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Marchionni E, Guadagnolo D, Mastromoro G, Pizzuti A. Prenatal Genome-Wide Sequencing analysis (Exome or Genome) in detecting pathogenic Single Nucleotide Variants in fetal Central Nervous System Anomalies: systematic review and meta-analysis. Eur J Hum Genet 2024; 32:759-769. [PMID: 38486024 PMCID: PMC11219734 DOI: 10.1038/s41431-024-01590-2] [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: 09/16/2023] [Revised: 02/04/2024] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
Prenatal Exome (pES) or Genome (pGS) Sequencing analysis showed a significant incremental diagnostic yield over karyotype and chromosomal microarray analysis (CMA) in fetal structural anomalies. Optimized indications and detection rates in different fetal anomalies are still under investigation. The aim of this study was to assess the incremental diagnostic yield in prenatally diagnosed Central Nervous System (CNS) anomalies. A systematic review on antenatal CNS anomalies was performed according to PRISMA guidelines, including n = 12 paper, accounting for 428 fetuses. Results were pooled in a meta-analysis fitting a logistic random mixed-effect model. The effect of interest was the incremental diagnostic rate of pES over karyotype/CMA in detecting likely pathogenic/pathogenic Single Nucleotide Variants (SNVs). A further meta-analysis adding the available pGS studies (including diagnostic coding SNVs only) and submeta-analysis on three CNS subcategories were also performed. The pooled incremental diagnostic yield estimate of pES studies was 38% (95% C.I.: [29%;47%]) and 36% (95% C.I.: [28%;45%]) when including diagnostic SNVs of pGS studies. The point estimate of the effect resulted 22% (95% C.I.: [15%;31%]) in apparently isolated anomalies, 33% (95% C.I.: [22%;46%]) in CNS-only related anomalies (≥1) and 46% (95% C.I.: [38%;55%]) in non-isolated anomalies (either ≥ 2 anomalies in CNS, or CNS and extra-CNS). Meta-analysis showed a substantial diagnostic improvement in performing Prenatal Genome-Wide Sequencing analysis (Exome or Genome) over karyotype and CMA in CNS anomalies.
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Affiliation(s)
- Enrica Marchionni
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy.
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Gioia Mastromoro
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
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Qi Q, Jiang Y, Zhou X, Lü Y, Xiao R, Bai J, Lou H, Sun W, Lian Y, Hao N, Li M, Chang J. Whole-genome sequencing analysis in fetal structural anomalies: novel phenotype-genotype discoveries. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:664-671. [PMID: 37842862 DOI: 10.1002/uog.27517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023]
Abstract
OBJECTIVES The identification of structural variants and single-nucleotide variants is essential in finding molecular etiologies of monogenic genetic disorders. Whole-genome sequencing (WGS) is becoming more widespread in genetic disease diagnosis. However, data on its clinical utility remain limited in prenatal practice. We aimed to expand our understanding of implementing WGS in the genetic diagnosis of fetal structural anomalies. METHODS We employed trio WGS with a minimum coverage of 40× on the MGI DNBSEQ-T7 platform in a cohort of 17 fetuses presenting with aberrations detected by ultrasound, but uninformative findings of standard chromosomal microarray analysis (CMA) and exome sequencing (ES). RESULTS Causative genetic variants were identified in two families, with an increased diagnostic yield of 11.8% (2/17). Both were exon-level copy-number variants of small size (3.03 kb and 5.16 kb) and beyond the detection thresholds of CMA and ES. Moreover, to the best of our knowledge, we have described the first prenatal instance of the association of FGF8 with holoprosencephaly and facial deformities. CONCLUSIONS Our analysis demonstrates the clinical value of WGS in the diagnosis of the underlying etiology of fetuses with structural abnormalities, when routine genetic tests have failed to provide a diagnosis. Additionally, the novel variants and new fetal manifestations have expanded the mutational and phenotypic spectrums of BBS9 and FGF8. © 2023 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- Q Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Y Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - X Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Y Lü
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - R Xiao
- National Engineering Laboratory for Key Technology of Birth Defect Control and Prevention, Screening and Diagnostic R&D Center, Zhejiang, China
| | - J Bai
- Becreative Lab Co. Ltd, Beijing, China
| | - H Lou
- Becreative Lab Co. Ltd, Beijing, China
| | - W Sun
- Biosan Biochemical Technologies Co. Ltd., Zhejiang, China
| | - Y Lian
- Biosan Biochemical Technologies Co. Ltd., Zhejiang, China
| | - N Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - M Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - J Chang
- Department of Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
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Botos L, Szatmári E, Nagy GR. Prenatal and postnatal genetic testing toward personalized care: The non-invasive perinatal testing. Mol Cell Probes 2023; 72:101942. [PMID: 37951513 DOI: 10.1016/j.mcp.2023.101942] [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: 10/10/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
This article investigates how non-invasive prenatal testing and the incorporation of genomic sequencing into newborn screening postnatally are transforming perinatal care. They improve the accuracy of prenatal and neonatal screening, allowing for early interventions and personalized therapies. Non-invasive prenatal testing before birth and saliva-sample-based newborn genomic sequencing after birth can be collectively referred to as non-invasive perinatal testing. Non-invasive prenatal testing is particularly useful for aneuploidy, whereas performance markers worsen as DNA abnormalities shrink in size. Screening for clinically actionable diseases in childhood would be crucial to personalized medical therapy, as the postnatal period remains appropriate for screening for the great majority of monogenic disorders. While genomic data can help diagnose uncommon diseases, challenges like ethics and equity necessitate joint approaches for appropriate integration in this revolutionary journey toward personalized care.
