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The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes

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BRITISH JOURNAL OF HAEMATOLOGY 2016年第2期174卷 292-301页

作者： Olsson, Linda Zettermark, Sofia Biloglav, Andrea Castor, Anders Behrendtz, Mikael Forestier, Erik Paulsson, Kajsa Johansson, Bertil Lund Univ Div Clin Genet Dept Lab Med Lund Sweden Dept Clin Genet Div Lab Med Off Med Serv Lund Sweden Skane Univ Hosp Dept Paediat Lund Sweden Linkoping Univ Hosp Dept Paediat Linkoping Sweden Umea Univ Dept Med Biosci Umea Sweden

Cytogenetic analyses of a consecutive series of 67 paediatric (median age 8 years;range 0-17) de novo acute myeloid leukaemia (AML) patients revealed aberrations in 55 (82%) cases. The most common subgroups were KMT2A rearrangement (29%), normal karyotype (15%), RUNX1-RUNX1T1 (10%), deletions of 5q, 7q and/or 17p (9%), myeloid leukaemia associated with Down syndrome (7%), PML-RARA (7%) and CBFBMYH11 (5%). single nucleotide polymorphism array (SNP-A) analysis and exon sequencing of 100 genes, performed in 52 and 40 cases, respectively (39 overlapping), revealed >= 1 aberration in 89%;when adding cytogenetic data, this frequency increased to 98%. Uniparental isodisomies (UPIDs) were detected in 13% and copy number aberrations (CNAs) in 63% (median 2/case);three UPIDs and 22 CNAs were recurrent. Twenty-two genes were targeted by focal CNAs, including AEBP2 and PHF6 deletions and genes involved in AML-associated gene fusions. Deep sequencing identified mutations in 65% of cases (median 1/case). In total, 60 mutations were found in 30 genes, primarily those encoding signalling proteins (47%), transcription factors (25%), or epigenetic modifiers (13%). Twelve genes (BCOR, CEBPA, FLT3, GATA1, KIT, KRAS, NOTCH1, NPM1, NRAS, PTPN11, SMC3 and TP53) were recurrently mutated. We conclude that SNP-A and deep sequencing analyses complement the cytogenetic diagnosis of paediatric AML.

关键词： paediatric acute myeloid leukaemia single nucleotide polymorphism array targeted deep exon sequencing

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Concurrent exome-targeted next-generation sequencing and single nucleotide polymorphism array to identify the causative genetic aberrations of isolated Mayer-Rokitansky-Kuster-Hauser syndrome

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HUMAN REPRODUCTION 2015年第7期30卷 1732-1742页

作者： Chen, Mei-Jou Wei, Shin-Yi Yang, Wei-Shiung Wu, Tsai-Tzu Li, Huei-Ying Ho, Hong-Nerng Yang, Yu-Shih Chen, Pei-Lung Natl Taiwan Univ Hosp Dept Obstet & Gynecol Taipei 100 Taiwan Natl Taiwan Univ Hosp Dept Internal Med Taipei 100 Taiwan Natl Taiwan Univ Grad Inst Clin Med Coll Med Taipei 100 Taiwan Natl Taiwan Univ Res Ctr Dev Biol & Regenerat Med Taipei 100 Taiwan Natl Taiwan Univ Grad Inst Mol Med Coll Med Taipei 100 Taiwan Natl Taiwan Univ Hosp Dept Med Genet Taipei 100 Taiwan Natl Taiwan Univ Coll Med Grad Inst Med Genom & Prote Taipei 100 Taiwan

