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Improved assay performance of SNP array over conventional karyotyping in analyzing products of conception

Improved assay performance of SNP array over conventional ka...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Lin Shaobin Zhou Yi Luo Yanmin Fang Qun Chen Baojiang Fetal Medicine Center Department of Obstetrics and Gynecology First Affiliated Hospital of Sun Yat-Sen University

Objective Conventional karyotyping has been a routine method to identify chromosome abnormalities in products of conception(POC). However, this manner is being transformed by single nucleotide polymorphism(SNP) array, which has advantages over karyotyping including higher resolution, dispensing with cell culture and so on. This study was to evaluate the advantage of high-resolution SNP array in identifying genetic aberrations in POC. Method 155 POC specimens including 139 from first-trimester miscarriage and 16 from secondtrimester miscarriage were collected consecutively. SNP array was performed on these samples in parallel with G-banded *** SNP array obtained test success rate of 98.1%(152/155) that was higher than that in karyotyping(133/155, 85.8%). It yielded a 63.8%(97/152) abnormality rate, and the frequency of various chromosome abnormalities was agreement with other previous studies. Results between array and karyotyping demonstrated 94.0%(125/133) concordance. SNP array obtained additional aberrations in 3.8%(5/133) cases unidentified by karyotyping, which included 3 cases with whole-genome uniparental disomy(UPD), 1 case with pathogenic copy number variation(CNV) and 1 case with del(4)(q35.1 q35.2) and dup(12)(q24.31 q24.33). However, chromosome translocations presented in 2 cases and tetraploidy presented in 1 case were detected by karyotyping instead of array. Additionally, 2 out of 3 cases with mosaic trisomy were revealed by array but recognized as pure trisomy by karyotyping. Conclusion This study demonstrated that SNP array had certain advantages over G-banded karyotyping, including higher success rate, additional detection of CNVs and UPD, and improved sensitivity to mosaicism, so it would be an alternative method to karyotyping in clinical genetic practice.

关键词： SNP Improved assay performance of SNP array over conventional karyotyping in analyzing products of conception

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Novel promoter polymorphisms in HTR2A gene are associated with schizophrenia in Chinese

Novel promoter polymorphisms in HTR2A gene are associated wi...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： sun qianqian Huang Xiaoye Niu Weibo Yu Tao Chen Shiqing Li Xingwang Wu Xi Shi Lei Cao Yanfei Zhang Rui Bi Yan Xu Fei Yang Fengping Wang Lu Li Weidong Xu Yifeng He Lin He Guang Bio-X Institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education) Shanghai Jiao Tong University Institute for Nutritional Sciences Shanghai Institutes of Biological Sciences Chinese Academy of Sciences Shanghai Key Laboratory of Psychotic Disorders Shanghai Institute of Mental Health Institutes of Biomedical Sciences Fudan University

Objective Schizophrenia is a common psychiatric disorder involved with various genetic and envi ronmental risk factors. Previous studies suggested HTR2 A gene(5-hydroxytryptamine/serotonin receptor2 A) and its nearby polymorphisms were associated with schizophrenic phenotypes and a ntipsychotic efficacies. Method The current study reexamined the association between HTR2 A gene and schizophrenia i n the Han Chinese population according to analyzing its seven intronic or promoter polymorphism s(rs7322347, rs1923882, rs643627, rs6311, rs1328685, rs731245, rs732821). Genotyping was routinely performed for these polymorphisms in 893 sporadic schizophrenics and 611 ethnically m atched controls. Result Three novel promoter polymorphisms were nominally associated with schizophrenia in all ele frequencies(rs1328685:P=0.0415;rs731245: P=0.0497;rs732821: P=0.0382) or genotype fr equencies(rs1328685: P=0.0221). We also found the existence of a strong LD(linkage disequilibrium) block among four consecutive polymorphisms(rs6311, rs1328685, rs731245, rs732821), but no obvious haplotype associated with schizophrenia. Conclusion We found three novel promoter polymorphisms were nominally associated with schiz ophrenia in Chinese Han population.

