibirica provenances. Heights （H）, basal diameters （BD）, survival rates （SR） and crown lengths （CL） of different families were measured as primary outcomes in different growth years. Results of data analyses demonstrated high coefficients of phenotypic variation （PCV） and heritability （H2） for H, BD and CL at 18 years after introduction. PCV and H2 increased with age. Correlations of＆amp;nbsp;growth traits between any two growth years were all significantly positive, but the correlation coefficient was smaller when the growth year interval was larger. Correlations between H and the original environment factors decreased gradually, indicating that with long-term subsistence in the new environment, the influence of the source environment declined. Colligation of multiple traits to estimate provenances showed that Novosibirsk, Tomsk, and Altai Mountains had higher survival rates and biomass, and proved more suitable for introduction and plantation in the Greater Xing’an Range in China.

关键词： Pinus sibirica provenance genetic testing variation selection

PICOTEES:a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants from Chinese children cohorts

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Journal of genetics and Genomics 2024年第2期51卷 243-251页

作者： Xinran Dong Yulan Lu Lanting Guo Chuan Li Qi Ni Bingbing Wu Huijun Wang Lin Yang Songyang Wu Qi Sun Hao Zheng Wenhao Zhou Shuang Wang Center for Molecular Medicine Children's Hospital of Fudan UniversityShanghai 201102China Key Laboratory of Birth Defects Children's Hospital of Fudan UniversityShanghai 201102China Department of Bioinformatics Hangzhou Nuowei Information Technology Co.LtdHangzhouZhejiang 310000China The Third Research Institute of the Ministry of Public Security Shanghai 200031China Xiamen Campus of Children's Hospital of Fudan University XiamenFujian 361006China Institutes for Systems genetics West China HospitalChengduSichuan 610041China Shanghai Putuo People's Hospital Tongji UniversityShanghai 200060China

The growth in biomedical data resources has raised potential privacy concerns and risks of genetic information leakage. For instance, exome sequencing aids clinical decisions by comparing data through web services, but it requires significant trust between users and providers. To alleviate privacy concerns, the most commonly used strategy is to anonymize sensitive data. Unfortunately, studies have shown that anonymization is insufficient to protect against reidentification attacks. Recently, privacy-preserving technologies have been applied to preserve application utility while protecting the privacy of biomedical data. We present the PICOTEES framework, a privacy-preserving online service of phenotype exploration for genetic-diagnostic variants (https://***:3000/). PICOTEES enables privacy-preserving queries of the phenotype spectrum for a single variant by utilizing trusted execution environment technology, which can protect the privacy of the user's query information, backend models, and data, as well as the final results. We demonstrate the utility and performance of PICOTEES by exploring a bioinformatics dataset. The dataset is from a cohort containing 20,909 genetic testing patients with 3,152,508 variants from the Children's Hospital of Fudan University in China, dominated by the Chinese Han population (>99.9%). Our query results yield a large number of unreported diagnostic variants and previously reported pathogenicity.

关键词： Privacy protecti on Rare diseases in children genetic testing Web system Trusted executi on envir onment

Molecularly defined adult-type hypolactasia in school-aged children with a previous history of cow's milk allergy

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World Journal of Gastroenterology 2006年第14期12卷 2264-2268页

作者： Heli Rasinper Kristiina Saarinen Anna Pelkonen Irma Jrvel Erkki Savilahti Kaija-Leena Kolho Department of Medical genetics University of Helsinki Finland Hospital for Children and Adolescents University of Helsinki Finland Department of Allergology Skin and Allergy Hospital Helsinki University Central HospitalHelsinkiFinland Department of Medical genetics University of Helsinki Finland Laboratory of Molecular GeneticsHelsinki University HospitalHelsinkiFinland

AIM： To assess the role of lactase non-persistence/per- sistence in school-aged children and their milk-related symptoms. METHODS： The genotypes for the C/T-13910 variant associated with lactase non-persistence/ persistence were determined using PCR-minisequencing in a group of 172 children with a mean age of 8.6 years （SE = 0.02, 93 boys） participating in a follow-up study for cow＇s milk allergy. The parents were asked to assess their children＇s milk consumption and abdominal symptoms. RESULTS： The presence of allergy to cow＇s milk was not associated with the C/C-13910 genotype related with a decline of lactase enzyme activity during childhood （lactase non-persistence）. The frequency of the C/C-13910 genotype （16%） was similar to published figures for the prevalence of adult-type hypolactasia in Finland. The majority of the children （90%） in this series consumed milk but 26% of their families suspected that their children had milk-related symptoms. Forty-eight percent of the children with the C/C-13910 genotype did not drink milk at all or consumed a low lactose containing diet prior to the genotyping （P〈 0.004 when compared to the other genotypes）. CONCLUSION： Analysis of the C/T-13910 polymorphism is an easy and reliable method for excluding adult-type hypolactasia in children with milk-related symptoms. Genotyping for this variant can be used to advise diets for children with a previous history of cow＇s milk allergy.

关键词： Adult-type hypolactasia Primary lactose malabsorption genetic testing Cow's milk allergy