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Okano S, Makita Y, Kimura K, Fukuda I, Miyamoto A, Tanaka H. Wisconsin syndrome with brain volume laterality: a case report and review of the literature. J Med Case Rep 2022; 16:153. [PMID: 35428363 PMCID: PMC9013138 DOI: 10.1186/s13256-022-03332-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 02/13/2022] [Indexed: 11/13/2022] Open
Abstract
Background Wisconsin syndrome is a congenital anomaly caused by a 3q interstitial deletion. It is associated with characteristic facies and developmental delays. Only 33 cases with a deletion estimated to be in the associated region 3q25 have been reported. Case report We present the case of a 5-year-old Japanese girl with a 3q24q25.2 deletion. Her facial features corresponded to the Wisconsin syndrome phenotype, and she exhibited brain volume laterality, which has not been reported previously. Conclusion The clinical features of our case may contribute to narrowing down the list of candidate genes of Wisconsin syndrome.
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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Xie X, Wu X, Su L, Cai M, Li Y, Huang H, Xu L. Application of Single Nucleotide Polymorphism Microarray in Prenatal Diagnosis of Fetuses with Central Nervous System Abnormalities. Int J Gen Med 2021; 14:4239-4246. [PMID: 34393503 PMCID: PMC8354765 DOI: 10.2147/ijgm.s323899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023] Open
Abstract
Background The current gold standard of karyotype analysis for prenatal diagnosis of fetuses with central nervous system (CNS) abnormalities has some limitations. Here, we assessed the value of single nucleotide polymorphism (SNP) arrays as a diagnostic tool. Methods The results of prenatal diagnosis of 344 fetuses with CNS abnormalities as determined by ultrasonographic screening were retrospectively analyzed. All fetuses underwent chromosomal karyotype analysis and genome-wide SNP array analysis simultaneously. The resultant rates and frequencies of genomic abnormalities were compared. Results Karyotype analysis found 45 (13.2%) abnormal CNS cases, while SNP array found 60 (17.4%) cases. SNP array detected 23 (6.7%) cases of submicroscopic abnormalities that karyotype analysis did not find. The detection rate of karyotype analysis was 8.1% in the group with isolated CNS anomalies, but 16.5% in the group with CNS abnormalities plus extra ultrasound anomalies. Detection rates of SNP array were 12.4% and 20.8% in these two groups, respectively. Statistical analysis showed that the detection rates of both methods were significantly higher in the group with CNS malformations and other ultrasound anomalies than in the group with isolated CNS anomalies. Abnormal chromosomes were detected most frequently in fetuses with holoprosencephaly. Conclusion Genome-wide SNP array technology can significantly improve the positive detection rate of fetuses with CNS abnormalities. Combining karyotype analysis and SNP array technology is recommended for detecting the development of fetuses with abnormal CNS.
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Affiliation(s)
- Xiaorui Xie
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Xiaoqing Wu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Linjuan Su
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou, People's Republic of China
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Lan L, She L, Zhang B, He Y, Zheng Z. Prenatal diagnosis of 913 fetuses samples using copy number variation sequencing. J Gene Med 2021; 23:e3324. [PMID: 33615614 PMCID: PMC8243933 DOI: 10.1002/jgm.3324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/22/2021] [Accepted: 02/14/2021] [Indexed: 12/30/2022] Open
Abstract
Background The present study aimed to explore the etiological relationship between fetal abnormalities and copy number variations (CNVs) with the aim of intervening and preventing the birth of children with birth defects in time. Methods Samples of 913 fetuses with puncture indications were collected from January 2017 to December 2019. Karyotype analysis and CNV sequencing (CNV‐seq) testing was performed for fetuses with ultrasonic abnormalities, a high risk of Down’s syndrome and an adverse birth history. All cases were followed up. Results In total, 123 cases (13.47%) had abnormal karyotypes, including 109 cases with chromosome number abnormalities and 14 cases of chromosomal structural abnormalities. Thirty‐seven (4.05%) cases with pathogenic CNVs were detected. The detection rate of pathogenicity CNVs was 12.82% for mixed indications, followed by 7.5% for an adverse birth history, 5.88% at high risk of non‐invasive prenatal testing, 5.00% with an abnormal ultrasonic marker, 1.89% at high risk of screening for Down's syndrome and 1.45% with advanced maternal age. There were 12 (1.31%) cases with microduplications and 25 (2.74%) cases with microdeletions. Trisomy 21 (39.02%), trisomy 18 (13.82%) and Turner syndrome (9.76%) were the top three chromosome abnormalities. There were 104, 746 and 63 cases in the 11–13 weeks, 14–27 weeks 28–38 weeks gestational ages, respectively. The abnormal rates of fetal chromosome aneuploidy and the rate of pathogenic CNVs were decreased and increased with the increase of gestational age (p < 0.05), respectively. Conclusions Compared with karyotype analysis, CNV‐seq can improve the detection rate of chromosomal abnormalities. CNV‐seq combined karyotype analysis should be performed simultaneously in fetuses with puncture indications.
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Affiliation(s)
- Liubing Lan
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Lingna She
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Ultrasonic Department, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Bosen Zhang
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Ultrasonic Department, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Yanhong He
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Zhiyuan Zheng
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
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Xia M, Yang X, Fu J, Teng Z, Lv Y, Yu L. Application of chromosome microarray analysis in prenatal diagnosis. BMC Pregnancy Childbirth 2020; 20:696. [PMID: 33198662 PMCID: PMC7667803 DOI: 10.1186/s12884-020-03368-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
Background To explore the application value of chromosomal microarray analysis (CMA) in prenatal diagnosis. Methods The results of chromosome karyotype analysis and CMA of 477 cases undergoing amniocentesis were analyzed. The results of the no ultrasound abnormality group and the ultrasound abnormality group were compared separately. Within the ultrasound abnormality group, the results of the ultrasound structural malformation group, the ultrasound soft index abnormality group, and other ultrasound abnormality (including abnormal amniotic fluid volume and fetal growth restriction) groups were compared. Results Abnormal chromosome and CMA results were found in a total of 71 cases (15.88%, 71/447), which can be broken down into a total of 23 karyotype abnormalities (5.15%, 23/447), consisting of 18 cases of aneuploidy (4.03%, 18/447), 2 cases of unbalanced chromosome rearrangements (0.44%, 2/447), and 3 cases of chimerism (0.67%, 3/447); 17 cases with detection of pathogenic copy number variations (pCNVs) (3.80%, 17/447); and 31 cases of detection of clinical variants of unknown significance (VOUS) (6.93%, 31/447). CMA detected 3.8% more genetic abnormalities than karyotype analysis (in addition to the abnormalities detected simultaneously by karyotype analysis). Between the no ultrasound abnormality group and the ultrasound abnormality group, there was an extremely significant difference in the detection rate of an abnormal chromosomal karyotype (P < 0.01) and of VOUS (P < 0.01), but there was no significant difference in the detection rate of pCNV (P > 0.05). Comparing the ultrasound structural malformation group, the ultrasound soft index abnormality group, and the other ultrasound abnormality group, there were no significant differences in the detection rate of abnormal chromosomal karyotypes (P > 0.05), pCNV (P > 0.05) or VOUS (P > 0.05). Conclusions The detection rate of chromosomal karyotype abnormalities in prenatal diagnosis in cases with no ultrasound abnormalities was higher. For cases with fetal ultrasound structural abnormalities, when compared with traditional karyotype analysis, CMA can improve the detection rate of fetal genetic abnormalities. However, the no ultrasound abnormality group also had a high VOUS abnormality detection rate, so it is necessary to strictly define the CMA indications.
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Affiliation(s)
- Mingjing Xia
- Department of Obstetrics, Weihai Maternal and Child Health Hospital, the Affiliated Weihai Second Municipal Hospital of Qingdao University, Weihai, China.
| | - Xinhong Yang
- Department of Obstetrics, Weihai Maternal and Child Health Hospital, the Affiliated Weihai Second Municipal Hospital of Qingdao University, Weihai, China
| | - Jing Fu
- Department of Obstetrics, Weihai Maternal and Child Health Hospital, the Affiliated Weihai Second Municipal Hospital of Qingdao University, Weihai, China
| | - Zhenjuan Teng
- Department of Obstetrics, Weihai Maternal and Child Health Hospital, the Affiliated Weihai Second Municipal Hospital of Qingdao University, Weihai, China
| | - Yan Lv
- Department of Obstetrics, Weihai Maternal and Child Health Hospital, the Affiliated Weihai Second Municipal Hospital of Qingdao University, Weihai, China
| | - Lixia Yu
- Department of Obstetrics, Weihai Maternal and Child Health Hospital, the Affiliated Weihai Second Municipal Hospital of Qingdao University, Weihai, China
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Santirocco M, Plaja A, Rodó C, Valenzuela I, Arévalo S, Castells N, Abuli A, Tizzano E, Maiz N, Carreras E. Chromosomal microarray analysis in fetuses with central nervous system anomalies: An 8-year long observational study from a tertiary care university hospital. Prenat Diagn 2020; 41:123-135. [PMID: 32926442 DOI: 10.1002/pd.5829] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/01/2020] [Accepted: 09/08/2020] [Indexed: 01/08/2023]
Abstract
OBJECTIVES To evaluate the prevalence of DNA copy number variants (CNVs) detected with array comparative genomic hybridization (CGH) in fetuses with central nervous system (CNS) anomalies. Secondary objectives were to describe the prevalence of CNV in specific CNS abnormalities, in isolated defects or associated with other malformations or fetal growth restriction (FGR). METHODS Observational cohort study in 238 fetuses with CNS anomalies in which an array-CGH had been performed between January 2009 and December 2017. Pathogenic CNV and variants of unknown significance (VUS) were reported. RESULTS Pathogenic CNVs were found in 16/238 cases (6.7%), VUS in 18/238 (7.6%), and normal result in 204/238 (85.7%) cases. Pathogenic CNVs were more frequent in posterior fossa anomalies (cerebellar hypoplasia 33%, megacisterna magna 20%), moderate ventriculomegaly (11%) and spina bifida (3.7%). Pathogenic CNVs and VUS were found in 7/182 (3.8%) and 14/182 (7.7%) cases of isolated anomalies, in 9/49 (18.4%) and 4/49 (8.2%) presenting another malformation, and in 0/7 and 0/7 cases with associated FGR (P = .001, P = .741, respectively). CONCLUSION These results provide strong evidence toward performing array in fetuses with CNS anomalies, particular in cases of posterior fossa anomalies. The prevalence of pathogenic CNVs is higher in association with other malformations.