关键词： HTR Novel promoter polymorphisms in HTR2A gene are associated with schizophrenia in Chinese

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A novel compound heterozygous variants in the LHCGR gene identified in a leydig cell hypoplasia type 1 pedigree

A novel compound heterozygous variants in the LHCGR gene ide...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Xu Yufei Chen Yulin Hu Xuyun Li Guoqing Wang xiumin Shen Yiping Wang Jian Department of Medical Genetics and Molecular Diagnostic Laboratory Shanghai Children's Medical CenterShanghai Jiao Tong University School of Medicine Department of Laboratory Medicine Boston Children's Hospital

Objective Leydig cell hypoplasia（LCH） is a rare disease and one of the causes of male disorder of sexual differentiation（DSD） in severe cases. Mutations in the LH/chorionic gonadotrophin receptor（LHCGR） gene leading to dysfunction of the receptor account for the underlying pathogenicity. Two subtypes have been classified based on clinical severity. This study aimed to analyze the clinical presentation and diagnosis as well as molecular characteristics of a patient with LCH type 1. Method Clinical data including medical history, hormone profiles, imaging examination, etc. were collected and analyzed from the patient. The pedigree was performed by the next generation sequencing（NGS） technology using peripheral blood genomic DNA, and the relevant mutations identified by NGS were verified with Sanger sequencing. Result We describe a 5-year-old social gender female patient presented with male pseudohermaphroditism, lateral inguinal hernia companied by abnormal hormone tests. The molecular test revealed a novel compound heterozygous variants in the LHCGR gene, including a splice site mutation（c.681-1 G>A） and a frameshift variant（c.1582585 del ATAT, ***528*）, which could be categorized into "pathogenic" according to the criteria recommended by the American College of Medical Genetics and Genomics（ACMG）. Conclusion We identified a novel compound heterozygous variants in the LHCGR gene in a LCH patient, and expanded the genotype-phenotype correlation spectrum of LHCGR variants. Further researches on the receptor function will contribute to better understand and clarify the relationship between the structure and action of LHCGR.

关键词： LHCGR A novel compound heterozygous variants in the LHCGR gene identified in a leydig cell hypoplasia type 1 pedigree

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Genetic Diagnosis in a Big Chinese Family with Polycystic Kidney Disease and Thalassemia Minor

Genetic Diagnosis in a Big Chinese Family with Polycystic Ki...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Xiong Jun Miao Yun Chen Jianfan Xu Huiling Huang Huajie Xu Xiangmin Xiong Fu Department of Medical Genetics Southern Medical University Department of Organ Transplantation Nanfang Hospital

Objective To identify genetic defects in a large family with polycystic kidney disease and thalasse mia minor. Method Whole genome next-generation sequencing was performed on the proband and clinical e valuation was taken in the whole family. Then Sanger sequencing was used to identify the mutati ons discovered by NGS in family. The pathogenic potential of the variants were evaluated by Poly Phen-2, SIFT algorithm and Mutation taster. In vivo kidney assays of immunohistochemistry, west ern blot, immunofluorescence and TUNEL were performed to investigate the differences of PC1 e xpression, proliferation and apoptosis between the proband and normal control. Result Five members were found having the PKD and six members took thalassemia minor. The proband also had sistus inversus totalis besides PKD and thalassemia minor. A novel PKD1 trunc ation mutation(c.3903 del C, p.A1302 Pfs) was found co-segregated with the renal disease in famil y. And a big α-thalassemia deletion(*** deletion, SEA deletion) connected to the thalasse mia minor was confirmed. In vivo kidney assays showed a higher PC1 level in the dilated renal tu bule and increased proliferation and apoptosis. Besides, four members harbored the COL4 A5 p.G935 V(rs78972735), which was annotated as pathogenic in db SNP and HGMD, while they have no clinical symptom of Alport syndromes. Conclusion A novel pathogenic PKD1 mutation(c.3903 del C) and a thalassemia SEA deletion w as found responsible for the clinical symptoms of the family. And the COL4 a5 variant(c.G2858 T, rs78972735) is not pathogenic alone.

