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Chromosomal Copy Number Variation Analysis in Pregnancy Products from Recurrent and Sporadic Miscarriage Using Next-Generation Sequencing. Reprod Sci 2022; 29:2927-2936. [PMID: 35578104 DOI: 10.1007/s43032-022-00969-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 05/07/2022] [Indexed: 10/18/2022]
Abstract
Chromosomal abnormality is one of the causes of fetal miscarriage. The potential differences of fetal chromosomal abnormalities in sporadic miscarriage (SM) and recurrent miscarriage (RM) remain unclear. The purpose of this study was to investigate copy number variations (CNVs) in SM and RM to provide useful genetic guidance for pregnancy and prenatal diagnosis. Four hundred eight samples of aborted fetuses were analyzed by CNV sequencing, and further functional enrichment analysis was performed. Chromosomal abnormalities were identified in 218 (53.4%) fetuses. There were 62 cases (15.2%) with structural chromosomal abnormalities, including 41 with VUS CNVs, 8 with pathogenic CNVs (pCNVs), and 5 with likely pCNVs. Duplications or deletions of 7p22, 8p22, 8p23, and Xp22.31 were significantly more common in RM cases and therefore believed to be related to RM. A total of 289 genes were identified, and 29 different functions were enriched as potential RM candidate genes and functions, which were mainly concentrated in 4 functional categories: chemokines and chemotaxis, protease activity and protein modification, defense response to bacterial and fungal infections, and immune response. The results of this study may improve our understanding of the etiology of RM and contribute to the establishment of a population-based genetic marker information for RM.
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Huang H, Cai M, Xue H, Xu L, Lin N. Single nucleotide polymorphism array in genetic evaluation of fetal ultrasound abnormalities: a retrospective follow-up study. Am J Transl Res 2022; 14:3516-3524. [PMID: 35702125 PMCID: PMC9185077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Fetal ultrasound abnormalities may be complicated by cognitive dysfunction or developmental retardation, and ultrasonography cannot detect these problems; therefore, chromosome detection is required in fetuses with ultrasound abnormalities. To examine the effectiveness of single nucleotide polymorphism (SNP) array in genetic diagnosis of fetal ultrasound abnormalities, the prenatal samples of 805 pregnant women with fetal ultrasound abnormalities were collected for SNP array and karyotyping analysis. A 95.5% percentage of normal karyotypes and 4.5% percentage of abnormal karyotypes were observed, and aneuploidy was detected in 28 fetuses with abnormal karyotypes. SNP array identified 89 positives, including 55 cases (6.8%) with pathogenic copy number variation (CNVs) and 34 (4.2%) with variants of unknown significance (VOUS). In addition to 36 cases showing consistent results with karyotyping, SNP array detected 19 additional cases with pathogenic CNVs, including microdeletion/microduplication syndromes in 18 cases and uniparental disomy in one case. The detection rate of pathogenic CNVs was highest in fetuses with structural abnormalities of multiple systems complicated by non-structural abnormalities (13.7%) and lowest in those with structural abnormalities of a single system (4.2%). Presence of pathogenic CNVs was 12.2% in fetuses with structural abnormalities in the urinary system, followed by in the skeletal system (10.3%), while no pathogenic CNVs were identified in fetuses with structural abnormalities in the head and face, the respiratory system or the digestive system. An 89.6% follow-up rate was seen in the study sample, and 55 fetuses with pathogenic CNVs identified by SNP array were all given induction of labor. Our data demonstrate that SNP array improves the detection of genetics aberrations in fetuses with prenatal ultrasound abnormality relative to karyotyping.
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Affiliation(s)
- Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect Fuzhou 350001, Fujian, China
| | - Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect Fuzhou 350001, Fujian, China
| | - Huili Xue
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect Fuzhou 350001, Fujian, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect Fuzhou 350001, Fujian, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect Fuzhou 350001, Fujian, China
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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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Chen L, Wang L, Yin D, Tang F, Zeng Y, Zhu H, Wang J. Analysis of autosomal dominant genes impacted by copy number loss in 24,844 fetuses without structural abnormalities. BMC Genomics 2022; 23:94. [PMID: 35109792 PMCID: PMC8812209 DOI: 10.1186/s12864-022-08340-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/28/2022] [Indexed: 12/03/2022] Open
Abstract
Background The broad application of high-resolution chromosome detection technology in prenatal diagnosis has identified copy number loss (CNL) involving autosomal dominant (AD) genes in certain fetuses. Exon sequencing of fetuses exhibiting structural anomalies yields diagnostic information in up to 20% of cases. However, there is currently no relevant literature about the genetic origin and pregnancy outcome of CNL involving AD genes in fetuses without structural abnormalities. Results This was a prospective study involving pregnant women who underwent amniocentesis for fetal copy number variation sequencing (CNVseq). Detection of parent-of-origin was suggested in cases of samples with CNL involving AD genes and the pregnancy outcome was monitored. Amniotic fluid samples from 24,844 fetuses without structural abnormalities were successfully tested via CNVseq. The results showed that 134 fetuses (0.5%) had small CNL (< 10 Mb) containing AD genes, after excluding microdeletion and microduplication syndrome and polymorphisms. By monitoring the pregnancy outcomes of the 134 fetuses, we found that 104 (77.6%) were good, 13 (9.7%) were adverse, and 17 (12.7%) pregnant women voluntarily chose to terminate pregnancy. Of the 13 fetuses with adverse pregnancy outcomes, only 2 fetuses had phenotypes consistent with those of diseases caused by AD genes involved in CNL. Conclusions The overall prognosis for fetuses without family history or structural abnormalities but with small CNL containing AD genes detected during pregnancy is good. The genetic origin, overlap status of established haploinsufficient gene and/or region, size of the CNL, and genetic mode may affect the pathogenicity of the CNL. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08340-y.
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Affiliation(s)
- Lin Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Daishu Yin
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Feng Tang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yang Zeng
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Hongmei Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China.
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Choi J, Jeon S, Kim D, Chua M, Do S. A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database: CNV extraction, transformation, and loading AI (CNV-ETLAI). Comput Biol Med 2022; 144:105332. [DOI: 10.1016/j.compbiomed.2022.105332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/08/2022] [Accepted: 02/16/2022] [Indexed: 11/24/2022]
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Single nucleotide polymorphism array versus karyotype for prenatal diagnosis in fetuses with abnormal ultrasound: A systematic review and meta-analysis. Eur J Obstet Gynecol Reprod Biol 2022; 271:235-244. [DOI: 10.1016/j.ejogrb.2022.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 11/22/2022]
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Xie M, Li J, Hu H, Wang P, Cong X, Li J, Dai L, Lu Y, Zhang W. Development and validation of a novel 26-plex system for prenatal diagnosis with forensic markers. Int J Legal Med 2022; 136:527-537. [PMID: 35102446 DOI: 10.1007/s00414-022-02780-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 01/18/2022] [Indexed: 10/19/2022]
Abstract
Short tandem repeat (STR) loci are commonly used in forensic casework, such as personal identification and paternity testing. In recent years, STR has also been widely used for rapid, accurate and automated prenatal diagnosis, known as quantitative fluorescent PCR (QF-PCR). Despite their usefulness, the current systems often lack the power to detect mosaicism for Turner syndrome. In this study, we developed a novel 26-plex system that combined the 22 STRs in chromosome 21/18/13/X, 3 sex loci and 1 quality control marker (TAF9L). The system was generated to achieve greater diagnostic power of trisomy 21/18/13 and sex chromosome abnormalities. Studies of the sensitivity, specificity, stability and accuracy were performed according to the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. Compared with the results of the chromosomal microarray analysis (CMA)/copy number variation sequencing (CNV-seq), the detection ratio of non-mosaic chromosome abnormalities of this system in the identification of chromosome 21/18/13/X/Y aneuploidies reached 100%, and the rate of negative results was consistently 100% based on 203 prenatal diagnosis sample analyses. In addition, our results suggested that this panel was a useful tool for mosaicism for Turner syndrome cases. Interestingly, we found one case with large segment loss of chromosome X, which indicated that we should be alert to this situation when the STR genotype of the parent-child is inconsistent in forensic genetics. In summary, this study demonstrated that our system is an accurate, cost-effective and rapid approach for the detection of chromosome numerical abnormalities in prenatal diagnosis.
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Affiliation(s)
- Mingkun Xie
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Huan Hu
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Panpan Wang
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Xueqi Cong
- Beijing Microread Genetics Co., Ltd., Beijing, China
| | - Jingzhi Li
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Lei Dai
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Yang Lu
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China
| | - Weishe Zhang
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, China.
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Rodriguez-Flores JL, Messai-Badji R, Robay A, Temanni R, Syed N, Markovic M, Al-Khayat E, Qafoud F, Nawaz Z, Badii R, Al-Sarraj Y, Mbarek H, Al-Muftah W, Alvi M, Rostami MR, Cruzado JCM, Mezey JG, Shakaki AA, Malek JA, Greenblatt MB, Fakhro KA, Machaca K, Al-Nabet A, Afifi N, Brooks A, Ismail SI, Althani A, Crystal RG. The QChip1 knowledgebase and microarray for precision medicine in Qatar. NPJ Genom Med 2022; 7:3. [PMID: 35046417 PMCID: PMC8770564 DOI: 10.1038/s41525-021-00270-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 11/04/2021] [Indexed: 12/28/2022] Open
Abstract
Risk genes for Mendelian (single-gene) disorders (SGDs) are consistent across populations, but pathogenic risk variants that cause SGDs are typically population-private. The goal was to develop "QChip1," an inexpensive genotyping microarray to comprehensively screen newborns, couples, and patients for SGD risk variants in Qatar, a small nation on the Arabian Peninsula with a high degree of consanguinity. Over 108 variants in 8445 Qatari were identified for inclusion in a genotyping array containing 165,695 probes for 83,542 known and potentially pathogenic variants in 3438 SGDs. QChip1 had a concordance with whole-genome sequencing of 99.1%. Testing of QChip1 with 2707 Qatari genomes identified 32,674 risk variants, an average of 134 pathogenic alleles per Qatari genome. The most common pathogenic variants were those causing homocystinuria (1.12% risk allele frequency), and Stargardt disease (2.07%). The majority (85%) of Qatari SGD pathogenic variants were not present in Western populations such as European American, South Asian American, and African American in New York City and European and Afro-Caribbean in Puerto Rico; and only 50% were observed in a broad collection of data across the Greater Middle East including Kuwait, Iran, and United Arab Emirates. This study demonstrates the feasibility of developing accurate screening tools to identify SGD risk variants in understudied populations, and the need for ancestry-specific SGD screening tools.
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Affiliation(s)
- Juan L Rodriguez-Flores
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | - Ramzi Temanni
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Monika Markovic
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Eiman Al-Khayat
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Fatima Qafoud
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Zafar Nawaz
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Ramin Badii
- Weill Cornell Medicine, Doha, Qatar
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | | | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
| | | | | | | | | | - Jason G Mezey
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | | | | | - Matthew B Greenblatt
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Khalid A Fakhro
- Weill Cornell Medicine, Doha, Qatar
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Ajayeb Al-Nabet
- Diagnostic Genomic Division, Hamad Medical Corporation, Doha, Qatar
| | - Nahla Afifi
- Qatar Biobank for Medical Research, Qatar Foundation, Doha, Qatar
| | - Andrew Brooks
- RUCDR Infinite Biologics, Piscataway, NJ, USA
- Department of Genetics, Rutgers University, New Brunswick, NJ, USA
| | | | - Asmaa Althani
- Qatar Genome Program, Qatar Foundation, Doha, Qatar
- Biomedical Research Center, Qatar University, Doha, Qatar
| | - Ronald G Crystal
- Department of Genetic Medicine, Weill Cornell Medicine, New York, NY, USA.
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Meng X, Jiang L. Prenatal detection of chromosomal abnormalities and copy number variants in fetuses with congenital gastrointestinal obstruction. BMC Pregnancy Childbirth 2022; 22:50. [PMID: 35045821 PMCID: PMC8772214 DOI: 10.1186/s12884-022-04401-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/12/2022] [Indexed: 12/13/2022] Open
Abstract
Background Congenital gastrointestinal obstruction (CGIO) mainly refers to the stenosis or atresia of any part from the esophagus to the anus and is one of the most common surgical causes in the neonatal period. The concept of genetic factors as an etiology of CGIO has been accepted, but investigations about CGIO have mainly focused on aneuploidy, and the focus has been on duodenal obstruction. The objective of this study was to evaluate the risk of chromosome aberrations (including numeric and structural aberrations) in different types of CGIO. A second objective was to assess the risk of abnormal CNVs detected by copy number variation sequencing (CNV-seq) in fetuses with different types of CGIO. Methods Data from pregnancies referred for invasive testing and CNV-seq due to sonographic diagnosis of fetal CGIO from 2015 to 2020 were obtained retrospectively from the computerized database. The rates of chromosome aberrations and abnormal CNV-seq findings for isolated CGIOs and complicated CGIOs and different types of CGIOs were calculated. Results Of the 240 fetuses with CGIO that underwent karyotyping, the detection rate of karyotype abnormalities in complicated CGIO was significantly higher than that of the isolated group (33.8% vs. 10.8%, p < 0.01). Ninety-three cases with normal karyotypes further underwent CNV-seq, and CNV-seq revealed an incremental diagnostic value of 9.7% over conventional karyotyping. In addition, the incremental diagnostic yield of CNV-seq analysis in complicated CGIOs (20%) was higher than that in isolated CGIOs (4.8%), and the highest prevalence of pathogenic CNVs/likely pathogenic CNVs was found in the duodenal stenosis/atresia group (17.5%), followed by the anorectal malformation group (15.4%). The 13q deletion, 10q26 deletion, 4q24 deletion, and 2p24 might be additional genetic etiologies of duodenal stenosis/atresia. Conclusions The risk of pathogenic chromosomal abnormalities and CNVs increased in the complicated CGIO group compared to that in the isolated CGIO group, especially when fetuses presented duodenal obstruction (DO) and anorectal malformation. CNV-seq was recommended to detect submicroscopic chromosomal aberrations for DO and anorectal malformation when the karyotype was normal. The relationship between genotypes and phenotypes needs to be explored in the future to facilitate prenatal diagnosis of fetal CGIO and yield new clues into their etiologies.