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Affiliation(s)
- Maddalena Santirocco
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alberto Plaja
- Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Carlota Rodó
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Silvia Arévalo
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Neus Castells
- Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Anna Abuli
- Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Eduardo Tizzano
- Universitat Autònoma de Barcelona, Bellaterra, Spain.,Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Nerea Maiz
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elena Carreras
- Maternal-Fetal Medicine Department, Obstetrics Department, Vall d'Hebron Hospital Universitari, Barcelona, Spain.,Universitat Autònoma de Barcelona, Bellaterra, Spain
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HU J, QIAN Y, SUN Y, YU J, LUO Y, DONG M. [Application of single nucleotide polymorphism microarray in clinical diagnosis of intellectual disability or retardation]. Zhejiang Da Xue Xue Bao Yi Xue Ban 2019; 48:420-428. [PMID: 31901047 PMCID: PMC8800802 DOI: 10.3785/j.issn.1008-9292.2019.08.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/28/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To assess the clinical application of single nucleotide polymorphism microarray (SNP array) in patients with intellectual disability/developmental delay(ID/DD). METHODS SNP array was performed to detect genome-wide DNA copy number variants (CNVs) for 145 patients with ID/DD in Women's Hospital, Zhejiang University School of Medicine from January 2013 to June 2018. The CNVs were analyzed by CHAS software and related databases. RESULTS Among 145 patients, pathogenic chromosomal abnormalities were detected in 32 cases, including 26 cases of pathogenic CNVs and 6 cases of likely pathogenic CNVs. Meanwhile, 18 cases of uncertain clinical significance and 14 cases of likely benign were identified, no significant abnormalities were found in 81 cases (including benign). CONCLUSIONS SNP array is effective for detecting chromosomal abnormalities in patients with ID/DD with high efficiency and resolution.
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Affiliation(s)
| | | | | | | | | | - Minyue DONG
- 董旻岳(1964—), 男, 博士, 主任医师, 博士生导师, 主要从事生殖遗传学研究; E-mail:
;
https://orcid.org/0000-0002-4344-7924
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YU J, SUN Y, HU J, QIAN Y, LUO Y, DONG M. [Single nucleotide polymorphism microarray in prenatal diagnosis of fetuses with absent nasal bone]. Zhejiang Da Xue Xue Bao Yi Xue Ban 2019; 48:414-419. [PMID: 31901046 PMCID: PMC8800805 DOI: 10.3785/j.issn.1008-9292.2019.08.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/24/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To assess the clinical application of single nucleotide polymorphism microarray (SNP array) in prenatal genetic diagnosis for fetuses with absent nasal bone. METHODS Seventy four fetuses with absent nasal bone detected by prenatal ultrasound scanning were recruited from Women's Hospital, Zhejiang University School of Medicine during June 2015 and October 2018. The chromosome karyotypes analysis and SNP array were performed. The correlation between absent fetal nasal bone and chromosome copy number variants was analyzed. RESULTS Among 74 fetuses, 19 were detected to have chromosomal abnormalities, including 16 cases of trisomy-21, 1 case of trisomy-18 and two cases of micro-deletion/duplication. Among 46 cases with isolated absence of nasal bone, 3 had trisomy-21, and 1 had a micro-duplication. Absence of nasal bone in association with nuchal translucency thickening had a higher rate of abnormal karyotypes compared with isolated absence of nasal bone (χ2=32.27,P<0.01). CONCLUSIONS Fetuses with absent nasal bone and nuchal translucency thickening are likely to have chromosome abnormalities, and SNP array testing is recommended to exclude the chromosome abnormalities.
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Affiliation(s)
| | | | | | | | | | - Minyue DONG
- 董旻岳(1964—), 男, 博士, 主任医师, 博士生导师, 主要从事生殖遗传学研究; E-mail:
;
https://orcid.org/0000-0002-4344-7924
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Xu LL, Zhen L, Lou JW, Tang HS, Pan M, Han J, Yang X, Li DZ. Can cell-free DNA testing be used in pregnancies with isolated fetal omphalocele? Preliminary evidence from cytogenetic results of prenatal cases. J Matern Fetal Neonatal Med 2019; 34:624-628. [PMID: 31018788 DOI: 10.1080/14767058.2019.1611769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Objective: To evaluate whether cell-free DNA (cfDNA) testing could replace an invasive procedure in pregnancies with isolated fetal omphalocele.Study design: This was a retrospective study of all pregnancies with sonographically detected fetal omphalocele at three tertiary referral centers between 2012 and 2016. Invasive diagnostic testing was performed for genetic investigations using conventional karyotyping or chromosomal microarray. cfDNA testing was assumed to be offered to patients with isolated fetal omphalocele for screening for common aneuploidies.Results: Invasive genetic testing was performed in a total of 107 pregnancies with a fetal omphalocele. Abnormal karyotype was found in 66% (31/47) of nonisolated omphalocele cases and in 1.7% (1/60) of isolated omphalocele cases. No pathogenic copy number variations (CNVs) were detected in 59 cases with isolated omphalocele and normal karyotype. If cfDNA screening was used in cases with isolated omphalocele, the affected fetus with trisomy 18 would be detected, and no rare chromosomal aberrations or submicroscopic pathogenic CNVs would be missed.Conclusions: cfDNA testing could be recommended for prenatal genetic evaluation in pregnancies with isolated fetal omphalocele after thorough pretest counseling.Key Message: A very low percentage of aneuploidies and rare chromosomal/subchromosomal abnormalities are found in prenatal cases of isolated omphalocele. It seems that for pregnancies with isolated omphalocele, cfDNA testing represents an alternative for patients who choose to continue the pregnancies and are reluctant to undertake invasive diagnostic testing.
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Affiliation(s)
- Li-Li Xu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, China
| | - Ji-Wu Lou
- Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, China
| | - Hai-Shen Tang
- Prenatal Diagnosis Center, Dongguan Maternal and Children Healthcare Hospital, Dongguan, China
| | - Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center affiliated to Guangzhou Medical University, Guangzhou, China
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Martinez-Portilla RJ, Pauta M, Hawkins-Villarreal A, Rial-Crestelo M, Paz Y Miño F, Madrigal I, Figueras F, Borrell A. Added value of chromosomal microarray analysis over conventional karyotyping in stillbirth work-up: systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 53:590-597. [PMID: 30549343 DOI: 10.1002/uog.20198] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/14/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
OBJECTIVE To assess the added value of chromosomal microarray analysis (CMA) over conventional karyotyping to assess the genetic causes in stillbirth. METHODS To identify relevant studies, published in English or Spanish and without publication time restrictions, we performed a systematic search of PubMed, SCOPUS and ISI Web of Science databases, The Cochrane Library and the PROSPERO register of systematic reviews, for case series of fetal loss ≥ 20 weeks of gestation, with normal or suspected normal karyotype, undergoing CMA and with at least five subjects analyzed. To investigate quality, two reviewers evaluated independently the risk of bias using the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. For the meta-analysis, the incremental yield of CMA over karyotyping was assessed by single-proportion analysis using a random-effects model (weighting by inverse variance). We assessed heterogeneity between studies and performed a sensitivity analysis and a subgroup analysis of structurally abnormal (malformed or growth-restricted) and normal fetuses. RESULTS Included in the meta-analysis were seven studies involving 903 stillborn fetuses which had normal karyotype. The test success rate achieved by conventional cytogenetic analysis was 75%, while that for CMA was 90%. The incremental yield of CMA over conventional karyotyping based on the random-effects model was 4% (95% CI, 3-5%) for pathogenic copy-number variants (pCNVs) and 8% (95% CI, 4-17%) for variants of unknown significance. Subgroup analysis showed a 6% (95% CI, 4-10%) incremental yield of CMA for pCNVs in structurally abnormal fetuses and 3% (95% CI, 1-5%) incremental yield for those in structurally normal fetuses. The pCNV found most commonly was del22q11.21. CONCLUSIONS CMA, incorporated into the stillbirth work-up, improves both the test success rate and the detection of genetic anomalies compared with conventional karyotyping. To achieve a genetic diagnosis in stillbirth is particularly relevant for the purpose of counseling regarding future pregnancies. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- R J Martinez-Portilla
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Fetal Medicine and Therapy Research Center Mexico, on behalf of the Iberoamerican Research Network in Translational, Molecular and Maternal-Fetal Medicine, Mexico
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - M Pauta
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - A Hawkins-Villarreal
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - M Rial-Crestelo
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - F Paz Y Miño
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - I Madrigal
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
| | - F Figueras
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
- Center for Biomedical Research on Rare Diseases (CIBER-ER), Madrid, Spain
| | - A Borrell
- BCNatal, Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clínic de Ginecologia, Obstetricia i Neonatologia Fetal i+D Fetal Medicine Research Center, Universitat de Barcelona, Barcelona, Catalonia, Spain
- IDIBAPS, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Center of Biomedical Diagnosis, Hospital Clinic Barcelona, Barcelona, Catalonia, Spain
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11
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Rudolf G, Lovrečić L, Tul N, Teran N, Peterlin B. The frequency of CNVs in a cohort population of consecutive fetuses with congenital anomalies after the termination of pregnancy. Mol Genet Genomic Med 2019; 7:e658. [PMID: 31004418 PMCID: PMC6565594 DOI: 10.1002/mgg3.658] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The implementation of molecular karyotyping has resulted in an improved diagnostic yield in the genetic diagnostics of congenital anomalies, detected prenatally or after the termination of pregnancy. However, the systematic epidemiologic ascertainment of copy number variations in the etiology of congenital anomalies has not yet been sufficiently explored. METHODS Consecutive fetuses, altogether 204, with major single or multiple congenital anomalies were ascertained by using the SLOCAT registry for the period from 2011 to 2015. After excluding aneuploidies by using conventional karyotyping or Quantitative Fluorescence-Polymerase Chain Reaction, array comparative genomic hybridization was performed for the detection of copy number variations. RESULTS We identified pathogenic or likely pathogenic copy number variations in 14 fetuses (6.8%); 2.9% in fetuses with isolated, and 3.9% in fetuses with multiple congenital anomalies. Additionally, aneuploidies and major structural chromosomal abnormalities were detected in 40.2%. CONCLUSION Our systematic approach of ascertaining congenital anomalies resulted in explaining the etiology of congenital anomalies in 47% of fetuses after the termination of pregnancy. By using array comparative genomic hybridization, we found that copy number variations represent an important part in the etiology of multiple, as well as isolated congenital anomalies, which indicates the importance of analyzing copy number variations in the diagnostic approach of fetuses with congenital anomalies after the termination of pregnancy.