STUDY QUESTION: Can the use of whole-exome sequencing (WES) together with single nucleotide polymorphism (SNP) array help to identify novel causative genes of isolated Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome? SUMMARY ANSWER: OR4M2 (olfactory receptor, family 4, subfamily M, member 2) and PDE11A (phosphodiesterase 11A) gene loss-of-function variants as well as deletions at 15q11.2, 19q13.31, 1p36.21, and 1q44 were identified as possible commonly altered regions in patients with type 1 MRKH. WHAT IS KNOWN ALREADY: The isolated form of Mullerian aplasia is the most common subtype of MRKH syndrome, which invariably leads to difficulties producing offspring in affected women. However, there is little information currently available to allow for genetic testing and counseling to be performed for those affected by this syndrome. STUDY DESIGN, SIZE AND DURATION: This was a case-series genetic study. A total of seven consecutive unrelated women with type 1 MRKH were enrolled. The enrollment and experimental procedures were performed over a 2-year period. PARTICIPANTS/MATERIALS, SETTING, METHODS: Whole exome-targeted next-generation sequencing and SNP array (Affymetrix Genome-Wide Human SNP array 6.0) were performed on the first five unrelated women with type 1 MRKH syndrome. The data were combined, and the '3-hit principal' was applied on a genome-wide scale to search for the common causative genes. Quantitative PCR (qPCR) and Sanger sequencing were used to validate the identified genomic copy number losses and variants. Replication tests using direct Sanger sequencing and qPCR were performed on the remaining two women with type 1 MRKH syndrome to support the credibility of the potential candidate genes and deletions. MAIN RESULTS AND THE ROLE OF CHANCE: A total of 3443 damaging variants based on WES were shown to intersect with 1336 copy number variations (deletions) derived from the SNP array. Four highly recurrent deletions at 15q11.2 (80%), 19q13.31 (40%), 1p36.21

关键词： next-generation sequencing whole-exome sequencing single nucleotide polymorphism array Mayer-Rokitansky-Kuster-Hauser syndrome Mullerian aplasia

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Improved assay performance of single nucleotide polymorphism array over conventional karyotyping in analyzing products of conception

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JOURNAL OF THE CHINESE MEDICAL ASSOCIATION 2015年第7期78卷 408-413页

作者： Lin, Shao-Bin Xie, Ying-Jun Chen, Zheng Zhou, Yi Wu, Jian-Zhu Zhang, Zhi-Qiang Shi, Shan-Shan Chen, Bao-Jiang Fang, Qun Sun Yat Sen Univ Fetal Med Ctr Dept Obstet & Gynecol Affiliated Hosp 1 Guangzhou 510080 Guangdong Peoples R China Sun Yat Sen Univ Dept Med Genet Zhongshan Med Coll Guangzhou 510080 Guangdong Peoples R China Jinan Univ Dept Fetal Med Ctr Affiliated Hosp 1 Guangzhou Guangdong Peoples R China

Background: Conventional karyotyping has been a routine method to identify chromosome abnormalities in products of conception. However, this process is being transformed by single nucleotide polymorphism (SNP) array, which has advantages over karyotyping, including higher resolution and dispensing with cell culture. Therefore, the purpose of this study was to evaluate the advantage of high-resolution SNP array in identifying genetic aberrations in products of conception. Methods: We consecutively collected 155 products of conception specimens, including 139 from first-trimester miscarriage and 16 from second-trimester miscarriage. SNP array was performed on these samples in parallel with G-banded karyotyping. Results: The test success rate was 98.1% (152/155) using SNP array, which was higher than that using karyotyping (133/155, 85.8%). It yielded a 63.8% (97/152) abnormality rate, and the frequency of various chromosome abnormalities was in agreement with other previous studies. The results between array and karyotyping demonstrated a 94.0% (125/133) concordance. SNP array obtained additional aberrations in 3.8% (5/133) of those cases unidentified by karyotyping, which included three cases with whole-genome uniparental disomy, one with pathogenic copy number variation, and one with del(4)(q35.1q35.2) and dup(12)(q24.31q24.33). However, chromosome translocations presented in two cases and tetraploidy presented in one case were detected by karyotyping instead of array. Additionally, two out of three 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 a higher success rate, additional detection of copy number variations and uniparental disomy, and improved sensitivity to mosaicism. Therefore, it would be an alternative method to karyotyping in clinical genetic practice. Copyright (C) 2015 Elsevier Taiwan LLC and th

关键词： copy number variation karyotyping products of conception single nucleotide polymorphism array uniparental disomy

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Identification of copy number variations in three Chinese horse breeds using 70K single nucleotide polymorphism BeadChip array

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ANIMAL GENETICS 2016年第5期47卷 560-569页