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Hu H, Zhang R, Ma Y, Luo Y, Pan Y, Xu J, Jiang L, Wang D. Prenatal Diagnosis and Genetic Analysis of 21q21.1-q21.2 Aberrations in Seven Chinese Pedigrees. Front Genet 2022; 12:731815. [PMID: 34992628 PMCID: PMC8724545 DOI: 10.3389/fgene.2021.731815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Chromosomal aberrations contribute to human phenotypic diversity and disease susceptibility, but it is difficult to assess their pathogenic effects in the clinic. Therefore, it is of great value to report new cases of chromosomal aberrations associated with normal phenotypes or clinical abnormalities. Methods: This was a retrospective analysis of seven pedigrees that carried 21q21.1–q21.2 aberrations. G-banding and single-nucleotide polymorphism array techniques were used to analyze chromosomal karyotypes and copy number variations in the fetuses and their family members. Results: All fetuses and their family members showed normal karyotypes in seven pedigrees. Here, it was revealed that six fetuses carried maternally inherited 21q21.1–q21.2 duplications, ranging from 1 to 2.7 Mb, but none of the mothers had an abnormal phenotype. In one fetus, an 8.7 Mb deletion of 21q21.1–q21.2 was found. An analysis of the pedigree showed that the deletion was also observed in the mother, brother, and maternal grandmother, but no abnormal phenotypes were found. Conclusion: This study identified 21q21.1–q21.2 aberrations in Chinese pedigrees. The carriers of 21q21.1–q21.2 duplications had no clinical consequences based on their phenotypes, and the 21q21.1–q21.2 deletion was transmitted through three generations of normal individuals. This provides benign clinical evidence for pathogenic assessment of 21q21.1–q21.2 duplication and deletion, which was considered a variant of uncertain significance and a likely pathogenic variant in previous reports.
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Affiliation(s)
- Huamei Hu
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Rong Zhang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yongyi Ma
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yanmei Luo
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yan Pan
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Juchun Xu
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lupin Jiang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Dan Wang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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Cai M, Lin N, Fan X, Chen X, Xu S, Fu X, Xu L, Huang H. Fetal Aberrant Right Subclavian Artery: Associated Anomalies, Genetic Etiology, and Postnatal Outcomes in a Retrospective Cohort Study. Front Pediatr 2022; 10:895562. [PMID: 35722491 PMCID: PMC9203729 DOI: 10.3389/fped.2022.895562] [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: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Aberrant right subclavian artery (ARSA) is becoming increasingly common in fetuses. However, there are relatively fewer studies regarding the genetic etiology of ARSA. We performed a genetic analysis of fetuses with ARSA and followed up on the pregnancy outcomes to evaluate the prognosis of the fetuses, providing information for prenatal and eugenic consultations. METHODS This retrospective study included 112 pregnant females whose fetuses were diagnosed with ARSA from December 2016 to February 2021. Fetal karyotype analysis and single-nucleotide polymorphism (SNP) array were performed. RESULTS The 112 fetuses were divided into two groups: the isolated ARSA group (n = 48, 42.9%) and the non-isolated ARSA group (ARSA with other ultrasound abnormalities, n = 64, 57.1%). The total rate of pathogenic copy number variation (CNV) observed using karyotype analysis (3/8) and SNP array (5/8) was 7.1% (8/112). The rates of pathogenic CNV in the isolated and non-isolated ARSA groups were 4.2% (2/48) and 9.4% (6/64), respectively. No significant difference was observed between the two groups (P = 0.463). The results of genetic analysis influenced the parents' decision to terminate the pregnancy. During the follow-up examination, fetuses with ARSA without pathogenic CNV were found to have normal growth and development after birth. CONCLUSION Fetuses with isolated ARSA have a low probability of being diagnosed with pathogenic CNV. However, when ARSA is complicated with other ultrasound abnormalities, the risk of pathogenic CNV remarkably increases. Prenatal genetic counseling and SNP-array should be recommended for better assessment of fetal prognosis.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiangqun Fan
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shiyi Xu
- Guangxi Medical University, Guangxi, China
| | - Xianguo Fu
- Department of Prenatal Diagnosis, Ningde Municipal Hospital, Ningde Normal University, Ningde, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Zhang Z, Pan L, Chen K, Tan R. Prenatal ultrasound features and genetic analysis for 17q12 microdeletion syndrome. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:1370-1374. [PMID: 35232906 PMCID: PMC10930568 DOI: 10.11817/j.issn.1672-7347.2021.210412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVES The 17q12 microdeletion syndrome is a type of syndrome caused by a deletion of 1.4 to 1.8 Mb in the 17q12 region of the chromosome. The main clinical features of the syndrome are structural or functional abnormalities in the kidney and urethra, type 5 diabetes, and neurodevelopmental or neuropsychiatric disorders. The diverse range of phenotypes associated with 17q12 microdeletion limited clinical recognition and diagnosis. In addition, the phenotypic description of this microdeletion is mainly about postpartum. Due to the rarity of the 17q12 microdeletion itself, studies on the prenatal phenotype of the 17q12 microdeletion are limited. This study aims to analyze the prenatal ultrasound features of 17q12 microdeletion, and to investigate the possibility of genotype-phenotype relationship for providing evidence for genetic counseling in such pregnancies. METHODS A total of 3 320 pregnant women and their fetuses were collected for the detection of chromosome copy number variation sequencing (CNV-Seq) due to different ultrasound anomalies in Xiangya Hospital of Central South University. The clinical data of pregnant women and their fetuses who were found to harbor 17q12 microdeletion were reviewed, including maternal age, fetus ultrasound findings, gestational week of the invasive procedure, CNV-Seq results, and the pregnancy outcome. CNV-Seq was tested in the parents to verify whether the abnormality was de novo or inherited. The prenatal ultrasound features and CNV-Seq test results of these 12 fetuses were analyzed and their pregnancy outcomes were followed up. RESULTS Approximately 0.36% (12/3 320) of fetuses were detected to have 17q12 microdeletion, all characterized as renal abnormalities, accounting for 4.2% (12/288) of all prenatal ultrasound with renal abnormalities, accounting for 48% (12/25) of prenatal ultrasound with renal abnormalities and pathogenic chromosomal abnormalities. The sizes of 17q12 deletion ranged from 1.4 to 1.7 Mb, and all of them included the HNF1B gene. Nine cases were de novo, 2 inherited from the mother, and 1 inherited from father. Among 12 fetuses with 17q12 deletion, 11 cases of prenatal ultrasound suggested bilateral hyperechogenic kidneys and 1 case only showed renal cyst, in which 3 fetuses with enlarged kidneys, 1 with clubfeet, and 1 with subependymal cyst. Pregnancy outcomes were available for 11 of the 12 fetuses. Of them, the parents of 9 fetuses with de novo deletion chose to terminate the pregnancy, and 2 live birth babies inherited from their mother with normal renal function had persistent renal echogenicity enhancement after birth. CONCLUSIONS Bilateral hyperechogenic kidneys show strikingly correlation with 17q12 microdeletion, suggesting the necessity of chromosome copy numbers detection for fetuses with hyperechogenic kidneys.
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Affiliation(s)
- Zhenhui Zhang
- Department of Obstetrics, First Hospital of Changsha, Changsha 410005.
| | - Lijuan Pan
- Department of Obstetrics, Xiangya Hospital, Central South University, Changsha 410008.
| | - Kuifang Chen
- Department of Obstetrics, Xiangya Hospital, Central South University, Changsha 410008
| | - Rong Tan
- Department of Ultrasonography, First Hospital of Changsha, Changsha 410005, China
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Prenatal Diagnosis by Array Comparative Genomic Hybridization in Fetuses with Cardiac Abnormalities. Genes (Basel) 2021; 12:genes12122021. [PMID: 34946970 PMCID: PMC8701951 DOI: 10.3390/genes12122021] [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: 11/08/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Congenital heart defects (CHDs) appear in 8–10 out of 1000 live born newborns and are one of the most common causes of deaths. In fetuses, the congenital heart defects are found even 3–5 times more often. Currently, microarray comparative genomic hybridization (array CGH) is recommended by worldwide scientific organizations as a first-line test in the prenatal diagnosis of fetuses with sonographic abnormalities, especially cardiac defects. We present the results of the application of array CGH in 484 cases with prenatally diagnosed congenital heart diseases by fetal ultrasound scanning (256 isolated CHD and 228 CHD coexisting with other malformations). We identified pathogenic aberrations and likely pathogenic genetic loci for CHD in 165 fetuses and 9 copy number variants (CNVs) of unknown clinical significance. Prenatal array-CGH is a useful method allowing the identification of all unbalanced aberrations (number and structure) with a much higher resolution than the currently applied traditional assessment techniques karyotype. Due to this ability, we identified the etiology of heart defects in 37% of cases.
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Monier I, Receveur A, Houfflin-Debarge V, Goua V, Castaigne V, Jouannic JM, Mousty E, Saliou AH, Bouchghoul H, Rousseau T, Valat AS, Groussolles M, Fuchs F, Benoist G, Degre S, Massardier J, Tsatsaris V, Kleinfinger P, Zeitlin J, Benachi A. Should prenatal chromosomal microarray analysis be offered for isolated fetal growth restriction? A French multicenter study. Am J Obstet Gynecol 2021; 225:676.e1-676.e15. [PMID: 34058167 DOI: 10.1016/j.ajog.2021.05.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/07/2021] [Accepted: 05/15/2021] [Indexed: 11/16/2022]
Abstract
BACKGROUND Compared with standard karyotype, chromosomal microarray analysis improves the detection of genetic anomalies and is thus recommended in many prenatal indications. However, evidence is still lacking on the clinical utility of chromosomal microarray analysis in cases of isolated fetal growth restriction. OBJECTIVE This study aimed to estimate the proportion of copy number variants detected by chromosomal microarray analysis and the incremental yield of chromosomal microarray analysis compared with karyotype in the detection of genetic abnormalities in fetuses with isolated fetal growth restriction. STUDY DESIGN This retrospective study included all singleton fetuses diagnosed with fetal growth restriction and no structural ultrasound anomalies and referred to 13 French fetal medicine centers over 1 year in 2016. Fetal growth restriction was defined as an estimated fetal weight of <tenth percentile for gestational age identified in ultrasound reports. For this analysis, we selected fetuses who underwent invasive genetic testing with karyotype and chromosomal microarray analysis results. Data were obtained from medical records and ultrasound databases and postmortem and placental examination reports in case of spontaneous stillbirths and terminations of pregnancy. Following the American College of Medical Genetics and Genomics guidelines, copy number variants were classified into 5 groups as following: pathogenic, likely pathogenic, variant of unknown significance, likely benign, and benign. RESULTS Of 682 referred fetuses diagnosed with isolated fetal growth restriction, both karyotype and chromosomal microarray analysis were performed in 146 fetuses. Overall, the detection rate of genetic anomalies found by chromosomal microarray analysis was estimated to be 7.5% (11 of 146 [95% confidence interval, 3.3-11.8]), including 10 copy number variants classified as pathogenic and 1 copy number variant classified as likely pathogenic. Among the 139 fetuses with normal karyotype, 5 were detected with pathogenic and likely pathogenic copy number variants, resulting in an incremental yield of 3.6% (95% confidence interval, 0.5-6.6) in chromosomal microarray analysis compared with karyotype. All fetuses detected with pathogenic or likely pathogenic copy number variants resulted in terminations of pregnancy. In addition, 3 fetuses with normal karyotype were detected with a variant of unknown significance (2.1%). Among the 7 fetuses with abnormal karyotype, chromosomal microarray analysis did not detect trisomy 18 mosaicism in all fetuses. CONCLUSION Our study found that compared with karyotype, chromosomal microarray analysis improves the detection of genetic anomalies in fetuses diagnosed with isolated fetal growth restriction. These results support the use of chromosomal microarray analysis in addition to karyotype for isolated fetal growth restriction.
