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Ferrari A, Pennestrì F, Bonciani M, Banfi G, Vainieri M, Tomaiuolo R. The role of patient-reported experiences in disclosing genetic prenatal testing: Findings from a large-scale survey on pregnant women. Eur J Obstet Gynecol Reprod Biol X 2024; 23:100327. [PMID: 39130210 PMCID: PMC11315116 DOI: 10.1016/j.eurox.2024.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 08/13/2024] Open
Abstract
Introduction Pregnant women can choose from different prenatal genetic tests throughout their maternity journey. We aim to investigate the clinical, societal, and economic determinants influencing the selection of different options (non-invasive, invasive, or both). Methods A systematic survey focusing on maternity pathways was launched by the Region of Tuscany, Italy, to collect data on pregnant women's experience, outcomes and satisfaction levels. Drawing from this survey, we retrospectively analyzed data on women who filled out the second-trimester questionnaire between March 2019 and February 2023 (n = 27,337), providing complete data on relevant variables. Logistic regression models were applied to identify the factors contributing to a higher likelihood of opting for non-invasive prenatal testing (NIPT) and invasive testing. Results Among the participants, 42.7 % chose only NIPT, 3.8 % opted for invasive tests exclusively, 1.3 % underwent both tests, and 52.2 % did not pursue any genetic testing. NIPT was more often chosen by older, Italian, highly educated, nulliparous women, who perceived better health, were employed (versus unemployed), had higher economic status, planned pregnancy, received hospital-based care (versus counseling center), under gynecologist supervision (versus midwife), not opted for combined testing and received pregnancy vaccinations. Conversely, invasive testing was more prevalent among older women but less common among those who were nulliparous, had Italian nationality, and had a perceived better health status. This group also tended to experience unplanned and high-risk pregnancy, did not take folate during pregnancy, received public hospital-based assistance, less frequently chose combined tests or NIPT, and had frequent delays in examinations. Conclusions Various factors beyond clinical considerations influence the selection of a prenatal test. Therefore, NIPT pathways should include balanced, high-quality information about benefits and limitations, ensuring laboratory specialists' active and integrated involvement in decision-making.
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Affiliation(s)
- Amerigo Ferrari
- Institute of Management, MeS (Management and Health) Laboratory, Scuola Superiore Sant’Anna, Pisa, Italy
- Department of Clinical and Experimental Medicine, Division of Obstetrics and Gynecology, University of Pisa, Pisa, Italy
| | | | - Manila Bonciani
- Institute of Management, MeS (Management and Health) Laboratory, Scuola Superiore Sant’Anna, Pisa, Italy
- Meyer Center for Health and Happiness, A. Meyer Children's Hospital, Florence, Italy
| | - Giuseppe Banfi
- IRCCS Ospedale Galeazzi Sant’Ambrogio, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Milena Vainieri
- Institute of Management, MeS (Management and Health) Laboratory, Scuola Superiore Sant’Anna, Pisa, Italy
| | - Rossella Tomaiuolo
- IRCCS Ospedale Galeazzi Sant’Ambrogio, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
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2
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Tang Z, Wang S, Li X, Hu C, Zhai Q, Wang J, Ye Q, Liu J, Zhang G, Guo Y, Su F, Liu H, Guan L, Jiang C, Chen J, Li M, Ren F, Zhang Y, Huang M, Li L, Zhang H, Hou G, Jin X, Chen F, Zhu H, Li L, Zeng J, Xiao H, Zhou A, Feng L, Gao Y, Liu G. Longitudinal integrative cell-free DNA analysis in gestational diabetes mellitus. Cell Rep Med 2024; 5:101660. [PMID: 39059385 DOI: 10.1016/j.xcrm.2024.101660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 05/13/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024]
Abstract
Gestational diabetes mellitus (GDM) presents varied manifestations throughout pregnancy and poses a complex clinical challenge. High-depth cell-free DNA (cfDNA) sequencing analysis holds promise in advancing our understanding of GDM pathogenesis and prediction. In 299 women with GDM and 299 matched healthy pregnant women, distinct cfDNA fragment characteristics associated with GDM are identified throughout pregnancy. Integrating cfDNA profiles with lipidomic and single-cell transcriptomic data elucidates functional changes linked to altered lipid metabolism processes in GDM. Transcription start site (TSS) scores in 50 feature genes are used as the cfDNA signature to distinguish GDM cases from controls effectively. Notably, differential coverage of the islet acinar marker gene PRSS1 emerges as a valuable biomarker for GDM. A specialized neural network model is developed, predicting GDM occurrence and validated across two independent cohorts. This research underscores the high-depth cfDNA early prediction and characterization of GDM, offering insights into its molecular underpinnings and potential clinical applications.
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Affiliation(s)
- Zhuangyuan Tang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China
| | - Shuo Wang
- Tianjin Women and Children's Health Center, Tianjin 300070, China
| | - Xi Li
- BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430074, China
| | | | | | - Jing Wang
- Tianjin Women and Children's Health Center, Tianjin 300070, China
| | - Qingshi Ye
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China
| | - Jinnan Liu
- Tianjin Women and Children's Health Center, Tianjin 300070, China
| | | | - Yuanyuan Guo
- Tianjin Women and Children's Health Center, Tianjin 300070, China
| | | | - Huikun Liu
- Tianjin Women and Children's Health Center, Tianjin 300070, China
| | - Lingyao Guan
- China National GeneBank, BGI, Shenzhen 518083, China
| | - Chang Jiang
- Tianjin Women and Children's Health Center, Tianjin 300070, China
| | - Jiayu Chen
- China National GeneBank, BGI, Shenzhen 518083, China
| | - Min Li
- Tianjin Women and Children's Health Center, Tianjin 300070, China
| | - Fangyi Ren
- China National GeneBank, BGI, Shenzhen 518083, China
| | - Yu Zhang
- Tianjin Women and Children's Health Center, Tianjin 300070, China
| | - Minjuan Huang
- China National GeneBank, BGI, Shenzhen 518083, China
| | - Lingguo Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China
| | | | | | - Xin Jin
- Tianjin Women and Children's Health Center, Tianjin 300070, China; The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | | | | | - Linxuan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; BGI Research, Shenzhen 518083, China
| | - Jingyu Zeng
- BGI Research, Shenzhen 518083, China; College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Han Xiao
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aifen Zhou
- Institute of Maternal and Child Health, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China; Department of Obstetrics, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lingyan Feng
- Tianjin Women and Children's Health Center, Tianjin 300070, China.
| | - Ya Gao
- BGI Research, Shenzhen 518083, China; Shenzhen Engineering Laboratory for Birth Defects Screening, Shenzhen, China.
| | - Gongshu Liu
- Tianjin Women and Children's Health Center, Tianjin 300070, China.
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3
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Becking EC, Henneman L, Crombag NMTH, Bertorotta J, Rijsbergen Y, Bax CJ, van Vliet-Lachotzki E, Scheffer PG, Bekker MN. Perspectives of pregnant women on broadening the scope of noninvasive prenatal testing from screening for foetal aneuploidies to prediction of adverse pregnancy outcomes: A qualitative study. Prenat Diagn 2024; 44:1033-1042. [PMID: 38877376 DOI: 10.1002/pd.6621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/28/2024] [Accepted: 05/30/2024] [Indexed: 06/16/2024]
Abstract
OBJECTIVE To explore the perspectives of pregnant women on broadening the scope of noninvasive prenatal testing (NIPT) from screening for foetal aneuploidies to prediction of adverse pregnancy outcomes. METHODS Four online focus groups (n = 23 participants) and 14 individual semi-structured interviews were conducted. Participants included pregnant women with and without a history of adverse pregnancy outcomes. RESULTS Both women at low and high risk of adverse pregnancy outcomes had a positive attitude towards using NIPT to predict adverse pregnancy outcomes. Perceived benefits included the possibility to potentially improve maternal and foetal outcomes by taking risk-reducing measures and/or intensified monitoring during pregnancy and the ability to mentally prepare for the potential adverse outcome. Perceived concerns included anxiety and stress caused by a high-risk test result, a false sense of control over pregnancy, and potential false reassurance. Additionally, women reasoned that broadening the scope of NIPT could increase the complexity of prenatal screening and raised concerns on the combined screening aims in one test (prediction of adverse pregnancy outcomes to improve foetal and maternal health vs. screening for foetal aneuploidies to increase reproductive autonomy). On a societal level, considerations on the risk of medicalising pregnancy and overall pressure to opt for NIPT were mentioned. CONCLUSION In general, pregnant women have a positive attitude towards broadening the scope of NIPT to the prediction of pregnancy outcomes, although some concerns are acknowledged.
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Affiliation(s)
- Ellis C Becking
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Lidewij Henneman
- Department of Human Genetics, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands
| | - Neeltje M T H Crombag
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Janneke Bertorotta
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ylana Rijsbergen
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Caroline J Bax
- Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands
- Department of Obstetrics, Amsterdam UMC, Location AMC, Amsterdam, the Netherlands
| | | | - Peter G Scheffer
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mireille N Bekker
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
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4
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Becking EC, Scheffer PG, Henrichs J, Bax CJ, Crombag NMTH, Weiss MM, Macville MVE, Van Opstal D, Boon EMJ, Sistermans EA, Henneman L, Schuit E, Bekker MN. Fetal fraction of cell-free DNA in noninvasive prenatal testing and adverse pregnancy outcomes: a nationwide retrospective cohort study of 56,110 pregnant women. Am J Obstet Gynecol 2024; 231:244.e1-244.e18. [PMID: 38097030 DOI: 10.1016/j.ajog.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/05/2023] [Accepted: 12/06/2023] [Indexed: 01/11/2024]
Abstract
BACKGROUND Noninvasive prenatal testing by cell-free DNA analysis is offered to pregnant women worldwide to screen for fetal aneuploidies. In noninvasive prenatal testing, the fetal fraction of cell-free DNA in the maternal circulation is measured as a quality control parameter. Given that fetal cell-free DNA originates from the placenta, the fetal fraction might also reflect placental health and maternal pregnancy adaptation. OBJECTIVE This study aimed to assess the association between the fetal fraction and adverse pregnancy outcomes. STUDY DESIGN We performed a retrospective cohort study of women with singleton pregnancies opting for noninvasive prenatal testing between June 2018 and June 2019 within the Dutch nationwide implementation study (Trial by Dutch Laboratories for Evaluation of Non-Invasive Prenatal Testing [TRIDENT]-2). Multivariable logistic regression analysis was used to assess associations between fetal fraction and adverse pregnancy outcomes. Fetal fraction was assessed as a continuous variable and as <10th percentile, corresponding to a fetal fraction <2.5%. RESULTS The cohort comprised 56,110 pregnancies. In the analysis of fetal fraction as a continuous variable, a decrease in fetal fraction was associated with increased risk of hypertensive disorders of pregnancy (adjusted odds ratio, 2.27 [95% confidence interval, 1.89-2.78]), small for gestational age neonates <10th percentile (adjusted odds ratio, 1.37 [1.28-1.45]) and <2.3rd percentile (adjusted odds ratio, 2.63 [1.96-3.57]), and spontaneous preterm birth from 24 to 37 weeks of gestation (adjusted odds ratio, 1.02 [1.01-1.03]). No association was found for fetal congenital anomalies (adjusted odds ratio, 1.02 [1.00-1.04]), stillbirth (adjusted odds ratio, 1.02 [0.96-1.08]), or neonatal death (adjusted odds ratio, 1.02 [0.96-1.08]). Similar associations were found for adverse pregnancy outcomes when fetal fraction was <10th percentile. CONCLUSION In early pregnancy, a low fetal fraction is associated with increased risk of adverse pregnancy outcomes. These findings can be used to expand the potential of noninvasive prenatal testing in the future, enabling the prediction of pregnancy complications and facilitating tailored pregnancy management through intensified monitoring or preventive measures.
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Affiliation(s)
- Ellis C Becking
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Peter G Scheffer
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jens Henrichs
- Department of Midwifery Science, VU University Medical Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Caroline J Bax
- Department of Obstetrics and Gynaecology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction and Development research institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Neeltje M T H Crombag
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Marjan M Weiss
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Merryn V E Macville
- Department of Clinical Genetics, GROW School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Elles M J Boon
- Department of Human Genetics, VU University Medical Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Erik A Sistermans
- Amsterdam Reproduction and Development research institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands; Department of Human Genetics, VU University Medical Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Lidewij Henneman
- Amsterdam Reproduction and Development research institute, Amsterdam University Medical Centers, Amsterdam, the Netherlands; Department of Human Genetics, VU University Medical Center Amsterdam, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | - Ewoud Schuit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mireille N Bekker
- Department of Obstetrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
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5
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Kong C, Yin G, Wang X, Sun Y. In Utero Gene Therapy and its Application in Genetic Hearing Loss. Adv Biol (Weinh) 2024:e2400193. [PMID: 39007241 DOI: 10.1002/adbi.202400193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/03/2024] [Indexed: 07/16/2024]
Abstract
For monogenic genetic diseases, in utero gene therapy (IUGT) shows the potential for early prevention against irreversible and lethal pathological changes. Moreover, animal models have also demonstrated the effectiveness of IUGT in the treatment of coagulation disorders, hemoglobinopathies, neurogenetic disorders, and metabolic and pulmonary diseases. For major alpha thalassemia and severe osteogenesis imperfecta, in utero stem cell transplantation has entered the phase I clinical trial stage. Within the realm of the inner ear, genetic hearing loss significantly hampers speech, cognitive, and intellectual development in children. Nowadays, gene therapies offer substantial promise for deafness, with the success of clinical trials in autosomal recessive deafness 9 using AAV-OTOF gene therapy. However, the majority of genetic mutations that cause deafness affect the development of cochlear structures before the birth of fetuses. Thus, gene therapy before alterations in cochlear structure leading to hearing loss has promising applications. In this review, addressing advances in various fields of IUGT, the progress, and application of IUGT in the treatment of genetic hearing loss are focused, in particular its implementation methods and unique advantages.