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Affiliation(s)
- Lilla Botos
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Erzsébet Szatmári
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Gyula Richárd Nagy
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary; Intelligenetic Healthcare Services Ltd., Budapest, Hungary.
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Khera HK, Mishra R. Nucleic Acid Based Testing (NABing): A Game Changer Technology for Public Health. Mol Biotechnol 2023:10.1007/s12033-023-00870-4. [PMID: 37695473 DOI: 10.1007/s12033-023-00870-4] [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: 04/28/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Timely and accurate detection of the causal agent of a disease is crucial to restrict suffering and save lives. Mere symptoms are often not enough to detect the root cause of the disease. Better diagnostics applied for screening at a population level and sensitive detection assays remain the crucial component of disease surveillance which may include clinical, plant, and environmental samples, including wastewater. The recent advances in genome sequencing, nucleic acid amplification, and detection methods have revolutionized nucleic acid-based testing (NABing) and screening assays. A typical NABing assay consists of three modules: isolation of the nucleic acid from the collected sample, identification of the target sequence, and final reading the target with the help of a signal, which may be in the form of color, fluorescence, etc. Here, we review current NABing assays covering the different aspects of all three modules. We also describe the frequently used target amplification or signal amplification procedures along with the variety of applications of this fast-evolving technology and challenges in implementation of NABing in the context of disease management especially in low-resource settings.
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Affiliation(s)
- Harvinder Kour Khera
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
| | - Rakesh Mishra
- Tata Institute for Genetics and Society, New inStem Building NCBS Campus, GKVK Post, Bellary Road, Bengaluru, 560065, India.
- CSIR-Centre for Cellular and Molecular Biology, Uppal Rd, IICT Colony, Habsiguda, Hyderabad, Telangana, 500007, India.
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Krieger KL, Mann EK, Lee KJ, Bolterstein E, Jebakumar D, Ittmann MM, Dal Zotto VL, Shaban M, Sreekumar A, Gassman NR. Spatial mapping of the DNA adducts in cancer. DNA Repair (Amst) 2023; 128:103529. [PMID: 37390674 PMCID: PMC10330576 DOI: 10.1016/j.dnarep.2023.103529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
DNA adducts and strand breaks are induced by various exogenous and endogenous agents. Accumulation of DNA damage is implicated in many disease processes, including cancer, aging, and neurodegeneration. The continuous acquisition of DNA damage from exogenous and endogenous stressors coupled with defects in DNA repair pathways contribute to the accumulation of DNA damage within the genome and genomic instability. While mutational burden offers some insight into the level of DNA damage a cell may have experienced and subsequently repaired, it does not quantify DNA adducts and strand breaks. Mutational burden also infers the identity of the DNA damage. With advances in DNA adduct detection and quantification methods, there is an opportunity to identify DNA adducts driving mutagenesis and correlate with a known exposome. However, most DNA adduct detection methods require isolation or separation of the DNA and its adducts from the context of the nuclei. Mass spectrometry, comet assays, and other techniques precisely quantify lesion types but lose the nuclear context and even tissue context of the DNA damage. The growth in spatial analysis technologies offers a novel opportunity to leverage DNA damage detection with nuclear and tissue context. However, we lack a wealth of techniques capable of detecting DNA damage in situ. Here, we review the limited existing in situ DNA damage detection methods and examine their potential to offer spatial analysis of DNA adducts in tumors or other tissues. We also offer a perspective on the need for spatial analysis of DNA damage in situ and highlight Repair Assisted Damage Detection (RADD) as an in situ DNA adduct technique with the potential to integrate with spatial analysis and the challenges to be addressed.