关键词： Genetic Diagnosis in a Big Chinese Family with Polycystic Kidney Disease and Thalassemia Minor

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Epigenetic Memory Affects Hematopoietic Efficiency of i PSCs Derived from PBMCs and KRAS Enhanced the Differentiation to CD34+ Cell

Epigenetic Memory Affects Hematopoietic Efficiency of i PSCs...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Fan Di Niu Xiaohua Song Bing Sun Xiaofang The Third Affiliated Hospital of Guangzhou Medical University

Objective Several studies have discussed the possibility that donor cell type may influence the e pigenetics and differentiation potential of i PSCs, but it remains unclear whether i PSCs derived fro m different tissue sources reserve their epigenetic memory. Method we clarify that i PSCs obtained from different tissues exhibit specific epigenetic patterns. We determined the DNA methylation profiles of 18 human cell lines, including h ESC lines, adult fi broblast cell-derived i PSC lines, peripheral blood-derived mononuclear cell-derived i PSC lines, a mniotic cell-derived i PSC lines and their corresponding parent cell lines. Result We found that the catalog of tissue-specific DNA methylation was preserved in the i PSC li ne as epigenetic memory during reprogramming. In addition, we observed that epigenetic memor y influences the in vitro differentiation potential and that among the i PSCs derived from three type s of somatic cell, the i PSCs from PBMCs showed high efficiency of hematopoietic differentiation. Furthermore, we found that tissue-specific expression of KRAS in both PBMCs and i PSCs derive d from PBMCs. Bisulfite sequencing proved a tissue specific DNA methylation exiting in the gene body of KRAS. Conclusion Our results demonstrated that tissue memory was passed from somatic cells to i PS cells via preservation of Cp G methylation;KRAS carried a specific memory of PBMCs in its gene body, which benefits the hematopoietic efficiency of PBMC-derived i PSCs. Our finding suggested that the tissue memory of PBMCs may offer a new avenue for therapeutic interventions against h ematologic diseases based on the i PSC technique.

关键词： Epigenetic Memory Affects Hematopoietic Efficiency of i PSCs Derived from PBMCs and KRAS Enhanced the Differentiation to CD34 PBMCs

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Concurrent Genetic Diagnosis of Beta Thalassemia Mutation and Aneuploidy Screening at Single-Cell Level

Concurrent Genetic Diagnosis of Beta Thalassemia Mutation an...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Liu Wei Qiang Liu Jian Qiao He Wen Yin Du Hong Zi Zhang Hui Min Hu Dan Sun Xiao Fang Third affiliated hospital of guangzhou medical university

Objective The purpose of this study is to evaluate the WGA efficiency at HBB gene region between two most popular WGA method, MALBAC and MDA. Thus to chose the best WGA method for pre-implantation genetic diagnosis of β-thalassemia disorders. Method For WGA efficiency evaluation, 11 samples each contained single-fibroblast cell, 11 samples contained two-fibroblast cells and 11 samples contained five--fibroblast cells were prepared for subsequent genetic analysis. For comparison, each 8 of cell types were used to evaluate the efficiency of MDA method. 48 single-blastomeres derived from discarded embryos, which were donated from IVF Center, were also amplified using MALBAC and MDA. Highthroughput sequencing with low depth was performed to evaluation the HBB detection rate, allele dropout rates and chromosomal copy number variation status between these two methods. Result The success rate of chromosmal copy number variation detection in fibroblasts samples was 100% in MALBAC group and 91.67% in MDA group;However, the successful WGA rate in single-blastomere samples was 87.50% when using MALBAC method group while it was 79.17% in MDA method group. The ADO of two HBB allele rate was 4.55%(3/66) in MALBAC group and it increased to 22.5%(9/40) when in MDA group. ADO rate of 60 SNP sites whic was close to the HBB gene was 2.98% in MALBAC and 5.19% in MDA group. Conclusion MALBAC has a higher level of uniformity, specificity and lower ADO ratio in PGD for β-thalassemia at single cell level than that of MDA;Combined with haplotype analysis with SNP markers, MALBAC is superior to MDA in PGD of β-thalassemia disease.