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Affiliation(s)
- Isabelle Monier
- Obstetrical, Perinatal and Pediatric Epidemiology Research Team, Epidemiology and Statistics Research Center, Université de Paris, Institut national de la santé et de la recherche médicale, Institut national de la recherche agronomique, Paris, France; Department of Obstetrics and Gynaecology, Antoine Béclère Hospital, AP-HP, Paris Saclay University, Clamart, France.
| | - Aline Receveur
- Department of Cytogenetics and Reproductive Biology, Antoine Béclère Hospital, AP-HP, Paris Saclay University, Clamart, France
| | | | - Valérie Goua
- Department of Obstetrics and Gynaecology, Poitiers University Hospital, Poitiers, France
| | - Vanina Castaigne
- Department of Obstetrics and Gynaecology, Centre Hospitalier Intercommunal de Créteil, Créteil, France
| | - Jean-Marie Jouannic
- Fetal Medicine Department, Armand-Trousseau Hospital, AP-HP, Sorbonne University, Paris, France
| | - Eve Mousty
- Department of Gynaecology and Obstetrics, Nîmes University Hospital, Nîmes, France
| | - Anne-Hélène Saliou
- Department of Obstetrics and Gynaecology, Brest University Hospital, Brest, France
| | - Hanane Bouchghoul
- Department of Obstetrics and Gynaecology, Bicêtre Hospital, AP-HP, Paris Saclay University, Le Kremlin Bicêtre, France
| | - Thierry Rousseau
- Department of Obstetrics and Gynaecology, Dijon University Hospital, Dijon, France
| | - Anne-Sylvie Valat
- Department of Obstetrics and Gynaecology, Lens Hospital, Lens, France
| | - Marion Groussolles
- Department of Obstetrics and Gynecology, Paule de Viguier Hospital, Toulouse University Hospital, Toulouse, France
| | - Florent Fuchs
- Department of Obstetrics and Gynecology, Montpellier University Hospital Center, Montpellier, France
| | - Guillaume Benoist
- Department of Obstetrics and Gynecology, Caen University Hospital Center, Caen, France
| | - Sophie Degre
- Department of Obstetrics and Gynecology, Le Havre University Hospital Center, Le Havre, France
| | - Jérôme Massardier
- Department of Obstetrics and Gynecology, Hospices Civils de Lyon, Bron, France
| | - Vassilis Tsatsaris
- Department of Obstetrics and Gynecology, Cochin Hospital, AP-HP, Paris-Descartes University, Paris, France
| | | | - Jennifer Zeitlin
- Obstetrical, Perinatal and Pediatric Epidemiology Research Team, Epidemiology and Statistics Research Center, Université de Paris, Institut national de la santé et de la recherche médicale, Institut national de la recherche agronomique, Paris, France
| | - Alexandra Benachi
- Department of Obstetrics and Gynaecology, Antoine Béclère Hospital, AP-HP, Paris Saclay University, Clamart, France
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Meyer R, Bar-Yosef O, Barzilay E, Radinsky I, Segal CK, Ziv-Baran T, Shani H, Levin G, Katorza E. The Significance of Fetal Brain Ventricular Asymmetry Without Dilation. JOURNAL OF ULTRASOUND IN MEDICINE : OFFICIAL JOURNAL OF THE AMERICAN INSTITUTE OF ULTRASOUND IN MEDICINE 2021; 40:2413-2419. [PMID: 33427340 DOI: 10.1002/jum.15626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/22/2020] [Accepted: 12/25/2020] [Indexed: 06/12/2023]
Abstract
OBJECTIVES Fetal brain non-dilated ventricular asymmetry (NDVA) is a common finding on prenatal ultrasound exams. However, the optimal prenatal management in these cases remains unknown. We aimed to evaluate the benefit of prenatal genetic and magnetic resonance imaging (MRI) exams performed in cases of fetal NDVA detected on ultrasound. METHODS A historical cohort study from a tertiary medical center. Singleton pregnancies with fetal brain NDVA diagnosed on ultrasound were included. We defined ventricular asymmetry as a difference of ≥2.0 mm between the lateral ventricles and ventricular dilation as ventricular width of >10.0 mm. Outcomes were evaluated with genetic exams (karyotype and chromosomal microarray analysis [CMA]) and fetal brain MRI. RESULTS During the study period, there were 145 cases diagnosed with NDVA on ultrasound that comprised the cohort study. The rate of abnormal karyotype was 1.8% (1/56) and of abnormal CMA was 10% (3/30). The rate of minor additional CNS findings did not differ between ultrasound and MRI (3.4 versus 2.8%, respectively, p = .74). No major additional fetal brain findings were detected on MRI performed after ultrasound. CONCLUSIONS In cases diagnosed with NDVA on ultrasound, no significant additional anomalies were detected on fetal brain MRI. The rate of abnormal genetic tests was relatively high and warrants further studies.
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Affiliation(s)
- Raanan Meyer
- Department of Obstetrics and Gynecology, Sheba Medical Center, Ramat-Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Omer Bar-Yosef
- Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
- Pediatric Neurology Unit, Sheba Medical Center, Ramat-Gan, Israel
| | - Eran Barzilay
- Department of Obstetrics and Gynecology, Samson Assuta Ashdod University Hospital, Ashdod, Israel
| | - Igal Radinsky
- Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Chen Key Segal
- School of Medicine, Semmelweis University, Budapest, Hungary
| | - Tomer Ziv-Baran
- Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Hagit Shani
- Department of Obstetrics and Gynecology, Sheba Medical Center, Ramat-Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Gabriel Levin
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eldad Katorza
- Department of Obstetrics and Gynecology, Sheba Medical Center, Ramat-Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
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Filges I, Miny P, Holzgreve W, Tercanli S. How genomics is changing the practice of prenatal testing. J Perinat Med 2021; 49:1003-1010. [PMID: 34214293 DOI: 10.1515/jpm-2021-0220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 11/15/2022]
Abstract
New genomic laboratory technology namely microarrays and high throughput sequencing (HTS) as well as a steady progress in sonographic image capture and processing have changed the practice of prenatal diagnosis during the last decade fundamentally. Pregnancies at high risk for common trisomies are reliably identified by non-invasive prenatal testing (NIPT) and expert sonography has greatly improved the assessment of the fetal phenotype. Preconceptional comprehensive carrier screening using HTS is available for all parents, if they should wish to do so. A definite fetal diagnosis, however, will still require invasive testing for most conditions. Chromosomal microarrays (CMA) have greatly enhanced the resolution in the detection of chromosome anomalies and other causal copy number variations (CNV). Gene panel or whole exome sequencing (WES) is becoming the routine follow up of many anomalies detected by ultrasound after CNVs have been excluded. The benefits and limitations of the various screening as well as diagnostic options are perceived as complex by many who find it challenging to cope with the need for immediate choices. The communication of facts to ensure an informed decision making is obviously a growing challenge with the advent of the new genomic testing options. This contribution provides an overview of the current practice and policies in Switzerland.
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Affiliation(s)
- Isabel Filges
- Institut für Medizinische Genetik und Pathologie and Departement Klinische Forschung, Universitätsspital Basel, Basel, Switzerland
| | - Peter Miny
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Basel, Switzerland
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López-Carrasco A, Berbegall AP, Martín-Vañó S, Blanquer-Maceiras M, Castel V, Navarro S, Noguera R. Intra-Tumour Genetic Heterogeneity and Prognosis in High-Risk Neuroblastoma. Cancers (Basel) 2021; 13:5173. [PMID: 34680323 PMCID: PMC8534138 DOI: 10.3390/cancers13205173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Spatial ITH is defined by genomic and biological variations within a tumour acquired by tumour cell evolution under diverse microenvironments, and its role in NB patient prognosis is understudied. In this work, we applied pangenomic techniques to detect chromosomal aberrations in at least two different areas of each tumour and/or in simultaneously obtained solid and liquid biopsies, detecting ITH in the genomic profile of almost 40% of HR-NB. ITH was better detected when comparing one or more tumour pieces and liquid biopsy (50%) than between different tumour pieces (21%). Interestingly, we found that patients with ITH analysed by pangenomic techniques had a significantly better survival rate that those with non-heterogeneous tumours, especially in cases without MYCN amplification. Moreover, all patients in the studied cohort with high ITH (defined as 50% or more genomic aberration differences between areas of a tumour or simultaneously obtained samples) survived after 48 months. These results clearly support analysing at least two solid tumour areas (separately or mixed) and liquid samples to provide more accurate genomic diagnosis, prognosis and therapy options in HR-NB.
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Affiliation(s)
- Amparo López-Carrasco
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Ana P. Berbegall
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Susana Martín-Vañó
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Maite Blanquer-Maceiras
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Victoria Castel
- Clinical and Translational Oncology Research Group, Investigation Institute La Fe, 46026 Valencia, Spain;
| | - Samuel Navarro
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
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Song J, Zhang Q, Lu B, Gou Z, Wang T, Tang H, Xiang J, Jiang W, Deng X. Case Report: Candidate Genes Associated With Prenatal Ultrasound Anomalies in a Fetus With Prenatally Detected 1q23.3q31.2 Deletion. Front Genet 2021; 12:696624. [PMID: 34630509 PMCID: PMC8496901 DOI: 10.3389/fgene.2021.696624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Patients with deletions involving the long arm of chromosome 1 are rare, and the main aim of this study was to refine the genotype-phenotype correlation. Case Report: In this report, a 28-year-old pregnant woman, gravida 2 para 1, at 25+4 weeks of gestation underwent ultrasound examination in our institute. The ultrasonographic findings of the fetus were as follows: (1) fetal growth restriction; (2) cleft lip and palate; (3) bilateral renal hypoplasia; (4) lateral ventriculomegaly; (5) single umbilical artery; (6) absent stomach; (7) coronary sinus dilatation with persistent left superior vena cava, ventricular septal defect and unroofed coronary sinus syndrome. Chromosomal microarray analysis of amniotic fluid from the fetus revealed a 28.025 Mb deletion in 1q23.3q31.2, spanning from position 164,559,675 to 192,584,768 (hg19). Conclusion: Genotype-phenotype correlation might improve prenatal diagnosis of fetuses with chromosome 1q deletion. PBX1 could be a candidate gene for fetal growth restriction, renal hypoplasia and congenital heart disease. Fetal growth restriction was accompanied by decreased renal volume in the fetus. Combined with ultrasonic examination, the application of chromosomal microarray analysis will provide accurate prenatal diagnosis.
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Affiliation(s)
- Jiahao Song
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Qian Zhang
- Department of Obstetrics and Gynecology, The Affiliated Suzhou Hospital Nanjing Medical University, Suzhou, China
| | - Bing Lu
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zhongshan Gou
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ting Wang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital Nanjing Medical University, Suzhou, China
| | - Hui Tang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital Nanjing Medical University, Suzhou, China
| | - Jingjing Xiang
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital Nanjing Medical University, Suzhou, China
| | - Wei Jiang
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Xuedong Deng
- Center for Medical Ultrasound, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
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Hui L, Pynaker C, Kennedy J, Lewis S, Amor DJ, Walker SP, Halliday J. Study protocol: childhood outcomes of fetal genomic variants: the PrenatAL Microarray (PALM) cohort study. BMC Pediatr 2021; 21:447. [PMID: 34629048 PMCID: PMC8502634 DOI: 10.1186/s12887-021-02809-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/07/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The implementation of genomic testing in pregnancy means that couples have access to more information about their child's genetic make-up before birth than ever before. One of the resulting challenges is the management of genetic variations with unclear clinical significance. This population-based study will help to close this critical knowledge gap through a multidisciplinary cohort study of children with and without genomic copy number variants (CNVs) diagnosed before birth. By comparing children with prenatally-ascertained CNVs to children without a CNV, we aim to (1) examine their developmental, social-emotional and health status; (2) measure the impact of prenatal diagnosis of a CNV on maternal perceptions of child health, behavior and development; and (3) determine the proportion of prenatally-ascertained CNVs of unknown or uncertain significance that are reclassified as benign or pathogenic after 2 or more years. METHODS This study will establish and follow up a cohort of mother-child pairs who have had a prenatal diagnosis with a chromosomal microarray from 2013-2019 in the Australian state of Victoria. Children aged 12 months to 7 years will be assessed using validated, age-appropriate measures. The primary outcome measures will be the Wechsler Preschool and Primary Scale of Intelligence IV (WPSSI-IV) IQ score (2.5 to 7 year old's), the Ages and Stages Questionnaire (12-30 months old), and the Brief Infant- Toddler Social and Emotional Assessment (BITSEA) score. Clinical assessment by a pediatrician will also be performed. Secondary outcomes will be scores obtained from the: Vineland Adaptive Behavior Scale, Maternal Postnatal Attachment Questionnaire, the Vulnerable Child Scale, Profile of Mood States, Parent Sense of Competence Scale. A descriptive analysis of the reclassification rates of CNVs after ≥2 years will be performed. DISCUSSION This study protocol describes the first Australian cohort study following children after prenatal diagnostic testing with chromosomal microarray. It will provide long-term outcomes of fetal genomic variants to guide evidence-based pre-and postnatal care. This, in turn, will inform future efforts to mitigate the negative consequences of conveying genomic uncertainty during pregnancy. TRIAL REGISTRATION ACTRN12620000446965p ; Registered on April 6, 2020.
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Affiliation(s)
- Lisa Hui
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC, Australia.
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia.
- Mercy Hospital for Women, Heidelberg, VIC, Australia.
- Northern Health, Epping, VIC, Australia.
| | - Cecilia Pynaker
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC, Australia
| | - Joanne Kennedy
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Sharon Lewis
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - David J Amor
- Mercy Hospital for Women, Heidelberg, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Neurodisability and Rehabilitation group, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC, Australia
| | - Susan P Walker
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
- Mercy Hospital for Women, Heidelberg, VIC, Australia
| | - Jane Halliday
- Reproductive Epidemiology group, Murdoch Children's Research Institute, Flemington Rd, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
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Chau MHK, Qian J, Chen Z, Li Y, Zheng Y, Tse WT, Kwok YK, Leung TY, Dong Z, Choy KW. Trio-Based Low-Pass Genome Sequencing Reveals Characteristics and Significance of Rare Copy Number Variants in Prenatal Diagnosis. Front Genet 2021; 12:742325. [PMID: 34616436 PMCID: PMC8488434 DOI: 10.3389/fgene.2021.742325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/25/2021] [Indexed: 01/22/2023] Open
Abstract
Background: Low-pass genome sequencing (GS) detects clinically significant copy number variants (CNVs) in prenatal diagnosis. However, detection at improved resolutions leads to an increase in the number of CNVs identified, increasing the difficulty of clinical interpretation and management. Methods: Trio-based low-pass GS was performed in 315 pregnancies undergoing invasive testing. Rare CNVs detected in the fetuses were investigated. The characteristics of rare CNVs were described and compared to curated CNVs in other studies. Results: A total of 603 rare CNVs, namely, 597 constitutional and 6 mosaic CNVs, were detected in 272 fetuses (272/315, 86.3%), providing 1.9 rare CNVs per fetus (603/315). Most CNVs were smaller than 1 Mb (562/603, 93.2%), while 1% (6/603) were mosaic. Forty-six de novo (7.6%, 46/603) CNVs were detected in 11.4% (36/315) of the cases. Eighty-four CNVs (74 fetuses, 23.5%) involved disease-causing genes of which the mode of inheritance was crucial for interpretation and assessment of recurrence risk. Overall, 31 pathogenic/likely pathogenic CNVs were detected, among which 25.8% (8/31) were small (<100 kb; n = 3) or mosaic CNVs (n = 5). Conclusion: We examined the landscape of rare CNVs with parental inheritance assignment and demonstrated that they occur frequently in prenatal diagnosis. This information has clinical implications regarding genetic counseling and consideration for trio-based CNV analysis.