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Affiliation(s)
- Chenyang Kong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Ge Yin
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiaohui Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yu Sun
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Otorhinolaryngology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
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6
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Norton ME, Risch N. The Inclusion of Race in Prenatal Screening Algorithms. Clin Chem 2024; 70:891-893. [PMID: 38842043 DOI: 10.1093/clinchem/hvae073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 04/24/2024] [Indexed: 06/07/2024]
Affiliation(s)
- Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, United States
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, United States
| | - Neil Risch
- Institute of Human Genetics, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
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Luo X, Jiang P, Ma J, Li Z, Zhou J, Wei X, A J, Chai J, Lv Y, Cheng P, Cao C, A X. Circulating free DNA as a diagnostic marker for echinococcosis: a systematic review and meta-analysis. Front Microbiol 2024; 15:1413532. [PMID: 39021627 PMCID: PMC11251952 DOI: 10.3389/fmicb.2024.1413532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024] Open
Abstract
Introduction Echinococcosis is a chronic zoonotic disease caused by tapeworms of the genus Echinococcus. The World Health Organization (WHO) has identified encapsulated disease as one of 17 neglected diseases to be controlled or eliminated by 2050. There is no accurate, early, non-invasive molecular diagnostic method to detect echinococcosis. The feasibility of circulating free DNA as a diagnostic method for echinococcosis has yielded inconclusive results in a number of published studies. However, there has been no systematic evaluation to date assessing the overall performance of these assays. We report here the first meta-analysis assessing the diagnostic accuracy of cfDNA in plasma, serum, and urine for echinococcosis. Methods We systematically searched PubMed, Embase, Cochrane Library, China National Knowledge Infrastructure (CNKI), and WeiPu databases up to 17 January 2024, for relevant studies. All analyses were performed using RevMan 5.3, Meta-DiSc 1.4, Stata 17.0, and R 4.3.1 software. The sensitivity, specificity, and other accuracy indicators of circulating free DNA for the diagnosis of echinococcosis were summarized. Subgroup analyses and meta-regression were performed to identify sources of heterogeneity. Results A total of 7 studies included 218 patients with echinococcosis and 214 controls (156 healthy controls, 32 other disease controls (non-hydatid patients), and 26 non-study-targeted echinococcosis controls were included). Summary estimates of the diagnostic accuracy of cfDNA in the diagnosis of echinococcosis were as follows: sensitivity (SEN) of 0.51 (95% CI: 0.45-0.56); specificity (SPE) of 0.99 (95% CI: 0.97-0.99); positive likelihood ratio (PLR) of 11.82 (95% CI: 6.74-20.74); negative likelihood ratio (NLR) of 0.57 (95% CI: 0.41-0.80); diagnostic ratio (DOR) of 36.63 (95% CI: 13.75-97.59); and area under the curve (AUC) value of 0.98 (95% CI: 0.96-1.00). Conclusion Existing evidence indicates that the combined specificity of circulating cfDNA for echinococcosis is high. However, the combined sensitivity performance is unsatisfactory due to significant inter-study heterogeneity. To strengthen the validity and accuracy of our findings, further large-scale prospective studies are required.Systematic review registrationThe systematic review was registered in the International Prospective Register of Systematic Reviews PROSPERO [CRD42023454158]. https://www.crd.york.ac.uk/PROSPERO/.
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Affiliation(s)
- Xiaoqin Luo
- Qinghai University, Xining, China
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | | | | | - Zian Li
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | - Jianwu Zhou
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | | | - Jide A
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | - Jinping Chai
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
| | - Yanke Lv
- Qinghai University, Xining, China
| | | | | | - Xiangren A
- Qinghai University, Xining, China
- Department of Clinical Laboratory, Qinghai Provincial People’s Hospital, Xining, China
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Abstract
This review delves into the rapidly evolving landscape of liquid biopsy technologies based on cell-free DNA (cfDNA) and cell-free RNA (cfRNA) and their increasingly prominent role in precision medicine. With the advent of high-throughput DNA sequencing, the use of cfDNA and cfRNA has revolutionized noninvasive clinical testing. Here, we explore the physical characteristics of cfDNA and cfRNA, present an overview of the essential engineering tools used by the field, and highlight clinical applications, including noninvasive prenatal testing, cancer testing, organ transplantation surveillance, and infectious disease testing. Finally, we discuss emerging technologies and the broadening scope of liquid biopsies to new areas of diagnostic medicine.
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Affiliation(s)
- Conor Loy
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Lauren Ahmann
- Department of Pathology, Stanford University, Stanford, California, USA;
| | - Iwijn De Vlaminck
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA;
| | - Wei Gu
- Department of Pathology, Stanford University, Stanford, California, USA;
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9
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Liang D, Lin Y, Luo C, Li H, Hu P, Xu Z. Noninvasive prenatal screening in a pregnant woman with a history of stem cell transplant from a male donor: A case report and literature review. Mol Genet Genomic Med 2024; 12:e2479. [PMID: 38860502 PMCID: PMC11165337 DOI: 10.1002/mgg3.2479] [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: 01/08/2024] [Revised: 05/08/2024] [Accepted: 05/23/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND As a screening method, inaccuracies in noninvasive prenatal screening (NIPS) exist, which are often attributable to biological factors. One such factor is the history of transplantation. However, there are still limited reports on such NIPS cases. METHODS We report an NIPS case of a pregnant woman who had received a stem cell transplant from a male donor. To determine the karyotype in the woman's original cell, we performed chromosome microarray analysis (CMA) on her postnatal blood and oral mucosa. To comprehensively estimate the cell-free DNA (cfDNA) composition, we further performed standard NIPS procedures on the postnatal plasma. Moreover, we reviewed all published relevant NIPS case reports about pregnant women with transplantation history. RESULTS NIPS showed a low-risk result for common trisomies with a fetal fraction of 65.80%. CMA on maternal white blood cells showed a nonmosaic male karyotype, while the oral mucosa showed a nonmosaic female karyotype. The proportion of donor's cfDNA in postnatal plasma was 94.73% based on the Y-chromosome reads ratio. The composition of cfDNA in maternal plasma was estimated as follows: prenatally, 13.60% maternal, 65.80% donor, and 20.60% fetal/placental, whereas postnatally, 5.27% maternal and 94.73% donor. CONCLUSIONS This study expanded our understanding of the influence of stem cell transplantation on NIPS, allowing us to optimize NIPS management for these women.
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Affiliation(s)
- Dong Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingJiangsuChina
| | - Ying Lin
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingJiangsuChina
| | - Chunyu Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingJiangsuChina
| | - Hang Li
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingJiangsuChina
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingJiangsuChina
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical UniversityNanjing Women and Children's Healthcare HospitalNanjingJiangsuChina
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10
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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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11
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Xu Y, Lou J, Qian Y, Jin P, Qian Y, Hong J, Xu Y, Yin Y, Yi S, Dong M. Performance of noninvasive prenatal screening for fetal sex chromosome aneuploidies in a cohort of 116,862 pregnancies. Expert Rev Mol Diagn 2024; 24:467-472. [PMID: 38526221 DOI: 10.1080/14737159.2024.2333951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/20/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND Noninvasive prenatal screening (NIPS) has shown good performance in screening common aneuploidies. However, its performance in detecting fetal sex chromosome aneuploidies (SCAs) needs to be evaluated in a large cohort. RESEARCH DESIGN AND METHODS In this retrospective observation, a total of 116,862 women underwent NIPS based on DNA nanoball sequencing from 2015 to 2022. SCAs were diagnosed based on karyotyping or chromosomal microarray analysis (CMA). Among them, 2,084 singleton pregnancies received karyotyping and/or CMA. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NIPS for fetal SCAs were evaluated. RESULTS The sensitivity was 97.7% (95%CI, 87.7-99.9), 87.3% (95% CI, 76.5-94.4), 96.1% (95%CI, 86.5-99.5), and 95.7% (95% CI, 78.1-99.9), the PPV was 25.8% (95%CI, 19.2-33.2), 80.9% (95%CI, 69.5-89.4), 79.0% (95%CI, 66.8-88.3), and 53.7% (95%CI, 37.4-69.3) for 45,X, 47,XXY, 47,XXX, and 47,XYY, respectively. The specificity was 94.1% (95%CI, 93.0-95.1) for 45,X, and more than 99.0% for sex chromosome trisomy (SCT). The NPV was over 99.0% for all. CONCLUSIONS NIPS screening for fetal SCAs has high sensitivity, specificity and NPV. The PPV of SCAs was moderate, but that of 45,X was lower than that of SCTs. Invasive prenatal diagnosis should be recommended for high-risk patients.
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Affiliation(s)
- Yanfei Xu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jianbo Lou
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Obstetrics and Gynecology, Shaoxing Maternal and Child Health Care Hospital, Shaoxing, China
| | - Yeqing Qian
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
| | - Pengzhen Jin
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yangwen Qian
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiawei Hong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuqing Xu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yixuan Yin
- Hangzhou Women's Hospital, Prenatal Diagnosis Center, Hangzhou, China
| | - Songjia Yi
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Minyue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, China
- Department of Reproductive Medicine, Key Laboratory of Women's Reproductive Health of Zhejiang Province, Hangzhou, China
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12
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Morisi N, Virzì GM, Ferrarini M, Alfano G, Zanella M, Ronco C, Donati G. Exploring the Role of Cell-Free Nucleic Acids and Peritoneal Dialysis: A Narrative Review. Genes (Basel) 2024; 15:553. [PMID: 38790182 PMCID: PMC11121405 DOI: 10.3390/genes15050553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
INTRODUCTION Cell-free nucleic acids (cf-NAs) represent a promising biomarker of various pathological and physiological conditions. Since its discovery in 1948, cf-NAs gained prognostic value in oncology, immunology, and other relevant fields. In peritoneal dialysis (PD), blood purification is performed by exposing the peritoneal membrane. Relevant sections: Complications of PD such as acute peritonitis and peritoneal membrane aging are often critical in PD patient management. In this review, we focused on bacterial DNA, cell-free DNA, mitochondrial DNA (mtDNA), microRNA (miRNA), and their potential uses as biomarkers for monitoring PD and its complications. For instance, the isolation of bacterial DNA in early acute peritonitis allows bacterial identification and subsequent therapy implementation. Cell-free DNA in peritoneal dialysis effluent (PDE) represents a marker of stress of the peritoneal membrane in both acute and chronic PD complications. Moreover, miRNA are promising hallmarks of peritoneal membrane remodeling and aging, even before its manifestation. In this scenario, with multiple cytokines involved, mtDNA could be considered equally meaningful to determine tissue inflammation. CONCLUSIONS This review explores the relevance of cf-NAs in PD, demonstrating its promising role for both diagnosis and treatment. Further studies are necessary to implement the use of cf-NAs in PD clinical practice.
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Affiliation(s)
- Niccolò Morisi
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
| | - Grazia Maria Virzì
- Department of Nephrology, Dialysis and Transplant, St. Bortolo Hospital, 36100 Vicenza, Italy
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Marco Ferrarini
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
| | - Gaetano Alfano
- Nephrology Dialysis and Transplant Unit, University Hospital of Modena, 41124 Modena, Italy
| | - Monica Zanella
- Department of Nephrology, Dialysis and Transplant, St. Bortolo Hospital, 36100 Vicenza, Italy
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Claudio Ronco
- IRRIV-International Renal Research Institute Vicenza-Foundation, 36100 Vicenza, Italy
| | - Gabriele Donati
- Surgical, Medical, Dental and Morphological Sciences Department (CHIMOMO), University of Modena and Reggio Emilia, 41124 Modena, Italy; (N.M.)
