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Shen G, Li W, Zhang Y, Chen L. Next-generation sequencing based newborn screening and comparative analysis with MS/MS. BMC Pediatr 2024; 24:230. [PMID: 38561707 PMCID: PMC10985934 DOI: 10.1186/s12887-024-04718-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Newborn screening (NBS), such as tandem mass spectrometry (MS/MS), may yield false positive/negative results. Next-generation sequencing (NGS) has the potential to provide increased data output, efficiencies, and applications. This study aimed to analyze the types and distribution of pathogenic gene mutations in newborns in Huzhou, Zhejiang province, China and explore the applicability of NGS and MS/MS in NBS. METHODS Blood spot samples from 1263 newborns were collected. NGS was employed to screen for pathogenic variants in 542 disease-causing genes, and detected variants were validated using Sanger sequencing. Simultaneously, 26 inherited metabolic diseases (IMD) were screened using MS/MS. Positive or suspicious samples identified through MS/MS were cross-referenced with the results of NGS. RESULTS Among all newborns, 328 had no gene mutations detected. NGS revealed at least one gene mutation in 935 newborns, with a mutation rate of 74.0%. The top 5 genes were FLG, GJB2, UGT1A1, USH2A, and DUOX2. According to American College of Medical Genetics guidelines, gene mutations in 260 cases were classified as pathogenic or likely pathogenic mutation, with a positive rate of 20.6%. The top 5 genes were UGT1A1, FLG, GJB2, MEFV, and G6PD. MS/MS identified 18 positive or suspicious samples for IMD and 1245 negative samples. Verification of these cases by NGS results showed no pathogenic mutations, resulting in a false positive rate of 1.4% (18/1263). CONCLUSION NBS using NGS technology broadened the range of diseases screened, and enhanced the accuracy of diagnoses in comparison to MS/MS for screening IMD. Combining NGS and biochemical screening would improve the efficiency of current NBS.
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Affiliation(s)
- Guosong Shen
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China.
| | - Wenwen Li
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China
| | - Yaqin Zhang
- Medical Laboratory Center, Huzhou Maternity & Child Health Care Hospital, Huzhou, Zhejiang Province, 313000, China
| | - Lyuyan Chen
- Institut for Neuroscience, Technical University of Munich, 80802, Munich, Germany
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2
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Sun X, Zhang Y, Xin S, Jin L, Cao Q, Wang H, Wang K, Liu X, Tang C, Li W, Li Z, Wen X, Yang G, Guo C, Liu Z, Ye L. NOTCH3 promotes docetaxel resistance of prostate cancer cells through regulating TUBB3 and MAPK signaling pathway. Cancer Sci 2024; 115:412-426. [PMID: 38115797 PMCID: PMC10859609 DOI: 10.1111/cas.16040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/12/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
Docetaxel is the preferred chemotherapeutic agent in patients with castrate-resistant prostate cancer (CRPC). However, patients eventually develop docetaxel resistance and in the absence of effective treatment options. Consequently, it is essential to investigate the mechanisms generating docetaxel resistance and develop novel alternative therapeutic targets. RNA sequencing was undertaken on docetaxel-sensitive and docetaxel-resistant prostate cancer (PCa) cells. Subsequently, chemoresistance, cancer stemness, and lipid metabolism were investigated. To obtain insight into the precise activities and action mechanisms of NOTCH3 in docetaxel-resistant PCa, immunoprecipitation, mass spectrometry, ChIP, luciferase reporter assay, cell metabolism, and animal experiments were performed. Through RNA sequencing analysis, we found that NOTCH3 expression was markedly higher in docetaxel-resistant cells relative to parental cells, and that this trend was continued in docetaxel-resistant PCa tissues. Experiments in vitro and in vivo revealed that NOTCH3 enhanced stemness, lipid metabolism, and docetaxel resistance in PCa. Mechanistically, NOTCH3 is bound to TUBB3 and activates the MAPK signaling pathway. Moreover, NOTCH3 was directly regulated by MEF2A in docetaxel-resistant cells. Notably, targeting NOTCH3 and the MEF2A/TUBB3 signaling axis was related to docetaxel chemoresistance in PCa. Overall, these results demonstrated that NOTCH3 fostered stemness, lipid metabolism, and docetaxel resistance in PCa via the TUBB3 and MAPK signaling pathways. Therefore, NOTCH3 may be employed as a prognostic biomarker in PCa patients. NOTCH3 could be a therapeutic target for PCa patients, particularly those who have developed docetaxel resistance.
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Affiliation(s)
- Xianchao Sun
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of UrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Ying Zhang
- Department of UrologyThe Second Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Shiyong Xin
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Liang Jin
- Department of Urology, Shanghai Tenth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Qiong Cao
- Department of PathologyThe Third Affiliated Hospital of Henan University of Science and TechnologyLuoyangChina
| | - Hong Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Keyi Wang
- Department of Urology, Shanghai Tenth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Xiang Liu
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Chaozhi Tang
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Weiyi Li
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Urology, Shanghai Tenth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Ziyao Li
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Xiaofei Wen
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Guosheng Yang
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Changcheng Guo
- Department of Urology, Shanghai Tenth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Zhiyu Liu
- Department of UrologyThe Second Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Lin Ye
- Department of Urology, Shanghai East Hospital, School of MedicineTongji UniversityShanghaiChina
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3
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Wang JZ, Yuan D, Yang XH, Sun CH, Hou LL, Zhang Y, Gao YX. Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study. Front Cell Infect Microbiol 2024; 13:1291980. [PMID: 38264726 PMCID: PMC10803656 DOI: 10.3389/fcimb.2023.1291980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Pneumonia are the leading cause of death worldwide, and antibiotic treatment remains fundamental. However, conventional sputum smears or cultures are still inefficient for obtaining pathogenic microorganisms.Metagenomic next-generation sequencing (mNGS) has shown great value in nucleic acid detection, however, the NGS results for lower respiratory tract microorganisms are still poorly studied. Methods This study dealt with investigating the efficacy of mNGS in detecting pathogens in the lower respiratory tract of patients with pulmonary infections. A total of 112 patients admitted at the First Affiliated Hospital of Zhengzhou University between April 30, 2018, and June 30, 2020, were enrolled in this retrospective study. The bronchoalveolar lavage fluid (BALF) was obtained from lower respiratory tract from each patient. Routine methods (bacterial smear and culture) and mNGS were employed for the identification of pathogenic microorganisms in BALF. Results The average patient age was 53.0 years, with 94.6% (106/112) obtaining pathogenic microorganism results. The total mNGS detection rate of pathogenic microorganisms significantly surpassed conventional methods (93.7% vs. 32.1%, P < 0.05). Notably, 75% of patients (84/112) were found to have bacteria by mNGS, but only 28.6% (32/112) were found to have bacteria by conventional approaches. The most commonly detected bacteria included Acinetobacter baumannii (19.6%), Klebsiella pneumoniae (17.9%), Pseudomonas aeruginosa (14.3%), Staphylococcus faecium (12.5%), Enterococcus faecium (12.5%), and Haemophilus parainfluenzae (11.6%). In 29.5% (33/112) of patients, fungi were identified using mNGS, including 23 cases of Candida albicans (20.5%), 18 of Pneumocystis carinii (16.1%), and 10 of Aspergillus (8.9%). However, only 7.1 % (8/112) of individuals were found to have fungi when conventional procedures were used. The mNGS detection rate of viruses was significantly higher than the conventional method rate (43.8% vs. 0.9%, P < 0.05). The most commonly detected viruses included Epstein-Barr virus (15.2%), cytomegalovirus (13.4%), circovirus (8.9%), human coronavirus (4.5%), and rhinovirus (4.5%). Only 29.4% (33/112) of patients were positive, whereas 5.4% (6/112) of patients were negative for both detection methods as shown by Kappa analysis, indicating poor consistency between the two methods (P = 0.340; Kappa analysis). Conclusion Significant benefits of mNGS have been shown in the detection of pathogenic microorganisms in patients with pulmonary infection. For those with suboptimal therapeutic responses, mNGS can provide an etiological basis, aiding in precise anti-infective treatment.
