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Guha S, Reddi HV, Aarabi M, DiStefano M, Wakeling E, Dungan JS, Gregg AR. Laboratory testing for preconception/prenatal carrier screening: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2024; 26:101137. [PMID: 38814327 DOI: 10.1016/j.gim.2024.101137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 05/31/2024] Open
Abstract
Carrier screening has historically assessed a relatively small number of autosomal recessive and X-linked conditions selected based on frequency in a specific subpopulation and association with severe morbidity or mortality. Advances in genomic technologies enable simultaneous screening of individuals for several conditions. The American College of Medical Genetics and Genomics recently published a clinical practice resource that presents a framework when offering screening for autosomal recessive and X-linked conditions during pregnancy and preconception and recommends a tier-based approach when considering the number of conditions to screen for and their frequency within the US population in general. This laboratory technical standard aims to complement the practice resource and to put forth considerations for clinical laboratories and clinicians who offer preconception/prenatal carrier screening.
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Affiliation(s)
| | - Honey V Reddi
- Department of Pathology and Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI
| | - Mahmoud Aarabi
- UPMC Medical Genetics and Genomics Laboratories, UPMC Magee-Womens Hospital, Pittsburgh, PA; Departments of Pathology and Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | - Jeffrey S Dungan
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Anthony R Gregg
- Department of Obstetrics and Gynecology, Prisma Health, Columbia, SC
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2
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Go M, Shim SH. Genomic aspects in reproductive medicine. Clin Exp Reprod Med 2024; 51:91-101. [PMID: 38263590 PMCID: PMC11140259 DOI: 10.5653/cerm.2023.06303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/29/2023] [Accepted: 09/21/2023] [Indexed: 01/25/2024] Open
Abstract
Infertility is a complex disease characterized by extreme genetic heterogeneity, compounded by various environmental factors. While there are exceptions, individual genetic and genomic variations related to infertility are typically rare, often family-specific, and may serve as susceptibility factors rather than direct causes of the disease. Consequently, identifying the cause of infertility and developing prevention and treatment strategies based on these factors remain challenging tasks, even in the modern genomic era. In this review, we first examine the genetic and genomic variations associated with infertility, and subsequently summarize the concepts and methods of preimplantation genetic testing in light of advances in genome analysis technology.
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Affiliation(s)
- Minyeon Go
- Department of Biomedical Science, College of Life Science, CHA University, Pocheon, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Pocheon, Republic of Korea
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3
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Scarano C, Veneruso I, De Simone RR, Di Bonito G, Secondino A, D’Argenio V. The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences. Biomolecules 2024; 14:568. [PMID: 38785975 PMCID: PMC11117673 DOI: 10.3390/biom14050568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The understanding of the human genome has been greatly improved by the advent of next-generation sequencing technologies (NGS). Despite the undeniable advantages responsible for their widespread diffusion, these methods have some constraints, mainly related to short read length and the need for PCR amplification. As a consequence, long-read sequencers, called third-generation sequencing (TGS), have been developed, promising to overcome NGS. Starting from the first prototype, TGS has progressively ameliorated its chemistries by improving both read length and base-calling accuracy, as well as simultaneously reducing the costs/base. Based on these premises, TGS is showing its potential in many fields, including the analysis of difficult-to-sequence genomic regions, structural variations detection, RNA expression profiling, DNA methylation study, and metagenomic analyses. Protocol standardization and the development of easy-to-use pipelines for data analysis will enhance TGS use, also opening the way for their routine applications in diagnostic contexts.