- Nephrology Dialysis and Transplant Unit, University Hospital of Modena, 41124 Modena, Italy
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13
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Raymond Y, Fernando S, Menezes M, Mol BW, McLennan A, da Silva Costa F, Hardy T, Rolnik DL. Placental, maternal, fetal, and technical origins of false-positive cell-free DNA screening results. Am J Obstet Gynecol 2024; 230:381-389. [PMID: 38008147 DOI: 10.1016/j.ajog.2023.11.1240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Accepted: 11/16/2023] [Indexed: 11/28/2023]
Abstract
The introduction of noninvasive prenatal testing has resulted in substantial reductions to previously accepted false-positive rates of prenatal screening. Despite this, the possibility of false-positive results remains a challenging consideration in clinical practice, particularly considering the increasing uptake of genome-wide noninvasive prenatal testing, and the subsequent increased proportion of high-risk results attributable to various biological events besides fetal aneuploidy. Confined placental mosaicism, whereby chromosome anomalies exclusively affect the placenta, is perhaps the most widely accepted cause of false-positive noninvasive prenatal testing. There remains, however, a substantial degree of ambiguity in the literature pertaining to the clinical ramifications of confined placental mosaicism and its potential association with placental insufficiency, and consequentially adverse pregnancy outcomes including fetal growth restriction. Other causes of false-positive noninvasive prenatal testing include vanishing twin syndrome, in which the cell-free DNA from a demised aneuploidy-affected twin triggers a high-risk result, technical failures, and maternal origins of abnormal cell-free DNA such as uterine fibroids or unrecognized mosaicisms. Most concerningly, maternal malignancies are also a documented cause of false-positive screening results. In this review, we compile what is currently known about the various causes of false-positive noninvasive prenatal testing.
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Affiliation(s)
- Yvette Raymond
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia.
| | - Shavi Fernando
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia; Monash Women's, Monash Health, Melbourne, Australia; Monash Obstetrics, Melbourne, Australia
| | - Melody Menezes
- Monash Ultrasound for Women, Melbourne, Australia; Department of Paediatrics, The University of Melbourne, Melbourne, Australia; Monash IVF Group, Melbourne, Australia
| | - Ben W Mol
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia; Monash Women's, Monash Health, Melbourne, Australia; Centre for Women's Health Research, The University of Aberdeen, Aberdeen, UK
| | - Andrew McLennan
- Sydney Ultrasound for Women, Sydney, Australia; Discipline of Obstetrics, Gynaecology and Neonatology, The University of Sydney, Sydney, Australia
| | - Fabricio da Silva Costa
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Queensland, Australia; School of Medicine and Dentistry, Griffith University, Gold Coast, Queensland, Australia
| | - Tristan Hardy
- Monash IVF Group, Melbourne, Australia; Repromed Adelaide, Dulwich, Australia
| | - Daniel L Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Melbourne, Australia; Monash Women's, Monash Health, Melbourne, Australia; Monash Ultrasound for Women, Melbourne, Australia
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14
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Díaz del Arco C, Fernández Aceñero MJ, Ortega Medina L. Liquid biopsy for gastric cancer: Techniques, applications, and future directions. World J Gastroenterol 2024; 30:1680-1705. [PMID: 38617733 PMCID: PMC11008373 DOI: 10.3748/wjg.v30.i12.1680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
After the study of circulating tumor cells in blood through liquid biopsy (LB), this technique has evolved to encompass the analysis of multiple materials originating from the tumor, such as nucleic acids, extracellular vesicles, tumor-educated platelets, and other metabolites. Additionally, research has extended to include the examination of samples other than blood or plasma, such as saliva, gastric juice, urine, or stool. LB techniques are diverse, intricate, and variable. They must be highly sensitive, and pre-analytical, patient, and tumor-related factors significantly influence the detection threshold, diagnostic method selection, and potential results. Consequently, the implementation of LB in clinical practice still faces several challenges. The potential applications of LB range from early cancer detection to guiding targeted therapy or immunotherapy in both early and advanced cancer cases, monitoring treatment response, early identification of relapses, or assessing patient risk. On the other hand, gastric cancer (GC) is a disease often diagnosed at advanced stages. Despite recent advances in molecular understanding, the currently available treatment options have not substantially improved the prognosis for many of these patients. The application of LB in GC could be highly valuable as a non-invasive method for early diagnosis and for enhancing the management and outcomes of these patients. In this comprehensive review, from a pathologist's perspective, we provide an overview of the main options available in LB, delve into the fundamental principles of the most studied techniques, explore the potential utility of LB application in the context of GC, and address the obstacles that need to be overcome in the future to make this innovative technique a game-changer in cancer diagnosis and treatment within clinical practice.
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Affiliation(s)
- Cristina Díaz del Arco
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - M Jesús Fernández Aceñero
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Luis Ortega Medina
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
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15
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Anees F, Montoya DA, Pisetsky DS, Payne CK. DNA corona on nanoparticles leads to an enhanced immunostimulatory effect with implications for autoimmune diseases. Proc Natl Acad Sci U S A 2024; 121:e2319634121. [PMID: 38442162 PMCID: PMC10945806 DOI: 10.1073/pnas.2319634121] [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: 11/08/2023] [Accepted: 02/03/2024] [Indexed: 03/07/2024] Open
Abstract
Autoimmune and inflammatory diseases are highly complex, limiting treatment and the development of new therapies. Recent work has shown that cell-free DNA bound to biological microparticles is linked to systemic lupus erythematosus, a prototypic autoimmune disease. However, the heterogeneity and technical challenges associated with the study of biological particles have hindered a mechanistic understanding of their role. Our goal was to develop a well-controlled DNA-particle model system to understand how DNA-particle complexes affect cells. We first characterized the adsorption of DNA on the surface of polystyrene nanoparticles (200 nm and 2 µm) using transmission electron microscopy, dynamic light scattering, and colorimetric DNA concentration assays. We found that DNA adsorbed on the surface of nanoparticles was resistant to degradation by DNase 1. Macrophage cells incubated with the DNA-nanoparticle complexes had increased production of pro-inflammatory cytokines tumor necrosis factor alpha (TNF-α) and interleukin 6 (IL-6). We probed two intracellular DNA sensing pathways, toll-like receptor 9 (TLR9) and cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING), to determine how cells sense the DNA-nanoparticle complexes. We found that the cGAS-STING pathway is the primary route for the interaction between DNA-nanoparticles and macrophages. These studies provide a molecular and cellular-level understanding of DNA-nanoparticle-macrophage interactions. In addition, this work provides the mechanistic information necessary for future in vivo experiments to elucidate the role of DNA-particle interactions in autoimmune diseases, providing a unique experimental framework to develop novel therapeutic approaches.
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Affiliation(s)
- Faisal Anees
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
| | - Diego A. Montoya
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
| | - David S. Pisetsky
- Division of Rheumatology and Immunology, Duke University Medical Center, and Medical Research Service, Durham VA Medical Center, Durham, NC27705
| | - Christine K. Payne
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC27708
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16
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Thorsen SU, Moseholm KF, Clausen FB. Circulating cell-free DNA and its association with cardiovascular disease: what we know and future perspectives. Curr Opin Lipidol 2024; 35:14-19. [PMID: 37800671 DOI: 10.1097/mol.0000000000000907] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
PURPOSE OF REVIEW The aim of this review is to explore a possible link between cell-free DNA (cfDNA) and cardiovascular disease (CVD), which may hold valuable potential for future diagnostics. RECENT FINDINGS cfDNA has become topic of high interest across several medical fields. cfDNA is used as a diagnostic biomarker in cancer, prenatal care, and transplantation. In addition, cfDNA may play an unrecognized role in biological processes that are involved in or underlying various disease states, for example, inflammation. Elevated levels of cfDNA are associated with various elements of CVD, cardio-metabolic risk factors, and autoimmune diseases. Mitochondrial cfDNA and neutrophil extracellular traps may play distinct roles. Total circulating cfDNA may reflect the unspecific accumulation of stressors and the organism's susceptibility and resilience to such stressors. As such, cfDNA, in a stressful situation, may provide predictive value for future development of CVD. We suggest exploring such possibility through a large-scale prospective cohort study of pregnant women. SUMMARY There is no doubt that cfDNA is a valuable biomarker. For CVD, its potential is indicated but less explored. New studies may identify cfDNA as a valuable circulating cardiovascular risk marker to help improve risk stratification.
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Affiliation(s)
| | - Kristine Frøsig Moseholm
- Department of Public Health, Section of Epidemiology, University of Copenhagen, Copenhagen, Denmark
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17
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Parijs I, Brison N, Vancoillie L, Baetens M, Blaumeiser B, Boulanger S, Désir J, Dimitrov B, Fieremans N, Janssens K, Janssens S, Marichal A, Menten B, Meunier C, Van Berkel K, Van Den Bogaert A, Devriendt K, Van Den Bogaert K, Vermeesch JR. Population screening for 15q11-q13 duplications: corroboration of the difference in impact between maternally and paternally inherited alleles. Eur J Hum Genet 2024; 32:31-36. [PMID: 37029316 PMCID: PMC10772068 DOI: 10.1038/s41431-023-01336-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 04/09/2023] Open
Abstract
Maternally inherited 15q11-q13 duplications are generally found to cause more severe neurodevelopmental anomalies compared to paternally inherited duplications. However, this assessment is mainly inferred from the study of patient populations, causing an ascertainment bias towards patients at the more severe end of the phenotypic spectrum. Here, we analyze the low coverage genome-wide cell-free DNA sequencing data obtained from pregnant women during non-invasive prenatal screening (NIPS). We detect 23 15q11-q13 duplications in 333,187 pregnant women (0.0069%), with an approximately equal distribution between maternal and paternal duplications. Maternally inherited duplications are always associated with a clinical phenotype (ranging from learning difficulties to intellectual impairment, epilepsy and psychiatric disorders), while paternal duplications are normal or associated with milder phenotypes (mild learning difficulties and dyslexia). This data corroborates the difference in impact between paternally and maternally inherited 15q11-q13 duplications, contributing to the improvement of genetic counselling. We recommend reporting 15q11-q13 duplications identified during genome-wide NIPS with appropriate genetic counselling for these pregnant women in the interest of both mothers and future children.
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Affiliation(s)
- Ilse Parijs
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
| | - Nathalie Brison
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
| | - Machteld Baetens
- Center of Medical Genetics, University Hospital Ghent, Ghent, Belgium
| | - Bettina Blaumeiser
- Center of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Sébastien Boulanger
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Julie Désir
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Boyan Dimitrov
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, research group Reproduction and Genetics, Center for Medical Genetics, Brussels, Belgium
| | - Nathalie Fieremans
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, research group Reproduction and Genetics, Center for Medical Genetics, Brussels, Belgium
| | - Katrien Janssens
- Center of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Sandra Janssens
- Center of Medical Genetics, University Hospital Ghent, Ghent, Belgium
| | - Axel Marichal
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Björn Menten
- Center of Medical Genetics, University Hospital Ghent, Ghent, Belgium
| | - Colombine Meunier
- Center for Medical Genetics, Institut de Pathologie et de Génétique Gosselies, Charleroi, Belgium
| | - Kim Van Berkel
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, research group Reproduction and Genetics, Center for Medical Genetics, Brussels, Belgium
| | - Ann Van Den Bogaert
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, research group Reproduction and Genetics, Center for Medical Genetics, Brussels, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven-KU Leuven, Leuven, Belgium
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18
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Kong L, Li S, Zhao Z, Feng J, Fu X, Li H, Zhu J, Wang Y, Tang W, Yuan C, Li F, Han X, Wu D, Kong X, Sun L. Exploring factors impacting haplotype-based noninvasive prenatal diagnosis for single-gene recessive disorders. Clin Genet 2024; 105:52-61. [PMID: 37822034 DOI: 10.1111/cge.14434] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Haplotype-based noninvasive prenatal diagnosis (NIPD) is applicable for various recessive single-gene disorders in proband families. However, a comprehensive exploration of critical factors influencing the assay performance, such as fetal fraction, informative single nucleotide polymorphism (SNP) count, and recombination events, has yet to be performed. It is critical to identify key factors affecting NIPD performance, including its accuracy and success rate, and their impact on clinical diagnostics to guide clinical practice. We conducted a prospective study, recruiting 219 proband families with singleton pregnancies at risk for eight recessive single-gene disorders (Duchenne muscular dystrophy, spinal muscular atrophy, phenylketonuria, methylmalonic acidemia, hemophilia A, hemophilia B, non-syndromic hearing loss, and congenital adrenal hyperplasia) at 7-14 weeks of gestation. Haplotype-based NIPD was performed by evaluating the relative haplotype dosage (RHDO) in maternal circulation, and the results were validated via invasive prenatal diagnosis or newborn follow-ups. Among the 219 families, the median gestational age at first blood draw was 8+5 weeks. Initial testing succeeded for 190 families and failed for 29 due to low fetal fraction (16), insufficient informative SNPs (9), and homologous recombination near pathogenic variation (4). Among low fetal fraction families, successful testing was achieved for 11 cases after a redraw, while 5 remained inconclusive. Test failures linked to insufficient informative SNPs correlated with linkage disequilibrium near the genes, with F8 and MMUT exhibiting the highest associated failure rates (14.3% and 25%, respectively). Homologous recombination was relatively frequent around the DMD and SMN1 genes (8.8% and 4.8%, respectively) but led to detection failure in only 44.4% (4/9) of such cases. All NIPD results from the 201 successful families were consistent with invasive diagnostic findings or newborn follow-up. Fetal fraction, informative SNPs count, and homologous recombination are pivotal to NIPD performance. Redrawing blood effectively improves the success rate for low fetal fraction samples. However, informative SNPs count and homologous recombination rates vary significantly across genes, necessitating careful consideration in clinical practice. We have designed an in silico method based on linkage disequilibrium data to predict the number of informative SNPs. This can identify genomic regions where there might be an insufficient number of SNPs, thereby guiding panel design. With these factors properly accounted for, NIPD is highly accurate and reliable.