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Affiliation(s)
- Gorazd Rudolf
- Clinical Institute of Medical Genetics (CIMG), University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrečić
- Clinical Institute of Medical Genetics (CIMG), University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nataša Tul
- Department of Perinatology, Division of Gynaecology and Obstetrics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Nataša Teran
- Clinical Institute of Medical Genetics (CIMG), University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics (CIMG), University Medical Centre Ljubljana, Ljubljana, Slovenia
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12
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Tonni G, Palmisano M, Perez Zamarian AC, Rabachini Caetano AC, Santana EFM, Peixoto AB, Armbruster-Moraes E, Ruano R, Araujo Júnior E. Phenotype to genotype characterization by array-comparative genomic hydridization (a-CGH) in case of fetal malformations: A systematic review. Taiwan J Obstet Gynecol 2019; 58:15-28. [PMID: 30638470 DOI: 10.1016/j.tjog.2018.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 11/16/2022] Open
Abstract
The aim of the current review is to report a-CGH abnormalities identified in fetuses with prenatally diagnosed fetal malformations in whom a normal karyotype was diagnosed with conventional cytogenetic analysis. A systematic electronic search of databases (PubMed/Medline, EMBASE/SCOPUS) has been conducted from inception to May, 2017. Bibliographic analysis has been performed according to PRISMA statement for review. The following keywords were used: 'array-CGH' and 'fetal malformations" and "prenatal diagnosis"; alternatively, "microarray", "oligonucleotide array", "molecular biology", "antenatal diagnostics", "fetal diagnostics", "congenital malformations" and "ultrasound" were used to capture both "a-CGH" and "prenatal". One-hundred and twelve fetuses with prenatally diagnosed fetal malformations with normal karyotyping and a-CGH abnormalities detected are described. Single or multiple microarray abnormalities diagnosed have been classified in relation to different organ/system affected. The most frequent a-CGH abnormalities were detected in cases of congenital heart diseases (CDHs), multiple malformations and central nervous system (CNS) malformations. Maternal or paternal carrier-state was seen in 19.64% (22/112), of cases while the number of reported de novo mutations accounted for 46.42% (52/112) of all CNVs microarray abnormalities. Array-comparative genomic hydridization (a-CGH) may become an integral and complemantary genetic testing when fetal malformations are detected prenatally in fetuses with normal cytogenetic karyotype. In addition, a-CGH enables the identification of CNVs and VOUS and improves the calculation of recurrent risk and the genetic counseling.
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Affiliation(s)
- Gabriele Tonni
- Prenatal Diagnostic Service, Department of Obstetrics and Gynecology, Istituto di Ricerca a Carattere Clinico Scientifico (IRCCS) AUSL Reggio Emilia, Italy.
| | - Marcella Palmisano
- Prenatal Diagnostic Service, Department of Obstetrics and Gynecology, Istituto di Ricerca a Carattere Clinico Scientifico (IRCCS) AUSL Reggio Emilia, Italy
| | - Ana Cristina Perez Zamarian
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
| | - Ana Carolina Rabachini Caetano
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
| | - Eduardo Félix Martins Santana
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
| | - Alberto Borges Peixoto
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
| | - Edecio Armbruster-Moraes
- Discipline of Genetics, Faculty of Medicine of ABC (FMABC), Santo André-SP, Brazil; Department of Gynecology and Obstetrics, Faculty of Medicine of the University of São Paulo (FMUSP), São Paulo-SP, Brazil
| | - Rodrigo Ruano
- Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Edward Araujo Júnior
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
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13
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Li DZ, Tang HS. Chromosomal microarray analysis in pregnancies at risk for a molecular disorder. J Matern Fetal Neonatal Med 2019; 34:159-162. [PMID: 30651013 DOI: 10.1080/14767058.2019.1571577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Objective: The aim of this study was to evaluate the utility of chromosomal microarray (CMA) in patients who were solely referred for molecular diagnosis.Methods: During a 2-year period, CMA was the patients' choice, whether to opt for it or not, for those at risk for fetal hemoglobin Bart's disease or β-thalassemia major who were referred for invasive prenatal diagnosis and had a normal fetal genotype. CytoScan 750 K array (Affymetrix Inc., Santa Clara, CA) was used for CMA. The CMA testing results were collected.Results: There were 184 patients, who had a normal genotypic result, opting CMA testing without an obvious indication for fetal karyotyping. The median maternal age was 29 years (range, 17-34); the median gestational age was 13 weeks (range, 11-20). In two out of 184 (1.1%) cases unexpected de novo pathogenic microdeletions were found: a 3.2 Mb 22q11.21 microdeletion and a 0.8 Mb 16p11.2 microdeletion.Conclusions: Pregnancies at risk for thalassemia can also benefit from performing CMA. This information might be a part of the contents in comprehensive pretest counseling for those who are referred for diagnostic testing due to a molecular disorder.
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Affiliation(s)
- Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, PR China
| | - Hai-Shen Tang
- Prenatal Diagnosis Unit, Boai Hospital of Zhongshan, Zhongshan, PR China
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14
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Affiliation(s)
- Ji-Un Kang
- Department of Biomedical Laboratory Science, Korea Nazarene University, Cheonan, Korea
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15
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Guo W, Zhu X, Yan L, Qiao J. The present and future of whole-exome sequencing in studying and treating human reproductive disorders. J Genet Genomics 2018; 45:517-525. [DOI: 10.1016/j.jgg.2018.08.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/23/2018] [Accepted: 08/24/2018] [Indexed: 12/16/2022]
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16
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Ramineni A, Coman D. De Novo 3q22.3q24 Microdeletion in a Patient With Blepharophimosis-Ptosis-Epicanthus Inversus Syndrome, Dandy-Walker Malformation, and Wisconsin Syndrome. Child Neurol Open 2016; 3:2329048X16666362. [PMID: 28503614 PMCID: PMC5417291 DOI: 10.1177/2329048x16666362] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 01/22/2023] Open
Abstract
Interstitial deletions affecting the long arm of chromosome 3 have been associated with a broad phenotype. This has included the features of blepharophimosis–ptosis–epicanthus inversus syndrome, Dandy-Walker malformation, and the rare Wisconsin syndrome. The authors report a young female patient presenting with features consistent with all 3 of these syndromes. This has occurred in the context of a de novo 3q22.3q24 microdeletion including FOXL2, ZIC1, and ZIC4. This patient provides further evidence for the role of ZIC1 and ZIC4 in Dandy-Walker malformation and is the third reported case of Dandy-Walker malformation to have associated corpus callosum thinning. This patient is also only the seventh to be reported with the rare Wisconsin syndrome phenotype.
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Affiliation(s)
- Anand Ramineni
- Department of Paediatrics, The Wesley Hospital, Brisbane, Queensland, Australia.,Discipline of Paediatrics, UnitingCare Clinical School, Brisbane, Queensland, Australia.,Neuroscience Department, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia.,School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - David Coman
- Department of Paediatrics, The Wesley Hospital, Brisbane, Queensland, Australia.,Discipline of Paediatrics, UnitingCare Clinical School, Brisbane, Queensland, Australia.,Neuroscience Department, Lady Cilento Children's Hospital, Brisbane, Queensland, Australia.,School of Medicine, The University of Queensland, Brisbane, Queensland, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
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17
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Zhu H, Lin S, Huang L, He Z, Huang X, Zhou Y, Fang Q, Luo Y. Application of chromosomal microarray analysis in prenatal diagnosis of fetal growth restriction. Prenat Diagn 2016; 36:686-92. [PMID: 27221052 DOI: 10.1002/pd.4844] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/17/2016] [Accepted: 05/19/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Hui Zhu
- Fetal Medicine Center, Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Shaobin Lin
- Fetal Medicine Center, Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Linhuan Huang
- Fetal Medicine Center, Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Zhiming He
- Fetal Medicine Center, Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Xuan Huang
- Fetal Medicine Center, Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Yi Zhou
- Fetal Medicine Center, Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Qun Fang
- Fetal Medicine Center, Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Yanmin Luo
- Fetal Medicine Center, Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
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18
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Lazier J, Fruitman D, Lauzon J, Bernier F, Argiropoulos B, Chernos J, Caluseriu O, Simrose R, Thomas MA. Prenatal Array Comparative Genomic Hybridization in Fetuses With Structural Cardiac Anomalies. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2016; 38:619-26. [PMID: 27591345 DOI: 10.1016/j.jogc.2016.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/15/2016] [Indexed: 12/19/2022]
Abstract
OBJECTIVES To examine the diagnostic performance of array comparative genomic hybridization (CGH) for fetal cardiac anomalies in two medium-sized Canadian prenatal genetics clinics. METHODS We prospectively recruited 22 pregnant women with fetal structural cardiac anomalies, normal rapid aneuploidy detection, and FISH for 22q11.2 testing for array CGH analysis. RESULTS One case had an 8p deletion that was also visible on karyotype and included the GATA4 gene, which has been associated with congenital heart disease. Two cases had inherited pathogenic copy number variants (CNVs) of variable expressivity and penetrance: one was a duplication of 16p11.2 and the other a deletion of 15q11.2. One case had the incidental finding of being a carrier of a recessive disease unrelated to the cardiac anomaly. CONCLUSIONS Of these prospectively recruited cases of fetal cardiac anomalies, 14% had a pathogenic result on array CGH. Pathogenic CNVs of variable penetrance and expressivity were a significant proportion of the positive results identified. These CNVs are generally associated with neurodevelopmental issues and may or may not have been associated with the fetus' underlying congenital heart disease. Array CGH increases the diagnostic yield in this group of patients; however, certain CNVs remain a challenge for counselling in the prenatal setting.