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Affiliation(s)
- Carmela Scarano
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Iolanda Veneruso
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Rosa Redenta De Simone
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Gennaro Di Bonito
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Angela Secondino
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, Via Sergio Pansini 5, 80131 Napoli, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Via G. Salvatore 486, 80145 Napoli, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Via di Val Cannuta 247, 00166 Roma, Italy
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Ranieri A, La Monica I, Di Iorio MR, Lombardo B, Pastore L. Genetic Alterations in a Large Population of Italian Patients Affected by Neurodevelopmental Disorders. Genes (Basel) 2024; 15:427. [PMID: 38674362 PMCID: PMC11050211 DOI: 10.3390/genes15040427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Neurodevelopmental disorders are a group of complex multifactorial disorders characterized by cognitive impairment, communication deficits, abnormal behaviour, and/or motor skills resulting from abnormal neural development. Copy number variants (CNVs) are genetic alterations often associated with neurodevelopmental disorders. We evaluated the diagnostic efficacy of the array-comparative genomic hybridization (a-CGH) method and its relevance as a routine diagnostic test in patients with neurodevelopmental disorders for the identification of the molecular alterations underlying or contributing to the clinical manifestations. In the present study, we analysed 1800 subjects with neurodevelopmental disorders using a CGH microarray. We identified 208 (7%) pathogenetic CNVs, 2202 (78%) variants of uncertain significance (VOUS), and 504 (18%) benign CNVs in the 1800 patients analysed. Some alterations contain genes potentially related to neurodevelopmental disorders including CHRNA7, ANKS1B, ANKRD11, RBFOX1, ASTN2, GABRG3, SHANK2, KIF1A SETBP1, SNTG2, CTNNA2, TOP3B, CNTN4, CNTN5, and CNTN6. The identification of interesting significant genes related to neurological disorders with a-CGH is therefore an essential step in the diagnostic procedure, allowing a better understanding of both the pathophysiology of these disorders and the mechanisms underlying their clinical manifestations.
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Affiliation(s)
- Annaluisa Ranieri
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
| | - Ilaria La Monica
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Maria Rosaria Di Iorio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Barbara Lombardo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy; (A.R.); (I.L.M.); (M.R.D.I.); (L.P.)
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II, via Sergio Pansini 5, 80131 Naples, Italy
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Li Y, Liang L, Bai J, Zheng L, Qin T. Case report: Prenatal diagnosis in the fetus of a couple with both thalassemia and deafness genes. Front Genet 2023; 14:1258293. [PMID: 38146341 PMCID: PMC10749304 DOI: 10.3389/fgene.2023.1258293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023] Open
Abstract
Background: Prenatal diagnosis and genetic counseling play an important role in preventing and controlling birth defects. No reports were found of prenatal diagnosis of couples carrying both the thalassemia and deafness genes. In this study, we presented the prenatal screening and diagnosis of a couple with both thalassemia and deafness genes, contributing to better genetic counseling. Case Report: A couple visited our hospital for a routine prenatal examination. As required by the policy in our region, they underwent screening and genetic diagnosis for thalassemia. Meanwhile, they did not accept the recommendation to test for spinal muscular atrophy and deafness genes. The female was confirmed to be a Hb Quong Sze (Hb QS) carrier (αQSα/αα, βN/βN), and the male had Hb H disease combined with β-thalassemia (--SEA/αCSα, βCDs41-42 (-TTCT)/βN). A prenatal diagnosis of the fetus revealed a Hb CS heterozygote. Subsequent complementary testing showed that the male was a double heterozygote of the GJB2 gene c.299_300delAT combined with c.109G>A, and Sanger sequencing confirmed that the female was a carrier of c.508_511dup in the GJB2. Fortunately, the chorionic villi results indicated that the fetus was only a carrier of deafness. Conclusion: Since both partners carried thalassemia and deafness genes, the couple required prenatal diagnosis for the respective mutations. Expanded carrier screening (ECS) is a more advanced technology that can detect multiple disease genes simultaneously.