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Affiliation(s)
- Lingrong Kong
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shaojun Li
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhenhua Zhao
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jun Feng
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xinyu Fu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanyun Li
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingqi Zhu
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanan Wang
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weiqin Tang
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Chao Yuan
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Feifei Li
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xiujuan Han
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Di Wu
- Celula (China) Medical Technology Co., Ltd., Chengdu, China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
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19
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Nintao N, Manonai J, Wattanayingcharoenchai R, Bumrungphuet S, Hansahiranwadee W, Dulyaphat W, Somchit W, Wattanasirichaigoon D, Prakobpanich M, Tangshewinsirikul C. Effects of an animated educational video on knowledge of cell-free DNA screening among Thai pregnant women: a randomized control trial. BMC Pregnancy Childbirth 2023; 23:853. [PMID: 38082376 PMCID: PMC10714566 DOI: 10.1186/s12884-023-06170-8] [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: 05/16/2023] [Accepted: 12/03/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND In developing countries, pregnant women have insufficient knowledge about cell-free DNA screening. Reports from developed countries have found that various tools in prenatal genetic counseling can improve the knowledge of pregnant women who undergo cell-free DNA screening. Data are limited from developing countries where women have different baseline socio-educational backgrounds. The objective of this study was to compare the effects of an animated educational video combined with traditional counseling versus traditional counseling alone in changing pregnant women's knowledge of cell-free DNA screening. METHODS This study was a randomized control trial at an antenatal clinic. Eligible subjects who were Thai pregnant women, were randomized to either view or not view the 4-minute animated educational video explaining cell-free DNA screening. Both groups received traditional counseling. The women were asked to complete a Thai questionnaire assessing knowledge of the screening before and after intervention. The questionnaire consisted of three sections: demographic data of the research participants and their existing awareness about cell-free DNA testing; performance and limitations of cell-free DNA screening; and participants' attitudes toward the positive screening. Primary outcome was the change in knowledge scores. Secondary outcomes were attitudes toward positive screening test, levels of satisfaction with counseling, and screening acceptance rates. RESULTS Data from 83 women in the video group and 82 in the non-video group were analyzed. The knowledge score (range 0-18) change after counseling was significantly higher in the video group than the non-video group (+ 7.1 ± 3.3 vs + 4.2 ± 2.5; p = 0.03). There were no significant differences in attitudes toward positive screening test (p = 0.83), levels of satisfaction (p = 0.24), or screening acceptance rates (p = 0.15) between the groups. CONCLUSIONS Adding the video to traditional counseling was better than traditional counseling alone in improving pregnant women's knowledge about cell-free DNA screening. TRIAL REGISTRATION The study was retrospectively registered with the Thai Clinical Trials Registry (TCTR20210917001, 17/09/2021).
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Affiliation(s)
- Nutta Nintao
- Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Jittima Manonai
- Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rujira Wattanayingcharoenchai
- Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sommart Bumrungphuet
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wirada Hansahiranwadee
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Wirada Dulyaphat
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Werapath Somchit
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Maneerat Prakobpanich
- Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Chayada Tangshewinsirikul
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynaecology, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
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20
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Botos L, Szatmári E, Nagy GR. Prenatal and postnatal genetic testing toward personalized care: The non-invasive perinatal testing. Mol Cell Probes 2023; 72:101942. [PMID: 37951513 DOI: 10.1016/j.mcp.2023.101942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
This article investigates how non-invasive prenatal testing and the incorporation of genomic sequencing into newborn screening postnatally are transforming perinatal care. They improve the accuracy of prenatal and neonatal screening, allowing for early interventions and personalized therapies. Non-invasive prenatal testing before birth and saliva-sample-based newborn genomic sequencing after birth can be collectively referred to as non-invasive perinatal testing. Non-invasive prenatal testing is particularly useful for aneuploidy, whereas performance markers worsen as DNA abnormalities shrink in size. Screening for clinically actionable diseases in childhood would be crucial to personalized medical therapy, as the postnatal period remains appropriate for screening for the great majority of monogenic disorders. While genomic data can help diagnose uncommon diseases, challenges like ethics and equity necessitate joint approaches for appropriate integration in this revolutionary journey toward personalized care.
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Affiliation(s)
- Lilla Botos
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Erzsébet Szatmári
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Gyula Richárd Nagy
- Department of Obstetrics and Gynecology, Baross Street Division, Semmelweis University, Budapest, Hungary; Intelligenetic Healthcare Services Ltd., Budapest, Hungary.
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21
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Lenaerts L, Theunis M, Amant F, Vermeesch JR. Non-invasive prenatal testing: when results suggests maternal cancer. MED GENET-BERLIN 2023; 35:285-295. [PMID: 38835737 PMCID: PMC11006267 DOI: 10.1515/medgen-2023-2055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
It is now well-established that non-invasive prenatal testing (NIPT), originally designed to screen cell-free DNA (cfDNA) in maternal blood for the presence of common fetal trisomies, can lead to incidental detection of occult maternal malignancies. Retrospective evaluations have demonstrated that the detection of multiple copy number alterations in cfDNA is particularly suggestive of an incipient tumor and that cancer detection rates not only depend on tumor biology but also on applied NIPT technologies and downstream diagnostic investigations. Since the identification of a maternal cancer in pregnancy has implications for both woman and the unborn child, prospective studies are needed to provide evidence on best clinical practices and on clinical utility in terms of patient outcomes.
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Affiliation(s)
- Liesbeth Lenaerts
- Catholic University Leuven Department of Oncology, Laboratory of Gynecological Oncology Herestraat 49 - box 818 3000 Leuven Belgium
| | - Miel Theunis
- Catholic University Leuven Centre of Human Genetics Herestraat 49 - box 818 3000 Leuven Belgium
| | - Frédéric Amant
- Catholic University Leuven Department of Oncology, Laboratory of Gynecological Oncology Herestraat 49 - box 818 3000 Leuven Belgium
- Catholic University Leuven Department of Oncology, Laboratory for Gynecological Oncology Leuven Belgium
- University Hospitals Leuven Centre of Human Genetics Leuven Belgium
| | - Joris R Vermeesch
- Catholic University Leuven Centre of Human Genetics Herestraat 49 - box 818 3000 Leuven Belgium
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22
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Park JE, Kang KM, Kim H, Jang HY, Go M, Yang SH, Jeong D, Jeong H, Kim JC, Lim SY, Cha DH, Shim SH. Cell-Free Fetal DNA Screening Analysis in Korean Pregnant Women: Six Years of Experience and a Retrospective Study of 9327 Patients Analyzed from 2017 to 2022. J Pers Med 2023; 13:1468. [PMID: 37888079 PMCID: PMC10608624 DOI: 10.3390/jpm13101468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
Cell-free DNA (cfDNA) screening for normal fetal aneuploidy has been widely adopted worldwide due to its convenience, non-invasiveness, and high positive predictive rate. We retrospectively evaluated 9327 Korean women with single pregnancies who underwent a non-invasive prenatal test (NIPT) to investigate how various factors such as maternal weight, age, and the method of conception affect the fetal fraction (FF). The average FF was 9.15 ± 3.31%, which decreased significantly as the maternal body mass index (BMI) increased (p < 0.001). The highly obese group showed a 'no-call' rate of 8.01%, which is higher than that of the normal weight group (0.33%). The FF was 8.74 ± 3.20% when mothers were in their 40s, and lower than that when in their 30s (9.23 ± 3.34, p < 0.001) and in the natural pregnancy group (9.31% ± 3.33). The FF of male fetuses was observed to be approximately 2.76% higher on average than that of female fetuses. As the gestational age increased, there was no significant increase in the fraction of fetuses up to 21 weeks compared to that at 10-12 weeks, and a significant increase was observed in the case of 21 weeks or more. The FFs in the NIPT high-risk result group compared to that in the low-risk group were not significantly different (p = 0.62). In conclusion, BMI was the factor most associated with the fetal fraction. Although the NIPT is a highly prevalent method in prenatal analysis, factors affecting the fetal fraction should be thoroughly analyzed to obtain more accurate results.
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Affiliation(s)
- Ji Eun Park
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
| | - Kyung Min Kang
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
| | - Hyunjin Kim
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
| | - Hee Yeon Jang
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
| | - Minyeon Go
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
| | - So Hyun Yang
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
| | - Daeun Jeong
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (D.J.); (H.J.); (S.Y.L.)
| | - Hyeonmin Jeong
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (D.J.); (H.J.); (S.Y.L.)
| | - Jong Chul Kim
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
| | - Seo Young Lim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (D.J.); (H.J.); (S.Y.L.)
| | - Dong Hyun Cha
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 06125, Republic of Korea
| | - Sung Han Shim
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06125, Republic of Korea; (J.E.P.); (K.M.K.); (H.K.); (H.Y.J.); (M.G.); (S.H.Y.); (J.C.K.)
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (D.J.); (H.J.); (S.Y.L.)
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23
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Scott F, Smet ME, Elhindi J, Mogra R, Sunderland L, Ferreira A, Menezes M, Meagher S, McLennan A. Late first-trimester ultrasound findings can alter management after high-risk NIPT result. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2023; 62:497-503. [PMID: 37247395 DOI: 10.1002/uog.26272] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To evaluate the impact of detailed late first-trimester ultrasound (LFTU) on the positive predictive value (PPV) of a high-risk non-invasive prenatal test (NIPT) result for various chromosomal abnormalities. METHODS This was a retrospective study of all cases undergoing invasive prenatal testing from three tertiary providers of obstetric ultrasound over 4 years, each using NIPT as a first-line screening test. Data were collected from pre-NIPT ultrasound, NIPT, LFTU, placental serology and later ultrasound examinations. Prenatal testing for chromosomal abnormalities was performed by microarray, initially using array comparative genomic hybridization and then single nucleotide polymorphism (SNP) array for the last 2 years. Uniparental disomy testing was performed by SNP array during all 4 years. The majority of NIPT tests were analyzed using the Illumina platform, initially confined to the assessment of the common autosomal trisomies, sex chromosome aneuploidies and rare autosomal trisomies (RAT), then extending to genome-wide analysis for the last 2 years. RESULTS Amniocentesis or chorionic villus sampling (CVS) was performed on 2657 patients, 1352 (51%) of whom had undergone prior NIPT, with 612 (45%) of these returning a high-risk result and meeting the inclusion criteria for the study. LFTU findings significantly affected the PPV of the NIPT result for trisomies 13 (T13), 18 (T18) and 21 (T21), monosomy X (MX) and RAT but not for the other sex chromosomal abnormalities or segmental imbalances (> 7 Mb). Abnormal LFTU increased the PPV close to 100% for T13, T18, T21, MX and RAT. The magnitude of the change in PPV was highest for the most severe chromosomal abnormalities. When LFTU was normal, the incidence of confined placental mosaicism (CPM) was highest in those with a high-risk NIPT result for T13, followed by T18 and T21. After normal LFTU, the PPV for T21, T18, T13 and MX decreased to 68%, 57%, 5% and 25%, respectively. CONCLUSIONS LFTU after a high-risk NIPT result can alter the PPV for many chromosomal abnormalities, assisting counseling regarding invasive prenatal testing and pregnancy management. The high PPVs of NIPT for T21 and T18 are not sufficiently modified by normal LFTU findings to alter management. These at-risk patients should be offered CVS for earlier diagnosis, particularly given the low rate of CPM associated with these aneuploidies. Patients with a high-risk NIPT result for T13 and normal LFTU findings often wait for amniocentesis or avoid invasive testing altogether given the low PPV and higher rate of CPM in this context. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- F Scott
- Sydney Ultrasound for Women, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - M-E Smet
- Sydney Ultrasound for Women, Sydney, Australia
- Maternal-Fetal Medicine Department, Westmead Hospital, Sydney, Australia
| | - J Elhindi
- Maternal-Fetal Medicine Department, Westmead Hospital, Sydney, Australia
| | - R Mogra
- Sydney Ultrasound for Women, Sydney, Australia
- Department of Obstetrics and Gynaecology, Royal Prince Alfred Hospital, Sydney, Australia
| | - L Sunderland
- Department of Obstetrics and Gynaecology, Royal Prince Alfred Hospital, Sydney, Australia
| | - A Ferreira
- Sydney Ultrasound for Women, Sydney, Australia
- School of Women's and Children's Health, University of New South Wales, Sydney, Australia
| | - M Menezes
- Monash Ultrasound for Women, Melbourne, Australia
| | - S Meagher
- Monash Ultrasound for Women, Melbourne, Australia
| | - A McLennan
- Sydney Ultrasound for Women, Sydney, Australia
- School of Women's and Children's Health, University of Sydney, Sydney, Australia
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24
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Solomon BD, Chung WK. Artificial intelligence and the impact on medical genetics. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2023; 193:e32060. [PMID: 37565625 DOI: 10.1002/ajmg.c.32060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 07/24/2023] [Accepted: 07/29/2023] [Indexed: 08/12/2023]
Abstract
Virtually all areas of biomedicine will be increasingly affected by applications of artificial intelligence (AI). We discuss how AI may affect fields of medical genetics, including both clinicians and laboratorians. In addition to reviewing the anticipated impact, we provide recommendations for ways in which these groups may want to evolve in light of the influence of AI. We also briefly discuss how educational and training programs can play a key role in preparing the future workforce given these anticipated changes.