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Affiliation(s)
- Joanna Lazier
- Department of Medical Genetics, University of Calgary, Calgary AB
| | - Deborah Fruitman
- Department of Pediatrics, University of Calgary, Calgary AB; Section of Pediatric Cardiology, University of Calgary, Calgary AB
| | - Julie Lauzon
- Department of Medical Genetics, University of Calgary, Calgary AB; Department of Pediatrics, University of Calgary, Calgary AB; Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary AB
| | - Francois Bernier
- Department of Medical Genetics, University of Calgary, Calgary AB; Department of Pediatrics, University of Calgary, Calgary AB; Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary AB
| | - Bob Argiropoulos
- Cytogenetics Laboratory, Alberta Children's Hospital, Calgary AB
| | - Judy Chernos
- Cytogenetics Laboratory, Alberta Children's Hospital, Calgary AB
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton AB
| | - Rebecca Simrose
- Department of Obstetrics and Gynecology, University of Calgary, Calgary AB
| | - Mary Ann Thomas
- Department of Medical Genetics, University of Calgary, Calgary AB; Department of Pediatrics, University of Calgary, Calgary AB; Alberta Children's Hospital Research Institute for Child and Maternal Health, University of Calgary, Calgary AB
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19
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Tong H, Jin Y, Xu Y, Zou B, Ye H, Wu H, Kumar S, Pitman JL, Zhou G, Song Q. Prenatal diagnosis of trisomy 21, 18 and 13 by quantitative pyrosequencing of segmental duplications. Clin Genet 2016; 90:451-455. [PMID: 26948280 DOI: 10.1111/cge.12772] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/02/2016] [Accepted: 03/02/2016] [Indexed: 01/22/2023]
Abstract
Chromosomal aberration mostly occurs in chromosomes 21, 18 and 13, with an incidence approximately 1 out of 160 live births in humans, therefore making prenatal diagnosis necessary in clinics. Current methods have drawbacks such as time consuming, high cost, complicated operations and low sensitivity. In this paper, a novel method for rapid and accurate prenatal diagnosis of aneuploidy is proposed based on pyrosequencing, which quantitatively detects the peak height ratio (PHR) of different bases of segmental duplication. A direct polymerase chain reaction (PCR) approach was undertaken, where a small volume of amniotic fluid was used as the starting material without DNA extraction. Single-stranded DNA was prepared from PCR products and subsequently analyzed using pyrosequencing. The PHR between target and reference chromosome of 2.2 for euploid and 3:2 for a trisomy fetus were used as reference. The reference intervals and z scores were calculated for discrimination of aneuploidy. A total of 132 samples were collected, within trisomy 21 (n = 11), trisomy 18 (n = 3), trisomy 13 (n = 2), and unaffected controls (n = 116). A set of six segmental duplications were chosen for analysis. This method had consistent results with karyotyping analysis, a correct diagnosis with 100% sensitivity and 99.9% specificity.
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Affiliation(s)
- H Tong
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, China Pharmaceutical University, Nanjing, China
| | - Y Jin
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, China Pharmaceutical University, Nanjing, China
| | - Y Xu
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, China Pharmaceutical University, Nanjing, China
| | - B Zou
- Department of pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - H Ye
- Department of pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - H Wu
- Department of pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - S Kumar
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - J L Pitman
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - G Zhou
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, China Pharmaceutical University, Nanjing, China. .,Department of pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
| | - Q Song
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, China Pharmaceutical University, Nanjing, China. .,Department of pharmacology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China.
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20
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Leavitt K, Goldwaser T, Bhat G, Kalia I, Klugman SD, Dolan SM. Chromosomal microarray in prenatal diagnosis: case studies and clinical challenges. Per Med 2016; 13:249-255. [PMID: 29767605 DOI: 10.2217/pme-2015-0003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chromosomal microarray analysis (CMA) is a diagnostic tool used in the evaluation of pediatric patients with congenital anomalies or developmental and intellectual disability. In both the pediatric and prenatal patient population, CMA has been shown to have a higher detection rate of chromosomal abnormalities than conventional karyotype alone. Currently, the diagnostic yield of prenatal CMA is highest when applied to the evaluation of a fetus with multiple ultrasound anomalies. Challenges arise when CMA yields isolated findings not associated with a phenotype on ultrasound or variants of uncertain significance, which warrants evaluation of the risks, benefits, limitations and optimal incorporation of CMA into prenatal care. The clinical cases presented here will be used to illustrate these issues.
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Affiliation(s)
- Karla Leavitt
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Tamar Goldwaser
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Gifty Bhat
- Genetics Division, Department of Pediatrics, Montefiore Medical Center/Albert Einstein College of Medicine, The Children's Hospital at Montefiore, 3415 Bainbridge Ave., Bronx, NY 10467, USA
| | - Isha Kalia
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Susan D Klugman
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
| | - Siobhan M Dolan
- Division of Reproductive Genetics, Department of Obstetrics & Gynecology & Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine 1695 Eastchester Road Suite 301, Bronx, NY 10463, USA
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21
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Grande M, Jansen FAR, Blumenfeld YJ, Fisher A, Odibo AO, Haak MC, Borrell A. Genomic microarray in fetuses with increased nuchal translucency and normal karyotype: a systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 46:650-658. [PMID: 25900824 DOI: 10.1002/uog.14880] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/09/2015] [Accepted: 04/10/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVE To estimate the incremental yield of detecting copy number variants (CNVs) by genomic microarray over karyotyping in fetuses with increased nuchal translucency (NT) diagnosed by first-trimester ultrasound. METHODS This was a systematic review conducted in accordance with PRISMA criteria. We searched PubMed, Ovid MEDLINE and Web of Science for studies published between January 2009 and January 2015 that described CNVs in fetuses with increased NT, usually defined as ≥ 3.5 mm, and normal karyotype. Search terms included: fetal or prenatal, nuchal translucency or cystic hygroma or ultrasound anomaly, array comparative genomic hybridization or copy number variants, with related search terms. Risk differences were pooled to estimate the overall and stratified microarray incremental yield using RevMan. Quality assessment of included studies was performed using the Quality Assessment tool for Diagnostic Accuracy Studies (QUADAS-2) checklist. RESULTS Seventeen studies met the inclusion criteria for analysis. Meta-analysis indicated an incremental yield of 5.0% (95% CI, 2.0-8.0%) for the detection of CNVs using microarray when pooling results. Stratified analysis of microarray results demonstrated a 4.0% (95% CI, 2.0-7.0%) incremental yield in cases of isolated NT and 7.0% (95% CI, 2.0-12.0%) when other malformations were present. The most common pathogenic CNVs reported were 22q11.2 deletion, 22q11.2 duplication, 10q26.12q26.3 deletion and 12q21q22 deletion. The pooled prevalence for variants of uncertain significance was 1%. CONCLUSION The use of genomic microarray provides a 5.0% incremental yield of detecting CNVs in fetuses with increased NT and normal karyotype.
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Affiliation(s)
- M Grande
- Department of Maternal-Fetal Medicine, Institute of Gynecology, Obstetrics and Neonatology, Hospital Clinic of Barcelona, Catalonia, Spain
| | - F A R Jansen
- Leiden University Medical Center, Department of Obstetrics and Fetal Medicine, Leiden, The Netherlands
| | - Y J Blumenfeld
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - A Fisher
- Elliot Health System, Manchester, NH, USA
| | - A O Odibo
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of South Florida, Tampa, FL, USA
| | - M C Haak
- Leiden University Medical Center, Department of Obstetrics and Fetal Medicine, Leiden, The Netherlands
| | - A Borrell
- Department of Maternal-Fetal Medicine, Institute of Gynecology, Obstetrics and Neonatology, Hospital Clinic of Barcelona, Catalonia, Spain
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Prenatal Diagnosis of Central Nervous System Anomalies by High-Resolution Chromosomal Microarray Analysis. BIOMED RESEARCH INTERNATIONAL 2015; 2015:426379. [PMID: 26064910 PMCID: PMC4443641 DOI: 10.1155/2015/426379] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/07/2015] [Indexed: 12/20/2022]
Abstract
The aims of this study were to evaluate the contribution of chromosomal microarray analysis (CMA) in the prenatal diagnosis of fetuses with central nervous system (CNS) anomalies but normal chromosomal karyotype. A total of 46 fetuses with CNS anomalies with or without other ultrasound anomalies but normal karyotypes were evaluated by array-based comparative genomic hybridisation (aCGH) or single-nucleotide polymorphism (SNP) array. The result showed that CNVs were detected in 17 (37.0%) fetuses. Of these, CNVs identified in 5 (5/46, 10.9%) fetuses were considered to be likely pathogenic, and CNVs detected in 3 (3/46, 6.5%) fetuses were defined as being of uncertain clinical significance. Fetuses with CNS malformations plus other ultrasound anomalies had a higher rate of pathogenic CNVs than those with isolated CNS anomalies (13.6% versus 8.3%), but there was no significant difference (Fisher's exact test, P > 0.05). Pathogenic CNVs were detected most frequently in fetuses with Dandy-Walker syndrome (2/6, 33.3%) when compared with other types of neural malformations, and holoprosencephaly (2/7, 28.6%) ranked the second. CMA is valuable in prenatal genetic diagnosis of fetuses with CNS anomalies. It should be considered as part of prenatal diagnosis in fetuses with CNS malformations and normal karyotypes.
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Prenatal diagnosis and molecular cytogenetic characterization of chromosome 22q11.2 deletion syndrome associated with congenital heart defects. Taiwan J Obstet Gynecol 2015; 53:248-51. [PMID: 25017279 DOI: 10.1016/j.tjog.2014.04.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2014] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE To report prenatal diagnosis of 22q11.2 deletion syndrome in a pregnancy with congenital heart defects in the fetus. CASE REPORT A 26-year-old, primigravid woman was referred for counseling at 24 weeks of gestation because of abnormal ultrasound findings of fetal congenital heart defects. The Level II ultrasound revealed a singleton fetus with heart defects including overriding aorta, small pulmonary artery, and ventricular septal defect. Cordocentesis was performed. The DNA extracted from the cord blood was analyzed by multiplex ligation-dependent amplification (MLPA). The MLPA showed deletion in the DiGeorge syndrome (DGS) critical region of chromosome 22 low copy number repeat (LCR) 22-A∼C. Conventional cytogenetic analysis revealed a normal male karyotype. Repeated amniocentesis and cordocentesis were performed. Whole-genome array comparative genomic hybridization (aCGH) on cord blood was performed. aCGH detected a 3.07-Mb deletion at 22q11.21. Conventional cytogenetic analysis of cultured amniocytes revealed a karyotype 46,XY. Metaphase fluorescence in situ hybridization (FISH) analysis on cultured amniocytes confirmed an interstitial 22q11.2 deletion. CONCLUSION Prenatal ultrasound findings of congenital heart defects indicate that the fetuses are at increased risk for chromosome abnormalities. Studies for 22q11.2 deletion syndrome should be considered adjunct to conventional karyotyping. Although FISH has become a standard procedure for diagnosis of 22q11.2 deletion syndrome, MLPA can potentially diagnose a broader spectrum of abnormalities, and aCGH analysis has the advantage of refining the 22q11.2 deletion breakpoints and detecting uncharacterized chromosome rearrangements or genomic imbalances.