作者： Kader, Adiljan Liu, Xuexue Dong, Kunzhe Song, Shen Pan, Jianfei Yang, Min Chen, Xiaofei He, Xiaohong Jiang, Lin Ma, Yuehui Chinese Acad Agr Sci Key Lab Farm Anim Genet Resources & Utilizat Minist Agr China Inst Anim Sci 2 Yuanmingyuan West Rd Beijing 100193 Peoples R China Xinjiang Acad Anim Sci Urumqi 83000 Xinjiang Peoples R China ARS USDA Avian Dis & Oncol Lab E Lansing MI 48823 USA China Agr Univ Dept Anim Genet & Breeding Coll Anim Sci & Technol Beijing 100094 Peoples R China

Copy number variation (CNV), an essential form of genetic variation, has been increasingly recognized as one promising genetic marker in the analysis of animal genomes. Here, we used the Equine 70K single nucleotide polymorphism genotyping array for the genome-wide detection of CNVs in 96 horses from three diverse Chinese breeds: Debao pony (DB), Mongolian horse (MG) and Yili horse (YL). A total of 287 CNVs were determined and merged into 122 CNV regions (CNVRs) ranging from 199 bp to 2344 kb in size and distributed in a heterogeneous manner on chromosomes. These CNVRs were integrated with seven existing reports to generate a composite genome-wide dataset of 1558 equine CNVRs, revealing 69 (56.6%) novel CNVRs. The majority (69.7%) of the 122 CNVRs overlapped with 438 genes, whereas 30.3% were located in intergenic regions. Most of these genes were associated with common CNVRs, which were shared by divergent horse breeds. As many as 60, 42 and 91 genes overlapping with the breed-specific ss were identified in DB, MG and YL respectively. Among these genes, FGF11, SPEM1, PPARG, CIDEB, HIVEP1 and GALR may have potential relevance to breed-specific traits. These findings provide valuable information for understanding the equine genome and facilitating association studies of economically important traits with equine CNVRs in the future.

关键词： copy number variation region Debao pony growth single nucleotide polymorphism array

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Whole-Genome single nucleotide polymorphism array Analysis Is Complementary to Classical Cytogenetic Analysis in the Evaluation of Lymphoid Proliferations

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AMERICAN JOURNAL OF CLINICAL PATHOLOGY 2014年第2期141卷 247-255页

作者： Gibson, Sarah E. Luo, Jianhua Sathanoori, Malini Liao, Jun Surti, Urvashi Swerdlow, Steven H. Univ Pittsburgh Sch Med Dept Pathol Pittsburgh PA USA UPMC Magee Womens Hosp Pittsburgh Cytogenet Lab Pittsburgh PA 15213 USA

Objectives: To explore how much additional information single nucleotide polymorphism (SNP) arrays provide and whether they could partially replace classical cytogenetics. Methods: Twenty-six lymphoid proliferations with available cytogenetic studies were analyzed with the Affymetrix Genome-Wide Human SNP array 6.0 (Affymetrix, Santa Clara, CA). Results: Eleven of 26 cases demonstrated complete concordance between cytogenetics and SNP analysis, and 10 of 26 cases demonstrated partial concordance. Five discordant cases had copy number abnormalities (CNAs) with cytogenetics not identified with SNP arrays. While SNP analysis showed CNAs not apparent by cytogenetics in eight cases and helped clarify the karyotype in six cases, cytogenetics demonstrated CNAs not seen by SNP analysis in 15 cases as well as balanced translocations in 12 cases. Conclusions: The combination of cytogenetics and SNP analysis results in a higher overall yield in identifying numerical chromosomal abnormalities than either technique alone.

关键词： single nucleotide polymorphism array SNP Classical cytogenetics Lymphoma Lymphoid proliferations

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Prenatal diagnosis, ultrasound findings and pregnancy outcome of 7q11.23 deletion and duplication syndromes: what are the fetal features?