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Affiliation(s)
- Benjamin D Solomon
- Medical Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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25
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De Borre M, Che H, Yu Q, Lannoo L, De Ridder K, Vancoillie L, Dreesen P, Van Den Ackerveken M, Aerden M, Galle E, Breckpot J, Van Keirsbilck J, Gyselaers W, Devriendt K, Vermeesch JR, Van Calsteren K, Thienpont B. Cell-free DNA methylome analysis for early preeclampsia prediction. Nat Med 2023; 29:2206-2215. [PMID: 37640858 DOI: 10.1038/s41591-023-02510-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 07/22/2023] [Indexed: 08/31/2023]
Abstract
Preeclampsia (PE) is a leading cause for peripartal morbidity, especially if developing early in gestation. To enable prophylaxis in the prevention of PE, pregnancies at risk of PE must be identified early-in the first trimester. To identify at-risk pregnancies we profiled methylomes of plasma-derived, cell-free DNA from 498 pregnant women, of whom about one-third developed early-onset PE. We detected DNA methylation differences between control and PE pregnancies that enabled risk stratification at PE diagnosis but also presymptomatically, at around 12 weeks of gestation (range 9-14 weeks). The first-trimester risk prediction model was validated in an external cohort collected from two centers (area under the curve (AUC) = 0.75) and integrated with routinely available maternal risk factors (AUC = 0.85). The combined risk score correctly predicted 72% of patients with early-onset PE at 80% specificity. These preliminary results suggest that cell-free DNA methylation profiling is a promising tool for presymptomatic PE risk assessment, and has the potential to improve treatment and follow-up in the obstetric clinic.
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Affiliation(s)
- Marie De Borre
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Huiwen Che
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Qian Yu
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Lore Lannoo
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Kobe De Ridder
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Pauline Dreesen
- Faculty of Medicine and Life Science, Hasselt University, Hasselt, Belgium
| | - Mika Van Den Ackerveken
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Mio Aerden
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Eva Galle
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | | | | | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Joris Robert Vermeesch
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
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26
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Zhang F, Yin T, Tang X, Ma S, Meng Q, Song J, Wang Y, Men S, Wang L. Prenatal diagnosis of a case with complete and uniform tetrasomy 12p by the utility of noninvasive prenatal testing. J Assist Reprod Genet 2023; 40:2233-2240. [PMID: 37501006 PMCID: PMC10440312 DOI: 10.1007/s10815-023-02896-8] [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: 04/26/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023] Open
Abstract
PURPOSE To report a rare type of Pallister-Killian syndrome (PKS) diagnosed prenatally by the utility of non-invasive prenatal testing (NIPT). METHODS NIPT was performed in the first trimester. Conventional karyotyping and chromosomal microarray analysis (CMA) were performed on the amniotic samples in the second trimester. Copy number variation sequencing (CNV-seq) was used for the validation of fetal skin and the placental tissue after pregnancy termination. RESULTS NIPT results showed increased signal from chromosome 12p. Subsequent prenatal diagnostic testing by karyotype revealed 47, XY, +i (12p), and CMA displayed four copies of 12p: 12p13.33-12p11.1(173786_34835641) × 4. The CNV-seq results of the fetal skin and the fetal side of placenta showed four copies of 12p13.33-p11 and an estimated chimeric duplication of 34.08 Mb (chimerism ratio: 10%) in 12 p13.33-p11, respectively. However, no abnormality was detected by CNV-seq at the maternal side of placenta. CONCLUSIONS Our findings suggest that a positive signal from chromosome 12p on NIPT should raise suspicion for PKS. With the wide application of NIPT, the true positive of incidental finding is expected to increase.
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Affiliation(s)
- Fang Zhang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Ting Yin
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Xinxin Tang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Shanshan Ma
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Qian Meng
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Jiedong Song
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Yongan Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Shuai Men
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China
| | - Leilei Wang
- Department of Prenatal Diagnosis, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, 222000, People's Republic of China.
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27
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Berezina TA, Berezin AE. Cell-free DNA as a plausible biomarker of chronic kidney disease. Epigenomics 2023; 15:879-890. [PMID: 37791402 DOI: 10.2217/epi-2023-0255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Circulating cell-free DNA (cf-DNA) is released from dead and/or apoptotic leukocytes and due to neutrophil extracellular traps contributing to an inflammatory response. Previous clinical studies have reported that the peak concentrations and dynamic changes of cf-DNA may be used as a noninvasive biomarker of worsening kidney function as well as a guide to the management of kidney allograft rejection. We hypothesized that the pattern and dynamic changes of cf-DNA might be a plausible predictive biomarker for patients at risk of chronic kidney disease (CKD), including individuals with type 2 diabetes mellitus, heart failure, cardiovascular disease and established CKD. Along with it, pre- and posthemodialysis levels of serum cf-DNA appear to be a independent predictor for all-cause mortality in patients with end-stage kidney disease.
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Affiliation(s)
- Tetiana A Berezina
- VitaCenter, Department of Internal Medicine and Nephrology, Zaporozhye, 69000, Ukraine
| | - Alexander E Berezin
- Paracelsus Medical University, Department of Internal Medicine II, Division of Cardiology, Salzburg, 5020, Austria
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28
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Yu SCY, Choy LYL, Lo YMD. 'Longing' for the Next Generation of Liquid Biopsy: The Diagnostic Potential of Long Cell-Free DNA in Oncology and Prenatal Testing. Mol Diagn Ther 2023; 27:563-571. [PMID: 37474843 PMCID: PMC10435595 DOI: 10.1007/s40291-023-00661-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Liquid biopsy using cell-free DNA (cfDNA) has gained global interest as a molecular diagnostic tool. However, the analysis of cfDNA in cancer patients and pregnant women has been focused on short DNA molecules (e.g., ≤ 600 bp). With the detection of long cfDNA in the plasma of pregnant women and cancer patients in two recent studies, a new avenue of long cfDNA-based liquid biopsy has been opened. In this review, we summarize our current knowledge in this nascent field of long cfDNA analysis, focusing on the fragmentomic and epigenetic features of long cfDNA. In particular, long-read sequencing enabled single-molecule methylation analysis and subsequent determination of the tissue-of-origin of long cfDNA, which has promising clinical potential in prenatal and cancer testing. We also examine some of the limitations that may hinder the immediate clinical applications of long cfDNA analysis and the current efforts involved in addressing them. With concerted efforts in this area, it is hoped that long cfDNA analysis will add to the expanding armamentarium of liquid biopsy.
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Affiliation(s)
- Stephanie C Y Yu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China
| | - L Y Lois Choy
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China.
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.
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Moufarrej MN, Bianchi DW, Shaw GM, Stevenson DK, Quake SR. Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities. Annu Rev Biomed Data Sci 2023; 6:397-418. [PMID: 37196360 PMCID: PMC10528197 DOI: 10.1146/annurev-biodatasci-020722-094144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Prenatal screening using sequencing of circulating cell-free DNA has transformed obstetric care over the past decade and significantly reduced the number of invasive diagnostic procedures like amniocentesis for genetic disorders. Nonetheless, emergency care remains the only option for complications like preeclampsia and preterm birth, two of the most prevalent obstetrical syndromes. Advances in noninvasive prenatal testing expand the scope of precision medicine in obstetric care. In this review, we discuss advances, challenges, and possibilities toward the goal of providing proactive, personalized prenatal care. The highlighted advances focus mainly on cell-free nucleic acids; however, we also review research that uses signals from metabolomics, proteomics, intact cells, and the microbiome. We discuss ethical challenges in providing care. Finally, we look to future possibilities, including redefining disease taxonomy and moving from biomarker correlation to biological causation.
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Affiliation(s)
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development and Section on Prenatal Genomics and Fetal Therapy, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gary M Shaw
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - David K Stevenson
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, California, USA
- Chan Zuckerberg Initiative, Redwood City, California, USA
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Nguyen HM, Baradaran M, Daigle G, Nshimyumukiza L, Guertin JR, Reinharz D. Pregnant women's and policymakers' preferences for the expansion of noninvasive prenatal screening: A discrete choice experiment approach study. Health Sci Rep 2023; 6:e1516. [PMID: 37636285 PMCID: PMC10447874 DOI: 10.1002/hsr2.1516] [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: 05/01/2023] [Revised: 07/12/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Background and Aims Quantitative approaches for eliciting preferences for new interventions are mostly conducted by patients and rarely by policymakers. This study aimed to quantify the preferences of pregnant women and policymakers regarding the addition of a new test to prenatal screening programs for detecting chromosomal abnormalities. Methods A discrete choice experiment was conducted to measure the respondents' preferences for a new prenatal test. A seven-attribute instrument was built based on interviews with pregnant women and policymakers. The data were analyzed using robust conditional logistic regression and nested logit models. Results In total, 272 pregnant women and 24 policymakers completed the questionnaire (response rates of 48% and 55%, respectively). Overall, all attributes were statistically significant in the pregnant women group, whereas only three attributes (test performance, degree of test result certainty, and cost) were statistically significant in the policymakers group. Statistically significant differences in test performance and information were observed between the two groups. Conclusion Policymakers differed from pregnant women in their appraisal of attributes related to their preference for a new prenatal screening intervention. The low response rates observed in both groups suggest that further investigation of the relevance of this approach must be conducted.
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Affiliation(s)
- Hung Manh Nguyen
- Département de médecine sociale et préventiveUniversité LavalQuébecCanada
| | - Mohammad Baradaran
- Département de génie électrique et de génie informatiqueUniversité LavalQuébecCanada
| | - Gaétan Daigle
- Département de mathématiques et de statistiqueUniversité LavalQuébecCanada
| | - Leon Nshimyumukiza
- Institut national d'excellence en santé et en services sociauxQuébecCanada
- Faculté des sciences infirmièresUniversité LavalQuébecCanada
| | - Jason Robert Guertin
- Département de médecine sociale et préventiveUniversité LavalQuébecCanada
- Centre de Recherche du CHU de QuébecUniversité LavalQuébecCanada
| | - Daniel Reinharz
- Département de médecine sociale et préventiveUniversité LavalQuébecCanada
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31
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De Falco L, Pelo E, Qi Z, Novelli A. Editorial: Unravelling the basis of non-invasive prenatal screening results. Front Genet 2023; 14:1247764. [PMID: 37529782 PMCID: PMC10390063 DOI: 10.3389/fgene.2023.1247764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/05/2023] [Indexed: 08/03/2023] Open
Affiliation(s)
- Luigia De Falco
- AMES, Centro Polidiagnostico Strumentale, srl, Naples, Italy
| | - Elisabetta Pelo
- SOD Diagnostica Genetica, Azienda Ospedaliero Universitaria Careggi, Florence, Italy
| | - Zhongxia Qi
- Medical Center, Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Hou Y, Yang J, Deng F, Wang F, Peng H, Guo F, Wang D, Yin A. Association between cell-free DNA fetal fraction and pregnant character: a retrospective cohort study of 27,793 maternal plasmas. Sci Rep 2023; 13:11420. [PMID: 37452067 PMCID: PMC10349099 DOI: 10.1038/s41598-023-38151-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/04/2023] [Indexed: 07/18/2023] Open
Abstract
To determine the association between cell-free DNA fetal fraction (cffDNA) and various prenatal characters to better guide the clinical application of noninvasive prenatal screening (NIPS), a retrospective cohort study of 27,793 women with singleton pregnancies was conducted. Results indicated that no significant difference on cffDNA between trisomy/sex chromosome aneuploidy (SCA) and non-trisomy groups was found. However, the fetal fraction (FF) in the T18 and T13 subgroups were significantly lower than that in the non-trisomy group, while the FF in the T21 group was significantly higher than the non-trisomy group. Pearson's correlation analysis revealed a positive correlation between √FF and gestational week in the T21, SCA, and non-trisomy groups. A negative correlation between maternal age and √FF in T21 and non-trisomy cases was found, but a positive correlation in SCA group. Compared to the decreasing trend in FF in the T21 group, no significant difference was observed in the SCA group. The √FF level was negatively correlated to maternal BMI in T21 and non-trisomy group, while a positive correlation in SCA group. FF was close related to the result of NIPS and related maternal factors. Though NIPS has increased accuracy, the complexity still should be recognized especially in clinical practice.