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Affiliation(s)
- Youqiong Li
- Center for Medical Genetics and Prenatal Diagnosis, People’s Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
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Szalai C. Arguments for and against the whole-genome sequencing of newborns. Am J Transl Res 2023; 15:6255-6263. [PMID: 37969196 PMCID: PMC10641337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/11/2023] [Indexed: 11/17/2023]
Abstract
Recent decades have brought enormous progress in both genetics and genomics, as well as in information technology (IT). The sequence of the human genome is now known, and although our knowledge is far from complete, great progress has been made in understanding how the genome works. With the developments in storage capacity, artificial intelligence, and learning algorithms, we are now able to learn and interpret complex systems such as the human genome in a very short time. Perhaps the most important goal of learning about the human genome is to understand diseases better: how they develop; how their processes can be prevented or slowed down; and after diseases have developed, how they can be cured or their symptoms alleviated. The vast majority of diseases have a genetic background, i.e., genes, sequence variations, and gene-gene interactions play a role in most diseases to a greater or lesser extent. Accordingly, the first step is to discover which genes, or genomic variants, cause or contribute to the development of a particular disease in a given patient. Given that an individual's genome remains virtually unchanged throughout their life (with one or two exceptions, such as in the case of cancer, which is caused by somatic mutations), it might be considered advantageous to sequence the genome of every person at birth. In this paper, we set out to show the possible benefits of sequencing the entire genome of every human being at birth, while also discussing the main arguments against it.
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Affiliation(s)
- Csaba Szalai
- Department of Genetics, Cell and Immunobiology, Semmelweis University1089 Budapest, Hungary
- Heim Pál Children’s Hospital1089 Budapest, Hungary
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Anderson S. Current State of Dor Yeshorim, Expanded Carrier, and Newborn Screening: Benefits and Limitations. MCN Am J Matern Child Nurs 2023; 48:266-272. [PMID: 37326600 DOI: 10.1097/nmc.0000000000000939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
ABSTRACT Availability and accessibility of preconception and prenatal genetic carrier and newborn biochemical and genetic screening have grown exponentially over the past 2 decades and as such, it is challenging for clinicians to keep pace. Although genetic counseling or genetic consultation should be offered to all expectant and new parents for prenatal screening decisions and positive results, benefits and limitations of these tests and results must be known and familiar to perinatal and pediatric clinicians. A brief historical overview of Dor Yeshorim, preconception and prenatal expanded carrier, and newborn screening is presented, followed by discussion about the conditions screened and considerations surrounding the benefits and limitations of these tests in the practice setting.
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Affiliation(s)
- Sharon Anderson
- Sharon Anderson is the Associate Dean and Associate Professor, Division of Advanced Nursing Practice, Rutgers School of Nursing, Newark, NJ; and Advanced Practice Nurse, Rutgers Robert Wood Johnson Medical School, Medical Genetics, Child Health Institute of New Jersey, New Brunswick, NJ. Dr. Anderson can be reached via email at
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Veneruso I, Ranieri A, Falcone N, Tripodi L, Scarano C, La Monica I, Pastore L, Lombardo B, D’Argenio V. The Potential Usefulness of the Expanded Carrier Screening to Identify Hereditary Genetic Diseases: A Case Report from Real-World Data. Genes (Basel) 2023; 14:1651. [PMID: 37628702 PMCID: PMC10454493 DOI: 10.3390/genes14081651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 08/16/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Expanded carrier screening (ECS) means a comprehensive genetic analysis to evaluate an individual's carrier status. ECS is becoming more frequently used, thanks to the availability of techniques such as next generation sequencing (NGS) and array comparative genomic hybridization (aCGH), allowing for extensive genome-scale analyses. Here, we report the case of a couple who underwent ECS for a case of autism spectrum disorder in the male partner family. aCGH and whole-exome sequencing (WES) were performed in the couple. aCGH analysis identified in the female partner two deletions involving genes associated to behavioral and neurodevelopment disorders. No clinically relevant alterations were identified in the husband. Interestingly, WES analysis identified in the male partner a pathogenic variant in the LPL gene that is emerging as a novel candidate gene for autism. This case shows that ECS may be useful in clinical contexts, especially when both the partners are analyzed before conception, thus allowing the estimation of their risk to transmit an inherited condition. On the other side, there are several concerns related to possible incidental findings and difficult-to-interpret results. Once these limits are defined by the establishment of specific guidelines, ECS may have a greater diffusion.