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Srebniak MI, Van Opstal D, Joosten M, Diderich KEM, de Vries FAT, Riedijk S, Knapen MFCM, Go ATJI, Govaerts LCP, Galjaard RJH. Whole-genome array as a first-line cytogenetic test in prenatal diagnosis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2015; 45:363-372. [PMID: 25488734 DOI: 10.1002/uog.14745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 06/04/2023]
Affiliation(s)
- M I Srebniak
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
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Hayashi S, Yagi M, Morisaki I, Inazawa J. Identical deletion at 14q13.3 including PAX9 and NKX2-1 in siblings from mosaicism of unaffected parent. J Hum Genet 2015; 60:203-6. [DOI: 10.1038/jhg.2014.123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/18/2014] [Accepted: 12/19/2014] [Indexed: 01/19/2023]
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D'Amours G, Langlois M, Mathonnet G, Fetni R, Nizard S, Srour M, Tihy F, Phillips MS, Michaud JL, Lemyre E. SNP arrays: comparing diagnostic yields for four platforms in children with developmental delay. BMC Med Genomics 2014; 7:70. [PMID: 25539807 PMCID: PMC4299176 DOI: 10.1186/s12920-014-0070-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 12/11/2014] [Indexed: 11/28/2022] Open
Abstract
Background Molecular karyotyping is now the first-tier genetic test for patients affected with unexplained intellectual disability (ID) and/or multiple congenital anomalies (MCA), since it identifies a pathogenic copy number variation (CNV) in 10-14% of them. High-resolution microarrays combining molecular karyotyping and single nucleotide polymorphism (SNP) genotyping were recently introduced to the market. In addition to identifying CNVs, these platforms detect loss of heterozygosity (LOH), which can indicate the presence of a homozygous mutation or uniparental disomy. Since these abnormalities can be associated with ID and/or MCA, their detection is of particular interest for patients whose phenotype remains unexplained. However, the diagnostic yield obtained with these platforms is not confirmed, and the real clinical value of LOH detection has not been established. Methods We selected 21 children affected with ID, with or without congenital malformations, for whom standard genetic analyses failed to provide a diagnosis. We performed high-resolution SNP array analysis with four platforms (Affymetrix Genome-Wide Human SNP Array 6.0, Affymetrix Cytogenetics Whole-Genome 2.7 M array, Illumina HumanOmni1-Quad BeadChip, and Illumina HumanCytoSNP-12 DNA Analysis BeadChip) on whole-blood samples obtained from children and their parents to detect pathogenic CNVs and LOHs, and compared the results with those obtained on a moderate resolution array-based comparative genomic hybridization platform (NimbleGen CGX-12 Cytogenetics Array), already used in the clinical setting. Results We identified a total of four pathogenic CNVs in three patients, and all arrays successfully detected them. With the SNP arrays, we also identified a LOH containing a gene associated with a recessive disorder consistent with the patient’s phenotype (i.e., an informative LOH) in four children (including two siblings). A homozygous mutation within the informative LOH was found in three of these patients. Therefore, we were able to increase the diagnostic yield from 14.3% to 28.6% as a result of the information provided by LOHs. Conclusions This study shows the clinical usefulness of SNP arrays in children with ID, since they successfully detect pathogenic CNVs, identify informative LOHs that can lead to the diagnosis of a recessive disorder. It also highlights some challenges associated with the use of SNP arrays in a clinical laboratory. Electronic supplementary material The online version of this article (doi:10.1186/s12920-014-0070-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guylaine D'Amours
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada.
| | - Mathieu Langlois
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | | | - Raouf Fetni
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Département de pathologie, CHU Sainte-Justine, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Sonia Nizard
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Myriam Srour
- Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada.
| | - Frédérique Tihy
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pathologie et biologie cellulaire, Université de Montréal, Montréal, QC, Canada.
| | - Michael S Phillips
- Centre de pharmacogénomique, Institut de cardiologie de Montréal, Montréal, QC, Canada.
| | - Jacques L Michaud
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
| | - Emmanuelle Lemyre
- Service de génétique médicale, CHU Sainte-Justine, Montréal, QC, Canada. .,Centre de recherche, CHU Sainte-Justine, Montréal, QC, Canada. .,Faculté de médecine, Université de Montréal, Montréal, QC, Canada. .,Pédiatrie, Université de Montréal, Montréal, QC, Canada.
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Large cryptic genomic rearrangements with apparently normal karyotypes detected by array-CGH. Mol Cytogenet 2014; 7:82. [PMID: 25435912 PMCID: PMC4247713 DOI: 10.1186/s13039-014-0082-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 10/29/2014] [Indexed: 12/18/2022] Open
Abstract
Background Conventional karyotyping (550 bands resolution) is able to identify chromosomal aberrations >5-10 Mb, which represent a known cause of intellectual disability/developmental delay (ID/DD) and/or multiple congenital anomalies (MCA). Array-Comparative Genomic Hybridization (array-CGH) has increased the diagnostic yield of 15-20%. Results In a cohort of 700 ID/DD cases with or without MCA, including 15 prenatal diagnoses, we identified a subgroup of seven patients with a normal karyotype and a large complex rearrangement detected by array-CGH (at least 6, and up to 18 Mb). FISH analysis could be performed on six cases and showed that rearrangements were translocation derivatives, indistinguishable from a normal karyotype as they involved a similar band pattern and size. Five were inherited from a parent with a balanced translocation, whereas two were apparently de novo. Genes spanning the rearrangements could be associated with some phenotypic features in three cases (case 3: DOCK8; case 4: GATA3, AKR1C4; case 6: AS/PWS deletion, CHRNA7), and in two, likely disease genes were present (case 5: NR2F2, TP63, IGF1R; case 7: CDON). Three of our cases were prenatal diagnoses with an apparently normal karyotype. Conclusions Large complex rearrangements of up to 18 Mb, involving chromosomal regions with similar size and band appearance may be overlooked by conventional karyotyping. Array-CGH allows a precise chromosomal diagnosis and recurrence risk definition, further confirming this analysis as a first tier approach to clarify molecular bases of ID/DD and/or MCA. In prenatal tests, array-CGH is confirmed as an important tool to avoid false negative results due to karyotype intrinsic limit of detection.
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Charan P, Woodrow N, Walker SP, Ganesamoorthy D, McGillivray G, Palma-Dias R. High-resolution microarray in the assessment of fetal anomalies detected by ultrasound. Aust N Z J Obstet Gynaecol 2014; 54:46-52. [PMID: 24471846 DOI: 10.1111/ajo.12170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 11/18/2013] [Indexed: 12/27/2022]
Abstract
AIMS The main aim of this study was to determine the feasibility of using high-resolution microarray to assist with prenatal diagnosis of ultrasound-detected fetal abnormality and to describe the frequency of abnormal results in different categories of fetal anomalies. METHODS Prospective cross-sectional study was conducted on women diagnosed with a fetal anomaly (ies) between February 2009 and December 2011 who were offered testing by microarray analysis (Affymetrix 2.7M SNP) and fluorescent in situ hybridisation (FISH) instead of standard karyotyping. Fetal anomalies were categorised according to organ system involvement. RESULTS One hundred and eighteen women consented to testing with microarray. Eleven of one hundred eighteen (9.3%) cases had aneuploidy detected by FISH. Of the remaining 107, 23 (21.5%) had an abnormality detected on microarray, only three of which would have been detected using the combination of six-probe FISH and banded karyotype. The maximum expected yield for six-probe FISH and karyotype was thus 14/118 (11.8%), compared to 34/118 (28.8%), P < 0.0001. Of the 23 abnormalities detected with microarray, 10 (43%) were pathogenic, six (26%) were long continuous stretches of homozygosity and seven (30%) were of uncertain significance. The maximum yield was in cases with cardiovascular (100%); multiple (40%); central nervous system (CNS) (25%) and skeletal (9%) abnormalities. CONCLUSION This study has confirmed the feasibility of translation of microarray into clinical practice. 11.8% (14/118) of the cases would have a genetic basis of an abnormality with a FISH and banded karyotype. This figure is approximately tripled to 28.8% (34/118) if we offer FISH and microarray. High yield for imbalances are multiple, cardiovascular, CNS and skeletal abnormalities.
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Affiliation(s)
- Poonam Charan
- Pauline Gandel Imaging Centre, Royal Women's Hospital, Parkville, Victoria, Australia; Fetal Medicine Unit, Royal Women's Hospital, Parkville, Victoria, Australia
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Liu N, Yan J, Chen X, Song J, Wang B, Yao Y. Prenatal diagnosis of a de novo interstitial deletion of 11q (11q22.3 → q23.3) associated with abnormal ultrasound findings by array comparative genomic hybridization. Mol Cytogenet 2014; 7:62. [PMID: 25298785 PMCID: PMC4189608 DOI: 10.1186/s13039-014-0062-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Accepted: 08/26/2014] [Indexed: 11/29/2022] Open
Abstract
Background Conventional G-band karyotyping offers low-resolution detection of chromosome abnormalities and cannot provide information about the involved genomic content. On the other hand, array comparative genomic hybridization can offer a rapid and comprehensive detection of genomewide gains and losses with higher resolution, thus providing the genetic basis for prenatal diagnosis of fetal abnormalities. Case presentation A 35-year-old primigravid underwent cordocentesis at 28 weeks gestation due to the presence of polyhydramnios, intrauterine growth retardation, persistent right umbilical vein and mild stenosis of aortic arch at the ultrasound scan. Conventional G-band chromosome analysis revealed an apparently normal karyotype whereas the array CGH detected a de novo 8.97 Mb deletion at chromosome 11q22.3 → q23.3 and offered a precise characterization of the genetic defect. Conclusions The array CGH detected a de novo interstitial 11q deletion with its precise location and size which could be missed or confused by G-band chromosome analysis. The breakpoint was close to the folate sensitive rare fragile site FRA11B and the aphidicolin inducible common fragile site FRA11G, the co-localization fragile site could have caused instability and constitutional chromosomal breakage. This case study indicates that array CGH is a useful technique for detecting small unbalanced chromosomal abnormalities and should be an integral part of prenatal diagnosis for fetal malformations.