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Affiliation(s)
- Yaping Hou
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
| | - Jiexia Yang
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
| | - Fuli Deng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Fanghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Haishan Peng
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
| | - Fangfang Guo
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
| | - Dongmei Wang
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China
| | - Aihua Yin
- Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China.
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 510010, Guangdong, China.
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Nguyen HM, Lindsay C, Baradaran M, Guertin JR, Nshimyumukiza L, Soukkhaphone B, Reinharz D. Development of a discrete choice experiment questionnaire to elicit preferences by pregnant women and policymakers for the expansion of non-invasive prenatal screening. PLoS One 2023; 18:e0287653. [PMID: 37352239 PMCID: PMC10289448 DOI: 10.1371/journal.pone.0287653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 06/10/2023] [Indexed: 06/25/2023] Open
Abstract
OBJECTIVE An instrument for measuring intervention preferences applicable to both patients and policymakers would make it possible to better confront the needs of the supply and demand sides of the health care system. This study aimed to develop a discrete choice experiments (DCE) questionnaire to elicit the preferences of patients and policymakers. The instrument was specifically developed to estimate preferences for new conditions to be added to a screening program for fetal chromosomal anomalies. METHODS A DCE development study was conducted. The methods employed included a literature review, a qualitative study (based on individual semi-structured interviews, consultations, and a focus group discussion) with pregnant women and policymakers, and a pilot project with 33 pregnant women to validate the first version of the instrument and test the feasibility of its administration. RESULTS An initial list of 10 attributes was built based on a literature review and the qualitative research components of the study. Five attributes were built based on the responses provided by the participants from both groups. Eight attributes were consensually retained. A pilot project performed on 33 pregnant women led to a final instrument containing seven attributes: 'conditions to be screened', 'test performance', 'moment at gestational age to obtain the test result', 'degree of test result certainty to the severity of the disability', 'test sufficiency', 'information provided from test result', and 'cost related to the test'. CONCLUSION It is possible to reach a consensus on the construction of a DCE instrument intended to be administered to pregnant women and policymakers. However, complete validation of the consensual instrument is limited because there are too few voting members of health technology assessment agencies committees to statistically ascertain the relevance of the attributes and their levels.
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Affiliation(s)
- Hung Manh Nguyen
- Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada
| | - Carmen Lindsay
- Centre de Recherche du CHU de Québec, Université Laval, Québec, Canada
| | - Mohammad Baradaran
- Département de Génie Électrique et de Génie Informatique, Université Laval, Québec, Canada
| | - Jason Robert Guertin
- Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada
- Centre de Recherche du CHU de Québec, Université Laval, Québec, Canada
| | - Leon Nshimyumukiza
- Institut national D’excellence en Santé et en Services Sociaux, Québec, Canada
- Faculté des Sciences Infirmières, Université Laval, Québec, Canada
| | | | - Daniel Reinharz
- Département de Médecine Sociale et Préventive, Université Laval, Québec, Canada
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Rosner M, Horer S, Feichtinger M, Hengstschläger M. Multipotent fetal stem cells in reproductive biology research. Stem Cell Res Ther 2023; 14:157. [PMID: 37287077 DOI: 10.1186/s13287-023-03379-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/16/2023] [Indexed: 06/09/2023] Open
Abstract
Due to the limited accessibility of the in vivo situation, the scarcity of the human tissue, legal constraints, and ethical considerations, the underlying molecular mechanisms of disorders, such as preeclampsia, the pathological consequences of fetomaternal microchimerism, or infertility, are still not fully understood. And although substantial progress has already been made, the therapeutic strategies for reproductive system diseases are still facing limitations. In the recent years, it became more and more evident that stem cells are powerful tools for basic research in human reproduction and stem cell-based approaches moved into the center of endeavors to establish new clinical concepts. Multipotent fetal stem cells derived from the amniotic fluid, amniotic membrane, chorion leave, Wharton´s jelly, or placenta came to the fore because they are easy to acquire, are not associated with ethical concerns or covered by strict legal restrictions, and can be banked for autologous utilization later in life. Compared to adult stem cells, they exhibit a significantly higher differentiation potential and are much easier to propagate in vitro. Compared to pluripotent stem cells, they harbor less mutations, are not tumorigenic, and exhibit low immunogenicity. Studies on multipotent fetal stem cells can be invaluable to gain knowledge on the development of dysfunctional fetal cell types, to characterize the fetal stem cells migrating into the body of a pregnant woman in the context of fetomaternal microchimerism, and to obtain a more comprehensive picture of germ cell development in the course of in vitro differentiation experiments. The in vivo transplantation of fetal stem cells or their paracrine factors can mediate therapeutic effects in preeclampsia and can restore reproductive organ functions. Together with the use of fetal stem cell-derived gametes, such strategies could once help individuals, who do not develop functional gametes, to conceive genetically related children. Although there is still a long way to go, these developments regarding the usage of multipotent fetal stem cells in the clinic should continuously be accompanied by a wide and detailed ethical discussion.
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Affiliation(s)
- Margit Rosner
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Vienna, Austria
| | - Stefanie Horer
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Vienna, Austria
| | | | - Markus Hengstschläger
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Währinger Strasse 10, 1090, Vienna, Austria.
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35
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Jha P, Lenaerts L, Vermeesch J, Norton M, Amant F, Glanc P, Poder L. Noninvasive prenatal screening and maternal malignancy: role of imaging. Abdom Radiol (NY) 2023; 48:1590-1598. [PMID: 37095202 DOI: 10.1007/s00261-023-03913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 04/26/2023]
Abstract
Noninvasive prenatal screening (NIPS) tests for fetal chromosomal anomalies through maternal blood sampling. It is becoming widely available and standard of care for pregnant women in many countries. It is performed in the first trimester of pregnancy, usually between 9 and 12 weeks. Fragments of fetal cell-free deoxyribonucleic acid (DNA) floating in maternal plasma are detected and analyzed by this test to assess for chromosomal aberrations. Similarly, maternal tumor-derived cell-free DNA (ctDNA) released from the tumor cells also circulates in the plasma. Hence, the presence of genomic anomalies originating from maternal tumor-derived DNA may be detected on the NIPS-based fetal risk assessment in pregnant patients. Presence of multiple aneuploidies or autosomal monosomies are the most commonly reported NIPS abnormalities detected with occult maternal malignancies. When such results are received, the search for an occult maternal malignancy begins, in which imaging plays a crucial role. The most commonly detected malignancies via NIPS are leukemia, lymphoma, breast and colon cancers. Ultrasound is a reasonable radiation-free modality for imaging during pregnancy, specially when there are localizing symptoms or findings, such as palpable lumps. While there are no consensus guidelines on the imaging evaluation for these patients, when there are no localizing symptoms or clinically palpable findings, whole body MRI is recommended as the radiation-free modality of choice to search for an occult malignancy. Based on clinical symptoms, practice patterns, and available resources, breast ultrasound, chest radiographs, and targeted ultrasound evaluations can also be performed initially or as a follow-up for MRI findings. CT is reserved for exceptional circumstances due to its higher radiation dose. This article intends to increase awareness of this rare but stressful clinical scenario and guide imaging evaluation for occult malignancy detected via NIPS during pregnancy.
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Affiliation(s)
- Priyanka Jha
- Department of Radiology, Division of Body Imaging, Stanford University School of Medicine, Palo Alto, CA, USA.
| | | | - Joris Vermeesch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Centre of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Mary Norton
- Department of Obstetrics and Gynecology, University of California San Francisco, San Francisco, CA, USA
| | - Frédéric Amant
- Department of Oncology, KU Leuven, Leuven, Belgium
- Gynecology and Obstetrics, University Hospitals Leuven, Leuven, Belgium
- Center for Gynecological Oncology Amsterdam, Academic Medical Centre Amsterdam, University of Amsterdam, Amsterdam, The Netherlands
- The Netherlands Cancer Institute, Antoni Van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Phyllis Glanc
- Department of Radiology, Obstetrics & Gynecology, University of Toronto, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
| | - Liina Poder
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
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36
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Reappraisal of evolving methods in non-invasive prenatal screening: Discovery, biology and clinical utility. Heliyon 2023; 9:e13923. [PMID: 36879971 PMCID: PMC9984859 DOI: 10.1016/j.heliyon.2023.e13923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Non-invasive prenatal screening (NIPS) offers an opportunity to screen or determine features associated with the fetus. Earlier, prenatal testing was done with cytogenetic procedures like karyotyping or fluorescence in-situ hybridization, which necessitated invasive methods such as fetal blood sampling, chorionic villus sampling or amniocentesis. Over the last two decades, there has been a paradigm shift away from invasive prenatal diagnostic methods to non-invasive ones. NIPS tests heavily rely on cell-free fetal DNA (cffDNA). This DNA is released into the maternal circulation by placenta. Like cffDNA, fetal cells such as nucleated red blood cells, placental trophoblasts, leukocytes, and exosomes or fetal RNA circulating in maternal plasma, have enormous potential in non-invasive prenatal testing, but their use is still limited due to a number of limitations. Non-invasive approaches currently use circulating fetal DNA to assess the fetal genetic milieu. Methods with an acceptable detection rate and specificity such as sequencing, methylation, or PCR, have recently gained popularity in NIPS. Now that NIPS has established clinical significance in prenatal screening and diagnosis, it is critical to gain insights into and comprehend the genesis of NIPS de novo. The current review reappraises the development and emergence of non-invasive prenatal screen/test approaches, as well as their clinical application, with a focus, on the scope, benefits, and limitations.
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37
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Roszko KL, Guthrie L, Li X, Collins MT, de Castro LF, Boyce AM. Identification of GNAS Variants in Circulating Cell-Free DNA from Patients with Fibrous Dysplasia/McCune Albright Syndrome. J Bone Miner Res 2023; 38:443-450. [PMID: 36593655 DOI: 10.1002/jbmr.4766] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/20/2022] [Accepted: 12/29/2022] [Indexed: 01/04/2023]
Abstract
Fibrous dysplasia/McCune-Albright syndrome (FD/MAS) is a rare mosaic bone and endocrine disorder. Although most variants affect the GNAS R201 codon, obtaining a genetic diagnosis is difficult because not all cells harbor the variant, and an invasive biopsy may be required. We explored the presence of GNAS p.R201 variants in blood circulating cell free DNA (ccfDNA) using sensitive techniques of digital droplet polymerase chain reaction (PCR) (ddPCR) and competitive allele-specific TaqMan PCR (castPCR) in an effort to improve the genetic diagnosis of FD/MAS. We isolated ccfDNA from the plasma of 66 patients with a wide range of disease severity and performed both ddPCR and castPCR mutation analysis to search for GNAS p.R201H or R201C variants. We detected R201 variants in ccfDNA samples of 41 of 66 (62.1%) patients by either castPCR or ddPCR, and 45 of 66 (68.2%) of patients if the techniques were combined. Variant detection was more likely in patients with more severe disease. Skeletal disease burden score (SBS) was significantly higher in patients who had detectable variants, and SBS was a predictor of variant allele frequency. By ddPCR analysis, patients aged ≤30 years had higher detection rates, and higher variant allele frequencies, independent of disease burden. We detected variant DNA in only one patient with monostotic FD by ddPCR only. In summary, we have demonstrated that ccfDNA containing variant GNAS can be isolated from the plasma of patients with FD/MAS and that ddPCR and castPCR methods have similar variant detection rates. This methodology represents an important potential advancement in diagnosis for patients with FD/MAS, especially those younger than 30 years or with more severe disease. Published 2023. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Kelly L Roszko
- Skeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Lori Guthrie
- Skeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Xiaobai Li
- Biostatistics and Clinical Epidemiology Service, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael T Collins
- Skeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Luis F de Castro
- Skeletal Disorders and Mineral Homeostasis Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Alison M Boyce
- Metabolic Bone Disorders Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
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Eldem V, Kuralay SC, Özdoğan G, Özçelik GH, Aydın D, Çakmak G, Gürler MÖ, Çay SB, Çınar YU, Dikmen F, Yusuf I, Obut O, Kayalar Ö, Zararsız GE, Edizadeh M, Zararsız G, Akdeniz E, Özgür H, Tekin IM. Comprehensive analysis of circulating viral DNA in maternal plasma at population-scale using low-pass whole-genome sequencing. Genomics 2023; 115:110556. [PMID: 36599399 DOI: 10.1016/j.ygeno.2022.110556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 11/04/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023]
Abstract
As the most readily adopted molecular screening test, low-pass WGS of maternal plasma cell-free DNA for aneuploidy detection generates a vast amount of genomic data. This large-scale method also allows for high-throughput virome screening. NIPT sequencing data, yielding 6.57 terabases of data from 187.8 billion reads, from 12,951 pregnant Turkish women was used to investigate the prevalence and abundance of viral DNA in plasma. Among the 22 virus sequences identified in 12% of participants were human papillomavirus, herpesvirus, betaherpesvirus and anellovirus. We observed a unique pattern of circulating viral DNA with a high prevalence of papillomaviruses. The prevalence of herpesviruses/anellovirus was similar among Turkish, European and Dutch populations. Hepatitis B prevalence was remarkably low in Dutch, European and Turkish populations, but higher in China. WGS data revealed that herpesvirus/anelloviruses are naturally found in European populations. This represents the first comprehensive research on the plasma virome of pregnant Turkish women.