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Affiliation(s)
- Jin-zhu Wang
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ding Yuan
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiang-hong Yang
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Chang-hua Sun
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lin-lin Hou
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan Zhang
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yan-xia Gao
- Emergency Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Diderich KEM, Klapwijk JE, van der Schoot V, Brüggenwirth HT, Joosten M, Srebniak MI. Challenges and Pragmatic Solutions in Pre-Test and Post-Test Genetic Counseling for Prenatal Exome Sequencing. Appl Clin Genet 2023; 16:89-97. [PMID: 37216148 PMCID: PMC10198275 DOI: 10.2147/tacg.s411185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
The yield of genetic prenatal diagnosis has been notably improved by introducing whole genome chromosomal microarray (CMA) and prenatal exome sequencing (pES). However, together with increased numbers of diagnoses made, the need to manage challenging findings such as variants of unknown significance (VUS) and incidental findings (IF) also increased. We have summarized the current guidelines and recommendations and we have shown current solutions used in our tertiary center in the Netherlands. We discuss four of the most common clinical situations: fetus with normal pES results, fetus with a pathogenic finding explaining the fetal phenotype, fetus with a variant of uncertain clinical significance fitting the phenotype and fetus with a variant leading to an incidental diagnosis. Additionally, we reflect on solutions in order to facilitate genetic counseling in an NGS-era.
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Affiliation(s)
| | | | | | | | - Marieke Joosten
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
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5
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Bzdęga K, Kutkowska-Kaźmierczak A, Deutsch GH, Plaskota I, Smyk M, Niemiec M, Barczyk A, Obersztyn E, Modzelewski J, Lipska I, Stankiewicz P, Gajecka M, Rydzanicz M, Płoski R, Szczapa T, Karolak JA. Prenatal Detection of a FOXF1 Deletion in a Fetus with ACDMPV and Hydronephrosis. Genes (Basel) 2023; 14:genes14030563. [PMID: 36980834 PMCID: PMC10048226 DOI: 10.3390/genes14030563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/08/2023] [Accepted: 02/21/2023] [Indexed: 03/03/2023] Open
Abstract
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by the arrest of fetal lung formation, resulting in neonatal death due to acute respiratory failure and pulmonary arterial hypertension. Heterozygous single-nucleotide variants or copy-number variant (CNV) deletions involving the FOXF1 gene and/or its lung-specific enhancer are found in the vast majority of ACDMPV patients. ACDMPV is often accompanied by extrapulmonary malformations, including the gastrointestinal, cardiac, or genitourinary systems. Thus far, most of the described ACDMPV patients have been diagnosed post mortem, based on histologic evaluation of the lung tissue and/or genetic testing. Here, we report a case of a prenatally detected de novo CNV deletion (~0.74 Mb) involving the FOXF1 gene in a fetus with ACDMPV and hydronephrosis. Since ACDMPV is challenging to detect by ultrasound examination, the more widespread implementation of prenatal genetic testing can facilitate early diagnosis, improve appropriate genetic counselling, and further management.
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Affiliation(s)
- Katarzyna Bzdęga
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | | | - Gail H. Deutsch
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98105, USA
| | - Izabela Plaskota
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Marta Smyk
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Magdalena Niemiec
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Artur Barczyk
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Ewa Obersztyn
- Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Jan Modzelewski
- 1st Clinic of Obstetrics and Gynecology, Centre of Postgraduate Medical Education, 01-004 Warsaw, Poland
| | - Iwona Lipska
- Department of Pathomorphology, Wolski Hospital, 01-211 Warsaw, Poland
| | - Paweł Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Institute of Human Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland
| | - Małgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Tomasz Szczapa
- II Department of Neonatology, Neonatal Biophysical Monitoring and Cardiopulmonary Therapies Research Unit, Poznan University of Medical Science, 60-535 Poznan, Poland
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-806 Poznan, Poland
- Correspondence:
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6
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Berkowitz CL, Luks VL, Puc M, Peranteau WH. Molecular and Cellular In Utero Therapy. Clin Perinatol 2022; 49:811-820. [PMID: 36328600 DOI: 10.1016/j.clp.2022.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Significant advances in maternal-fetal medicine and gene sequencing technology have fostered a new frontier of in utero molecular and cellular therapeutics, including gene editing, enzyme replacement therapy, and stem cell transplantation to treat single-gene disorders with limited postnatal treatment strategies. In utero therapies take advantage of unique developmental properties of the fetus to allow for the correction of monogenic disorders before irreversible disease pathology develops. While early preclinical studies in animal models are encouraging, more studies are needed to further evaluate their safety and efficacy prior to widespread clinical use.
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Affiliation(s)
- Cara L Berkowitz
- Division of Pediatric General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Valerie L Luks
- Division of Pediatric General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Marcelina Puc
- Division of Pediatric General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - William H Peranteau
- Division of Pediatric General, Thoracic and Fetal Surgery, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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7
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Gayatri N, Ranganath P. Genetic Evaluation of the Parents Following Demise of the Index Case: Report of a Family with Fucosidosis. J Obstet Gynaecol India 2022; 72:369-371. [PMID: 35923507 PMCID: PMC9339439 DOI: 10.1007/s13224-020-01421-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 12/29/2020] [Indexed: 11/29/2022] Open
Abstract
It is common in obstetric practice to encounter couples who seek prenatal genetic counseling and testing in view of history of known or suspected genetic disorders in the previous offspring or in other family members. Recent advances in genetic testing techniques, especially the availability of the next-generation sequencing (NGS) technology, have greatly facilitated genetic evaluation of the proband and/or the consultand couple and enabled provision of accurate genetic counseling and prenatal genetic testing in such clinical scenarios. However, even in this era of NGS, comprehensive clinical history taking and detailed phenotype characterization through clinical examination and thorough perusal of available medical records, are very important and essential for accurate diagnosis, as reiterated by this report of a 30-year-old third gravida, who was referred for prenatal genetic counseling and testing, in view of history of death of the first offspring due to a suspected neurogenetic disorder. Retrospective clinical diagnosis for the deceased index child with the help of available medical records and reports, followed by relevant NGS-based clinical exome sequencing of the couple, helped to arrive at a definitive diagnosis of fucosidosis, based on which accurate prenatal genetic testing could be done.
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Outram SM, Brown JEH, Zamora AN, Sahin-Hodoglugil N, Ackerman SL. Parental Hopes and Understandings of the Value of Prenatal Diagnostic Genomic Sequencing: A Qualitative Analysis. Front Genet 2022; 13:883225. [PMID: 35923691 PMCID: PMC9339950 DOI: 10.3389/fgene.2022.883225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 06/24/2022] [Indexed: 11/29/2022] Open
Abstract
Objective: To provide qualitative empirical data on parental expectations of diagnostic prenatal genomic sequencing and the value of the results to families. Methods: We interviewed 15 families—mothers and/or fathers—who had had prenatal genomic sequencing about their expectations and their respective evaluations of the benefits of genomic sequencing. Results: Families’ hopes for genetic sequencing clustered around three themes: hoping to identify the cause of the fetal anomaly in a terminated pregnancy; hopes for guidance as to the likely outcome of current pregnancy; and hopes for information to support future family planning. In addition, hopes were discussed in terms of the potential for results to be beneficial in acquiring greater knowledge, while at the same time recognizing that new knowledge may raise more questions. Assessment of the value of sequencing largely mirrored these expectations when positive results seen. Negative results can also be seen as valuable in ruling out a genetic cause and in providing certainty that families had done everything that they could to know about the cause of fetal demise. Conclusion: It would appear that with guidance from genetic counsellors, families were largely able to navigate the many uncertainties of prenatal genomic sequencing and thus see themselves as benefitting from sequencing. However, support structures are essential to guide them through their expectations and interpretations of results to minimize possible harms. Engaging in the process of genomic sequencing was seen as beneficial in of itself to families who would otherwise be left without any options to seek diagnostic answers.