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Affiliation(s)
- Matthew Hoi Kin Chau
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Jicheng Qian
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Zihan Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Ying Li
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Yu Zheng
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Wing Ting Tse
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Shatin, Hong Kong, SAR China
| | - Zirui Dong
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, Hong Kong, SAR China.,Hong Kong Hub of Pediatric Excellence, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center For Medical Genetics, Shatin, Hong Kong, SAR China
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71
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Wu H, Huang Q, Zhang X, Yu Z, Zhong Z. Analysis of Genomic Copy Number Variation in Miscarriages During Early and Middle Pregnancy. Front Genet 2021; 12:732419. [PMID: 34603391 PMCID: PMC8484914 DOI: 10.3389/fgene.2021.732419] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/31/2021] [Indexed: 12/13/2022] Open
Abstract
The purpose of this study was to explore the copy number variations (CNVs) associated with miscarriage during early and middle pregnancy and provide useful genetic guidance for pregnancy and prenatal diagnosis. A total of 505 fetal specimens were collected and CNV sequencing (CNV-seq) analysis was performed to determine the types and clinical significance of CNVs, and relevant medical records were collected. The chromosomal abnormality rate was 54.3% (274/505), among which the numerical chromosomal abnormality rate was 40.0% (202/505) and structural chromosomal abnormality rate was 14.3% (72/505). Chromosomal monosomy mainly occurred on sex chromosomes, and chromosomal trisomy mainly occurred on chromosomes 16, 22, 21, 15, 13, and 9. The incidence of numerical chromosomal abnormalities in ≥35 year-old age pregnant women was significantly higher than <35 year-old age group. The highest incidence of pathogenic CNV (pCNV) was found in fetuses at ≤6 weeks of pregnancy (5.26%), and the incidence of variants of unknown significance (VOUS) CNVs decreased gradually with the increase of gestational age. The rate of chromosomal abnormalities of fetuses in early pregnancy (59.5%) was higher than that of fetuses in middle pregnancy (27.2%) (p < 0.001). There were 168 genes in VOUS + pCNV regions. 41 functions and 12 pathways (p < 0.05) were enriched of these genes by Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Some meaningful genetic etiology information such as genes and pathways has been obtained, it may provide useful genetic guidance for pregnancy and prenatal diagnosis.
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Affiliation(s)
- Heming Wu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, 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, China
| | - Qingyan Huang
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, 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, China
| | - Xia Zhang
- 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, China.,Center for Prenatal Diagnosis, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou, China
| | - Zhikang Yu
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, 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, China
| | - Zhixiong Zhong
- Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, 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, China
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72
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Wang J, Tang XX, Zhou Q, Yang S, Shi Y, Yu B, Zhang B, Wang LL. Prenatal Diagnostic Testing Following High-Risk Result from Serological Screening: Which Shall We Select? Int J Womens Health 2021; 13:879-888. [PMID: 34588820 PMCID: PMC8473719 DOI: 10.2147/ijwh.s324529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 09/04/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose We retrospectively analyzed the results of prenatal diagnosis in women with high-risk (HR) serological screening results, and discussed the reasonable application of diagnostic testing. Patients and Methods Diagnostic testing was done in 2239 pregnant women who had HR results from serological screening in two prenatal diagnosis centers. According to the HR results, they were divided into simple HR, HR combined with ultrasound abnormalities, and HR combined with other indication groups. After receiving counselling from clinicians, they were allowed to choose either the traditional karyotype analysis and/or chromosomal microarray analysis (CMA). Results Those who underwent CMA comprised 49.3%, 97.6%, and 100% of the HR group, HR combined with ultrasound abnormalities, and HR combined with other indication groups, respectively. Among the 100 (4.47%) clinically significant results, 55 (2.46%), 15 (0.67%), and 30 (1.34%) were chromosomal aneuploidies, chromosomal structural abnormalities, and pathogenic copy number variations (CNVs), respectively. The rate of abnormalities was 3.77%, 13.71%, and 19.05% in the simple HR, HR combined with ultrasound abnormalities, and HR combined with other indication groups, respectively. The increasing rate of clinical pathogenic CNVs was 1.34% using CMA in HR pregnant women, 9.52% in the HR combined with other indication group, and 1.24% in the simple HR group. Among the 573 women who chose both diagnostic tests, 45 had abnormal results. Only one case detected using karyotype analysis was missed on CMA. The incidence of chromosomal aneuploidy tended to increase with increase in HR values. However, chromosomal structural abnormalities and pathogenic CNVs did not increase. Conclusion CMA should be recommended as the first-line diagnostic testing for women with HR screening results, especially combined with other abnormal indications.
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Affiliation(s)
- Jing Wang
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, 213003, Jiangsu Province, People's Republic of China
| | - Xin-Xin Tang
- Lianyungang Maternal and Child Health Hospital Affiliated to Yangzhou University, Lianyungang, 222000, Jiangsu Province, People's Republic of China
| | - Qin Zhou
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, 213003, Jiangsu Province, People's Republic of China
| | - Shuting Yang
- Lianyungang Maternal and Child Health Hospital Affiliated to Yangzhou University, Lianyungang, 222000, Jiangsu Province, People's Republic of China
| | - Ye Shi
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, 213003, Jiangsu Province, People's Republic of China
| | - Bin Yu
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, 213003, Jiangsu Province, People's Republic of China
| | - Bin Zhang
- Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, 213003, Jiangsu Province, People's Republic of China
| | - Lei-Lei Wang
- Lianyungang Maternal and Child Health Hospital Affiliated to Yangzhou University, Lianyungang, 222000, Jiangsu Province, People's Republic of China
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73
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Ridnõi K, Muru K, Keernik M, Pajusalu S, Ustav EL, Tammur P, Mölter-Väär T, Kahre T, Šamarina U, Asser K, Szirko F, Reimand T, Õunap K. A two-year prospective study assessing the performance of fetal chromosomal microarray analysis and next-generation sequencing in high-risk pregnancies. Mol Genet Genomic Med 2021; 9:e1787. [PMID: 34486251 PMCID: PMC8580097 DOI: 10.1002/mgg3.1787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/22/2021] [Accepted: 08/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background Introduction of cell‐free fetal DNA (cff‐DNA) testing in maternal blood opened possibilities to improve the performance of combined first‐trimester screening (cFTS) in terms of better detection of trisomies and lowering invasive testing rate. The use of new molecular methods, such as chromosomal microarray analysis (CMA) and next‐generation sequencing (NGS), has shown benefits in prenatal diagnosis of chromosomal and genetic diseases, which are not detectable with cff‐DNA screening, but require an invasive procedure. Methods The objective of this study was to evaluate prospectively during two years performance of CMA and NGS in high‐risk pregnancies. Initially, we investigated 14,566 singleton pregnancies with cFTS. A total of 334 high‐risk pregnancies were selected for CMA diagnostic performance evaluation and 28 cases of highly dysmorphic fetuses for NGS analysis. CMA study group was divided into two groups based on the indications for testing; group A patients with high‐risk for trisomies after cFTS, but normal ultrasound and group B patients who met criteria for CMA as a first‐tier diagnostic test. Results The diagnostic yield of CMA was overall 3.6% (1.6% in Group A and 6.0% in Group B). In NGS analysis group, we report diagnostic yield of 17.9%. Conclusion The use of CMA in high‐risk pregnancies is justified and provides relevant clinical information in 3.6% of the cases. NGS analysis in fetuses with multiple anomalies shows promising results, but more investigations are needed for a better understanding of practical applications of this molecular diagnosis method in prenatal settings.
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Affiliation(s)
- Konstantin Ridnõi
- Centre for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kai Muru
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Maria Keernik
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Sander Pajusalu
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Pille Tammur
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Triin Mölter-Väär
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Tiina Kahre
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Ustina Šamarina
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Karin Asser
- Radiology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Ferenc Szirko
- Centre for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Katrin Õunap
- Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
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74
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Chen Y, Jiang Y, Chen B, Qian Y, Liu J, Yang M, Zhao B, Luo Q. Case Report: Whole Exome Sequencing Revealed Two Novel Mutations of PIEZO1 Implicated in Nonimmune Hydrops Fetalis. Front Genet 2021; 12:684555. [PMID: 34421994 PMCID: PMC8375471 DOI: 10.3389/fgene.2021.684555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Nonimmune hydrops fetalis (NIHF) is a serious and complex fetal condition. Prenatal diagnosis of hydrops fetalis is not difficult by ultrasound. However, determining the underlying etiology of NIHF remains a challenge which is essential to address for prenatal counseling. We extracted DNA from a proband prenatally diagnosed unexplained NIHF. Trio-whole exome sequencing (WES) was performed to filter candidate causative variants. Two gene mutations were identified as a compound heterozygous state in the proband. Both variants located on the PIEZO1 gene: c.3895C > T, a missense mutation in exon 27 paternally inherited; c.4030_4032del, a maternally inherited in-frame deletion in exon 28. Both variants were first reported to be related to NIHF. PIEZO1 gene mutations, leading to an autosomal recessive congenital lymphatic dysplasia, which can present as NIHF and partial or complete resolution postnatally. In conclusion, WES can aid in the elucidation of the genetic cause of NIHF and has a positive effect on the assessment of prognosis.
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Affiliation(s)
- Yuan Chen
- Department of Obstetrics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Jiang
- Department of Obstetrics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bangwu Chen
- Department of Obstetrics, Ninghai Maternal and Child health Care Hospital, Ningbo, China
| | - Yeqing Qian
- Department of Reproductive Genetics, Women's Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Jiao Liu
- Department of Obstetrics, Lishui Maternal and Child Health Care Hospital, Lishui, China
| | - Mengmeng Yang
- Department of Obstetrics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Baihui Zhao
- Department of Obstetrics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qiong Luo
- Department of Obstetrics, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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75
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Zhang F, Long W, Zhou Q, Wang J, Shi Y, Liu J, Wang Q. Is Prenatal Diagnosis Necessary for Fetal Isolated Nasal Bone Absence or Hypoplasia? Int J Gen Med 2021; 14:4435-4441. [PMID: 34408481 PMCID: PMC8364966 DOI: 10.2147/ijgm.s322359] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022] Open
Abstract
Purpose This study aimed to explore the value of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in the prenatal diagnosis of fetal isolated nasal bone absence (INBA) or isolated nasal bone hypoplasia (INBH). We hope to provide additional relevant information for clinical counseling. Patients and Methods From November 1, 2018, to March 1, 2020, 55 pregnant women with isolated nasal bone dysplasia were admitted to the Changzhou Maternity and Child Health Care Hospital. Based on the degree of abnormality, the patients were divided into two groups: INBA and INBH. CMA was performed on all patients. The clinical data and prenatal genetic diagnoses of the two groups were retrospectively analyzed. According to the requirements of WES for samples, 12 cases with negative CMA results were selected for the WES test. Results A total of 55 cases with INBA or INBH met the inclusion criteria. In 35INBA fetuses, there was one case of trisomy 21 and one case of 10q11.22 deletion (5.7Mb), and the abnormality rate was 5.71% (2/35). Compared with INBA fetuses, the abnormality rate was increased in the fetuses with INBH [15.00% (3/20)] (15.00% vs 5.71%); there was one case of 1q21.1 duplication (1.3Mb), one case of Xp22.31 duplication (1.67Mb), and one case of 4p deletion (7.6Mb). In a later retrospective study, two pathogenic variants were identified in two cases after the WES test; the abnormality rate was 16.67% (2/12), which involved RUNX2 and CDH4 genes, respectively. Conclusion A preliminary study confirmed that molecular prenatal diagnosis should be performed in fetuses with INBA or INBH. CMA followed by WES is an effective method.
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Affiliation(s)
- Feng Zhang
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Wei Long
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Qin Zhou
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Jing Wang
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Ye Shi
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Jianbing Liu
- Department of Medical Genetics, Changzhou Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Changzhou, Jiangsu Province, People's Republic of China
| | - Qiuwei Wang
- Clinical Laboratory, Changzhou Children's Hospital Affiliated to Nantong Medical University, Changzhou, Jiangsu Province, People's Republic of China
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76
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Berisha SZ, Shetty S, Prior TW, Mitchell AL. Cytogenetic and molecular diagnostic testing associated with prenatal and postnatal birth defects. Birth Defects Res 2021; 112:293-306. [PMID: 32115903 PMCID: PMC9290954 DOI: 10.1002/bdr2.1648] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 11/23/2022]
Abstract
Genetic testing is beneficial for patients and providers when in search of answers to medical problems related to the prenatal or early postnatal period. It can help to identify the cause or confirm a diagnosis associated with developmental delay, intellectual disability, dysmorphic features, heart defects, multiple malformations, short stature, stillbirth, neonatal death, or fertility problems. Genetic testing can be used to rule out single‐gene or chromosome abnormalities. Different diagnostic cytogenetic and molecular genetic techniques are applied in clinical genetics laboratories, from conventional ones to the state of the art chromosomal microarrays and next‐generation sequencing. Each of the genetic techniques or methods has its strengths and limitations, however different methods complement each‐other in trying to identify the genetic variation(s) responsible for a medical condition, especially the ones related to birth defects.