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Affiliation(s)
- Nian Liu
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Jiong Yan
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Xinlin Chen
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Jieping Song
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Bo Wang
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
| | - Yanyi Yao
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, Wuhan, 430070 China
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Hillman SC, Barton PM, Roberts TE, Maher ER, McMullan DM, Kilby MD. BAC chromosomal microarray for prenatal detection of chromosome anomalies in fetal ultrasound anomalies: an economic evaluation. Fetal Diagn Ther 2014; 36:49-58. [PMID: 24943865 DOI: 10.1159/000358387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 12/27/2013] [Indexed: 11/19/2022]
Abstract
INTRODUCTION To determine the cost-effectiveness of prenatal chromosomal microarray (CMA) when performed for structural anomalies on fetal ultrasound scan over conventional techniques. METHOD A decision tree was populated using data from a prospective cohort of women undergoing testing when a fetal ultrasound scan showed a structural abnormality. Nine strategies of testing were modeled including combinations of the tests: QFPCR, G-band karyotyping, CMA and FISH for DiGeorge (22q) microdeletion. RESULTS When CMA costs GBP 405 and using a 1-Mb BAC array it would cost GBP 24,600 for every additional case detected by CMA over a combination of QFPCR, followed by G-band karyotype, followed lastly by FISH (for DiGeorge syndrome). If CMA is performed instead of conventional karyotyping alone it costs GBP 33,000 for every additional case detected. However, if the cost of CMA is reduced to GBP 360 than when CMA is performed instead of conventional karyotyping alone it would cost GBP 9,768 for every additional case detected. DISCUSSION The use of a prenatal BAC CMA is not currently cost-effective when compared to other testing strategies. However, as CMA costs decrease and resolution (and detection rates) increase it is likely to become the cost-effective option of the future.
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Affiliation(s)
- Sarah C Hillman
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, Birmingham, UK
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Abstract
Determining a genetic diagnosis prenatally permits patients to make informed reproductive decisions and to be counseled about possible fetal outcomes. Therefore, it is important for the provider to be aware of the spectrum of genetic conditions and to use appropriate testing modality to obtain specific diagnosis. This article reviews genetic techniques available for prenatal diagnosis such as preimplantation genetic testing, chromosomal microarray, non-invasive prenatal screening, and next-generation sequencing. Chromosomal microarray has emerged as the first diagnostic test for evaluation of multiple congenital anomalies and developmental delay as most of the next-generation sequencing methods do not detect copy-number variants (CNVs). Exome sequencing and whole genome sequencing are time-consuming, so if this needs to be done to obtain an accurate genetic diagnosis, allow sufficient time.
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Yin A, Lu J, Liu C, Guo L, Wu J, Mai M, Zhong Y, Zhang X. A prenatal missed diagnosed case of submicroscopic chromosomal abnormalities by karyotyping: the clinical utility of array-based CGH in prenatal diagnostics. Mol Cytogenet 2014; 7:26. [PMID: 24735551 PMCID: PMC4005634 DOI: 10.1186/1755-8166-7-26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/26/2014] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Array-based comparative genomic hybridization possesses a number of significant advantages over conventional cytogenetic and other molecular cytogenetic techniques, providing a sensitive and comprehensive detection platform for unexpected imbalances in the genome wide. CASE PRESENTATION The newborn proband, demonstrated with craniofacial dysmorphism and multiple malformations, was born to a family with spontaneous abortions. This pregnancy was uneventful, except the prenatal ultrasound examination showed an increased nuchal translucency at 12(+) weeks of gestation. Cytogenetics revealed an apparently normal karyotype, and the couple decided to continue the pregnancy. Array-based CGH analysis was applied to the affected infant, identified a combination of 18p deletion and 7q duplication. Further study indicates that the unbalanced translocation was inherited from a balanced translocation carrier parent. CONCLUSIONS In review of the case, several overlooked points leading to the missed diagnosis should be discussed and certain quality control strategies should be adopted to avoid similar problems in the future. Array-based CGH and karyotyping techniques are complemented by diverse detection spectrum and resolutions, and a combination of these methods could help providing optimal genetic diagnosis. Given that the array-CGH analysis will not introduce additional risk to patients, it is reasonable to recommend those already undergoing invasive testing should take array-based CGH as an adjunct to conventional cytogenetic tests and other molecular cytogenetic analysis.
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Affiliation(s)
- Aihua Yin
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jian Lu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Chang Liu
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Li Guo
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Jing Wu
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Mingqin Mai
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Yanfang Zhong
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
| | - Xiaozhuang Zhang
- Prenatal Diagnosis Centre, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, Guangdong 510010, China
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Microarrays as a diagnostic tool in prenatal screening strategies: ethical reflection. Hum Genet 2014; 133:163-72. [PMID: 24077959 DOI: 10.1007/s00439-013-1365-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/18/2013] [Indexed: 01/09/2023]
Abstract
Genomic microarray analysis is increasingly being applied as a prenatal diagnostic tool. Microarrays enable searching the genome at a higher resolution and with higher sensitivity than conventional karyotyping for identifying clinically significant chromosomal abnormalities. As yet, no clear guidelines exist on whether microarrays should be applied prenatally for all indications or only in selected cases such as ultrasound abnormalities, whether a targeted or genome-wide array should be used, and what these should include exactly. In this paper, we present some ethical considerations on the prenatal use of microarrays. There is a strong consensus, at least in Western countries, that the aim of prenatal screening for foetal abnormalities should be understood as facilitating autonomous reproductive choice for prospective parents. The tests offered should be valid and useful to reach that purpose. Against this background, we address several ethical issues raised by the prenatal application of microarrays. First, we argue that the general distinction between a targeted and a genome-wide microarray needs to be scrutinised. Then we examine whether microarrays are 'suitable tests' to serve either a screening or a diagnostic purpose. Given the wide range of findings possibly generated by microarrays, the question arises whether microarrays actually promote or interfere with autonomous reproductive decision-making. Moreover, if variants of unknown clinical significance are identified, this adds to the burden and complexity of reproductive decision-making. We suggest a qualified use of microarrays in the prenatal context.
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de Wit MC, Srebniak MI, Govaerts LCP, Van Opstal D, Galjaard RJH, Go ATJI. Additional value of prenatal genomic array testing in fetuses with isolated structural ultrasound abnormalities and a normal karyotype: a systematic review of the literature. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2014; 43:139-146. [PMID: 23897843 DOI: 10.1002/uog.12575] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/19/2013] [Indexed: 06/02/2023]
Abstract
OBJECTIVE To establish the prevalence of submicroscopic genetic copy number variants (CNVs) in fetuses with a structural ultrasound anomaly (restricted to one anatomical system) and a normal karyotype. The aim was to determine the diagnostic and prognostic value of genomic array testing in these pregnancies. METHODS Embase and PubMed databases were systematically searched for all relevant articles on prevalence of pathogenic submicroscopic CNVs in fetuses with ultrasound anomalies. Reported cases were sorted into groups according to anatomical site of the detected ultrasound anomaly. The prevalence of causative submicroscopic CNVs was calculated for each group. RESULTS Combined data of the reviewed studies (n = 18) indicated that fetuses with an ultrasound anomaly restricted to one anatomical system (n = 2220) had a 3.1-7.9% chance of carrying a causative submicroscopic CNV, depending on the anatomical system affected. This chance increased to 9.1% for fetuses with multiple ultrasound anomalies (n = 1139). CONCLUSION This review indicates that 3.1-7.9% of fetuses with a structural ultrasound anomaly restricted to one anatomical system and a normal karyotype will show a submicroscopic CNV, which explains its phenotype and provides information for fetal prognosis. Therefore, we conclude that microarray has considerable diagnostic and prognostic value in these pregnancies.
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Affiliation(s)
- M C de Wit
- Department of Obstetrics and Gynecology, Erasmus Medical Centre, Rotterdam, The Netherlands
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Lonardo F. Genomic microarrays in prenatal diagnosis. World J Med Genet 2013; 3:14-21. [DOI: 10.5496/wjmg.v3.i4.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/13/2013] [Accepted: 08/09/2013] [Indexed: 02/06/2023] Open
Abstract
The application of microarray-based techniques for the diagnosis of genomic rearrangements has been steadily growing in popularity since its introduction in 2004. Given the many advantages of these techniques over conventional cytogenetics, there is increasing pressure towards their application in prenatal diagnosis. However, there remain several important issues that must be addressed. For example, microarray-based techniques (comparative genomic hybridization-based arrays and single nucleotide polymorphism-based arrays) allow detection of even very small genomic imbalances that can determine pathological clinical conditions. In addition, there are other copy number variations which represent normal variation, with no detectable effects on phenotype. Given the still incomplete knowledge of the changes in our genome and the associated phenotypes, microarray-based diagnosis is likely to find variants of uncertain and unknown clinical significance. The interpretation of these variants is now a major challenge for the medical geneticist, who often find it difficult to establish precise correlations between genotype and phenotype. There is sufficient available evidence to justify the use of microarray-based diagnostics for a select number of specific conditions, but there is also an inevitable trend towards ever wider application. It is very important that this drift does not progress in an unchecked and uncontrolled manner under the thrust of commercial interests. Therefore, we recommend that scientific societies be vigilant and take an advisory role in the adopting of these technologies as new scientific knowledge becomes available.
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Lee CG, Park SJ, Yun JN, Ko JM, Kim HJ, Yim SY, Sohn YB. Array-based comparative genomic hybridization in 190 Korean patients with developmental delay and/or intellectual disability: a single tertiary care university center study. Yonsei Med J 2013; 54:1463-70. [PMID: 24142652 PMCID: PMC3809862 DOI: 10.3349/ymj.2013.54.6.1463] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
PURPOSE This study analyzed and evaluated the demographic, clinical, and cytogenetic data [G-banded karyotyping and array-based comparative genomic hybridization (array CGH)] of patients with unexplained developmental delay or intellectual disability at a single Korean institution. MATERIALS AND METHODS We collected clinical and cytogenetic data based on retrospective charts at Ajou University Medical Center, Suwon, Korea from April 2008 to March 2012. RESULTS A total of 190 patients were identified. Mean age was 5.1±1.87 years. Array CGH yielded abnormal results in 26 of 190 patients (13.7%). Copy number losses were about two-fold more frequent than gains. A total of 61.5% of all patients had copy number losses. The most common deletion disorders included 22q11.2 deletion syndrome, 15q11.2q12 deletion and 18q deletion syndrome. Copy number gains were identified in 34.6% of patients, and common diseases among these included Potocki-Lupski syndrome, 15q11-13 duplication syndrome and duplication 22q. Abnormal karyotype with normal array CGH results was exhibited in 2.6% of patients; theses included balanced translocation (n=2), inversion (n=2) and low-level mosaicism (n=1). Facial abnormalities (p<0.001) and failure to thrive were (p<0.001) also more frequent in the group of patients with abnormal CGH findings. CONCLUSION Array CGH is a useful diagnostic tool in clinical settings in patients with developmental delay or intellectual disability combined with facial abnormalities or failure to thrive.
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Affiliation(s)
- Cha Gon Lee
- Department of Medical Genetics, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon 443-380, Korea.