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9
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Liautard-Haag C, Durif G, VanGoethem C, Baux D, Louis A, Cayrefourcq L, Lamairia M, Willems M, Zordan C, Dorian V, Rooryck C, Goizet C, Chaussenot A, Monteil L, Calvas P, Miry C, Favre R, Le Boette E, Fradin M, Roux AF, Cossée M, Koenig M, Alix-Panabière C, Guissart C, Vincent MC. Noninvasive prenatal diagnosis of genetic diseases induced by triplet repeat expansion by linked read haplotyping and Bayesian approach. Sci Rep 2022; 12:11423. [PMID: 35794169 PMCID: PMC9259573 DOI: 10.1038/s41598-022-15307-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractThe field of noninvasive prenatal diagnosis (NIPD) has undergone significant progress over the last decade. Direct haplotyping has been successfully applied for NIPD of few single-gene disorders. However, technical issues remain for triplet-repeat expansions. The objective of this study was to develop an NIPD approach for couples at risk of transmitting dynamic mutations. This method includes targeted enrichment for linked-read libraries and targeted maternal plasma DNA sequencing. We also developed an innovative Bayesian procedure to integrate the Hoobari fetal genotyping model for inferring the fetal haplotype and the targeted gene variant status. Our method of directly resolving parental haplotypes through targeted linked-read sequencing was smoothly performed using blood samples from families with Huntington’s disease or myotonic dystrophy type 1. The Bayesian analysis of transmission of parental haplotypes allowed defining the genotype of five fetuses. The predicted variant status of four of these fetuses was in agreement with the invasive prenatal diagnosis findings. Conversely, no conclusive result was obtained for the NIPD of fragile X syndrome. Although improvements should be made to achieve clinically acceptable accuracy, our study shows that linked-read sequencing and parental haplotype phasing can be successfully used for NIPD of triplet-repeat expansion diseases.Trial registration: NCT04698551_date of first registration: 07/01/2021.
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Brown JEH, Zamora AN, Outram S, Sparks TN, Lianoglou BR, Norstad M, Sahin Hodoglugil NN, Norton ME, Ackerman SL. “Let’s Just Wait Until She’s Born”: Temporal Factors That Shape Decision-Making for Prenatal Genomic Sequencing Amongst Families Underrepresented in Genomic Research. Front Genet 2022; 13:882703. [PMID: 35669190 PMCID: PMC9164104 DOI: 10.3389/fgene.2022.882703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/25/2022] [Indexed: 11/21/2022] Open
Abstract
Genomic sequencing has been increasingly utilized for prenatal diagnosis in recent years and this trend is likely to continue. However, decision-making for parents in the prenatal period is particularly fraught, and prenatal sequencing would significantly expand the complexity of managing health risk information, reproductive options, and healthcare access. This qualitative study investigates decision-making processes amongst parents who enrolled or declined to enroll in the prenatal arm of the California-based Program in Prenatal and Pediatric Genome Sequencing (P3EGS), a study in the Clinical Sequencing Evidence-Generating Research (CSER) consortium that offered whole exome sequencing for fetal anomalies with a focus on underrepresented groups in genomic research. Drawing on the views of 18 prenatal families who agreed to be interviewed after enrolling (n = 15) or declining to enroll (n = 3) in P3EGS, we observed that the timing of sequencing, coupled with unique considerations around experiences of time during pregnancy and prenatal testing, intersect with structural supports beyond the clinic to produce preferences for and against prenatal sequencing and to contain the threat of unwelcome, uncertain knowledge. Particularly for those without structural supports, finding out consequential information may be more palatable after the birth, when the first stage of the uncertain future has been revealed. Future research should examine the role of temporality in decision-making around prenatal genomic sequencing across diverse population cohorts, in order to observe more precisely the role that structural barriers play in patient preferences.
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Affiliation(s)
- Julia E. H. Brown
- Program in Bioethics, University of California, San Francisco (UCSF), San Francisco, CA, United States
- Institute for Health and Aging, UCSF, San Francisco, CA, United States
- *Correspondence: Julia E. H. Brown,
| | - Astrid N. Zamora
- Program in Bioethics, University of California, San Francisco (UCSF), San Francisco, CA, United States
| | - Simon Outram
- Program in Bioethics, University of California, San Francisco (UCSF), San Francisco, CA, United States
- Institute for Health and Aging, UCSF, San Francisco, CA, United States
- Department of Social and Behavioral Sciences, UCSF, San Francisco, CA, United States
| | - Teresa N. Sparks
- Department of Obstetrics, Gynecology, and Reproductive Sciences, UCSF, San Francisco, CA, United States
- Institute for Human Genetics, UCSF, San Francisco, CA, United States
- Center for Maternal Fetal Precision Medicine, UCSF, San Francisco, CA, United States
| | - Billie R. Lianoglou
- Center for Maternal Fetal Precision Medicine, UCSF, San Francisco, CA, United States
- Department of Surgery, UCSF, San Francisco, CA, United States
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, United States
| | - Matthew Norstad
- Program in Bioethics, University of California, San Francisco (UCSF), San Francisco, CA, United States
- Institute for Health and Aging, UCSF, San Francisco, CA, United States
| | | | - Mary E. Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, UCSF, San Francisco, CA, United States
- Institute for Human Genetics, UCSF, San Francisco, CA, United States
- Center for Maternal Fetal Precision Medicine, UCSF, San Francisco, CA, United States
| | - Sara L. Ackerman
- Program in Bioethics, University of California, San Francisco (UCSF), San Francisco, CA, United States
- Department of Social and Behavioral Sciences, UCSF, San Francisco, CA, United States
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Fei S, Gui Z, Feng D, Wang Z, Zheng M, Chen H, Sun L, Tao J, Han Z, Ju X, Gu M, Tan R, Li X. Association Between a TLR2 Gene Polymorphism (rs3804099) and Proteinuria in Kidney Transplantation Recipients. Front Genet 2022; 12:798001. [PMID: 35265098 PMCID: PMC8899217 DOI: 10.3389/fgene.2021.798001] [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: 10/19/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The occurrence of proteinuria is one of the evaluation indicators of transplanted kidney damage and becomes an independent risk factor for poor prognosis after kidney transplantation. Our research sought to understand these potential associations and detect the underlying impact of single-nucleotide polymorphisms (SNPs) on proteinuria in kidney transplant recipients. Materials and Methods: There were 200 recipients enrolled in this study, from which blood samples were extracted for SNP mutation–related gene detection. RNA sequencing was performed in kidney tissues after kidney transplantation, and the significantly differentially expressed genes (DEGs) were analyzed between the control group and the proteinuria group. Then, the intersection of genes with SNP mutations and DEGs was conducted to obtain the target genes. Multiple genetic models were used to investigate the relationship between SNPs and proteinuria. In addition, the effect of SNP mutation in the target gene was further validated in human renal podocytes. Results: According to the sequencing results, 26 significant SNP mutated genes and 532 DEGs were found associated with proteinuria after kidney transplantation. The intersection of SNP mutated genes and DEGs showed that the Toll-like receptor 2 (TLR2) gene was significantly increased in the transplanted renal tissues of patients with proteinuria after kidney transplantation, which was consistent with the results of immunohistochemical staining. Further inheritance model results confirmed that mutations at rs3804099 of the TLR2 gene had significant influence on the occurrence of proteinuria after kidney transplantation. In the in vitro validation, we found that, after the mutation of rs3804099 on the TLR2 gene, the protein expressions of podocalyxin and nephrin in podocytes were significantly decreased, while the protein expressions of desmin and apoptosis markers were significantly increased. The results of flow cytometry also showed that the mutation of rs3804099 on the TLR2 gene significantly increased the apoptotic rate of podocytes. Conclusion: Our study suggested that the mutation of rs3804099 on the TLR2 gene was significantly related to the generation of proteinuria after kidney transplantation. Our data provide insights into the prediction of proteinuria and may imply potential individualized therapy for patients after kidney transplantation.