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Affiliation(s)
- Stela Z Berisha
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Shashi Shetty
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Pathology, Case Western Reserve University, University Hospitals, Cleveland, Ohio
| | - Thomas W Prior
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Pathology, Case Western Reserve University, University Hospitals, Cleveland, Ohio
| | - Anna L Mitchell
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Genetics and Genome Sciences, Case Western Reserve University, University Hospitals, Cleveland, Ohio
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Larroya M, Tortajada M, Mensión E, Pauta M, Rodriguez-Revenga L, Borrell A. Have maternal or paternal ages any impact on the prenatal incidence of genomic copy number variants associated with fetal structural anomalies? PLoS One 2021; 16:e0253866. [PMID: 34242293 PMCID: PMC8270131 DOI: 10.1371/journal.pone.0253866] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 06/14/2021] [Indexed: 11/18/2022] Open
Abstract
The objective of this study was to determine whether maternal or paternal ages have any impact on the prenatal incidence of genomic copy number variants (CNV) in fetuses with structural anomalies. We conducted a non-paired case-control study (1:2 ratio) among pregnancies undergoing chromosomal microarray analysis (CMA) because of fetal ultrasound anomalies, from December 2012 to May 2020. Pregnancies with any pathogenic copy number variant (CNV), either microdeletion or microduplication, were defined as cases. Controls were selected as the next two pregnancies with the same indication for CMA but with a normal result. Logistic regression was used, adjusting by use of assisted reproductive technology (ART) and parental smoking. Stratified analysis was performed according to CNV type (de novo/inherited and recurrent/non-recurrent). The study included 189 pregnancies: 63 cases and 126 controls. Mean maternal age in cases was 33.1 (SD 4.6) years and 33.9 (SD 6.0) years in controls. Mean paternal mean age was 34.5 (SD 4.8) years in cases and 35.8 (SD 5.8) years in controls. No significant differences in maternal or paternal age were observed, neither in stratified analysis according to the CNV type. Moreover, the proportion of cases were not significantly different between non-advanced and advanced ages, either considering paternal or maternal ages. The presence of pathogenic CNV at CMA in fetuses with structural anomalies was not found to be associated with advanced paternal or maternal age.
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Affiliation(s)
- Marta Larroya
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clinic de Ginecologia, Obstetricia i Neonatologia, IDIBAPS, Fetal i+D Fetal Medicine Research and Centre for Biomedical Research on Rare Diseases (CIBER-ER), University of Barcelona, Barcelona, Catalonia, Spain
- * E-mail: (ML); (AB)
| | - Marta Tortajada
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clinic de Ginecologia, Obstetricia i Neonatologia, IDIBAPS, Fetal i+D Fetal Medicine Research and Centre for Biomedical Research on Rare Diseases (CIBER-ER), University of Barcelona, Barcelona, Catalonia, Spain
| | - Eduard Mensión
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clinic de Ginecologia, Obstetricia i Neonatologia, IDIBAPS, Fetal i+D Fetal Medicine Research and Centre for Biomedical Research on Rare Diseases (CIBER-ER), University of Barcelona, Barcelona, Catalonia, Spain
| | - Montse Pauta
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Laia Rodriguez-Revenga
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
- Biochemistry and Molecular Genetics Department, Hospital Clinic of Barcelona, Barcelona, Catalonia, Spain
- CIBER of Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Antoni Borrell
- BCNatal—Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Institut Clinic de Ginecologia, Obstetricia i Neonatologia, IDIBAPS, Fetal i+D Fetal Medicine Research and Centre for Biomedical Research on Rare Diseases (CIBER-ER), University of Barcelona, Barcelona, Catalonia, Spain
- * E-mail: (ML); (AB)
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Ali TM, Mateu-Brull E, Balaguer N, Dantas C, Borges HR, de Oliveira MQG, Rodrigo L, Campos-Galindo I, Navarro R, Milán M. Inherited unbalanced reciprocal translocation with 3q duplication and 5p deletion in a foetus revealed by cell-free foetal DNA (cffDNA) testing: a case report. Eur J Med Res 2021; 26:64. [PMID: 34187576 PMCID: PMC8243479 DOI: 10.1186/s40001-021-00535-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
Background Since 2011, screening maternal blood for cell-free foetal DNA (cffDNA) fragments has offered a robust clinical tool to classify pregnancy as low or high-risk for Down, Edwards, and Patau syndromes. With recent advances in molecular biology and improvements in data analysis algorithms, the screening’s scope of analysis continues to expand. Indeed, screening now encompassess additional conditions, including aneuploidies for sex chromosomes, microdeletions and microduplications, rare autosomal trisomies, and, more recently, segmental deletions and duplications called copy number variations (CNVs). Yet, the ability to detect CNVs creates a new challenge for cffDNA analysis in couples in which one member carries a structural rearrangement such as a translocation or inversion. Case presentation We report a segmental duplication of the long arm of chromosome 3 and a segmental deletion of the short arm of chromosome 5 detected by cffDNA analysis in a 25-year-old pregnant woman. The blood sample was sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay. G-band karyotyping in amniotic fluid only detected an abnormality in chromosome 5. Next-generation sequencing in amniocytes confirmed both abnormalities and identified breakpoints in 3q26.32q29 and 5p13.3p15. The foetus died at 21 weeks of gestation due to multiple abnormalities, and later G-band karyotyping in the parents revealed that the father was a carrier of a balanced reciprocal translocation [46,XY,t(3;5)(q26.2;p13)]. Maternal karyotype appeared normal. Conclusion This case provides evidence that extended cffDNA can detect, in addition to aneuploidies for whole chromosomes, large segmental aneuploidies. In some cases, this may indicate the presence of chromosomal rearrangements in a parent. Such abnormalities are outside the scope of standard cffDNA analysis targeting chromosomes 13, 18, 21, X, and Y, potentially leading to undiagnosed congenital conditions.
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Affiliation(s)
- Taccyanna M Ali
- Laboratório Igenomix, Laboratório de Genética E Medicina Reprodutiva, Sao Paulo, Sao Paulo, Brazil
| | - Emilia Mateu-Brull
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Nuria Balaguer
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Camila Dantas
- Laboratório Igenomix, Laboratório de Genética E Medicina Reprodutiva, Sao Paulo, Sao Paulo, Brazil
| | | | | | - Lorena Rodrigo
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Inmaculada Campos-Galindo
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Roser Navarro
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Miguel Milán
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain.
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Pang Y, Wang C, Tang J, Zhu J. Clinical application of noninvasive prenatal testing in the detection of fetal chromosomal diseases. Mol Cytogenet 2021; 14:31. [PMID: 34127051 PMCID: PMC8204420 DOI: 10.1186/s13039-021-00550-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/27/2021] [Indexed: 01/12/2023] Open
Abstract
Objective To assess the detection efficiency of noninvasive prenatal testing (NIPT) for fetal autosomal aneuploidy, sex chromosome aneuploidy (SCA), other chromosome aneuploidy, copy number variation (CNV), and to provide further data for clinical application of NIPT. Materials and methods 25,517 pregnant women who underwent NIPT testing in Anhui Province Maternity and Child Health Hospital from September 2019 to September 2020 were selected, and samples with high-risk test results were subjected to karyotype analysis for comparison by using amniotic fluid, with some samples subjected to further validation by chromosomal microarray analysis, and followed up for pregnancy outcome. Results A total of 25,517 pregnant women who received NIPT, 25,502 cases were tested successfully, and 294 high-risk samples (1.15%) were detected, there were 96 true positive samples, 117 false positive samples and 81 cases were refused further diagnosis. Samples with high risk of autosomal aneuploidy were detected in 71 cases (0.28%), and 51 cases were confirmed, including: trisomy 21 (T21) in 44 cases, trisomy 18 (T18) in 5 cases, and trisomy 13 (T13) in 2 cases; the positive predictive value (PPV) was 91.67%, 45.45%, and 33.33%, respectively, and the negative predictive value was 100%, the false positive rate (FPR) was 0.02%, 0.02%, and 0.02%, respectively.13 samples with high risk of mosaic trisomies 21, 18, and 13 were detected, and 1 case of T21mos was confirmed with a PPV of 8.33%. Samples with high risk of SCA were detected in 72 cases (0.28%), and the diagnosis was confirmed in 23 cases, with a PPV of 41.07% and a FPR of 0.13%. These included 3 cases of 45,X, 6 cases of 47,XXY, 8 cases of 47,XXX and 6 cases of 47,XYY, with PPVs of 12.00%, 50.00%, 72.73%, and 75.00%, respectively, and false-positive rates of 0.09%, 0.02%, 0.01% and 0.01% respectively. Samples with high risk of CNV were detected in 104 cases (0.41%) and confirmed in 18 cases, with a PPV of 32.14% and a FPR of 0.15%. Samples with high risk of other chromosomal aneuploidy were detected in 34 cases (0.13%), and the diagnosis was confirmed in 3 cases, which were T2, T9, and T16 respectively. The overall PPV for other chromosome aneuploidy was 12.50%, with a FPR of 0.08%. Conclusion NIPT is indicated for trisomies 21, 18 and 13 screening, especially for T21. It also has some certain reference value for SCA and CNV, but is not recommended for screening of other chromosomal aneuploidy.
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Affiliation(s)
- Yu Pang
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China.,Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Chaohong Wang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Junxiang Tang
- Maternity and Child Health Hospital of Anhui Province, Hefei, China
| | - Jiansheng Zhu
- Affiliated Maternity and Child Health Hospital of Anhui Medical University, Hefei, China. .,Maternity and Child Health Hospital of Anhui Province, Hefei, China.
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Chen L, Wang L, Tang F, Zeng Y, Yin D, Zhou C, Zhu H, Li L, Zhang L, Wang J. Copy number variation sequencing combined with quantitative fluorescence polymerase chain reaction in clinical application of pregnancy loss. J Assist Reprod Genet 2021; 38:2397-2404. [PMID: 34052955 DOI: 10.1007/s10815-021-02243-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/23/2021] [Indexed: 12/24/2022] Open
Abstract
PURPOSE In this study, we evaluated the feasibility of the combining CNV-seq and quantitative fluorescence polymerase chain reaction (QF-PCR) for miscarriage analysis in clinical practice. METHODS Over a 35-month period, a total of 389 fetal specimens including 356 chorionic villi and 33 fetal muscle tissues were analyzed by CNV-seq and QF-PCR. Relationships between the risk factors (e.g., advanced maternal age, abnormal pregnancy history, and gestational age) and incidence of these chromosomal abnormalities were further analyzed by subgroup. RESULTS Clinically significant chromosomal abnormalities were identified in 58.95% cases. Aneuploidy was the most common abnormality (46.84%), followed by polyploidy (8.16%) and structural chromosome anomalies (3.95%). In sub-group analysis, significant differences were found in the total frequency of chromosomal abnormalities between the early abortion and the late abortion group, as well as in the distribution of chromosomal abnormalities between the advanced and the younger maternal age group. Meanwhile, the results of the logistic regression analysis identified a trend suggesting that the percentage of fetal chromosomal abnormalities is significantly higher in advanced maternal age, lesser gestational age, and lesser number of prior miscarriages. CONCLUSION Our study suggests that CNV-seq and QF-PCR are efficient and reliable technologies in the fetal chromosome analysis of miscarriages and could be used as a routine selection method for the genetic analysis of spontaneous abortion.
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Affiliation(s)
- Lin Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Feng Tang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yang Zeng
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Daishu Yin
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Hongmei Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Linping Li
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Lili Zhang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China.
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Huang H, Wang Y, Zhang M, Lin N, An G, He D, Chen M, Chen L, Xu L. Diagnostic accuracy and value of chromosomal microarray analysis for chromosomal abnormalities in prenatal detection: A prospective clinical study. Medicine (Baltimore) 2021; 100:e25999. [PMID: 34011095 PMCID: PMC8137078 DOI: 10.1097/md.0000000000025999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 04/20/2021] [Indexed: 01/05/2023] Open
Abstract
Chromosomal microarray analysis (CMA) has emerged as a primary diagnostic tool for the evaluation of developmental delay and structural malformations in children. The aim of this study was to compare the accuracy and value of CMA and karyotyping on diagnosis of chromosomal abnormalities in Fujian province of South China.In the study, 410 clinical samples were collected from pregnant women between March 2015 and December 2016, including 3 villus (0.73%, 3/410), 296 amniotic fluid (72.20%, 296/410), and 111 umbilical cord blood (27.07%, 111/410). All samples were screening for chromosomal abnormalities by both using CMA and karyotyping.The success rate of CMA and karyotyping was 100% (410/410) and 99.27% (407/410), respectively. Sixty-one (14.88%, 61/410) samples were presented with chromosomal abnormalities by using CMA, whereas 47 (11.55%, 47/407) samples were shown with chromosomal abnormalities by using karyotyping. Thirty-one (8.61%, 31/360) samples with normal karyotypes were found to exist chromosomal abnormalities by using CMA. Receiver operating characteristic analysis showed that the area under the curve of karyotyping on the diagnosis of chromosomal abnormalities was 0.90 (95% confidence interval: 0.87-0.93), the sensitivity and specificity was 87.56% and 91.22%, respectively. The area under the curve of CMA on the diagnosis of chromosomal abnormalities was 0.93 (95% confidence interval: 0.90-0.95), with 90.68% sensitivity and 94.40% specificity. Notably, the combination of CMA and karyotyping could improve the diagnosis of chromosomal abnormalities.CMA has a better diagnostic value for screening chromosomal abnormalities, especially for those pregnant women with normal karyotypes. This study has guiding value for prenatal diagnosis in Fujian province of South China.