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Affiliation(s)
- Iolanda Veneruso
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Annaluisa Ranieri
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
| | - Noemi Falcone
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lorella Tripodi
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Carmela Scarano
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Ilaria La Monica
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
| | - Lucio Pastore
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Barbara Lombardo
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, Federico II University, via Sergio Pansini 5, 80131 Naples, Italy
| | - Valeria D’Argenio
- CEINGE-Biotecnologie Avanzate Franco Salvatore, via G. Salvatore 486, 80145 Naples, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, via di Val Cannuta 247, 00166 Rome, Italy
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Chen X, Xu Z, Lei X, Liang H, Wu F, Chen R, Guo Y, Xiong L. Amplicon sequencing-based carrier screening for 170 monogenic disorders among children with abnormal LC-MS/MS results. Clin Chim Acta 2023; 539:274-277. [PMID: 36574877 DOI: 10.1016/j.cca.2022.12.024] [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: 10/05/2022] [Revised: 12/13/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) has been suggested as a second-tier diagnostic test for newborn screening, which could help identify the carrier status of hundreds monogenic disorders with wider spectrum and earlier stage. METHODS Among the 1087 children (age from 27 min to 14 years old) underwent liquid chromatography-tandem mass spectrometry (LC-MS/MS), 290 individuals who had at least one abnormal value of LC-MS/MS measurements were sent for amplicon sequencing-based carrier screening (targeting 141 genes for 170 monogenic disorders). Multiplex polymerase chain reaction was used for amplicon capture and library preparation, the NextSeq 500 NGS platform (Illumina PE150) was used for sequencing. The identified clinical significant variants were further validated by Sanger sequencing. RESULTS Only 89 children carry none of clinical significant variants, other 201 individuals carry 1-4 variants in 63 genes (132 types; 317 in total: 171 pathogenic, 37 likely pathogenic, 29 variants of unknown significance, and 80 disease-associated functional polymorphisms). Besides the three missing samples with 4 variants, 91.1 % of identified variants (285 variants in 54 genes) were completely validated by Sanger sequencing. The most common genetic variants were in UGT1A1, GJB2, PAH, G6PD, and SLC25A13 (top 5 genes), which corresponding to Gilbert/Crigler-Najjar symdrome (n = 89), autosomal recessive hearing loss type 1A (n = 58), phenylketonuria (n = 12), glucose-6-phosphate dehydrogenease deficiency (n = 11) and Citrin deficiency (n = 9). More than 42 children present higher phenylalanine in LC-MS/MS, but only 12 of them were identified to carry clinical significant variants in PAH gene. CONCLUSION The amplicon sequencing-based carrier screening in our study could further clarify the abnormal LC-MS/MS results, which could also discover more monogenic disorders uncovered by LC-MS/MS screening.
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Affiliation(s)
- Xu Chen
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China; Institute of Maternal-Fetal Medicine, Baoan Women's and Children's Hospital, Shenzhen, China
| | - Zhongyao Xu
- Shenzhen Uni-medica Technology Co., Ltd, Shenzhen, China
| | - Xianghua Lei
- Shenzhen Uni-medica Technology Co., Ltd, Shenzhen, China
| | - Hui Liang
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China
| | - Feng Wu
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Ruoqing Chen
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yongchao Guo
- Shenzhen Uni-medica Technology Co., Ltd, Shenzhen, China
| | - Likuan Xiong
- Central Laboratory, Baoan Women's and Children's Hospital, Shenzhen, China; Shenzhen Key Laboratory of Birth Defects Research, Shenzhen, China.
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