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Affiliation(s)
- Shuang Fei
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Zeping Gui
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China.,Department of Urology, The Second Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Dengyuan Feng
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Zijie Wang
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Ming Zheng
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Hao Chen
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Li Sun
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Jun Tao
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Zhijian Han
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Xiaobing Ju
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Min Gu
- Department of Urology, The Second Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Ruoyun Tan
- Department of Urology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Xinli Li
- Department of Cardiology, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
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12
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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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13
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Gabriel H, Korinth D, Ritthaler M, Schulte B, Battke F, von Kaisenberg C, Wüstemann M, Schulze B, Friedrich-Freksa A, Pfeiffer L, Entezami M, Schröer A, Bürger J, Schwaibold EMC, Lebek H, Biskup S. Trio exome sequencing is highly relevant in prenatal diagnostics. Prenat Diagn 2021; 42:845-851. [PMID: 34958143 PMCID: PMC9305182 DOI: 10.1002/pd.6081] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/26/2022]
Abstract
Objective About 3% of newborns show malformations, with about 20% of the affected having genetic causes. Clarification of genetic diseases in postnatal diagnostics was significantly improved with high‐throughput sequencing, in particular through whole exome sequencing covering all protein‐coding regions. Here, we aim to extend the use of this technology to prenatal diagnostics. Method Between 07/2018 and 10/2020, 500 pregnancies with fetal ultrasound abnormalities were analyzed after genetic counseling as part of prenatal diagnostics using WES of the fetus and parents. Results Molecular genetic findings could explain ultrasound abnormalities in 38% of affected fetuses. In 47% of these, disease‐causing de novo variants were found. Pathogenic variants in genes with autosomal recessive or X‐linked inheritance were detected in more than one‐third (70/189 = 37%). The latter are associated with increased probability of recurrence, making their detection important for further pregnancies. Average time from sample receipt to report was 12 days in the recent cases. Conclusion Trio exome sequencing is a useful addition to prenatal diagnostics due to its high diagnostic yield and short processing time (comparable to chromosome analysis). It covers a wide spectrum of genetic changes. Comprehensive interdisciplinary counseling before and after diagnostics is indispensable.
What's already known about this topic?
It is known that about 20% of malformations in newborns can be associated with genetic causes. Whole‐exome sequencing, and especially trio exome sequencing, is an established and successful method in postnatal genetic diagnostics. Diagnostic yield for trio exome sequencing is around 37%.
What does this study add?
We show that trio exome sequencing is a fast and comprehensive method in prenatal diagnostics with diagnostic yield similar to that of postnatal trio exome sequencing. We provide case solution rates for different phenotypic observations from 19% for abnormalities of internal organs up to 52% for skeletal malformations.
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Affiliation(s)
| | - Dirk Korinth
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | | | | | | | | | - Max Wüstemann
- Zentrum für Pränatalmedizin Hannover, Hannover, Germany
| | | | | | - Lutz Pfeiffer
- Medicover Humangenetik Berlin-Lichtenberg, Berlin, Germany
| | | | | | | | | | - Holger Lebek
- Pränatale Diagnostik Berlin-Lichtenberg, Berlin, Germany
| | - Saskia Biskup
- Praxis für Humangenetik Tübingen, Tübingen, Germany.,CeGaT GmbH, Tübingen, Germany
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14
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Bai X, Zheng L, Ma S, Kan X. Prenatal diagnosis of chromosome 18 long arm deletion syndrome by high-throughput sequencing: Two case reports. Medicine (Baltimore) 2021; 100:e28143. [PMID: 34918667 PMCID: PMC8677896 DOI: 10.1097/md.0000000000028143] [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: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 01/05/2023] Open
Abstract
RATIONALE Chromosome 18 long arm deletion syndrome is a group of clinical syndromes caused by partial or total genetic material deletion of the long arm of chromosome 18 (18q), whose clinical manifestations are related to presentation and developmental abnormalities in various aspects such as intelligence, face, and movement. Prenatal diagnosis of this syndrome is challenging because of its low incidence and uncharacteristic prenatal clinical performance. In this paper, 2 cases of partial deletion of 18q found in prenatal amniotic fluid examination by high-throughput sequencing were reported and analyzed. PATIENT CONCERNS In patient 1, non-invasive prenatal gene detection at 21 + 2 weeks of gestation suggests a risk of trisomy 18. In patient 2, ultrasound examination at 21 + 2 weeks of gestation revealed a single live fetus, but it was difficult to pinpoint whether the fetus had only 1 umbilical artery to supply blood. DIAGNOSIS AND INTERVENTION The 18q deletion syndrome was diagnosed by chromosome karyotype analysis and high-throughput sequencing. OUTCOMES The pregnancies were terminated due to the abnormal chromosome. LESSON This report adds novel variants to the genetic profile of 18q deletion, in order to enrich the genetic data of long arm deletion of 18 chromosomes and provide better services for pre-screening, diagnosis, and genetic counseling for this disease.
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15
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Klapwijk JE, Srebniak MI, Go ATJI, Govaerts LCP, Lewis C, Hammond J, Hill M, Lou S, Vogel I, Ormond KE, Diderich KEM, Brüggenwirth HT, Riedijk SR. How to deal with uncertainty in prenatal genomics: A systematic review of guidelines and policies. Clin Genet 2021; 100:647-658. [PMID: 34155632 PMCID: PMC8596644 DOI: 10.1111/cge.14010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/21/2021] [Accepted: 06/08/2021] [Indexed: 12/01/2022]
Abstract
Exome sequencing (ES) enhanced the diagnostic yield of genetic testing, but has also increased the possibility of uncertain findings. Prenatal ES is increasingly being offered after a fetal abnormality is detected through ultrasound. It is important to know how to handle uncertainty in this particularly stressful period. This systematic review aimed to provide a comprehensive overview of guidelines available for addressing uncertainty related to prenatal chromosomal microarray (CMA) and ES. Ten uncertainty types associated with prenatal ES and CMA were identified and defined by an international multidisciplinary team. Medline (all) and Embase were systematically searched. Laboratory scientists, clinical geneticists, psychologists, and a fetal medicine specialist screened the papers and performed the data extraction. Nineteen papers were included. Recommendations generally emphasized the importance of trio analysis, clinical information, data sharing, validation and re-analysis, protocols, multidisciplinary teams, genetic counselling, whether to limit the possible scope of results, and when to report particular findings. This systematic review helps provide a vocabulary for uncertainties, and a compass to navigate uncertainties. Prenatal CMA and ES guidelines provide a strong starting point for determining how to handle uncertainty. Gaps in guidelines and recommendations were identified and discussed to provide direction for future research and policy making.