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Huang H, Cai M, Liu L, Xu L, Lin N. Effectiveness of Chromosomal Microarray Analysis for Prenatal Diagnosis of Fetal Echogenic Intracardiac Focus: A Single-Center Experience. Int J Gen Med 2021; 14:1991-1997. [PMID: 34045891 PMCID: PMC8149271 DOI: 10.2147/ijgm.s311800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Echogenic intracardiac focus (EIF) is a common ultrasound finding during pregnancy. However, the correlation between fetal EIF and cardiac abnormality remains in dispute until now. The study aimed to examine the association of fetal EIF with chromosomal abnormality by means of chromosomal microarray analysis (CMA). MATERIALS AND METHODS A total of 192 pregnant women with fetal EIF undergoing amniocentesis or umbilical cord blood puncture were recruited and assigned into groups A (8 cases with isolated EIF alone), B (75 cases with EIF and other cardiac malformations) and C (109 cases with EIF and extracardiac malformations). All fetuses underwent karyotyping analysis and CMA simultaneously. The detection of chromosomal abnormality and copy number variations (CNVs) were compared. RESULTS Chromosomal karyotyping identified 5 fetuses with chromosomal abnormality, including 3 cases with trisomy 21, one fetus with Turner's syndrome, and one fetus with chromosome 8 mosaicism, while CMA detected 6 additional fetuses with CNVs, including 2 fetuses with pathogenic CNVs and 4 fetuses with variants of uncertain significance (VOUS). There was no significant difference among groups A (0), B (5.33%) and C (6.42%) in terms of the prevalence of chromosomal abnormality (P> 0.05). Among the 4 fetuses with VOUS, pregnancy continued in 2 fetuses, and pregnancy was terminated in other 2 fetuses. CONCLUSION An isolated EIF may not correlate with chromosomal abnormality. However, CMA is recommended in fetuses with CMA complicated by other abnormal cardiac ultrasound findings, which facilitates the prediction of fetal outcomes during the genetic counseling and precision assessment of prognosis.
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Affiliation(s)
- Hailong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
| | - Meiying Cai
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
| | - Linyu Liu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
- School of Clinical Medicine, Fujian Medical University, Fuzhou City, Fujian Province, 350122, People’s Republic of China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
| | - Na Lin
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People’s Republic of China
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Gou L, Suo F, Wang Y, Wang N, Wu Q, Hu S, Wang P, Gu L, Zhang M, Wang C, Zhang Y, Yin X, Zhang P, Xu J, Wang X, Gu M. Clinical value for the detection of fetal chromosomal deletions/duplications by noninvasive prenatal testing in clinical practice. Mol Genet Genomic Med 2021; 9:e1687. [PMID: 33951332 PMCID: PMC8222853 DOI: 10.1002/mgg3.1687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/04/2021] [Accepted: 03/23/2021] [Indexed: 01/13/2023] Open
Abstract
Objective This study was to report the experiences on the clinical value of noninvasive prenatal testing (NIPT) for the screening of fetal chromosomal deletions/duplications. Methods We performed a retrospective analysis of a cohort of 20,439 pregnancies undergoing NIPT from March 2017 to September 2020 at a single center. Patients with positive NIPT results for fetal chromosomal deletions or duplications had options of invasive diagnostic testing or no further testing. The data were complied from all cases with positive NIPT results for chromosomal deletions/duplications. The positive predictive value (PPV) was calculated from tabulated data. Results In this cohort, positive NIPT results for fetal chromosomal deletions/duplications were found in 60 pregnant women. Of the positive samples, further invasive testing was performed in 39 cases, in which 9 cases were found to be true positive. The overall PPV for chromosomal deletions/duplications was 23.1%. In addition, fetal structural anomaly was found by ultrasound examination in three cases, in which the chromosomal deletions/duplications of three cases were not verified. Moreover, an unexpected pathogenic 8p23.3 deletion was identified by invasive testing in 1 fetus with a false positive NIPT screen for 3q27.3q29 duplication. Conclusions In summary, positive NIPT results of chromosomal deletions/duplications were not uncommon in clinical practice, whereas the PPV for the testing was low. Hence, potential risks and high percentage of false positives for these abnormal NIPT results might be informed to pregnant women before the choice made of invasive testing.
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Affiliation(s)
- Lingshan Gou
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Feng Suo
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yi Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Na Wang
- Department of Technology, Suzhou Beikang Medical Device Co. Ltd., Suzhou, China
| | - Qin Wu
- Zhejiang Biosan Biochemical Technologies Co. Ltd., Hangzhou, China
| | - Shunan Hu
- Office of Scientific Research & Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Peng Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Lize Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Man Zhang
- Zhejiang Biosan Biochemical Technologies Co. Ltd., Hangzhou, China
| | - Chuanxia Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yan Zhang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Xin Yin
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Peng Zhang
- Shenzhen Longgang Institute of Stomatology, Shenzhen Longgang E.N.T. Hospital, Shenzhen, China
| | - Jian Xu
- Shenzhen Longgang Institute of Stomatology, Shenzhen Longgang E.N.T. Hospital, Shenzhen, China
| | - Xingqi Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Maosheng Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
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Li Y, Zhang S, Snyder MP, Meador KJ. Precision medicine in women with epilepsy: The challenge, systematic review, and future direction. Epilepsy Behav 2021; 118:107928. [PMID: 33774354 PMCID: PMC8653993 DOI: 10.1016/j.yebeh.2021.107928] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 11/29/2022]
Abstract
Epilepsy is one of the most prevalent neurologic conditions, affecting almost 70 million people worldwide. In the United States, 1.3 million women with epilepsy (WWE) are in their active reproductive years. Women with epilepsy (WWE) face gender-specific challenges such as pregnancy, seizure exacerbation with hormonal pattern fluctuations, contraception, fertility, and menopause. Precision medicine, which applies state-of-the art molecular profiling to diagnostic, prognostic, and therapeutic problems, has the potential to advance the care of WWE by precisely tailoring individualized management to each patient's needs. For example, antiseizure medications (ASMs) are among the most common teratogens prescribed to women of childbearing potential. Teratogens act in a dose-dependent manner on a susceptible genotype. However, the genotypes at risk for ASM-induced teratogenic deficits are unknown. Here we summarize current challenging issues for WWE, review the state-of-art tools for clinical precision medicine approaches, perform a systematic review of pharmacogenomic approaches in management for WWE, and discuss potential future directions in this field. We envision a future in which precision medicine enables a new practice style that puts focus on early detection, prediction, and targeted therapies for WWE.
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Affiliation(s)
- Yi Li
- Department of Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Sai Zhang
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University School of Medicine, Stanford CA, 94305, USA
| | - Michael P. Snyder
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University School of Medicine, Stanford CA, 94305, USA
| | - Kimford J. Meador
- Department of Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA 94305, USA
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Benefit versus risk of chromosomal microarray analysis performed in pregnancies with normal and positive prenatal screening results: A retrospective study. PLoS One 2021; 16:e0250734. [PMID: 33901244 PMCID: PMC8075189 DOI: 10.1371/journal.pone.0250734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 04/12/2021] [Indexed: 11/19/2022] Open
Abstract
Background Most studies on chromosomal microarray analysis (CMA) and amniocentesis risks have not evaluated pregnancies with low risk for genetic diseases; therefore, the efficacy and safety of CMA and amniocentesis in this population are unclear. This study aimed to examine the benefits and risks of prenatal genetic diagnostic tests in pregnancies having low risk for chromosomal diseases. Methods and findings In this retrospective study, we used clinical data from a large database of 30,830 singleton pregnancies at gestational age 16–23 weeks who underwent amniocentesis for karyotyping with or without CMA. We collected socio-demographic, medical and obstetric information, along with prenatal screening, CMA and karyotyping results. Fetal loss events were also analysed. CMA was performed in 5,837 pregnancies with normal karyotype (CMA cohort). In this cohort, 4,174 women had normal prenatal screening results and the risk for identifying genetic abnormalities with >10% risk for intellectual disability by CMA was 1:102, with no significant difference between maternal age groups. The overall post-amniocentesis fetal loss rate was 1:1,401 for the entire cohort (n = 30,830) and 1:1,945 for the CMA cohort (n = 5,837). The main limitation of this study is the relatively short follow-up of 3 weeks, which may not have been sufficient for detecting all fetal loss events. Conclusion The low risk for post-amniocentesis fetal loss, compared to the rate of severe genetic abnormalities detected by CMA, suggests that even pregnant women with normal prenatal screening results should consider amniocentesis with CMA.
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Huang H, Cai M, Ma W, Lin N, Xu L. Chromosomal Microarray Analysis for the Prenatal Diagnosis in Fetuses with Nasal Bone Hypoplasia: A Retrospective Cohort Study. Risk Manag Healthc Policy 2021; 14:1533-1540. [PMID: 33889037 PMCID: PMC8054820 DOI: 10.2147/rmhp.s286038] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/27/2021] [Indexed: 01/03/2023] Open
Abstract
Background Previous studies have shown a strong correlation between fetal nasal bone hypoplasia and chromosomal anomaly; however, there is little knowledge on the associations of fetal nasal bone hypoplasia with chromosomal microdeletions and microduplications until now. Chromosomal microarray analysis (CMA) is a high-resolution molecular genetic tool that is effective to detect submicroscopic anomalies including chromosomal microdeletions and microduplications that cannot be detected by karyotyping. This study aimed to examine the performance of CMA for the prenatal diagnosis of nasal bone hypoplasia in the second and third trimesters. Subjects and Methods A total of 84 pregnant women in the second and third trimesters with fetal nasal bone hypoplasia, as revealed by ultrasound examinations, were enrolled, and all women underwent karyotyping and CMA with the Affymetrix CytoScan 750K GeneChip Platform. The subjects included 32 cases with fetal nasal bone hypoplasia alone and 52 cases with fetal nasal bone hypoplasia combined with other ultrasound abnormalities, and the prevalence of genomic abnormality was compared between these two groups. Results Karyotyping detected 21 cases of chromosomal anomaly in the 84 study subjects (21/84, 25%), including trisomy 21 (14 cases), trisomy 18 (3 cases), 46, del (4)(p16) karyotype (2 cases), 47, XYY syndrome (1 case) and 46, XY, del (5) (p15) karyotype (1 case). CMA detected additional four fetuses with pathogenic copy number variations (CNVs) and six fetuses with uncertain clinical significance (VOUS). No significant difference was detected in the prevalence of genomic abnormality in fetuses with nasal bone hypoplasia alone and in combination with other ultrasound abnormalities (13/32 vs 18/52; χ2 = 0.31, P > 0.05). The pregnancy was terminated in 21 fetuses detected with chromosomal abnormality and 4 fetuses detected with pathogenic CNVs. Among the other six fetuses detected with VOUS, the parents chose to continue the pregnancy, and the newborns all had normal clinical phenotypes. Conclusion In addition to chromosomal abnormalities identified in 21 fetuses by karyotyping, CMA detected additional 10 fetuses with abnormal CNVs (10/84, 11.9%) in the study population. CMA is a promising powerful tool for prenatal diagnosis that may provide valuable data for the accurate assessment of fetal prognosis and the decision of pregnancy continuation during the prenatal clinical counseling.
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Affiliation(s)
- Hailong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Meiying Cai
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Wei Ma
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China.,School of Clinical Medicine, Fujian Medical University, Fuzhou City, Fujian Province, 350122, People's Republic of China
| | - Na Lin
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou City, Fujian Province, 350001, People's Republic of China
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Patterson J, Wellesley D, Morgan S, Cilliers D, Allen S, Gardiner CA. Prenatal chromosome microarray: 'The UK experience'. A survey of reporting practices in UK genetic services (2012-2019). Prenat Diagn 2021; 41:661-667. [PMID: 33848363 DOI: 10.1002/pd.5944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/07/2021] [Accepted: 03/22/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND The value of chromosome microarray (CMA) in the prenatal detection of significant chromosome anomalies is well-established. To guide the introduction of this technique in routine clinical practice, the Joint Committee on Genomics in Medicine developed national UK guidelines for reporting prenatal CMA in 2015. OBJECTIVE To evaluate the UK experience of utilising prenatal CMA. METHOD A 36-item survey was distributed to all UK clinical genetics services (n = 23) in March 2019 requesting information pertaining to experience since diagnostic testing commenced and current practice (March 2018 to March 2019). RESULTS Eighteen UK genetics services currently offer prenatal CMA. A total of 14,554 tests had been performed. A pathogenic copy number variant was identified in 7.8% of tests overall, though the diagnostic rate increased to 8.4% in the final year of the survey. Variants of uncertain significance (VUS) were reported in 0.7% of tests, and 'actionable' incidental findings in 0.12%. CONCLUSION Diagnostic rate has improved over time, while reporting of VUS has decreased. Reviewing survey responses at a national level highlights variation in testing experience and practice, raising considerations both for future guideline development and implementation of other novel techniques including prenatal whole exome sequencing.
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Affiliation(s)
- Jenny Patterson
- West of Scotland Centre for Genomic Medicine, Laboratory Medicine Building, QEUH, Glasgow, UK
| | - Diana Wellesley
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, UK
| | - Sian Morgan
- All Wales Genetics Laboratory, Institute of Medical Genetics, University Hospital of Wales Heath Park, Cardiff, UK
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, ACE Building Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Carol A Gardiner
- West of Scotland Centre for Genomic Medicine, Laboratory Medicine Building, QEUH, Glasgow, UK
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Fan X, Huang H, Lin X, Xue H, Cai M, Lin N, Xu L. Performance of Chromosomal Microarray Analysis for Detection of Copy Number Variations in Fetal Echogenic Bowel. Risk Manag Healthc Policy 2021; 14:1431-1438. [PMID: 33859509 PMCID: PMC8044071 DOI: 10.2147/rmhp.s299806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Fetal echogenic bowel (FEB) is associated with an increased risk of poor pregnant outcomes; however, karyotyping fails to detect copy number variations (CNVs) in FEB. This study aimed to evaluate the performance of chromosomal microarray analysis (CMA) for detection of FEB. METHODS The medical records of 147 pregnant women with FEB recruited during December 2015 to December 2018 were retrospectively reviewed, and prenatal samples were collected for karyotyping and CMA. The detection of chromosomal abnormality was compared between karyotyping and CMA. RESULTS Karyotyping identified eight cases with abnormal karyotypes (5.44% prevalence), including four fetuses with pathogenic aneuploidy, three with chromosome polymorphism and one with balanced chromosome translocation. CMA identified 13 abnormal CNVs (8.84% prevalence), including 4 fetuses with pathogenic aneuploidy as detected by karyotyping and 9 additional CNVs with normal karyotypes; however, CMA failed to detect chromosome polymorphism and balanced chromosome translocation. In fetuses with isolated FEB, no cases presented pathogenic findings and CMA detected two cases with variants of uncertain significance (VOUS). In cases presenting FEB along with other ultrasound abnormalities, CMA detected three cases with pathogenic CNVs and four cases with VOUS in addition to four cases with aneuploidy. There was no significant difference in the detection of abnormal CNVs between the fetuses with echogenic bowel alone and along with other ultrasound abnormalities (10% vs 8.67%, P > 0.05). Except 9 fetuses lost to the follow-up, the other 138 fetuses with echogenic bowel were successfully followed up. Pregnancy was terminated in 5 fetuses with chromosomal abnormality, 2 with pathogenic CNVs and 1 with VOUS, and other 16 with normal karyotypes and CMA findings but showing ultrasound abnormalities or multiple malformations. CONCLUSION Isolated FEB is associated with a good prognosis, and a satisfactory pregnant outcome is expected for fetuses with echogenic bowel that are negative for chromosomal anomalies and other severe structure abnormalities. CMA shows an important value in the genetic diagnosis of FEB. As a supplement to karyotyping, CMA may improve the accuracy of prenatal diagnosis of fetal intestinal malformations in pregnant women with FEB.