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Shaffer LG, Rosenfeld JA. Microarray-based prenatal diagnosis for the identification of fetal chromosome abnormalities. Expert Rev Mol Diagn 2013; 13:601-11. [PMID: 23895129 DOI: 10.1586/14737159.2013.811912] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The goal of prenatal cytogenetic testing is to provide reassurance to the couple seeking testing for their pregnancy, identify chromosome abnormalities in the fetus, if present, and provide treatments and medical management for affected babies. Cytogenetic analysis of banded chromosomes has been the standard for identifying chromosome abnormalities in the fetus for over 40 years. With chromosome analysis, whole chromosome aneuploidies and large structural rearrangements can be identified. The sequencing of the human genome has provided the resources to develop molecular tools that allow higher resolution observations of human chromosomes. The future holds the promise of sequencing that may identify chromosomal imbalances and deleterious single nucleotide variants. This review will focus on the use of genomic microarrays for the testing and identification of chromosome anomalies in prenatal diagnosis and will discuss the future directions of fetal testing.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA.
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Liao C, Fu F, Li R, Xie GE, Zhang YL, Li J, Li DZ. Implementation of high-resolution SNP arrays in the investigation of fetuses with ultrasound malformations: 5 years of clinical experience. Clin Genet 2013; 86:264-9. [PMID: 24000829 DOI: 10.1111/cge.12271] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 08/22/2013] [Accepted: 08/30/2013] [Indexed: 12/20/2022]
Abstract
Chromosome microarray analysis (CMA) has proven to be a powerful tool in postnatal patients with intellectual disabilities, and it is increasingly used in prenatal diagnosis. However, its diagnostic capabilities in prenatal diagnosis vary, and clinical experiences have failed to establish a consensus regarding CMA indications, the design and resolution of microarrays, and the notification and interpretation of copy number variations (CNVs). We present our 5 years of clinical experience using whole-genome high-resolution single nucleotide polymorphism (SNP) arrays to investigate 446 fetuses that had structural malformations detected with ultrasound but for which standard karyotyping analysis showed normal karyotypes. CMA revealed genomic CNVs in 323 (72.4%) cases and clinically significant CNVs in 11.4% of the fetuses (51/446), including 2 cases of uniparental disomy (UPD) as well as 1 case of cryptic mosaic monosomy of chromosome X. Variants of unknown significance (VOUS) existed in 2.0% of the tested fetuses (9/446). Our results demonstrate the value of whole-genome high-resolution SNP arrays in fetuses with congenital malformations and give a higher detection rate of clinically significant genomic imbalance, especially for detecting UPD. Sufficient communication between technicians and genetic counselors, along with parental testing and comparison with data from in-house or international sources, can significantly reduce VOUS.
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Affiliation(s)
- C Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
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Callaway JLA, Shaffer LG, Chitty LS, Rosenfeld JA, Crolla JA. The clinical utility of microarray technologies applied to prenatal cytogenetics in the presence of a normal conventional karyotype: a review of the literature. Prenat Diagn 2013; 33:1119-23. [PMID: 23983223 PMCID: PMC4285999 DOI: 10.1002/pd.4209] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 06/24/2013] [Accepted: 07/22/2013] [Indexed: 12/22/2022]
Abstract
ABSTRACT The clinical utility of microarray technologies when used in the context of prenatal diagnosis lies in the technology's ability to detect submicroscopic copy number changes that are associated with clinically significant outcomes. We have carried out a systematic review of the literature to calculate the utility of prenatal microarrays in the presence of a normal conventional karyotype. Amongst 12 362 cases in studies that recruited cases from all prenatal ascertainment groups, 295/12 362 (2.4%) overall were reported to have copy number changes with associated clinical significance (pCNC), 201/3090 (6.5%) when ascertained with an abnormal ultrasound, 50/5108 (1.0%) when ascertained because of increased maternal age and 44/4164 (1.1%) for all other ascertainment groups (e.g. parental anxiety and abnormal serum screening result). When additional prenatal microarray studies are included in which ascertainment was restricted to fetuses with abnormal ultrasound scans, 262/3730 (7.0%) were reported to have pCNCs. © 2013 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.
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Hillman SC, McMullan DJ, Silcock L, Maher ER, Kilby MD. How does altering the resolution of chromosomal microarray analysis in the prenatal setting affect the rates of pathological and uncertain findings? J Matern Fetal Neonatal Med 2013; 27:649-57. [PMID: 23869996 DOI: 10.3109/14767058.2013.825601] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Chromosomal Microarray Analysis (CMA) has a higher detection rate of pathogenic chromosome abnormalities over conventional (G-band) karyotyping. The optimum resolution of CMA in the prenatal setting remains debatable. Our objective was to determine if an increased detection rate was obtained by performing differing resolution of CMA on the same fetal samples and whether this resulted in an increase in variants of uncertain clinical significance (VOUS). METHODS Sixty-two fetal cases initially underwent a 1 Mb targeted BAC microarray within a clinical diagnostic setting in addition to conventional karyotyping. At the conclusion of pregnancy, a higher resolution 60 K oligonucleotide microarray was performed. RESULTS The 1 Mb BAC analysis demonstrated a detection rate of pathogenic copy number variations (CNVs) in 4.1% (95% CI 2.1-7.6) of cases and a variation of unknown significance (VOUS) rate of 0.4% (95% CI 0.07-2.2) over conventional G-band karyotyping. The 60 K array had an additional pathogenic detection rate of 4.8% (95% CI 1.6-13.3) over the BAC array but also detected an additional 8% (95% CI 1.3-14.8) VOUS. CONCLUSION As the CMA platform resolution increases detection rates increase but are associated with an increase in VOUS rates. Our findings support the need for further large scale studies to inform the national consensus on the resolution required and on reporting of VOUS in the antenatal setting.
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Affiliation(s)
- S C Hillman
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, University of Birmingham , Edgbaston, Birmingham , UK
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Srebniak MI, Mout L, Van Opstal D, Galjaard RJH. 0.5 Mb array as a first-line prenatal cytogenetic test in cases without ultrasound abnormalities and its implementation in clinical practice. Hum Mutat 2013; 34:1298-303. [PMID: 23674485 DOI: 10.1002/humu.22355] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 05/02/2013] [Indexed: 01/08/2023]
Abstract
Using whole-genome array testing instead of karyotyping in prenatal diagnosis for all indications may be desirable because of the higher diagnostic yield and shorter reporting time. The goal of this research was finding the optimal array resolution that could replace routine prenatal karyotyping in cases without ultrasound abnormalities, for example, referred for advanced maternal age or abnormal first trimester screening. As variants of unknown clinical significance (VOUS), if reported, might complicate decision-making about continuation of pregnancy, such an optimal array resolution should have a high abnormality detection rate and reveal a minimal amount of VOUS. The array data of 465 fetuses were retrospectively evaluated with several resolution levels, and the Decipher microdeletion/microduplication syndrome list was reviewed to assess what could be theoretically missed with a lower resolution. A 0.5-Mb resolution showed a high diagnostic yield potential and significantly minimized the number of VOUS. Based on our experience, we recommend genomic SNP array as a first-tier test in prenatal diagnosis. The resolution should be chosen based on the indication. In cases of fetal ultrasound abnormalities or intrauterine fetal death (IUFD), high-resolution analysis should be done. In other cases, we advise replacing karyotyping by SNP array analysis with 0.5 Mb resolution.
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Hillman SC, McMullan DJ, Hall G, Togneri FS, James N, Maher EJ, Meller CH, Williams D, Wapner RJ, Maher ER, Kilby MD. Use of prenatal chromosomal microarray: prospective cohort study and systematic review and meta-analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 41:610-620. [PMID: 23512800 DOI: 10.1002/uog.12464] [Citation(s) in RCA: 189] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 02/25/2013] [Accepted: 03/01/2013] [Indexed: 06/01/2023]
Abstract
OBJECTIVES Chromosomal microarray analysis (CMA) is utilized in prenatal diagnosis to detect chromosomal abnormalities not visible by conventional karyotyping. A prospective cohort of women undergoing fetal CMA and karyotyping following abnormal prenatal ultrasound findings is presented in the context of a systematic review and meta-analysis of the literature describing detection rates by CMA and karyotyping. METHODS We performed a prospective cohort study of 243 women undergoing CMA alongside karyotyping when a structural abnormality was detected on prenatal ultrasound. A systematic review of the literature was also performed. MEDLINE (1970-Dec 2012), EMBASE (1980-Dec 2012) and CINAHL (1982-June 2012) databases were searched electronically. Selected studies included > 10 cases and prenatal CMA in addition to karyotyping. The search yielded 560 citations. Full papers were retrieved for 86, and 25 primary studies were included in the systematic review. RESULTS Our cohort study found an excess detection rate of abnormalities by CMA of 4.1% over conventional karyotyping when the clinical indication for testing was an abnormal fetal ultrasound finding; this was lower than the detection rate of 10% (95% CI, 8-13%) by meta-analysis. The rate of detection for variants of unknown significance (VOUS) was 2.1% (95% CI, 1.3-3.3%) when the indication for CMA was an abnormal scan finding. The VOUS detection rate was lower (1.4%; 95% CI, 0.5-3.7%) when any indication for prenatal CMA was meta-analyzed. CONCLUSION We present evidence for a higher detection rate by CMA than by karyotyping not just in the case of abnormal ultrasound findings but also in cases of other indications for invasive testing. It is likely that CMA will replace karyotyping in high-risk pregnancies.