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Affiliation(s)
| | | | - Attie T. J. I. Go
- Department of Obstetrics and Fetal MedicineErasmus MCRotterdamThe Netherlands
| | | | - Celine Lewis
- North Thames Genomic Laboratory HubGreat Ormond Street HospitalLondonUK
- Population, Policy and Practice DepartmentUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Jennifer Hammond
- North Thames Genomic Laboratory HubGreat Ormond Street HospitalLondonUK
- Genetic and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Melissa Hill
- North Thames Genomic Laboratory HubGreat Ormond Street HospitalLondonUK
- Genetic and Genomic MedicineUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Stina Lou
- Center for Fetal DiagnosticsAarhus University HospitalAarhusDenmark
| | - Ida Vogel
- Center for Fetal DiagnosticsAarhus University HospitalAarhusDenmark
- Department of Clinical MedicineAarhus UniversityAarhusDenmark
- Department of Clinical GeneticsAarhus University HospitalAarhusDenmark
| | - Kelly E. Ormond
- Department of Genetics and Stanford Center for Biomedical EthicsStanford University School of MedicineStanfordCaliforniaUSA
| | | | | | - Sam R. Riedijk
- Department of Clinical GeneticsErasmus MCRotterdamThe Netherlands
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16
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Mak C, Papassotiriou I, Zierk J, Kohse KP, Greaves RF, Geaghan SMD, Lang T, Loh TP. Emerging technologies in paediatric laboratory medicine. J LAB MED 2021. [DOI: 10.1515/labmed-2021-0097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Chloe Mak
- Department of Pathology , Princess Margaret Hospital , Hong Kong , P.R. China
| | - Ioannis Papassotiriou
- Department of Clinical Biochemistry , “Aghia Sophia” Children’s Hospital , Athens , Greece
| | - Jakob Zierk
- Department of Pediatrics and Adolescent Medicine , University Hospital Erlangen , Erlangen , Germany
| | - Klaus P. Kohse
- Faculty of Medicine and Health Sciences , University of Oldenburg , Oldenburg , Germany
- Institute for Laboratory Diagnostics and Microbiology, Klinikum , Oldenburg , Germany
| | - Ronda F. Greaves
- Victorian Clinical Genetics Services , Murdoch Children’s Research Institute , Melbourne , VIC , Australia
| | - Sharon M. D. Geaghan
- Department of Pathology , Pediatrics Division, Stanford University School of Medicine , Stanford , CA , USA
| | - Tim Lang
- Department of Clinical Biochemistry , University Hospital of North Durham , Durham , UK
| | - Tze Ping Loh
- Department of Laboratory Medicine , National University Hospital , Singapore , Singapore
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17
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Next Generation Sequencing Technology in Lung Cancer Diagnosis. BIOLOGY 2021; 10:biology10090864. [PMID: 34571741 PMCID: PMC8467994 DOI: 10.3390/biology10090864] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022]
Abstract
Simple Summary Lung cancer is still one of the most commonly diagnosed and deadliest cancers in the world. Its diagnosis at an early stage is highly necessary and will improve the standard of care of this disease. The aim of this article is to review the importance and applications of next generation sequencing in lung cancer diagnosis. As observed in many studies, next generation sequencing has been proven as a very helpful tool in the early detection of different types of cancers, including lung cancer, and has been used in the clinic, mainly due to its many advantages, such as low cost, speed, efficacy, low quantity usage of biological samples, and diversity. Abstract Lung cancer is still one of the most commonly diagnosed cancers, and one of the deadliest. The high death rate is mainly due to the late stage of diagnosis and low response rate to therapy. Previous and ongoing research studies have tried to discover new reliable and useful cbiomarkers for the diagnosis and prognosis of lung cancer. Next generation sequencing has become an essential tool in cancer diagnosis, prognosis, and evaluation of the treatment response. This article aims to review the leading research and clinical applications in lung cancer diagnosis using next generation sequencing. In this scope, we identified the most relevant articles that present the successful use of next generation sequencing in identifying biomarkers for early diagnosis correlated to lung cancer diagnosis and treatment. This technique can be used to evaluate a high number of biomarkers in a short period of time and from small biological samples, which makes NGS the preferred technique to develop clinical tests for personalized medicine using liquid biopsy, the new trend in oncology.
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18
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Schmitz D, Henn W. The fetus in the age of the genome. Hum Genet 2021; 141:1017-1026. [PMID: 34426855 PMCID: PMC9160108 DOI: 10.1007/s00439-021-02348-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/16/2021] [Indexed: 12/15/2022]
Abstract
Due to a number of recent achievements, the field of prenatal medicine is now on the verge of a profound transformation into prenatal genomic medicine. This transformation is expected to not only substantially expand the spectrum of prenatal diagnostic and screening possibilities, but finally also to advance fetal care and the prenatal management of certain fetal diseases and malformations. It will come along with new and profound challenges for the normative framework and clinical care pathways in prenatal (and reproductive) medicine. To adequately address the potential ethically challenging aspects without discarding the obvious benefits, several agents are required to engage in different debates. The permissibility of the sequencing of the whole fetal exome or genome will have to be examined from a philosophical and legal point of view, in particular with regard to conflicts with potential rights of future children. A second requirement is a societal debate on the question of priority setting and justice in relation to prenatal genomic testing. Third, a professional-ethical debate and positioning on the goal of prenatal genomic testing and a consequential re-structuring of clinical care pathways seems to be important. In all these efforts, it might be helpful to envisage the unborn rather not as a fetus, not as a separate moral subject and a second "patient", but in its unique physical connection with the pregnant woman, and to accept the moral quandaries implicitly given in this situation.
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Affiliation(s)
- Dagmar Schmitz
- Institute for History, Theory and Ethics in Medicine, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
| | - Wolfram Henn
- Institute of Human Genetics, Saarland University, Homburg/Saar, Germany
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19
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Abstract
ZusammenfassungDas Gendiagnostikgesetz (GenDG) verbietet seit 2010 die pränatale Diagnostik spätmanifestierender Erkrankungen (§ 15(2) GenDG). In seiner Begründung bezog sich der Gesetzgeber in Analogie zu internationalen Empfehlungen für den pädiatrischen Bereich vor allem auf das Recht des heranwachsenden Kindes bzw. des späteren Erwachsenen auf Nichtwissen. Mit diesem gesetzlichen Verbot hat Deutschland einen viel diskutierten Sonderweg in der Regulierung genetischer Pränataldiagnostik eingeschlagen. Seither jedoch hat sich nicht nur die Perspektive auf prädiktive Testungen im Kindesalter verändert. In zunehmendem Maße generieren auf das gesamte Genom abzielende Diagnostikangebote auch andere vorgeburtlich genetische Informationen, die – in ähnlicher Weise wie diejenigen zu spätmanifestierenden Erkrankungen eine potenzielle Gefahr für das Recht auf Nichtwissen der späteren Person darstellen. Es soll daher im Rahmen dieses Beitrages überprüft werden, inwiefern das deutsche Diagnostikverbot und dessen Bezug auf das Recht auf Nichtwissen des späteren Kindes eine tragfähige Basis zur Regulierung gendiagnostischer Untersuchungen in der Pränatalmedizin insgesamt darstellt bzw. zukünftig darstellen kann.Untersucht wird der Argumentationsgang des Diagnostikverbotes im Hinblick auf spätmanifestierende Erkrankungen vor dem Hintergrund der Entwicklungen in der prädiktiven (genomischen) Diagnostik. Eine Analyse des normativen Begründungsrahmens zeigt, dass nach wie vor deutlicher Klärungsbedarf hinsichtlich der philosophisch-ethischen Fundierung wie auch hinsichtlich der Interpretation eines Rechts auf Nichtwissen eines (zukünftigen) Kindes im Kontext von genetischer Diagnostik besteht. Darüber hinaus müssen auch Interessen des (zukünftigen) Kindes an eventuell möglich werdender pränataler Behandlung oder Prävention von Erkrankungen in die Abwägung miteinbezogen werden.Um zukünftigen Herausforderungen genomischer Pränataldiagnostik und -therapie begegnen zu können, müsste dringend geklärt werden, inwiefern Rechte zukünftiger Personen tatsächlich in der speziellen Situation der Schwangerschaft relevant sein können und mit welchen Pflichten diese für den Gesetzgeber, aber insbesondere auch für zukünftige Eltern und Ärzte einhergehen. Der Menschenrechtsdiskurs könnte hierfür eine tragfähige Basis und hilfreiche Strategien liefern.