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Affiliation(s)
- Xiangqun Fan
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Hailong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Xiyao Lin
- School of Clinical Medicine, Fujian Medical University, Fuzhou City, Fujian Province, 350122, People’s Republic of China
| | - Huili Xue
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Meiying Cai
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Na Lin
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
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Daum H, Stern S, Shkedi-Rafid S. Is it time for prenatal chromosomal-microarray analysis to all women? A review of the diagnostic yield in structurally normal fetuses. Curr Opin Obstet Gynecol 2021; 33:143-147. [PMID: 33620892 DOI: 10.1097/gco.0000000000000690] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Chromosomal-microarray analysis (CMA) is the first-tier test in pregnancies with structural malformations. Accumulating data show that pathogenic copy number variants (CNVs) can also be identified in structurally normal fetuses. We set out to summarize the published data on the diagnostic yield of CMA in structurally normal fetuses. RECENT FINDINGS Six studies summarize a total of 29,612 prenatal CMAs performed in structurally normal fetuses. The incidence of highly penetrant pathogenic/likely pathogenic CNVs is 0.4-2.5%. Variability was demonstrated in the timing of CMA testing and type of CNVs classified as pathogenic. The incidence of variants of uncertain significance is 0.4-5.4%. The prevalence of susceptibility loci is 0.3-0.7% when specified, and the incidence of CNVs associated with late onset disease is 0.1%. SUMMARY With a frequency of abnormal CNVs of 1:40 to 1:250 in structurally normal fetuses, it is recommended that all pregnant women be informed of the possibility to have CMA performed, even in the absence of malformations. Information should also be provided about uncertain and secondary findings.
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Affiliation(s)
- Hagit Daum
- Department of Genetics, Hadassah-Hebrew University Medical Center
- Faculty of Medicine, The Hebrew University of Jerusalem
| | - Shira Stern
- Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Shiri Shkedi-Rafid
- Department of Genetics, Hadassah-Hebrew University Medical Center
- Faculty of Medicine, The Hebrew University of Jerusalem
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The role of chromosomal microarray and exome sequencing in prenatal diagnosis. Curr Opin Obstet Gynecol 2021; 33:148-155. [PMID: 33620893 DOI: 10.1097/gco.0000000000000692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Advancements in technologies have revolutionized prenatal diagnosis. Chromosomal microarray analysis (CMA) became a proven method and was implemented to detect gains and losses of DNA and absence of heterozygosity across the genome. Next-generation sequencing technologies have brought opportunities and challenges to genetic testing. Exome sequencing detects single-nucleotide variants (SNVs) across the exome and its prenatal application is an emerging field. We reviewed the literature to define the role of CMA and exome sequencing in prenatal diagnosis. RECENT FINDING The application of exome sequencing in genetic diagnosis shows increased diagnostic yield and could be potentially implemented for prenatal diagnosis of fetuses with one or more ultrasound structural abnormalities or suspected monogenetic conditions. Although CMA is a gold standard for copy number variant (CNV) detection, large clinical cohort studies emphasized integrated CNV and SNV analyses for precise molecular diagnosis. Recent studies also suggest low-pass genome sequencing-based CNV detection can identify genome-wide imbalances at higher resolutions. SUMMARY Data suggest exome sequencing for SNVs and CMA for CNV detection are the most effective approach for prenatal genetic diagnosis. Emerging evidences show genome sequencing has the potential to replace CMA and even exome sequencing to become a comprehensive genetic test in the clinical diagnostic laboratory.
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91
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Bajaj Lall M, Agarwal S, Paliwal P, Saviour P, Joshi A, Joshi A, Mahajan S, Bijarnia-Mahay S, Dua Puri R, Verma IC. Prenatal Diagnosis by Chromosome Microarray Analysis, An Indian Experience. J Obstet Gynaecol India 2021; 71:156-167. [PMID: 34149218 PMCID: PMC8167018 DOI: 10.1007/s13224-020-01413-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 12/04/2020] [Indexed: 10/22/2022] Open
Abstract
BACKGROUND Karyotyping has been the gold standard for prenatal chromosome analysis. The resolution should be higher by chromosome microarray analysis (CMA). The challenge lies in recognizing benign and pathogenic or clinically significant copy number variations (pCNV) and variations of unknown significance (VOUS). The aim was to evaluate the diagnostic yield and clinical utility of CMA, to stratify the CMA results in various prenatal referral groups and to accumulate Indian data of pCNVs and VOUS for further interpretation to assist defined genetic counseling. METHODS Karyotyping and CMA were performed on consecutive referrals of 370 prenatal samples of amniotic fluid (n = 274) and chorionic villi (n = 96) from Indian pregnant women with high maternal age (n = 23), biochemical screen positive (n = 61), previous child abnormal (n = 59), abnormal fetal ultrasound (n = 205) and heterozygous parents (n = 22). RESULTS AND CONCLUSION The overall diagnostic yield of abnormal results was 5.40% by karyotyping and 9.18% by CMA. The highest percentage of pCNVs were found in the group with abnormal fetal ultrasound (5.40%) as compared to other groups, such as women with high maternal age (0.81%), biochemical screen positive (0.54%), previous abnormal offspring (0.81%) or heterozygous parents group (1.62%). Therefore, all women with abnormal fetal ultrasound must undergo CMA test for genotype-phenotype correlation. CMA detects known and rare deletion/duplication syndromes and characterizes marker chromosomes. Accumulation of CNV data will form an Indian Repository and also help to resolve the uncertainty of VOUS. Pretest and posttest genetic counseling is essential to convey benefits and limitations of CMA and help the patients to take informed decisions.
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Affiliation(s)
- Meena Bajaj Lall
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - Shruti Agarwal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - Preeti Paliwal
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - Pushpa Saviour
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - Anju Joshi
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - Arti Joshi
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - Surbhi Mahajan
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - Sunita Bijarnia-Mahay
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
| | - I. C. Verma
- Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, 110060 India
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92
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Li Y, Yan H, Chen J, Chen F, Jian W, Wang J, Ye X, Li Y, Li N, Chiu PCN, Chen M. The application of late amniocentesis: a retrospective study in a tertiary fetal medicine center in China. BMC Pregnancy Childbirth 2021; 21:266. [PMID: 33784964 PMCID: PMC8011189 DOI: 10.1186/s12884-021-03723-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Background To assess the indications and complications of late amniocentesis and the advanced genetic test results in a tertiary university fetal medical medicine unit. Methods In this retrospective study, women that underwent amniocentesis at 24+ 0 to 39+ 4 weeks, between January 2014 and December 2019, were recruited. Indications, complications, genetic test results, and pregnancy outcomes were reported for each pregnancy and compared with those who underwent the traditional amniocentesis at 16+ 0 to 23+ 6 weeks (control group). Information was retrieved from patient medical records, checked by research staff, and analyzed. Results Of the 1287 women (1321 fetuses) included in the late amniocentesis group, late detected sonographic abnormalities (85.5%) were the most common indication. The overall incidence of preterm birth and intrauterine demise after amniocentesis were 2.5 and 1.3%, respectively. Sixty-nine fetuses with aneuploidy (5.3%) and seventy-two fetuses with pathogenic copy number variations (5.5%) were identified by chromosomal microarray analysis. The maximal diagnostic yield (70%) was in the subgroup of fetuses with the abnormal diagnostic test results, followed by abnormal NIPT results (35.7%) and multiple abnormalities (23.8%). And 35.4% of the pregnancies were finally terminated. Conclusions Due to the high detection rates of advanced genetic technologies and the safety of the invasive procedure (3.9% vs 4.0%), it is reasonable to recommend late amniocentesis as an effective and reliable method to detect late-onset fetal abnormalities. However, chromosomal microarray and whole-exome sequencing may result in uncertain results like variants of uncertain significance. Comprehensive genetic counseling is necessary. Supplementary Information The online version contains supplementary material available at 10.1186/s12884-021-03723-7.
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Affiliation(s)
- Yingting Li
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Huanchen Yan
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Jingsi Chen
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Fei Chen
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Wei Jian
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Jiayan Wang
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Xiaoqing Ye
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Yufan Li
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Nan Li
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China
| | - Philip C N Chiu
- Department of Obstetrics and Gynecology, the University of Hong Kong, Hong Kong, China.,Shenzhen Key Laboratory of Fertility Regulation, the University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Min Chen
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, 63 Duobao Road, Liwan District, Guangzhou, China.
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93
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Bedei I, Wolter A, Weber A, Signore F, Axt-Fliedner R. Chances and Challenges of New Genetic Screening Technologies (NIPT) in Prenatal Medicine from a Clinical Perspective: A Narrative Review. Genes (Basel) 2021; 12:501. [PMID: 33805390 PMCID: PMC8065512 DOI: 10.3390/genes12040501] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
In 1959, 63 years after the death of John Langdon Down, Jérôme Lejeune discovered trisomy 21 as the genetic reason for Down syndrome. Screening for Down syndrome has been applied since the 1960s by using maternal age as the risk parameter. Since then, several advances have been made. First trimester screening, combining maternal age, maternal serum parameters and ultrasound findings, emerged in the 1990s with a detection rate (DR) of around 90-95% and a false positive rate (FPR) of around 5%, also looking for trisomy 13 and 18. With the development of high-resolution ultrasound, around 50% of fetal anomalies are now detected in the first trimester. Non-invasive prenatal testing (NIPT) for trisomy 21, 13 and 18 is a highly efficient screening method and has been applied as a first-line or a contingent screening approach all over the world since 2012, in some countries without a systematic screening program. Concomitant with the rise in technology, the possibility of screening for other genetic conditions by analysis of cfDNA, such as sex chromosome anomalies (SCAs), rare autosomal anomalies (RATs) and microdeletions and duplications, is offered by different providers to an often not preselected population of pregnant women. Most of the research in the field is done by commercial providers, and some of the tests are on the market without validated data on test performance. This raises difficulties in the counseling process and makes it nearly impossible to obtain informed consent. In parallel with the advent of new screening technologies, an expansion of diagnostic methods has begun to be applied after invasive procedures. The karyotype has been the gold standard for decades. Chromosomal microarrays (CMAs) able to detect deletions and duplications on a submicroscopic level have replaced the conventional karyotyping in many countries. Sequencing methods such as whole exome sequencing (WES) and whole genome sequencing (WGS) tremendously amplify the diagnostic yield in fetuses with ultrasound anomalies.
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Affiliation(s)
- Ivonne Bedei
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
| | - Aline Wolter
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
| | - Axel Weber
- Institute of Human Genetics, Justus Liebig University Giessen, 35392 Giessen, Germany;
| | - Fabrizio Signore
- Department of Obstetrics and Gynecology, Opedale S. Eugenio, 00144 Rome, Italy;
| | - Roland Axt-Fliedner
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
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Alyafee Y, Alam Q, Tuwaijri AA, Umair M, Haddad S, Alharbi M, Alrabiah H, Al-Ghuraibi M, Al-Showaier S, Alfadhel M. Next-Generation Sequencing-Based Pre-Implantation Genetic Testing for Aneuploidy (PGT-A): First Report from Saudi Arabia. Genes (Basel) 2021; 12:461. [PMID: 33804821 PMCID: PMC8063787 DOI: 10.3390/genes12040461] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/25/2022] Open
Abstract
Recently, high-throughput next-generation sequencing (NGS)-based preimplantation genetic testing for aneuploidies techniques came into use. This technique is essential for successful embryo transfer and accomplishing pregnancy, thus reducing the time and cost of additional cycles. In this study, we describe our first experience in introducing an NGS-based preimplantation genetic testing for aneuploidy (PGT-A) service using next-generation sequencing in King Abdulaziz Medical City located in Riyadh, Saudi Arabia. Our main goal was to report the successful implementation of this new technology in clinical practice and highlight the factors that may affect the results. In total, 200 blastomere biopsies were obtained from 36 in vitro fertilization (IVF) cycles from Saudi couples suffering from prolonged infertility or recurrent embryo transfer failure. NGS-based PGT-A was performed in all embryos. The results were analyzed in five age groups, showing that aneuploidy rates increased with maternal age. Moreover, the results also showed that complex abnormal embryos with (2-5) aneuploidy are the most common type of embryos. Additionally, our data showed that chromosome 16-related abnormality was the most frequent abnormality detected among all reported abnormalities. In conclusion, our study suggests that NGS-based PGT-A is an applicable and reliable technique for routine-based embryo screening, especially for couples suffering from recurrent miscarriages or multiple embryo transfer failures.