关键词： WGA SNP Concurrent Genetic Diagnosis of Beta Thalassemia Mutation and Aneuploidy Screening at Single-Cell Level

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A novel OCRL mutation causes Lowe syndrome in a Chinese family with two brothers

A novel OCRL mutation causes Lowe syndrome in a Chinese fami...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Zhang Xuelian Li Zhong Xu Huilin Huang Huajie Ma Di Chen Danna Chen Jianfan Xu Xiangmin Xiong Fu Department of Medical Genetics School of Basic Medical Sciences South Medical University Department of Neurology The Sixth Affiliated Hospital Sun Yat-sen University

Objective Lowe syndrome(oculo-cerebro-renal syndrome) is a rare X-linked recessive hereditary disease seen in approximately 1/200 000-1/500 000 births. In this study, we investigated the OC RL gene mutation in a Chinese Han family with Lowe syndrome and study the pathogenesis of th e mutation with OCRL gene. Method B ultrasound was used for clinical diagnosis. Peripheral venous blood was taken from th e family members. Polymerase chain reaction(PCR) was used for amplifying the OCRL gene and then analyzed with Sanger sequencing. The novel mutation of the pathogenesis was analyzed by bioinformatics, real-time PCR, subcellular localization and Western blot. Result Proband and his brother were diagnosed with Lowe syndrome. The Sanger sequencing s howed a novel mutation, c.1383 del A, a deletion mutation, in exon 14 of the OCRL gene. Their parents had no obvious clinical symptoms, only the mother carried the mutation site. The frameshift mutation generated a truncated protein that was expressed in transfected Human embryonic kidn ey(HEK) 293 T cells. Subcellular localization experiments showed that GFP-tagged of wild-type a nd mutant OCRL protein were located in the cytoplasm of HEK-293 T cells. Western blot analyze d that the protein expression of Co-transfection in HEK293 T cells with mutant expression plasmid s was significantly lower than wild type protein. Conclusion Our study suggests that the novel frameshift mutation(c.1383 del A) of OCRL gene le ads to a truncated protein and involves in Lowe syndrome pathogenesis with haploinsufficiency. T hese findings expand the mutation spectrum of OCRL gene, and provide theoretical basis for the treatment and genetic counseling of the Lowe syndrome family.

关键词： A novel OCRL mutation causes Lowe syndrome in a Chinese family with two brothers

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The Correlation between G6PD Deficiency and Malaria Infection Rates: Meta-analysis Study

The Correlation between G6PD Deficiency and Malaria Infectio...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Chen Xiao dan Zhang Zhi qiang Jiang Wei ying Liu Li Guangzhou women and children's medical center Department of Medical Genetics Zhongshan Medical College Sun Yat-Sen University

Objective The aim of the present study was to perform a meta-analysis to investigate whether G6 PD-deficiency decreases the risk of malaria infection. Method Keywords "glucose 6-phosphate-dehydrogenase or G6 PD, Plasmodium or Malaria, Infec tion Rates" were searched in different databases(Pub Med, Web of Science). Moreover, referenc e list of the published studies were examined to increase sensitivity and to select more studies. Af ter studying titles and abstracts of retrieved articles, excluding the repeated and unrelated ones, e valuating quality of articles were selected. Data was analyzed using Stata12.1 software. Result After performing systematic review, 9 papers were entered this meta-analysis and 3758 s ubjects were examined concerning the correlation between G6 PD deficiency and malaria infectio n. After performing a subgroup analysis, 7 papers were finally made fix effect model(I2=15.5%, C ochran‘s Q-tests: P=0.311>0.05) to compare the risk of malaria infection between G6 PD deficient patients and G6 PD-normal controls. The results were statistically significant.(RR=0.734, 95% CI: 0.638–0.845, P=0.001<0.05).Conclusion This meta-analysis showed that G6 PD-deficiency can decrease the risk of malaria in fection. The result suggests that we should pay more attention to the difference of resistance abili ty of malaria disease in G6 PD deficiency population in various regions, especially the order of sev erity in G6 PD deficiency in different regions.