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20
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He B, Chao W, Huang Z, Zeng J, Yang J, Luo D, Huang S, Pan H, Hao Y. Hsa_circ_001659 serves as a novel diagnostic and prognostic biomarker for colorectal cancer. Biochem Biophys Res Commun 2021; 551:100-106. [PMID: 33725570 DOI: 10.1016/j.bbrc.2021.02.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is prevalent worldwide and novel diagnostic and prognostic biomarkers are needed to improve precision medicine. Circular RNAs (circRNAs) are currently being considered as emerging tumor biomarkers. Herein, we aimed to explore the possible clinical application of circRNAs in the early diagnosis and prognostic prediction of CRC. First, candidate circRNA was selected by integrating analysis of Gene Expression Omnibus (GEO) database using GEO2R program. ROC curve analysis demonstrated the predictive values and likelihood ratios of circ_001659 were satisfactory for the diagnosis of CRC, including patients in early-stage disease or patients with carcinoembryonic antigen (CEA)-negative status. Moreover, serum circ_001659 may be a novel biomarker in the assessment of successful treatment and remission of cancer tracking. We further investigated the oncogenic role of circ_001659. In vivo and in vitro experiments indicated that circ_001659 could promote CRC cell invasion and migration. Mechanistically, circ_001659 was localized in the nucleus, recruited the RBBP5 to Vimentin promoter and increased H3K4 trimethylation level on the Vimentin promoter region, which epigenetically activated Vimentin transcription. Our findings demonstrate that circ_001659 could be a useful serum biomarker for CRC diagnosis and prognosis. Targeting circ_001659 and its pathway may be meaningful for treating patients with CRC.
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Affiliation(s)
- Baoyu He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200240, China; Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Guangxi, 545005, China
| | - Wei Chao
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Guangxi, 545005, China
| | - Zhizhuo Huang
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Guangxi, 545005, China
| | - Jianchao Zeng
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Guangxi, 545005, China
| | - Jie Yang
- Department of Hematology, The Fourth Affiliated Hospital of Guangxi Medical University, Guangxi, 545005, China; Department of Scientific Research and Education, The Fourth Affiliated Hospital of Guangxi Medical University, Guangxi, 545005, China
| | - Delan Luo
- Department of Gastroenterology, The First People's Hospital of Neijiang City, Sichuan, 641000, China
| | - Shishun Huang
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Guangxi, 545005, China
| | - Hongli Pan
- Medical Science Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Guangxi, 545005, China.
| | - Yujun Hao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200240, China.
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21
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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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22
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Huang H, Cai M, Wang Y, Liang B, Lin N, Xu L. SNP Array as a Tool for Prenatal Diagnosis of Congenital Heart Disease Screened by Echocardiography: Implications for Precision Assessment of Fetal Prognosis. Risk Manag Healthc Policy 2021; 14:345-355. [PMID: 33542665 PMCID: PMC7851374 DOI: 10.2147/rmhp.s286001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Objective This study aimed to examine the effectiveness of the SNP array for the prenatal diagnosis of congenital heart disease (CHD) screened by echocardiography. Patients and Methods A total of 356 pregnant women with fetal congenital heart malformations revealed by echocardiography at the Center for Prenatal Diagnosis of Fujian Maternal and Children Hospital during the period from November 2016 through July 2019 were recruited. The fetuses were assigned into three cohorts, including 142 with a single cardiac malformation, 106 with multiple cardiac malformations and 108 with cardiac and extracardiac malformations. All fetuses underwent chromosomal karyotyping and SNP array simultaneously, and the effectiveness of the SNP array for the prenatal diagnosis of CHD was evaluated. Results The overall prevalence of abnormal karyotypes was 9.3% among the 356 fetuses with CHD, and a higher proportion was found in fetuses with cardiac and extracardiac malformations (18.5%) than in those with single (5.6%) or multiple cardiac malformations (4.7%) (P<0.05). Consistent with karyotype analysis, SNP array detected an additional 25 fetuses with pathogenic copy number variations (CNVs), seven with variant of unknown significance (VOUS) and seven with benign CNVs, and a lower proportion of abnormal CNV was found in fetuses with a single cardiac malformation (4.2%) than in those with multiple cardiac malformations (9.4%) or cardiac and extracardiac malformations (14.8%) (P<0.05). Among the 33 fetuses with chromosomal abnormality, postnatal follow-up showed termination of pregnancy in 25 with pathogenic CNVs, one with VOUS, and six with normal karyotypes and SNP array findings but severe multiple malformations by ultrasonography. Conclusion SNP array increases the overall detection of abnormal CNVs by 9%, which improves the detection of CNVs associated with CHD. SNP array may serve as a tool for prenatal diagnosis of CHD that facilitates the discovery of pathogenic genes associated with CHD and provide valuable insights into the precision assessment of fetal prognosis during the prenatal counseling.
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Affiliation(s)
- Hailong Huang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Meiying Cai
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Yan Wang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Bin Liang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Na Lin
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Liangpu Xu
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
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23
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Yadav RM, Gupta M, Dalvi A, Bargir UA, Hule G, Shabrish S, Aluri J, Kulkarni M, Kambli P, Uppuluri R, Seshadri S, Jagadeesh S, Suresh B, Raja J, Taur P, Malaischamy S, Ghosh P, Mahalingam S, Kadam P, Lashkari HP, Tamhankar P, Tamhankar V, Mithbawkar S, Bhattad S, Jhawar P, Makam A, Bansal V, Prasad M, Govindaraj G, Guhan B, Bharadwaj Tallapaka K, Desai M, Raj R, Madkaikar MR. Prenatal Diagnosis for Primary Immunodeficiency Disorders-An Overview of the Indian Scenario. Front Immunol 2020; 11:612316. [PMID: 33365035 PMCID: PMC7750517 DOI: 10.3389/fimmu.2020.612316] [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: 09/30/2020] [Accepted: 11/04/2020] [Indexed: 01/13/2023] Open
Abstract
Prenatal Diagnosis (PND) forms an important part of primary preventive management for families having a child affected with primary immunodeficiency. Although individually sparse, collectively this group of genetic disorders represents a significant burden of disease. This paper discusses the prenatal services available for affected families at various centers across the country and the challenges and ethical considerations associated with genetic counseling. Mutation detection in the index case and analysis of chorionic villous sampling or amniocentesis remain the preferred procedures for PND and phenotypic analysis of cordocentesis sample is reserved for families with well-characterized index case seeking PND in the latter part of the second trimester of pregnancy. A total of 112 families were provided PND services in the last decade and the presence of an affected fetus was confirmed in 32 families. Post-test genetic counseling enabled the affected families to make an informed decision about the current pregnancy.