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BMC PREGNANCY AND CHILDBIRTH 2024年第1期24卷 727页

作者： Luo, Xiaojin Niu, Hongyan Zhou, Fei Chen, Xiaohang Pei, Yuanyuan Liu, Weiqiang Wei, Fengxiang Shantou Univ Longgang Dist Matern & Child Healthcare Hosp Shenz Genet Lab Longgang Matern & Child Inst Med Coll Shenzhen Guangdong Peoples R China

ObjectiveAnalyze the ultrasound findings, single nucleotide polymorphism array (SNP-array) results, and pregnancy outcomes of fetuses with 7q11.23 deletions and duplications in the second and third trimesters. Investigate the prenatal ultrasound characteristics and follow up information of these *** fetuses were diagnosed with 7q11.23 deletion and six with 7q11.23 duplication via SNP-array at the prenatal diagnosis center of a single Chinese tertiary medical center from January 2017 to May 2024. Maternal demographics, ultrasound findings, SNP-array results, pregnancy outcomes, and follow-up information were comprehensively reviewed and *** copy number variations (CNVs) ranged from 1.43 Mb to 1.78 Mb in cases of 7q11.23 deletions and from 1.42 Mb to 1.68 Mb in cases of 7q11.23 duplications. These CNVs encompassed 29 OMIM-listed genes, including ELN, DNAJC30, GTF2IRD1, and GTF2I. Among the seven cases of 7q11.23 deletion syndrome, six exhibited ultrasound abnormalities. The main clinical phenotypes included three cases of intrauterine growth restriction and four cases of cardiovascular system abnormalities, specifically two cases with ventricular septal defects, one case with aortic narrowing, and one case with supravalvular pulmonary stenosis. One case was particularly notable, exhibiting complex multi-organ structural malformations. Out of six cases of 7q11.23 duplication syndrome, five exhibited ultrasound abnormalities. These included two cases of cardiovascular abnormalities: one case with a widened left ventricle and another case with a shortened fetal humerus length. One case revealed complex multi-organ structural malformations, including hydronephrosis, a microgallbladder, and a cleft lip and palate. All seven cases of 7q11.23 deletions and three cases of 7q11.23 duplications opted for termination of the pregnancy. The remaining three cases of 7q11.23 duplications chose to continue the pregnancy. One case underwent surgical tr

关键词： 7q11.23 deletion syndrome 7q11.23 duplication Syndrome single nucleotide polymorphism array Prenatal diagnosis

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Endometriosis does not impact aneuploidy rates of products of conception in IVF population

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SCIENTIFIC REPORTS 2025年第1期15卷 1-9页

作者： Kong, Huijuan Fan, Wenqian Ye, Tian Du, Linqing Zhengzhou Univ Ctr Reprod Med Affiliated Hosp 1 Zhengzhou 450052 Peoples R China Zhengzhou Univ Henan Key Lab Reprod & Genet Affiliated Hosp 1 Zhengzhou 450052 Peoples R China Zhengzhou Univ Clin Res Ctr Henan Prov Obstetr & Gynaecol Dis Reprod Med Affiliated Hosp 1 Zhengzhou 450052 Peoples R China Zhengzhou Univ Affiliated Hosp 1 Henan Engn Lab Preimplantat Genet Diag & Screening Zhengzhou 450052 Peoples R China Zhengzhou Univ Dept Oncol Affiliated Hosp 1 1 Jianshe East Rd Zhengzhou 450000 Peoples R China

It has been debated whether endometriosis (EMS) adversely affects oocyte quality, potentially leading to a higher incidence of genetically unbalanced embryos or other egg factors that affect the developmental potential. In this study, we explored the effects of endometriosis on risk of chromosomally aberrant in miscarried products of conception (POC) after assisted reproductive treatment (ART), including fresh and frozen cycles. Miscarried POCs were collected from EMS patients (N = 102) and non-EMS patients (N = 441). single nucleotide polymorphism (SNP) array analysis was conducted on all collected samples. Propensity score matching (PSM, ratio of 1:4) based on maternal age was applied in data analysis. Logistic regression analysis was performed to identify risk factors for chromosomal aberration-induced miscarriage between the two cohorts. A total of 228 (41.99% of 543) conceptuses were identified as having chromosomal aberrations. The results showed that women with EMS had a significantly lower antral follicle count (AFC) (10 +/- 5 vs. 14 +/- 7, P < 0.01) compared to the control group. Additionally, the EMS group had a relatively lower anti-Mullerian hormone (AMH), higher basal follicle stimulating hormone (FSH) and fewer oocytes, (P > 0.05). There was no significant difference in the chromosomal aberration rate of POCs between EMS and non-EMS groups (35.29% vs. 43.54%;odds ratio (OR) = 1.03, 95% confidence intervals (CIs) 0.79-1.35). This is the first study to show that EMS maybe associated with decreased ovarian reserve, but not related to chromosomal abnormalities in POCs. These results suggest that chromosomal abnormalities may not be the only cause of miscarriage in EMS patients.