关键词： Meta-analysis Study The Correlation between G6PD Deficiency and Malaria Infection Rates

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Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders

Skeleton Genetics: a comprehensive database for genes and mu...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Chen Chong Xu Chenyang Xiang Yanbao Li Huanzheng Xu Xueqin Tang Shaohua Department of Genetics of Dingli Clinical Medical School Key Laboratory of Birth Defects of Wenzhou Wen zhou Central Hospital School of Laboratory Medicine and Life Science Wenzhou Medical University

Objective Genetic skeletal disorders(GSD) involving the skeletal system arise through disturban ces in the complex processes of skeletal development, growth and homeostasis and remain a dia gnostic challenge because of their clinical heterogeneity and genetic variety. Over the past decad es, tremendous effort platforms have been made to explore the complex heterogeneity, and mass ive new genes and mutations have been identified in different GSD, but the information supplied by literature is still limited and it is hard to meet the further needs of scientists and clinicians. Method Based on the standards of NCGSD-2015, we performed comprehensive searches for GS D-related publications and databases to obtain a complete list of mutation information associated with GSD and using Human Phenotype Ontology and OMIM to describe phenotypic information. Result We developed the first comprehensive and annotated genetic skeletal disorders database, named ?Skeleton Genetics‘, which contains information about all GSD-related knowledge includin g 8225 mutations in 357 genes, with detailed information associated with 481 clinical diseases(2260 clinical phenotype) classified in 42 groups defined by molecular, biochemical and/or radiogra phic criteria from 1698 publications. Further annotations were performed to each entry including Gene Ontology, pathways analysis, protein-protein interaction, mutation annotations, disease-disease clustering and gene-disease networking. Furthermore, by using concise search methods, int uitive graphical displays, convenient browsing functions and constantly updatable features, Conclusion Skeleton Genetics could serve as a central and integrative database for unveiling the genetic and pathways predispositions of GSD. Database URL: http://101.200.211.232/skeletong enetics/

关键词： GSD Ontology Skeleton Genetics a comprehensive database for genes and mutations related to genetic skeletal disorders

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Fructose 1,6-bisphosphatase deficiency diagnosed by the targeted-next generation sequencing

Fructose 1,6-bisphosphatase deficiency diagnosed by the targ...

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中华医学会第十五次全国医学遗传学学术会议暨中国医师协会医学遗传医师分会第一届全国学术会议暨2016年浙江省医学遗传学年会

作者： Li Niu Chang Guoying Xu Yufei Li Juan Yu Tingting Qin Yanrong Wang Xiumin Wang Jian Shanghai Children's Medical Center Shanghai Jiaotong University School of Medicine

Objective Fructose-1,6-bisphosphatase（FBPase） deficiency is a rare, autosomal recessive inherited disease caused by the mutation of FBP1 gene and may cause sudden unexpected infant death because of severe hypoglycemia. The symptoms（hypoglycemia, ketosis, acidosis, hyperlactacidemia, and convulsion） of affected individuals are easily confused with several other endocrine genopathies, including hereditary fructose intolerance and phosphoglucomutase *** aimed to perform genetic sequencing to screen disease-causing genes of the four patients and try to give the molecular diagnostic results. Method In the present study, we described the clinical features of four Chinese pediatric patients who were strongly suspected to have inherited metabolic diseases. Targrted-next generation sequencing was used to screen for causal variants in the genome, and the clinically relevant variants were subsequently verified using Sanger sequencing. Result 3 frameshift（c.704 del C, c.72029 del, and c.960 dup G）, 2 missense（D119 N and G164 S） and one splicing（c.825+1 G>A） of FBP1 gene were identified in our four patients, of them, two mutations（c.704 del C, and c.72029 del） were novel. Further in vitro studies in COS-7 cell line demonstrated that the mutation of D119 N had no impact on the protein expression but decreased the enzyme activity, and with which the clinical significance of D119 N can be determined to be likely pathogenic. Conclusion In conclusion, based on the DNA sequencing and functional studies, all of our four patients were finally diagnosed with FBPase deficiency, this report expends the variation spectrum of FBP1 gene.

关键词： Fructose 1,6-bisphosphatase deficiency diagnosed by the targeted-next generation sequencing FBP

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