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Affiliation(s)
- Reetika Malik Yadav
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Maya Gupta
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Aparna Dalvi
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Umair Ahmed Bargir
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Gouri Hule
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Snehal Shabrish
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Jahnavi Aluri
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Manasi Kulkarni
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Priyanka Kambli
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
| | - Ramya Uppuluri
- Department of Pediatric Hematology-Oncology, Blood Marrow Transplantation, Apollo Hospitals, Chennai, India
| | - Suresh Seshadri
- Department of Clinical Genetics & Genetic Counseling, Mediscan Systems, Chennai, India
| | - Sujatha Jagadeesh
- Department of Clinical Genetics & Genetic Counseling, Mediscan Systems, Chennai, India
| | - Beena Suresh
- Department of Clinical Genetics & Genetic Counseling, Mediscan Systems, Chennai, India
| | - Jayarekha Raja
- Department of Clinical Genetics & Genetic Counseling, Mediscan Systems, Chennai, India
| | - Prasad Taur
- Department of Immunology and Department of Pediatric Hemato-Oncology, Bai Jerbai Wadia Hospital for Children, Mumbai, India
| | | | | | | | - Priya Kadam
- MedGenome Labs Private Limited, Bangalore, India
| | - Harsha Prasada Lashkari
- Department of Pediatrics, Kasturba Medical College Hospital, Manipal Academy of Higher Education, Mangalore, India
| | | | | | | | - Sagar Bhattad
- Division of Pediatric Immunology and Rheumatology, Department of Pediatrics, Aster CMI Hospital, Bangalore, India
| | - Prerna Jhawar
- Department of Fetal Medicine, Motherhood Hospital, Bangalore, India
| | - Adinarayan Makam
- Department of Fetal Medicine, Adi Advanced Centre for Fetal Care, Bangalore, India
| | - Vandana Bansal
- Fetal Medicine Department Surya Hospitals, Mumbai, India
| | | | - Geeta Govindaraj
- Department of Pediatrics, Government Medical College, Kozhikode, Calicut, India
| | - Beena Guhan
- Department of Pediatrics, Government Medical College, Kozhikode, Calicut, India
| | | | - Mukesh Desai
- Department of Immunology and Department of Pediatric Hemato-Oncology, Bai Jerbai Wadia Hospital for Children, Mumbai, India
| | - Revathi Raj
- Department of Pediatric Hematology-Oncology, Blood Marrow Transplantation, Apollo Hospitals, Chennai, India
| | - Manisha Rajan Madkaikar
- Center of Excellence for PIDs, Department of Pediatric Immunology and Leucocyte Biology, ICMR-National Institute of Immunohaematology, Mumbai, India
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24
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Prenatal Detection of Uniparental Disomies (UPD): Intended and Incidental Finding in the Era of Next Generation Genomics. Genes (Basel) 2020; 11:genes11121454. [PMID: 33287348 PMCID: PMC7761756 DOI: 10.3390/genes11121454] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022] Open
Abstract
Prenatal detection of uniparental disomy (UPD) is a methodological challenge, and a positive testing result requires comprehensive considerations on the clinical consequences as well as ethical issues. Whereas prenatal testing for UPD in families which are prone to UPD formation (e.g., in case of chromosomal variants, imprinting disorders) is often embedded in genetic counselling, the incidental identification of UPD is often more difficult to manage. With the increasing application of high-resolution test systems enabling the identification of UPD, an increase in pregnancies with incidental detection of UPD can be expected. This paper will cover the current knowledge on uniparental disomies, their clinical consequences with focus on prenatal testing, genetic aspects and predispositions, genetic counselling, as well as methods (conventional tests and high-throughput assays).
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25
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Abstract
The introduction of noninvasive prenatal screening (NIPS) using cell-free DNA (cfDNA) is the newest option for aneuploidy screening during pregnancy. Compared with other aneuploidy screening options, NIPS offers a higher detection rate for trisomy 21 with a low false-positive rate. However, pretest and post-test patient counseling is essential and should include a discussion of the benefits and limitations, the screening rather than diagnostic nature of the test, and the association of a test failure with an increased risk of aneuploidy. Refer patients for genetic counseling when appropriate, particularly if test failure occurs due to a low fetal fraction or if maternal mosaicism or malignancy is suspected.
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26
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Kiani AK, Paolacci S, Scanzano P, Michelini S, Capodicasa N, D'Agruma L, Notarangelo A, Tonini G, Piccinelli D, Farshid KR, Petralia P, Fulcheri E, Buffelli F, Chiurazzi P, Terranova C, Plotti F, Angioli R, Castori M, Pös O, Szemes T, Bertelli M. Prenatal genetic diagnosis: Fetal therapy as a possible solution to a positive test. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:e2020021. [PMID: 33170180 PMCID: PMC8023142 DOI: 10.23750/abm.v91i13-s.10534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/17/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUND Fetal abnormalities cause 20% of perinatal deaths. Advances in prenatal genetic and other types of screening offer great opportunities for identifying high risk pregnancies. METHODS Through a literature search, here we summarise what are the prenatal diagnostic technique that are being used and how those techniques may allow for prenatal interventions. RESULTS Next generation sequencing and non-invasive prenatal testing are fundamental for clinical diagnostics because of their sensitivity and accuracy in identifying point mutations, aneuploidies, and microdeletions, respectively. Timely identification of genetic disorders and other fetal abnormalities enables early intervention, such as in-utero gene therapy, fetal drug therapy and prenatal surgery. CONCLUSION Prenatal intervention is mainly focused on conditions that may cause death or lifelong disabilities, like spina bifida, congenital diaphragm hernia and sacrococcygeal teratoma; and may be an alternative therapeutic option to termination of pregnancy. However, it is not yet widely available, due to lack of specialized centers.
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Affiliation(s)
| | | | | | - Sandro Michelini
- Department of Rehabilitation, San Giovanni Battista Hospital, Rome, Italy.
| | | | - Leonardo D'Agruma
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
| | - Angelantonio Notarangelo
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
| | - Gerolamo Tonini
- Surgical Department, Unit of Urology, Poliambulanza Foundation, Brescia, Italy.
| | - Daniela Piccinelli
- Department of Mother and Child Health, Unit of Obstetrics and Gynecology, Poliambulanza Foundation, Brescia, Italy.
| | | | | | - Ezio Fulcheri
- UOSD Fetal and Perinatal Pathology, Department of Translational Research, Laboratory Medicine, Diagnostics and Services, IRCCS Giannina Gaslini Institute, Genoa, Italy.
| | - Francesca Buffelli
- UOSD Fetal and Perinatal Pathology, Department of Translational Research, Laboratory Medicine, Diagnostics and Services, IRCCS Giannina Gaslini Institute, Genoa, Italy.
| | - Pietro Chiurazzi
- Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Genetica Medica, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome Italy.
| | - Corrado Terranova
- University Campus Bio Medico of Rome, Department of Obstetrics and Gynecology, Rome, Italy.
| | - Francesco Plotti
- University Campus Bio Medico of Rome, Department of Obstetrics and Gynecology, Rome, Italy.
| | - Roberto Angioli
- University Campus Bio Medico of Rome, Department of Obstetrics and Gynecology, Rome, Italy.
| | - Marco Castori
- Division of Medical Genetics, Fondazione IRCCS-Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG), Italy.
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia.
| | - Tomas Szemes
- 14 Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia; Geneton Ltd., Bratislava, Slovakia; Comenius University Science Park, Bratislava, Slovakia.
| | - Matteo Bertelli
- MAGI EUREGIO, Bolzano, Italy; MAGI'S LAB, Rovereto (TN), Italy; EBTNA-LAB, Rovereto (TN), Italy.