关键词： Endometriosis single nucleotide polymorphism array Miscarriage Chromosomal abnormality ART

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Extragonadal germ cell tumors: A clinicopathologic study with emphasis on molecular features, clinical outcomes and associated secondary malignancies

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HUMAN PATHOLOGY 2024年 148卷 41-50页

作者： Abdulfatah, Eman Brown, Noah A. Davenport, Matthew S. Reichert, Zachery R. Camelo-Piragua, Sandra Heider, Amer Huang, Tao Vaishampayan, Ulka N. Skala, Stephanie L. Montgomery, Jeffrey S. Chinnaiyan, Arul M. Kaffenberger, Samuel D. Bawa, Pushpinder Shao, Lina Mehra, Rohit Univ Michigan Dept Pathol 2800 Plymouth RdBldg 35 Ann Arbor MI 48109 USA Univ Michigan Dept Radiol Med Sch Ann Arbor MI USA Michigan Ctr Translat Pathol Ann Arbor MI USA Univ Michigan Dept Urol Med Sch Ann Arbor MI USA Michigan Med Rogel Canc Ctr Ann Arbor MI USA Howard Hughes Med Inst Ann Arbor MI USA Dept Internal Med Div Hematol Oncol Ann Arbor MI USA

Extragonadal germ cell tumors (EGCTs) are rare, representing <5% of all germ cell tumors (GCTs). Whilst EGCTs share morphological and immunohistochemical features with their gonadal counterparts, they tend to be more aggressive and are frequently associated with secondary somatic malignancies. The aim of our study was to evaluate the clinical, morphological and immunohistochemical features, and to analyze tumors for chromosomal abnormalities of 12p, in addition to any novel genetic alterations, in a series of EGCTs. Seventy-seven EGCTs were included. Anterior mediastinum was the most common anatomic site, followed by central nervous system, retroperitoneum, sacroccygeal area, and neck. Whole genome SNP array identified isochromosome 12p in 26% of tumors. Additional cytogenetic abnormalities included the presence of gain of chr 21 in 37% of tumors. Somatictype malignancies were identified in 8% of patients. Disease progression (metastasis and/or recurrence) was documented in 8 patients, most of whom died from their relapse. Three patients who died of disease had somatictype malignancies. Mediastinal seminomas had a significantly better overall survival when compared to mediastinal non-seminomatous GCTs. Our study demonstrates that EGCTs share similar histologic features, but diverse clinical outcomes compared to their gonadal counterparts. Outcomes vary according to anatomic location and histologic subtypes. Our data corroborate that somatic-type malignancies are frequently encountered in mediastinal EGCTs and that their presence portends a poorer prognosis.

关键词： Extragonadal Germ cell Isochromosome i12p Mediastinal Retroperitoneal Secondary somatic transformation Seminoma Embryonal carcinoma Teratoma Yolk sac tumor Choriocarcinoma single nucleotide polymorphism array

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Ultrasound Phenotype, Genetic Analysis, and Pregnancy Outcomes of Fetuses With 1p36 Deletion Syndrome

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MOLECULAR GENETICS & GENOMIC MEDICINE 2025年第5期13卷

作者： Cai, Meiying Lin, Na Chen, Xuemei Huang, Hailong Guo, Nan Lin, Jiansong Xu, Liangpu Fujian Med Univ Fujian Matern & Child Hlth Hosp Coll Clin Med Obstet & Gynecol & Pediat Med Genet Diag & Therapy CtrFujian Key Lab Prenat Fuzhou Peoples R China Fujian Med Univ Fujian Maternal & Child Hlth Hosp Coll Clin Med Obstet & Gynecol & Pediat Dept Pathol Fuzhou Peoples R China