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Affiliation(s)
- Yusra Alyafee
- King Abdullah International Medical Research Center (KAIMRC), Medical Genomics Research Department, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (Y.A.); (Q.A.); (A.A.T.); (M.U.); (S.H.); (M.A.)
| | - Qamre Alam
- King Abdullah International Medical Research Center (KAIMRC), Medical Genomics Research Department, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (Y.A.); (Q.A.); (A.A.T.); (M.U.); (S.H.); (M.A.)
| | - Abeer Al Tuwaijri
- King Abdullah International Medical Research Center (KAIMRC), Medical Genomics Research Department, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (Y.A.); (Q.A.); (A.A.T.); (M.U.); (S.H.); (M.A.)
| | - Muhammad Umair
- King Abdullah International Medical Research Center (KAIMRC), Medical Genomics Research Department, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (Y.A.); (Q.A.); (A.A.T.); (M.U.); (S.H.); (M.A.)
| | - Shahad Haddad
- King Abdullah International Medical Research Center (KAIMRC), Medical Genomics Research Department, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (Y.A.); (Q.A.); (A.A.T.); (M.U.); (S.H.); (M.A.)
| | - Meshael Alharbi
- King Abdullah International Medical Research Center (KAIMRC), Medical Genomics Research Department, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (Y.A.); (Q.A.); (A.A.T.); (M.U.); (S.H.); (M.A.)
| | - Hayat Alrabiah
- Reproductive Endocrinology and Infertility Unit, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (H.A.); (M.A.-G.); (S.A.-S.)
| | - Maha Al-Ghuraibi
- Reproductive Endocrinology and Infertility Unit, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (H.A.); (M.A.-G.); (S.A.-S.)
| | - Sahar Al-Showaier
- Reproductive Endocrinology and Infertility Unit, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (H.A.); (M.A.-G.); (S.A.-S.)
| | - Majid Alfadhel
- King Abdullah International Medical Research Center (KAIMRC), Medical Genomics Research Department, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia; (Y.A.); (Q.A.); (A.A.T.); (M.U.); (S.H.); (M.A.)
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh 11426, Saudi Arabia
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Levy B, Hoffmann ER, McCoy RC, Grati FR. Chromosomal mosaicism: Origins and clinical implications in preimplantation and prenatal diagnosis. Prenat Diagn 2021; 41:631-641. [PMID: 33720449 DOI: 10.1002/pd.5931] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/03/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
The diagnosis of chromosomal mosaicism in the preimplantation and prenatal stage is fraught with uncertainty and multiple factors need to be considered in order to gauge the likely impact. The clinical effects of chromosomal mosaicism are directly linked to the type of the imbalance (size, gene content, and copy number), the timing of the initial event leading to mosaicism during embryogenesis/fetal development, the distribution of the abnormal cells throughout the various tissues within the body as well as the ratio of normal/abnormal cells within each of those tissues. Additional factors such as assay noise and culture artifacts also have an impact on the significance and management of mosaic cases. Genetic counseling is an important part of educating patients about the likelihood of having a liveborn with a chromosome abnormality and these risks differ according to the time of ascertainment and the tissue where the mosaic cells were initially discovered. Each situation needs to be assessed on a case-by-case basis and counseled accordingly. This review will discuss the clinical impact of finding mosaicism through: embryo biopsy, chorionic villus sampling, amniocentesis, and noninvasive prenatal testing using cell-free DNA.
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Affiliation(s)
- Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Eva R Hoffmann
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Francesca R Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays, S.p.A. (Impact Lab), Busto Arsizio, Varese, Italy
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Sahajpal NS, Barseghyan H, Kolhe R, Hastie A, Chaubey A. Optical Genome Mapping as a Next-Generation Cytogenomic Tool for Detection of Structural and Copy Number Variations for Prenatal Genomic Analyses. Genes (Basel) 2021; 12:398. [PMID: 33799648 PMCID: PMC8001299 DOI: 10.3390/genes12030398] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/26/2021] [Accepted: 03/05/2021] [Indexed: 01/07/2023] Open
Abstract
Global medical associations (ACOG, ISUOG, ACMG) recommend diagnostic prenatal testing for the detection and prevention of genetic disorders. Historically, cytogenetic methods such as karyotype analysis, fluorescent in situ hybridization (FISH) and chromosomal microarray (CMA) are utilized worldwide to diagnose common syndromes. However, the limitations of each of these methods, either performed in tandem or simultaneously, demonstrates the need of a revolutionary technology that can alleviate the need for multiple technologies. Optical genome mapping (OGM) is a novel method that fills this void by being able to detect all classes of structural variations (SVs), including copy number variations (CNVs). OGM is being adopted by laboratories as a tool for both postnatal constitutional genetic disorders and hematological malignancies. This commentary highlights the potential for OGM to become a standard of care in prenatal genetic testing based on its capability to comprehensively identify large balanced and unbalanced SVs (currently the strength of karyotyping and metaphase FISH), CNVs (by CMA), repeat contraction disorders (by Southern blotting) and multiple repeat expansion disorders (by PCR-based methods or Southern blotting). Next-generation sequencing (NGS) methods are excellent at detecting sequence variants, but they are unable to accurately resolve repeat regions of the genome, which limits their ability to detect all classes of SVs. Notably, multiple molecular methods are used to identify repeat expansion and contraction disorders in routine clinical laboratories around the world. With non-invasive prenatal testing (NIPT) becoming the standard of care screening assay for all global pregnancies, we anticipate that OGM can provide a high-resolution, cytogenomic assay to be employed following a positive NIPT screen or for high-risk pregnancies with an abnormal ultrasound. Accurate detection of all types of genetic disorders by OGM, such as liveborn aneuploidies, sex chromosome anomalies, microdeletion/microduplication syndromes, repeat expansion/contraction disorders is key to reducing the global burden of genetic disorders.
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Affiliation(s)
- Nikhil Shri Sahajpal
- Department of Pathology, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (R.K.)
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children’s National Hospital, Washington, DC 20010, USA;
- Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
- Bionano Genomics Inc., San Diego, CA 92121, USA;
| | - Ravindra Kolhe
- Department of Pathology, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (R.K.)
| | - Alex Hastie
- Bionano Genomics Inc., San Diego, CA 92121, USA;
| | - Alka Chaubey
- Department of Pathology, Augusta University, Augusta, GA 30912, USA; (N.S.S.); (R.K.)
- Bionano Genomics Inc., San Diego, CA 92121, USA;
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97
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胡 睿, 胡 婷, 张 竹, 王 嘉, 李 勤, 杨 运, 肖 莉, 朱 红, 李 玲, 张 李, 王 和, 刘 珊. [Application of Array-based Comparative Genomic Hybridization in Diagnostic Assessment of Abnormal Prenatal Serological Screening Results of Down's Syndrome]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2021; 52:319-325. [PMID: 33829709 PMCID: PMC10408917 DOI: 10.12182/20210360602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Indexed: 11/23/2022]
Abstract
OBJECTIVE To explore the application of array-based comparative genomic hybridization (a-CGH) technology in the prenatal diagnostic assessment of abnormal serological prenatal screening results of Down's syndrome (DS). METHODS A total of 3 578 amniotic fluid samples from pregnant women who underwent amniocentesis for prenatal diagnosis solely due to abnormal serological prenatal screening results were selected. The samples were categorized into 3 groups, 2 624 in the high-risk group, 662 in the borderline-risk group, and 292 in the abnormal multiple of median (MoM) group. a-CGH was performed on the Agilent CGX ™ (8×60K) platform and the data were analyzed by the Genoglyphix ® software. RESULTS The overall detection rate of chromosomal abnormalities was 3.38% (121/3 578). Among the chromosomal abnormalities, 49.59% (60/121) was aneuploidies, 42.15% (51/121) was pathogenic copy number variants (pCNVs), and 8.26% (10/121) was likely pathogenic CNVs (lpCNVs). The detection rate of copy number variant of uncertain significance (VUS) was 1.03% (37/3 578). In the high-risk, the borderline-risk and the abnormal MoM groups, the detection rate of chromosomal abnormalities was 3.54% (93/2 624), 2.87% (19/662) and 3.08% (9/292), respectively; the detection rate of p/lp CNVs was 1.64% (43/2 624), 1.81% (12/662) and 2.05% (6/292), respectively; the detection rate of trisomy 21 and trisomy 18 was 1.37% (36/2 624), 0.76% (5/662) and 0.34% (1/292) in the three groups, respectively. There were no significant differences in all the detection rate among these groups ( P>0.05). One sample with X(51)/XYY(49) confirmed by fluorescence in situ hybridization (FISH) was misdiagnosed by a-CGH. CONCLUSION Prenatal diagnosis with a-CGH is of great significance for reducing birth defects in pregnancies with abnormal serological prenatal screening results of DS. It can also be used to detect CNVs of microdeletion/microduplication syndromes.
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Affiliation(s)
- 睿 胡
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 婷 胡
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 竹 张
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 嘉敏 王
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 勤琴 李
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 运源 杨
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 莉柯 肖
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 红梅 朱
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 玲萍 李
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 李李 张
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 和 王
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
| | - 珊玲 刘
- 四川大学华西第二医院 妇产科教研室 (成都 610041)Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu 610041, China
- 出生缺陷与相关妇儿疾病教育部重点实验室(四川大学) (成都 610041)Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China
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98
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Hopkins MK, Dugoff L, Kuller JA. Exome Sequencing and Its Emerging Role in Prenatal Genetic Diagnosis. Obstet Gynecol Surv 2021; 75:317-320. [PMID: 32469417 DOI: 10.1097/ogx.0000000000000787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Importance Prenatal genetic diagnosis can guide pregnancy management and decision making. Genetic diagnosis has advanced rapidly, and chromosomal microarray has become widely used, in addition to conventional karyotype. Exome sequencing may provide an even higher detection rate of genetic anomalies and may be more commonly applied in the future. Objectives The objectives of this manuscript are to review current practices in prenatal genetic diagnosis, define exome sequencing, identify scenarios in which exome sequencing may be indicated, identify potential concerns regarding exome sequencing, and review the importance for the general obstetrician-gynecologist to understand exome sequencing technology and its uses. Evidence Acquisition A MEDLINE search of "prenatal genetic testing," "chromosomal microarray," "conventional karyotype," or "exome sequencing" in the review was performed. Results The evidence cited in this review includes 6 medical society committee opinions and 17 additional peer-reviewed journal articles that were original research or expert opinion summaries. Conclusions and Relevance Exome sequencing may be a useful prenatal genetic diagnostic tool in cases with ultrasound anomalies with previously normal chromosomal microarray and/or karyotype. As more data become available, technology improves, and costs fall, exome sequencing may become more widely used in prenatal genetic diagnosis.
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Affiliation(s)
| | - Lorraine Dugoff
- Professor, Divisions of Reproductive Genetics and Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Jeffrey A Kuller
- Professor, Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC
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99
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Huang X, Chen J, Hu W, Li L, He H, Guo H, Liao Q, Ye M, Tang D, Dai Y. A report on seven fetal cases associated with 15q11-q13 microdeletion and microduplication. Mol Genet Genomic Med 2021; 9:e1605. [PMID: 33538077 PMCID: PMC8104164 DOI: 10.1002/mgg3.1605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
Background The 15q11‐q13 region contains three breakpoints (BP1 to BP3), and copy number variations often occur in the region. Aims 15q11‐q13 microdeletion and microduplication are usually associated with Prader‐Willi and Angelman syndromes, respectively. It is not yet clear to what extent microdeletion and microduplication affect the physical health of the fetus and the child. In this study, we examined seven fetuses ranging in gestational age from 15 to 27 weeks. Materials & Methods Detailed prenatal screening and laboratory examinations were performed, while karyotype analysis and chromosomal microarray analysis (CMA) of the amniotic fluid and umbilical cord blood were applied for genetic analysis. Results CMA analysis showed that four fetuses harbored a microdeletion and one fetus showed a microduplication at 15q11.2 BP1‐BP2, two fetuses had a microdeletion at 15q11‐q13 BP2‐BP3, and one fetus had an additional microdeletion at 16p13.11. Discussion There is no clear standard for the clinical diagnosis of 15q11‐q13 microdeletion and microduplication, some of them have clinical phenotypes or are clinically affected. Conclusion Therefore, parents of such fetuses should be informed of the possibility of microdeletions or microduplications to mitigate the psychological burden, and medical consultation and assistance should be provided when communicating the results of the mid‐gestation screening.
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Affiliation(s)
- Xiuzhu Huang
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Jieping Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Wenlong Hu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Lu Li
- MOE Key Laboratory of Tumor Molecular Biology and Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China.,Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Huiyan He
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Hui Guo
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Qiuyan Liao
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Mei Ye
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
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100
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Guadagnolo D, Mastromoro G, Di Palma F, Pizzuti A, Marchionni E. Prenatal Exome Sequencing: Background, Current Practice and Future Perspectives-A Systematic Review. Diagnostics (Basel) 2021; 11:diagnostics11020224. [PMID: 33540854 PMCID: PMC7913004 DOI: 10.3390/diagnostics11020224] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 12/16/2022] Open
Abstract
The introduction of Next Generation Sequencing (NGS) technologies has exerted a significant impact on prenatal diagnosis. Prenatal Exome Sequencing (pES) is performed with increasing frequency in fetuses with structural anomalies and negative chromosomal analysis. The actual diagnostic value varies extensively, and the role of incidental/secondary or inconclusive findings and negative results has not been fully ascertained. We performed a systematic literature review to evaluate the diagnostic yield, as well as inconclusive and negative-result rates of pES. Papers were divided in two groups. The former includes fetuses presenting structural anomalies, regardless the involved organ; the latter focuses on specific class anomalies. Available findings on non-informative or negative results were gathered as well. In the first group, the weighted average diagnostic yield resulted 19%, and inconclusive finding rate 12%. In the second group, the percentages were extremely variable due to differences in sample sizes and inclusion criteria, which constitute major determinants of pES efficiency. Diagnostic pES availability and its application have a pivotal role in prenatal diagnosis, though more homogeneity in access criteria and a consensus on clinical management of controversial information management is envisageable to reach widespread use in the near future.
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Affiliation(s)
- Daniele Guadagnolo
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Francesca Di Palma
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Clinical Genomics Unit, IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo (FG), Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (G.M.); (F.D.P.); (A.P.)
- Correspondence:
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