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27
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Song J, Hu Y, Li W, Li H, Zheng H, Chen Y, Dong S, Liu L. Transcriptome analysis following enterovirus 71 and coxsackievirus A16 infection in respiratory epithelial cells. Arch Virol 2020; 165:2817-2828. [PMID: 32990841 PMCID: PMC7522011 DOI: 10.1007/s00705-020-04821-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/22/2020] [Indexed: 11/03/2022]
Abstract
Enterovirus 71 (EV-A71) and coxsackievirus A16 (CV-A16) are the major pathogens responsible for hand, foot and mouth disease (HFMD), but the mechanism by which these viruses cause disease remains unclear. In this study, we used transcriptome sequencing technology to investigate changes in the transcriptome profiles after infection with EV-A71 and CV-A16 in human bronchial epithelial (16HBE) cells. Using systematic bioinformatics analysis, we then searched for useful clues regarding the pathogenesis of HFMD. As a result, a total of 111 common differentially expressed genes were present in both EV-A71- and CV-A16-infected cells. A trend analysis of these 111 genes showed that 91 of them displayed the same trend in EV-A71 and CV-A16 infection, including 49 upregulated genes and 42 downregulated genes. These 91 genes were further used to conduct GO, pathway, and coexpression network analysis. It was discovered that enriched GO terms (such as histone acetylation and positive regulation of phosphorylation) and pathways (such as glycosylphosphatidylinositol (GPI)-anchor biosynthesis and DNA replication) might be closely associated with the pathogenic mechanism of these two viruses, and key genes (such as TBCK and GPC) might be involved in the progression of HFMD. Finally, we randomly selected 10 differentially expressed genes for qRT-PCR to validate the transcriptome sequencing data. The experimental qRT-PCR results were roughly in agreement with the results of transcriptome sequencing. Collectively, our results provide clues to the mechanism of pathogenesis of HFMD induced by EV-A71 and CV-A16.
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Affiliation(s)
- Jie Song
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650118, China.,Key Laboratory of Systemic Innovative Research on Virus Vaccine, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Yajie Hu
- Department of Respiratory Medicine, The First People's Hospital of Yunnan Province, Kunming, 650002, China
| | - Weiyu Li
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650118, China
| | - Hui Li
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650118, China
| | - Huiwen Zheng
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650118, China
| | - Yanli Chen
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650118, China.,Key Laboratory of Systemic Innovative Research on Virus Vaccine, Chinese Academy of Medical Sciences, Kunming, 650118, China
| | - Shaozhong Dong
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650118, China.
| | - Longding Liu
- Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Institute of Medical Biology, Chinese Academy of Medical Science and Peking Union Medical College, Kunming, 650118, China. .,Key Laboratory of Systemic Innovative Research on Virus Vaccine, Chinese Academy of Medical Sciences, Kunming, 650118, China.
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28
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Single Circulating Fetal Trophoblastic Cells Eligible for Non Invasive Prenatal Diagnosis: the Exception Rather than the Rule. Sci Rep 2020; 10:9861. [PMID: 32555262 PMCID: PMC7300110 DOI: 10.1038/s41598-020-66923-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/20/2020] [Indexed: 12/18/2022] Open
Abstract
Non-Invasive Prenatal Diagnosis (NIPD), based on the analysis of circulating cell-free fetal DNA (cff-DNA), is successfully implemented for an increasing number of monogenic diseases. However, technical issues related to cff-DNA characteristics remain, and not all mutations can be screened with this method, particularly triplet expansion mutations that frequently concern prenatal diagnosis requests. The objective of this study was to develop an approach to isolate and analyze Circulating Trophoblastic Fetal Cells (CFTCs) for NIPD of monogenic diseases caused by triplet repeat expansion or point mutations. We developed a method for CFTC isolation based on DEPArray sorting and used Huntington’s disease as the clinical model for CFTC-based NIPD. Then, we investigated whether CFTC isolation and Whole Genome Amplification (WGA) could be used for NIPD in couples at risk of transmitting different monogenic diseases. Our data show that the allele drop-out rate was 3-fold higher in CFTCs than in maternal cells processed in the same way. Moreover, we give new insights into CFTCs by compiling data obtained by extensive molecular testing by microsatellite multiplex PCR genotyping and by WGA followed by mini-exome sequencing. CFTCs appear to be often characterized by a random state of genomic degradation.
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29
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Mone F, O'Connor C, Hamilton S, Quinlan-Jones E, Allen S, Marton T, Williams D, Kilby MD. Evolution of a prenatal genetic clinic-A 10-year cohort study. Prenat Diagn 2020; 40:618-625. [PMID: 32037575 DOI: 10.1002/pd.5661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/19/2020] [Accepted: 01/25/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To (a) evaluate the proportion of women where a unifying genetic diagnosis was obtained following assessment of an observed pattern of fetal anomalies and (b) assess trends in genetic testing in a joint fetal-medicine genetic clinic. METHOD Retrospective cohort study of all women attending the clinic. Outcomes included (a) indication for referral, (b) genetic test performed and (c) diagnoses obtained. RESULTS From 2008 to 2019, 256 patients were referred and reviewed, of which 23% (n = 59) were consanguineous. The main indication for referral was the observed pattern of fetal anomalies. Over 10 years, the number of patients reviewed increased from 11 to 35 per annum. A unifying genetic diagnosis was obtained in 43.2% (n = 79/183), the majority of which were diagnosed prenatally (50.6% [n = 40/79]). The main investigation(s) that was the ultimate diagnostic test was targeted gene panel sequencing 34.2% (n = 27/79), with this and exome sequencing becoming the dominant genetic test by 2019. Pregnancies reviewed due to an abnormal karyotype or microarray decreased as an indication for referral during the study period (21.6% [n = 16/74] 2008-2012 vs 16.5% [n = 30/182] in 2012-2019). CONCLUSION A prenatal genetic clinic with a structured multi-disciplinary team approach may be successful in obtaining a unifying prenatal genetic diagnosis.
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Affiliation(s)
- Fionnuala Mone
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.,West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Clare O'Connor
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Susan Hamilton
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Quinlan-Jones
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Tamas Marton
- West Midlands Perinatal Pathology Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Denise Williams
- West Midlands Regional Genetics Laboratory and Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Mark D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK.,Institute of Metabolism and Systems Research, College of Medical & Dental Sciences, University of Birmingham, Birmingham, UK
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30
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Meler E, Sisterna S, Borrell A. Genetic syndromes associated with isolated fetal growth restriction. Prenat Diagn 2020; 40:432-446. [PMID: 31891188 DOI: 10.1002/pd.5635] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 11/30/2019] [Accepted: 12/02/2019] [Indexed: 12/20/2022]
Abstract
Early onset fetal growth restriction (FGR) may be due to impaired placentation, environmental or toxic exposure, congenital infections or genetic abnormalities. Remarkable research, mainly based on retrospective series, has been published on the diverse genetic causes. Those have become more and more relevant with the improvement in the accuracy of the analysis techniques and the rising of breakthrough genomewide methods such as the whole genome sequencing. However, no publication has presented an integrated view of management of those fetuses with an early and severe affection. In this review, we explored to which extent genetic syndromes can cause FGR fetuses without structural defects. The most common chromosomal abnormalities (Triploidies and Trisomy 18), submicroscopic chromosomal anomalies (22q11.2 microduplication syndrome) and single gene disorders (often associated with mild ultrasound findings) related to early and severe FGR had been analysed. Finally, we addressed the impact of epigenetic marks on fetal growth, a matter of growing importance. At the end of this review, we should be able to provide an adequate counseling to parents in terms of diagnosis, prognosis and management of those pregnancies.
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Affiliation(s)
- Eva Meler
- 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, University of Barcelona, Fetal i+D Fetal Medicine Research, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Catalonia, Spain
| | - Silvina Sisterna
- Clinical Genetics and Prenatal Diagnosis, Hospital Privado de Comunidad - Maternal Fetal Medicine, Clínica Colon - Reproduction and human genetics center CRECER. Mar del Plata, Buenos Aires, Argentina
| | - 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, University of Barcelona, Fetal i+D Fetal Medicine Research, and Centre for Biomedical Research on Rare Diseases (CIBER-ER), Barcelona, Catalonia, Spain
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31
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Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
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Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
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