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Affiliation(s)
- S C Hillman
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham, UK
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Ferraris A, Bernardini L, Sabolic Avramovska V, Zanni G, Loddo S, Sukarova-Angelovska E, Parisi V, Capalbo A, Tumini S, Travaglini L, Mancini F, Duma F, Barresi S, Novelli A, Mercuri E, Tarani L, Bertini E, Dallapiccola B, Valente EM. Dandy-Walker malformation and Wisconsin syndrome: novel cases add further insight into the genotype-phenotype correlations of 3q23q25 deletions. Orphanet J Rare Dis 2013; 8:75. [PMID: 23679990 PMCID: PMC3667004 DOI: 10.1186/1750-1172-8-75] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/10/2013] [Indexed: 01/09/2023] Open
Abstract
Background The Dandy-Walker malformation (DWM) is one of the commonest congenital cerebellar defects, and can be associated with multiple congenital anomalies and chromosomal syndromes. The occurrence of overlapping 3q deletions including the ZIC1 and ZIC4 genes in few patients, along with data from mouse models, have implicated both genes in the pathogenesis of DWM. Methods and results Using a SNP-array approach, we recently identified three novel patients carrying heterozygous 3q deletions encompassing ZIC1 and ZIC4. Magnetic resonance imaging showed that only two had a typical DWM, while the third did not present any defect of the DWM spectrum. SNP-array analysis in further eleven children diagnosed with DWM failed to identify deletions of ZIC1-ZIC4. The clinical phenotype of the three 3q deleted patients included multiple congenital anomalies and peculiar facial appearance, related to the localization and extension of each deletion. In particular, phenotypes resulted from the variable combination of three recognizable patterns: DWM (with incomplete penetrance); blepharophimosis, ptosis, and epicanthus inversus syndrome; and Wisconsin syndrome (WS), recently mapped to 3q. Conclusions Our data indicate that the 3q deletion is a rare defect associated with DWM, and suggest that the hemizygosity of ZIC1-ZIC4 genes is neither necessary nor sufficient per se to cause this condition. Furthermore, based on a detailed comparison of clinical features and molecular data from 3q deleted patients, we propose clinical diagnostic criteria and refine the critical region for WS.
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Affiliation(s)
- Alessandro Ferraris
- Mendel Laboratory, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy
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Vestergaard EM, Christensen R, Petersen OB, Vogel I. Prenatal diagnosis: array comparative genomic hybridization in fetuses with abnormal sonographic findings. Acta Obstet Gynecol Scand 2013; 92:762-8. [PMID: 23590624 DOI: 10.1111/aogs.12146] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 04/10/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To evaluate the clinical value of a high-resolution whole-genome array method for examination of genomic imbalances in prenatal samples (46 amniotic fluid, 17 chorionic villus, and 26 products of conception) from fetuses with abnormal ultrasound, in a clinical setting where more than 90% of pregnant women receive first-trimester combined screening and a second-trimester anomaly scan. DESIGN Cross-sectional study. SETTING Fetal medicine units (national healthcare system) in Central and North Denmark Regions from March 2009 to April 2012. SAMPLES Eighty-nine samples obtained at 11.5-35.0 (mean 19.3) gestational weeks, either during ongoing pregnancy or after termination. METHODS DNA was extracted directly from amniotic fluid cells and chorionic villus samples, or from cultured cells, and examined with 80-kb resolution oligonucleotide array-based comparative genomic hybridization (aCGH). MAIN OUTCOME MEASURES Clinically significant copy number variations identified by aCGH. RESULTS We detected clinically significant copy number variations in 11 fetuses (12%, confidence interval 6.0-19%) with structural malformations. Three fetuses (3.4%) had uncertain clinical significant variations and incidental findings. CONCLUSIONS aCGH is a valuable diagnostic tool when fetal malformations are detected. More affected fetuses may be diagnosed at an earlier gestational age providing better possibilities for postnatal treatment and allowing for women to decide earlier on termination of pregnancy. When a normal result has reduced the risk of significant chromosomal aberration, aCGH may facilitate parental decision-making on whether to continue the pregnancy.
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An improved method to extract DNA from 1 ml of uncultured amniotic fluid from patients at less than 16 weeks' gestation. PLoS One 2013; 8:e59956. [PMID: 23565177 PMCID: PMC3614959 DOI: 10.1371/journal.pone.0059956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/20/2013] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to develop an improved technique for DNA extraction from 1 ml of uncultured AF from patients with a gestational age less than 16 weeks and to allow the use of array-CGH without DNA amplification. The DNA extraction protocol was tested in a series of 90 samples including 41 of uncultured AF at less than 16 weeks of gestation. Statistical analyses were performed using linear regression. To evaluate the sensitivity and the specificity of array-CGH on 1 ml of uncultured AF, five samples with an abnormal karyotype (three with aneuploidy, two with structural abnormalities) and five with a normal karyotype were studied. This protocol was reproducible and we were able to show a great improvement with higher yield of DNA obtained from all patients, including those with a gestational age less than 16 weeks (p = 0.003). All chromosomal abnormalities were detected and characterized by array-CGH and normal samples showed normal profiles. This new DNA extraction protocol associated with array-CGH analysis could be used in prenatal testing even when gestational age is less than 16 weeks, especially in cases with abnormal ultrasound findings.
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Mademont-Soler I, Morales C, Soler A, Martínez-Crespo JM, Shen Y, Margarit E, Clusellas N, Obón M, Wu BL, Sánchez A. Prenatal diagnosis of chromosomal abnormalities in fetuses with abnormal cardiac ultrasound findings: evaluation of chromosomal microarray-based analysis. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2013; 41:375-382. [PMID: 23233332 DOI: 10.1002/uog.12372] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/06/2012] [Indexed: 06/01/2023]
Abstract
OBJECTIVES To assess the frequency of karyotype abnormalities and chromosome 22q11.2 deletion syndrome among fetuses with abnormal cardiac ultrasound findings, and to evaluate the clinical value of chromosomal microarray-based analysis (CMA) in the study of such pregnancies. METHODS First, we carried out retrospective analysis of karyotype abnormalities and 22q11.2 deletion syndrome cases diagnosed between January 2009 and December 2011 in our center among fetuses with abnormal cardiac ultrasound findings (n = 276). Second, CMA was performed in 51 of the fetuses with such findings, normal karyotype and negative or no 22q11.2 deletion syndrome study, and in the only fetus with a heart defect and an apparently balanced de novo chromosomal rearrangement. RESULTS Out of the 276 pregnancies with abnormal cardiac ultrasound findings, karyotyping revealed a chromosomal abnormality in 44 (15.9%). Of fetuses with normal karyotype in which 22q11.2 deletion syndrome studies were performed, 6.4% (5/78) had this microdeletion syndrome. Among fetuses with abnormal cardiac findings, normal karyotype and negative or no 22q11.2 deletion syndrome study that underwent CMA, the detection rate of pathogenic copy number variants not detected by conventional cytogenetics was 2.0% (1/51), and no variants of uncertain clinical significance were found. In the fetus with a heart defect and an apparently balanced de novo chromosomal rearrangement, CMA revealed that the rearrangement was not truly balanced. CONCLUSIONS In the assessment of genetic abnormalities in pregnancies with abnormal cardiac ultrasound findings, the diagnostic yield may be increased by 2% if CMA is used as a complementary tool to conventional cytogenetics. Our results suggest that CMA could be a good alternative to karyotyping in these pregnancies.
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Affiliation(s)
- I Mademont-Soler
- Servei de Bioquímica i Genètica Molecular, Hospital Clínic, Barcelona, Spain
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Wei Y, Xu F, Li P. Technology-Driven and Evidence-Based Genomic Analysis for Integrated Pediatric and Prenatal Genetics Evaluation. J Genet Genomics 2013; 40:1-14. [DOI: 10.1016/j.jgg.2012.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 12/14/2012] [Indexed: 10/27/2022]
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KANG JIUN, KOO SUNHOE. Clinical implementation of chromosomal microarray technology in prenatal diagnosis (Review). Mol Med Rep 2012; 6:1219-22. [DOI: 10.3892/mmr.2012.1116] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 09/17/2012] [Indexed: 11/06/2022] Open
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Shaffer LG, Rosenfeld JA, Dabell MP, Coppinger J, Bandholz AM, Ellison JW, Ravnan JB, Torchia BS, Ballif BC, Fisher AJ. Detection rates of clinically significant genomic alterations by microarray analysis for specific anomalies detected by ultrasound. Prenat Diagn 2012; 32:986-95. [PMID: 22847778 PMCID: PMC3509216 DOI: 10.1002/pd.3943] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Revised: 06/01/2012] [Accepted: 06/26/2012] [Indexed: 12/18/2022]
Abstract
OBJECTIVE The aim of this study is to understand the diagnostic utility of comparative genomic hybridization (CGH)-based microarrays for pregnancies with abnormal ultrasound findings. METHODS We performed a retrospective analysis of 2858 pregnancies with abnormal ultrasounds and normal karyotypes (when performed) tested in our laboratory using CGH microarrays targeted to known chromosomal syndromes with later versions providing backbone coverage of the entire genome. Abnormalities were stratified according to organ system involvement. Detection rates for clinically significant findings among these categories were calculated. RESULTS Clinically significant genomic alterations were identified in cases with a single ultrasound anomaly (n = 99/1773, 5.6%), anomalies in two or more organ systems (n = 77/808, 9.5%), isolated growth abnormalities (n = 2/76, 2.6%), and soft markers (n = 2/77, 2.6%). The following anomalies in isolation or with additional anomalies had particularly high detection rates: holoprosencephaly (n = 9/85, 10.6%), posterior fossa defects (n = 21/144, 14.6%), skeletal anomalies (n = 15/140, 10.7%), ventricular septal defect (n = 14/132, 10.6%), hypoplastic left heart (n = 11/68, 16.2%), and cleft lip/palate (n = 14/136, 10.3%). CONCLUSIONS Microarray analysis identified clinically significant genomic alterations in 6.5% of cases with one or more abnormal ultrasound findings; the majority were below the resolution of karyotyping. Larger data sets such as this allow for sub-stratification by specific anomalies to determine risks for genomic alterations detectable by microarray analysis.
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Affiliation(s)
- Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington, USA.
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Hillman SC, McMullan DJ, Williams D, Maher ER, Kilby MD. Microarray comparative genomic hybridization in prenatal diagnosis: a review. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2012; 40:385-391. [PMID: 22887694 DOI: 10.1002/uog.11180] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/13/2012] [Indexed: 06/01/2023]
Abstract
G-band chromosomal karyotyping of fetal cells obtained by invasive prenatal testing has been used since the 1960s to identify structural chromosomal anomalies. Prenatal testing is usually performed in response to parental request, increased risk of fetal chromosomal abnormality associated with advanced maternal age, a high-risk screening test and/or the presence of a congenital malformation identified by ultrasonography. The results of karyotyping may inform the long-term prognosis (e.g. aneuploidy being associated with a poor outcome or microscopic chromosomal anomalies predicting global neurodevelopmental morbidity). Relatively recent advances in microarray technology are now enabling high-resolution genome-wide evaluation for DNA copy number abnormalities (e.g. deletions or duplications). While such technological advances promise increased sensitivity and specificity they can also pose difficult challenges of interpretation and clinical management. This review aims to give interested clinicians without an extensive prior knowledge of microarray technology, an overview of its use in prenatal diagnosis, the literature to date, advantages, potential pitfalls and experience from our own tertiary center.
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Affiliation(s)
- S C Hillman
- School of Clinical and Experimental Medicine, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham, UK
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