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Affiliation(s)
- Vahap Eldem
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey.
| | - Selim Can Kuralay
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Gülperi Özdoğan
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | | | - Dilşah Aydın
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Gökçe Çakmak
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | | | - Selahattin Barış Çay
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Yusuf Ulaş Çınar
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Fatih Dikmen
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Ishak Yusuf
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Onur Obut
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Özgecan Kayalar
- Koc University Research Center for Translational Medicine (KUTTAM), Koc University School of Medicine, Istanbul 34010, Turkey
| | - Gözde Ertürk Zararsız
- Department of Biostatistics, Erciyes University Medical Faculty, Kayseri 38280, Turkey; Erciyes University, Drug Application and Research Center (ERFARMA), Kayseri 38280, Turkey
| | - Masoud Edizadeh
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Gökmen Zararsız
- Department of Biostatistics, Erciyes University Medical Faculty, Kayseri 38280, Turkey; Erciyes University, Drug Application and Research Center (ERFARMA), Kayseri 38280, Turkey
| | - Eren Akdeniz
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Hilal Özgür
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
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The amniotic fluid proteome changes with term labor and informs biomarker discovery in maternal plasma. Sci Rep 2023; 13:3136. [PMID: 36823217 PMCID: PMC9950459 DOI: 10.1038/s41598-023-28157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/13/2023] [Indexed: 02/25/2023] Open
Abstract
The intra-uterine components of labor, namely, myometrial contractility, cervical ripening, and decidua/membrane activation, have been extensively characterized and involve a local pro-inflammatory milieu of cellular and soluble immune mediators. Targeted profiling has demonstrated that such processes extend to the intra-amniotic space, yet unbiased analyses of the proteome of human amniotic fluid during labor are lacking. Herein, we utilized an aptamer-based platform to characterize 1,310 amniotic fluid proteins and found that the proteome undergoes substantial changes with term labor (251 proteins with differential abundance, q < 0.1, and fold change > 1.25). Proteins with increased abundance in labor are enriched for immune and inflammatory processes, consistent with prior reports of labor-associated changes in the intra-uterine space. By integrating the amniotic fluid proteome with previously generated placental-derived single-cell RNA-seq data, we demonstrated the labor-driven upregulation of signatures corresponding to stromal-3 and decidual cells. We also determined that changes in amniotic fluid protein abundance are reflected in the maternal plasma proteome. Collectively, these findings provide novel insights into the amniotic fluid proteome in term labor and support its potential use as a source of biomarkers to distinguish between true and false labor by using maternal blood samples.
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Becking EC, Linthorst J, Patton S, Gutowska-Ding W, Goodall R, Khawaja F, Morgan F, Deans Z, Chitty LS, Bekker MN, Scheffer PG, Sistermans EA. Variability in Fetal Fraction Estimation: Comparing Fetal Fractions Reported by Noninvasive Prenatal Testing Providers Globally. Clin Chem 2023; 69:160-167. [PMID: 36576352 DOI: 10.1093/clinchem/hvac207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/07/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Fetal fraction (FF) measurement is considered important for reliable noninvasive prenatal testing (NIPT). Using minimal FF threshold as a quality parameter is under debate. We evaluated the variability in reported FFs of individual samples between providers and laboratories and within a single laboratory. METHODS Genomic quality assessment and European Molecular Genetics Quality Network provide joint proficiency testing for NIPT. We compared reported FFs across all laboratories and stratified according to test methodologies. A single sample was sequenced repeatedly and FF estimated by 2 bioinformatics methods: Veriseq2 and SeqFF. Finally, we compared FFs by Veriseq and SeqFF in 87 351 NIPT samples. RESULTS For each proficiency test sample we observed a large variability in reported FF, SDs and CVs ranging from 1.7 to 3.6 and 17.0 to 35.8, respectively. FF measurements reported by single nucleotide polymorphism-based methods had smaller SDs (0.5 to 2.4) compared to whole genome sequencing-based methods (1.8 to 2.9). In the internal quality assessment, SDs were similar between SeqFF (SD 1.0) and Veriseq v2 (SD 0.9), but mean FF by Veriseq v2 was higher compared to SeqFF (9.0 vs 6.4, P 0.001). In patient samples, reported FFs were on average 1.12-points higher in Veriseq than in SeqFF (P 0.001). CONCLUSIONS Current methods do not allow for a reliable and consistent FF estimation. Our data show estimated FF should be regarded as a laboratory-specific range, rather than a precise number. Applying strict universal minimum thresholds might result in unnecessary test failures and should be used with caution.
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Affiliation(s)
- Ellis C Becking
- Department of Obstetrics, Division of Women and Baby, Wilhelmina Childrens Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jasper Linthorst
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development, Amsterdam, The Netherlands
| | - Simon Patton
- Manchester Science Park, EMQN CIC, Manchester, UK
| | | | | | - Farrah Khawaja
- Genomics Quality Assessment, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Fiona Morgan
- Genomics Quality Assessment, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Zandra Deans
- Genomics Quality Assessment, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust and Genetics and Genomics, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Mireille N Bekker
- Department of Obstetrics, Division of Women and Baby, Wilhelmina Childrens Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter G Scheffer
- Department of Obstetrics, Division of Women and Baby, Wilhelmina Childrens Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erik A Sistermans
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development, Amsterdam, The Netherlands
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Tian M, Feng L, Li J, Zhang R. Focus on the frontier issue: progress in noninvasive prenatal screening for fetal trisomy from clinical perspectives. Crit Rev Clin Lab Sci 2023; 60:248-269. [PMID: 36647189 DOI: 10.1080/10408363.2022.2162843] [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: 01/18/2023]
Abstract
The discovery of cell-free fetal DNA (cffDNA) in maternal blood and the rapid development of massively parallel sequencing have revolutionized prenatal testing from invasive to noninvasive. Noninvasive prenatal screening (NIPS) based on cffDNA enables the detection of fetal trisomy through sequencing, comparison, and bioassays. Its accuracy is better than that of traditional screening methods, and it is the most advanced clinical application of high-throughput sequencing technologies. However, the existing sequencing methods are limited by high costs and complex sequencing procedures. These limitations restrict the availability of NIPS for pregnant women. Many amplification methods have been developed to overcome the limitations of sequencing methods. The rapid development of non-sequencing methods has not been accompanied by reviews to summarize them. In this review, we initially describe the detection principles for sequencing-based NIPS. We summarize the rapidly evolving amplification technologies, focusing on the need to reduce costs and simplify the procedures. To ensure that the testing systems are feasible and that the testing processes are reliable, we expand our vision to the clinic. We evaluate the clinical validity of NIPS in terms of sensitivity, specificity, and positive predictive value. Finally, we summarize the application guidelines and discuss the corresponding quality control methods for NIPS. In addition to cffDNA, extracellular vesicle DNA, RNA, protein/peptide, and fetal cells can also be detected as biomarkers of NIPS. With the development of prenatal testing, NIPS has become increasingly important. Notably, NIPS is a screening test instead of a diagnostic test. The testing methods and procedures used in the NIPS process require standardization.
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Affiliation(s)
- Meng Tian
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Lei Feng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, P. R. China.,Peking University Fifth School of Clinical Medicine, Beijing, P. R. China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China
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Xiang L, Zhu J, Deng K, Li Q, Tao J, Li M, Wang Y, Yuan X, Yao Y, Li X. Non-invasive prenatal testing for the detection of trisomies 21, 18, and 13 in pregnant women with various clinical indications: A multicenter observational study of 1,854,148 women in China. Prenat Diagn 2023. [PMID: 36639250 DOI: 10.1002/pd.6312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
OBJECTIVE This study aimed to evaluate the performance of noninvasive prenatal testing (NIPT) for detecting three common trisomies (T21, T18, and T13) in pregnant women with diverse clinical indications. METHODS Frequencies of NIPT, of high chance of having one of the three trisomies, and of confirmed trisomies were determined for women with each of seven clinical indications in a national cross-sectional survey of approximately 300 prenatal diagnosis centers. Data were collected for the period from October 1, 2016 to September 30, 2018 using the Prenatal Diagnosis Technology Management On-line Information System. The performance of NIPT for detecting the three trisomies in pregnant women with different clinical indications was assessed in terms of sensitivity, specificity, positive predictive value (PPV), negative predictive value, and the corresponding 95% confidence intervals. RESULTS A total of 5766 true positive cases for T21, T18, and T13 were detected among 1,854,148 samples, giving an overall detection rate of 0.31% (95% CI: 0.30%-0.32%). Most positive cases were associated with "NT thickening" (1.18%) and "advanced maternal age" (0.51%). The detection sensitivities of NIPT were 99.60% for T21, 99.14% for T18, and 100% for T13, while the corresponding specificities were 99.90%, 99.94%, and 99.95%. The corresponding PPVs were 69.77%, 47.24%, and 22.36%. NIPT showed high sensitivity and specificity, regardless of clinical indication. In contrast, PPV for three trisomies varied widely between 9.09% and 66.46% depending on the clinical indication. Across seven clinical indications, PPV ranged from 50.62% to 73.09% for T21, 20.00%-58.33% for T18, and 4.17%-47.37% for T13. The highest PPVs were 73.09% for T21 in pregnancies involving "advanced maternal age", 58.33% for T18 in pregnancies with "NT thickening", and 47.37% for T13 in pregnancies with "NT thickening". CONCLUSIONS NIPT shows high sensitivity and specificity for detecting T21, T18, and T13 in pregnant women with different clinical indications. However, PPV depends strongly on clinical indication, highlighting the need to strengthen education and genetic counseling about prenatal screening.
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Affiliation(s)
- Liangcheng Xiang
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jun Zhu
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Kui Deng
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Qi Li
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jing Tao
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mingrong Li
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yanping Wang
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xuelian Yuan
- National Office for Maternal and Child Health Surveillance of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongna Yao
- National Center for Birth Defect Monitoring of China, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohong Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China.,Sichuan Birth Defects Clinical Research Center, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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Rosner M, Hengstschläger M. Amniotic Fluid Stem Cells: What They Are and What They Can Become. Curr Stem Cell Res Ther 2023; 18:7-16. [PMID: 34895127 DOI: 10.2174/1574888x16666211210143640] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/21/2021] [Accepted: 11/15/2021] [Indexed: 11/22/2022]
Abstract
In the last two decades, fetal amniotic fluid stem cells progressively attracted attention in the context of both basic research and the development of innovative therapeutic concepts. They exhibit broadly multipotent plasticity with the ability to differentiate into cells of all three embryonic germ layers and low immunogenicity. They are convenient to maintain, highly proliferative, genomically stable, non-tumorigenic, perfectly amenable to genetic modifications, and do not raise ethical concerns. However, it is important to note that among the various fetal amniotic fluid cells, only c-Kit+ amniotic fluid stem cells represent a distinct entity showing the full spectrum of these features. Since amniotic fluid additionally contains numerous terminally differentiated cells and progenitor cells with more limited differentiation potentials, it is of highest relevance to always precisely describe the isolation procedure and characteristics of the used amniotic fluid-derived cell type. It is of obvious interest for scientists, clinicians, and patients alike to be able to rely on up-todate and concisely separated pictures of the utilities as well as the limitations of terminally differentiated amniotic fluid cells, amniotic fluid-derived progenitor cells, and c-Kit+ amniotic fluid stem cells, to drive these distinct cellular models towards as many individual clinical applications as possible.