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Affiliation(s)
- Kimiko L Krieger
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA
| | - Elise K Mann
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Kevin J Lee
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Elyse Bolterstein
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Deborah Jebakumar
- Department of Anatomic Pathology, Baylor Scott & White Medical Center, Temple, TX 76508, USA; Texas A&M College of Medicine, Temple, TX 76508, USA
| | - Michael M Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA; Human Tissue Acquisition & Pathology Shared Resource, Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Valeria L Dal Zotto
- Department of Pathology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Mohamed Shaban
- Department of Electrical and Computer Engineering, University of South Alabama, Mobile, AL 36688, USA
| | - Arun Sreekumar
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Translational Metabolism and Health Disparities (C-TMH), Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Natalie R Gassman
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Huang W, Shi X, Chen Y, Zhang Q, Peng J, Zheng S, Wu K. Comparative pharyngeal cartilage developmental toxicity of bisphenol A, bisphenol S and bisphenol AF to zebrafish (Danio rerio) larvae: A combination of morphometry and global transcriptome analyses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161702. [PMID: 36681333 DOI: 10.1016/j.scitotenv.2023.161702] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/17/2022] [Accepted: 01/15/2023] [Indexed: 01/21/2023]
Abstract
Exposure to BPA is recently shown to affect cartilage development in teleost fishes; whether BPS and BPAF, its two most frequently used phenolic analogues have similar effect, however, remains unclear. Here, we utilize zebrafish (Danio rerio) as an in-vivo larval model for systematic comparison of the pharyngeal arch-derived cartilage developmental toxicity of BPA, BPS and BPAF. Zebrafish are continuously exposed to three bisphenol analogues (3-BPs) at a range of concentrations since the embryonic stage (0.5 hpf), and identified cartilage malformations of the mandibular and hyoid pharyngeal arches at larval stage (120 hpf). BPA and BPAF prolong length and broaden cartilage angles; however, BPS shortens length and narrows the angles of skull cartilages. The results of the comparative transcriptome show that FoxO and MAPK signaling pathways are closely associated with the toxicity of BPA and BPAF, while BPS exposure affects energy metabolism-related pathways. Moreover, exposure to 3-BPs have an impact on the oxidative stress status. Our data collectively indicate that BPS and BPAF may not be safer than BPA regarding the impact on pharyngeal cartilage development in fish model, the mechanisms still need explorations, and that these two analogues should be applied with caution.
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Affiliation(s)
- Wenlong Huang
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515041, Guangdong, China.
| | - Xiaoling Shi
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Yuequn Chen
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Qiong Zhang
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Jiajun Peng
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Shukai Zheng
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Kusheng Wu
- Department of Preventive Medicine, Shantou University Medical College, Shantou 515041, Guangdong, China.
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Diagnostic potential of the amniotic fluid cells transcriptome in deciphering mendelian disease: a proof-of-concept. NPJ Genom Med 2022; 7:74. [PMID: 36577754 PMCID: PMC9797484 DOI: 10.1038/s41525-022-00347-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) is emerging in genetic diagnoses as it provides functional support for the interpretation of variants of uncertain significance. However, the use of amniotic fluid (AF) cells for RNA-seq has not yet been explored. Here, we examined the expression of clinically relevant genes in AF cells (n = 48) compared with whole blood and fibroblasts. The number of well-expressed genes in AF cells was comparable to that in fibroblasts and much higher than that in blood across different disease categories. We found AF cells RNA-seq feasible and beneficial in prenatal diagnosis (n = 4) as transcriptomic data elucidated the molecular consequence leading to the pathogenicity upgrade of variants in CHD7 and COL1A2 and revising the in silico prediction of a variant in MYRF. AF cells RNA-seq could become a reasonable choice for postnatal patients with advantages over fibroblasts and blood as it prevents invasive procedures.
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