BackgroundThe intrauterine ultrasound phenotype, genotype, pregnancy outcome, and neonatal prognosis of fetuses with 1p36 deletion syndrome were retrospectively analyzed, as previous reports are *** women (25,000) who underwent interventional prenatal diagnosis between December 2016 and March 2024 were selected. Fetal villus tissue, amniotic fluid, or umbilical cord blood were extracted for single nucleotide polymorphism array (SNP-array) detection under ultrasound *** fetuses had 1p36 deletions involving fragments that were 0.46-22.5 Mb. Six and seven fetuses had large and small copy number variation (CNV) fragment deletions in the 1p36 region, respectively. Two fetuses had normal ultrasound phenotypes, three underwent early spontaneous abortion, one had isolated ventricular septal defect, one had isolated mild ventriculomegaly, two had mild ventriculomegaly associated with increased renal echogenicity, one had mild ventriculomegaly associated with ventricular septal defect, one had severe ventriculomegaly associated with ventricular septal defect and fetal growth restriction, one had tricuspid valve dysplasia, and one had nasal bone dysplasia. Three 1p36 deletions were de novo, and one was paternally inherited. There were three cases of early spontaneous abortion, seven terminations, and three routine postnatal ***-resolution SNP-arrays are suitable for the prenatal diagnosis of 1p36 deletion syndrome.

关键词： cardiac development prenatal single nucleotide polymorphism array ventriculomegaly

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Prenatal diagnosis of Simpson-Golabi-Behmel syndrome type 1 with an 814 kb Xq26.2 deletion with the initial presentation of a thick nuchal fold

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TAIWANESE JOURNAL OF OBSTETRICS & GYNECOLOGY 2023年第1期62卷 163-166页

作者： Peng, Hsiu-Huei Yu, Chung Jen Chen, Yi Chi Hsu, Chin-Chieh Chang, Shuenn-Dyh Chueh, Ho -Yen Chang, Yao-Lung Cheng, Po -Jen Lee, Yen-Chang Chang Gung Mem Hosp Lin Ko Med Ctr Tao Yuan Taiwan Hungchi Women & Childrens Hosp Tao Yuan Taiwan Chang Gung Mem Hosp Dept Obstet & Gynecol 5 Fu Hsing St Tao Yuan Taiwan

Objective: Simpson-Golabi-Behmel syndrome type 1 (SGBS1) is a rare X-linked recessive disorder characterized by overgrowth and multiple anomalies. Most clinical diagnoses of SGBS1 are made post-natally. We present the case of a pregnant woman in whom the fetus presented with a thick nuchal fold 5.6 mm at 15 weeks of gestation, leading to the prenatal diagnosis of SGBS1 with Xq26.2 (133408101-134221889) deletion. Case report: We report the case of a 34-year-old pregnant woman with the initial presentation of fetal thick nuchal fold 5.6 mm at 15 weeks of gestation. Amniocentesis of the fetal karyotype revealed a normal 46, XY, and single nucleotide polymorphism array showed Xq26.2 (133408101-134221889) deletion. Prenatal ultrasound at 21 weeks of gestation revealed a thick nuchal fold, hepatomegaly, nephromegaly, congenital diaphragmatic hernia, hypospadias, and polyhydramnios. Fetal magnetic resonance imaging revealed hepatomegaly, nephromegaly, congenital diaphragmatic hernia, and right lung hypoplasia. The woman had her pregnancy terminated at 24 weeks of gestation. The proband had a general appearance of low-set ears, hypertelorism, a large tongue, and hypospadias and some unique findings on autopsy, including hepatomegaly, right hiatal hernia, liver extensive extramedullary hema-topoiesis, kidney marked congestion, and focal hemorrhage. Discussion: The main prenatal ultrasound findings that alert clinical doctors about the possible diagnosis of SGBS1 included macrosomia, polyhydramnios, organomegaly, renal malformations, congenital dia-phragmatic hernia, and cardiac anomalies. Our case underscores the importance of fetal karyotyping combined with single nucleotide polymorphism array when a thick nuchal fold is found. Genetic counseling is essential in SGBS1, and prenatal testing or preimplantation testing for subsequent preg-nancies is necessary to identify possible pathogenic variants. (c) 2023 Taiwan Association of Obstetrics & Gynecology. Publishing services b

关键词： Simpson-golabi-behmel syndrome type 1 Xq26 2 deletion GPC3 gene deletion Prenatal diagnosis single nucleotide polymorphism array

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