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Affiliation(s)
- Margit Rosner
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Markus Hengstschläger
- Institute of Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
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Chaddha M, Rai H, Gupta R, Thakral D. Integrated analysis of circulating cell free nucleic acids for cancer genotyping and immune phenotyping of tumor microenvironment. Front Genet 2023; 14:1138625. [PMID: 37091783 PMCID: PMC10117686 DOI: 10.3389/fgene.2023.1138625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/15/2023] [Indexed: 04/25/2023] Open
Abstract
The circulating cell-free nucleic acids (ccfNAs) consist of a heterogenous cocktail of both single (ssNA) and double-stranded (dsNA) nucleic acids. These ccfNAs are secreted into the blood circulation by both healthy and malignant cells via various mechanisms including apoptosis, necrosis, and active secretion. The major source of ccfNAs are the cells of hematopoietic system under healthy conditions. These ccfNAs include fragmented circulating cell free DNA (ccfDNA), coding or messenger RNA (mRNA), long non-coding RNA (lncRNA), microRNA (miRNA), and mitochondrial DNA/RNA (mtDNA and mtRNA), that serve as prospective biomarkers in assessment of various clinical conditions. For, e.g., free fetal DNA and RNA migrate into the maternal plasma, whereas circulating tumor DNA (ctDNA) has clinical relevance in diagnostic, prognostic, therapeutic targeting, and disease progression monitoring to improve precision medicine in cancer. The epigenetic modifications of ccfDNA as well as circulating cell-free RNA (ccfRNA) such as miRNA and lncRNA show disease-related variations and hold potential as epigenetic biomarkers. The messenger RNA present in the circulation or the circulating cell free mRNA (ccf-mRNA) and long non-coding RNA (ccf-lncRNA) have gradually become substantial in liquid biopsy by acting as effective biomarkers to assess various aspects of disease diagnosis and prognosis. Conversely, the simultaneous characterization of coding and non-coding RNAs in human biofluids still poses a significant hurdle. Moreover, a comprehensive assessment of ccfRNA that may reflect the tumor microenvironment is being explored. In this review, we focus on the novel approaches for exploring ccfDNA and ccfRNAs, specifically ccf-mRNA as biomarkers in clinical diagnosis and prognosis of cancer. Integrating the detection of circulating tumor DNA (ctDNA) for cancer genotyping in conjunction with ccfRNA both quantitatively and qualitatively, may potentially hold immense promise towards precision medicine. The current challenges and future directions in deciphering the complexity of cancer networks based on the dynamic state of ccfNAs will be discussed.
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Affiliation(s)
| | | | - Ritu Gupta
- *Correspondence: Deepshi Thakral, ; Ritu Gupta,
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Clinical impacts of genome-wide noninvasive prenatal testing for rare autosomal trisomy. Am J Obstet Gynecol MFM 2023; 5:100790. [PMID: 36377092 DOI: 10.1016/j.ajogmf.2022.100790] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genome-wide noninvasive prenatal testing identifies several rare autosomal trisomies in the general obstetrical population, but its use is questioned by its low positive predictive value. Furthermore, the origin of rare autosomal trisomies and the clinical effect of reporting them has not been sufficiently investigated. In addition, professional societies express their need for data assessing the clinical use of genome-wide noninvasive prenatal testing for rare autosomal trisomies for years. OBJECTIVE This study aimed to investigate the origin of rare autosomal trisomies and the clinical effect of disclosing rare autosomal trisomies in clinical settings. STUDY DESIGN Women who received noninvasive prenatal testing between March 2021 and March 2022 were prospectively enrolled. Clinical follow-up and cytogenetic and molecular investigations were performed. Posthoc analysis was performed to investigate the association between placental mosaicism and clinical outcomes. RESULTS Overall, 154 rare autosomal trisomies were identified in 89,242 pregnancies (0.17%) through noninvasive prenatal testing. In the 120 cases in which cytogenetic and molecular investigations were carried out, the rare autosomal trisomies were found to originate from true fetal mosaicism (n=5), uniparental disomy (n=5), maternal mosaic trisomy (n=3), maternal malignancy (n=1), and confined placental mosaicism (n=106). Clinical follow-up showed that 40% of all rare autosomal trisomy cases had adverse perinatal outcomes. In women with false-positive noninvasive prenatal testing results originating from confined placental mosaicism, the frequency of adverse perinatal outcomes was 26%. More importantly, the placental mosaicism ratio revealed by noninvasive prenatal testing was significantly higher in women who experienced adverse perinatal outcomes than those who did not (0.688 vs 0.332; P<.001). CONCLUSION Women with noninvasive prenatal testing results indicative of rare autosomal trisomies are at risk of adverse perinatal outcomes, and that risk can be stratified using chromosomes and the mosaicism ratio revealed by noninvasive prenatal testing. Our data are valuable for obstetrical caregivers advising a patient with a noninvasive prenatal testing result indicative of a rare autosomal trisomy and a false-positive diagnosis and for managing risks during pregnancy.
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Pacault M, Verebi C, Champion M, Orhant L, Perrier A, Girodon E, Leturcq F, Vidaud D, Férec C, Bienvenu T, Daveau R, Nectoux J. Non-invasive prenatal diagnosis of single gene disorders with enhanced relative haplotype dosage analysis for diagnostic implementation. PLoS One 2023; 18:e0280976. [PMID: 37093806 PMCID: PMC10124834 DOI: 10.1371/journal.pone.0280976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 04/05/2023] [Indexed: 04/25/2023] Open
Abstract
Non-invasive prenatal diagnosis of single-gene disorders (SGD-NIPD) has been widely accepted, but is mostly limited to the exclusion of either paternal or de novo mutations. Indeed, it is still difficult to infer the inheritance of the maternal allele from cell-free DNA (cfDNA) analysis. Based on the study of maternal haplotype imbalance in cfDNA, relative haplotype dosage (RHDO) was developed to address this challenge. Although RHDO has been shown to be reliable, robust control of statistical error and explicit delineation of critical parameters for assessing the quality of the analysis have not been fully addressed. We present here a universal and adaptable enhanced-RHDO (eRHDO) procedure through an automated bioinformatics pipeline with a didactic visualization of the results, aiming to be applied for any SGD-NIPD in routine care. A training cohort of 43 families carrying CFTR, NF1, DMD, or F8 mutations allowed the characterization and optimal setting of several adjustable data variables, such as minimum sequencing depth, type 1 and type 2 statistical errors, as well as the quality assessment of intermediate steps and final results by block score and concordance score. Validation was successfully performed on a test cohort of 56 pregnancies. Finally, computer simulations were used to estimate the effect of fetal-fraction, sequencing depth and number of informative SNPs on the quality of results. Our workflow proved to be robust, as we obtained conclusive and correctly inferred fetal genotypes in 94.9% of cases, with no false-negative or false-positive results. By standardizing data generation and analysis, we fully describe a turnkey protocol for laboratories wishing to offer eRHDO-based non-invasive prenatal diagnosis for single-gene disorders as an alternative to conventional prenatal diagnosis.
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Affiliation(s)
- Mathilde Pacault
- Laboratoire de Génétique Moléculaire et Histocompatibilité, Brest, France
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Camille Verebi
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | | | - Lucie Orhant
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Alexandre Perrier
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Emmanuelle Girodon
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - France Leturcq
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Dominique Vidaud
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Claude Férec
- Laboratoire de Génétique Moléculaire et Histocompatibilité, Brest, France
| | - Thierry Bienvenu
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
| | - Romain Daveau
- MOABI, Plateforme bio-informatique AP-HP, Département I&D, DSI, Paris, France
| | - Juliette Nectoux
- Service de Médecine Génomique des maladies de système et d'organe, APHP.Centre - Université Paris Cité, Hôpital Cochin, Paris, France
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van der Meij KRM, Henneman L, Sistermans EA. Non-invasive prenatal testing for everybody or contingent screening? Prenat Diagn 2022; 43:443-447. [PMID: 36575900 DOI: 10.1002/pd.6296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022]
Affiliation(s)
- Karuna R M van der Meij
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Lidewij Henneman
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
| | - Erik A Sistermans
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, Amsterdam, The Netherlands
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Experiences of pregnant women with genome-wide non-invasive prenatal testing in a national screening program. Eur J Hum Genet 2022; 31:555-561. [PMID: 36481825 PMCID: PMC10172316 DOI: 10.1038/s41431-022-01248-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
AbstractPregnant women’s perspectives should be included in the dialogue surrounding the expanding offers of non-invasive prenatal testing (NIPT), especially now that technological possibilities are rapidly increasing. This study evaluated women’s experiences with the offer of genome-wide (GW) first-tier NIPT in a national screening program. A nationwide pre-and post-test questionnaire was completed by 473 pregnant women choosing between targeted NIPT (trisomies 21, 18 and 13 only) and GW-NIPT (also other findings) within the Dutch TRIDENT-2 study. Measures included satisfaction, reasons for or against choosing GW-NIPT, anxiety, and opinion on the future scope of NIPT. Most respondents (90.4%) were glad to have been offered the choice between GW-NIPT and targeted NIPT; 76.5% chose GW-NIPT. Main reasons to choose GW-NIPT were ‘wanting as much information as possible regarding the child’s health’ (38.6%) and ‘to be prepared for everything’ (23.8%). Main reasons to choose targeted NIPT were ‘avoiding uncertain results/outcomes’ (33.7%) and ‘not wanting to unnecessarily worry’ (32.6%). Nearly all respondents received a low-risk NIPT result (98.7%). No differences were found in anxiety between women choosing GW-NIPT and targeted NIPT. Most respondents were favorable toward future prenatal screening for a range of conditions, including life-threatening disorders, mental disabilities, disorders treatable in pregnancy and severe physical disabilities, regardless of their choice for GW-NIPT or targeted NIPT. In conclusion, women who chose first-tier NIPT were satisfied with the choice between GW-NIPT and targeted NIPT, and most women were favorable toward a broader future screening offer. Our results contribute to the debate concerning the expansion of NIPT.
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Dowlut-McElroy T, Davis S, Howell S, Gutmark-Little I, Bamba V, Prakash S, Patel S, Fadoju D, Vijayakanthi N, Haag M, Hennerich D, Dugoff L, Shankar RK. Cell-free DNA screening positive for monosomy X: clinical evaluation and management of suspected maternal or fetal Turner syndrome. Am J Obstet Gynecol 2022; 227:862-870. [PMID: 35841934 PMCID: PMC9729468 DOI: 10.1016/j.ajog.2022.07.004] [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: 05/05/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/27/2023]
Abstract
Initially provided as an alternative to evaluation of serum analytes and nuchal translucency for the assessment of pregnancies at high risk of trisomy 21, cell-free DNA screening for fetal aneuploidy, also referred to as noninvasive prenatal screening, can now also screen for fetal sex chromosome anomalies such as monosomy X as early as 9 to 10 weeks of gestation. Early identification of Turner syndrome, a sex chromosome anomaly resulting from the complete or partial absence of the second X chromosome, allows medical interventions such as optimizing obstetrical outcomes, hormone replacement therapy, fertility preservation and support, and improved neurocognitive outcomes. However, cell-free DNA screening for sex chromosome anomalies and monosomy X in particular is associated with high false-positive rates and low positive predictive value. A cell-free DNA result positive for monosomy X may represent fetal Turner syndrome, maternal Turner syndrome, or confined placental mosaicism. A positive screen for monosomy X with discordant results of diagnostic fetal karyotype presents unique interpretation and management challenges because of potential implications for previously unrecognized maternal Turner syndrome. The current international consensus clinical practice guidelines for the care of individuals with Turner syndrome throughout the lifespan do not specifically address management of individuals with a cell-free DNA screen positive for monosomy X. This study aimed to provide context and expert-driven recommendations for maternal and/or fetal evaluation and management when cell-free DNA screening is positive for monosomy X. We highlight unique challenges of cell-free DNA screening that is incidentally positive for monosomy X, present recommendations for determining if the result is a true-positive, and discuss when diagnosis of Turner syndrome is applicable to the fetus vs the mother. Whereas we defer the subsequent management of confirmed Turner syndrome to the clinical practice guidelines, we highlight unique considerations for individuals initially identified through cell-free DNA screening.
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Affiliation(s)
- Tazim Dowlut-McElroy
- Pediatric and Adolescent Gynecology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD; Department of Surgery, Children's National Hospital, Washington, DC.
| | - Shanlee Davis
- eXtraOrdinarY Kids Turner Syndrome Clinic, Children's Hospital Colorado, Aurora, CO; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO
| | - Susan Howell
- eXtraOrdinarY Kids Turner Syndrome Clinic, Children's Hospital Colorado, Aurora, CO; Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO
| | - Iris Gutmark-Little
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Vaneeta Bamba
- Division of Endocrinology, Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Siddharth Prakash
- Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX
| | - Sheetal Patel
- Division of Pediatric Cardiology, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Doris Fadoju
- Division of Pediatric Endocrinology, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA
| | - Nandini Vijayakanthi
- Division of Pediatric Endocrinology, Emory University School of Medicine, Children's Healthcare of Atlanta, Atlanta, GA
| | - Mary Haag
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO
| | - Deborrah Hennerich
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, CO
| | - Lorraine Dugoff
- Divisions of Reproductive Genetics and Maternal Fetal Medicine, Department of Obstetrics and Gynecology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Roopa Kanakatti Shankar
- Division of Endocrinology, Children's National Hospital, George Washington University School of Medicine and Health Sciences, Washington, DC
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Xiang J, Peng Z. Applications of Noninvasive Prenatal Testing for Subchromosomal Copy Number Variations Using Cell-Free DNA. Clin Lab Med 2022; 42:613-625. [PMID: 36368786 DOI: 10.1016/j.cll.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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