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Pan Y, Pan X, Zhuang D, Zhou Y, Xue J, Wu S, Chen C, Li H. A statistical investigation of parameters associated with low cell-free fetal DNA fraction in maternal plasma for noninvasive prenatal testing. J Matern Fetal Neonatal Med 2024; 37:2338440. [PMID: 38604949 DOI: 10.1080/14767058.2024.2338440] [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: 10/13/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) is the most common method for prenatal aneuploidy screening. Low fetal fraction (LFF) is the primary reason for NIPT failure. Consequently, factors associated with LFF should be elucidated for optimal clinical implementation of NIPT. METHODS In this study, NIPT data from January 2019 to December 2022 from the laboratory records and obstetrical and neonatal data from the electronic medical records were collected and analyzed. Subjects with FF >3.50% were assigned to the control group, subjects with FF <3.50% once were assigned to the LFF group, and subjects with FF <3.50% twice were assigned to the repetitive low fetal fraction (RLFF) group. Factors, including body mass index (BMI), gestational age, maternal age, twin pregnancy, and in vitro fertilization (IVF) known to be associated with LFF were assessed by Kruskal-Wallis H test and logistic regression. Clinical data on first trimester pregnancy-associated plasma protein-A (PAPP-A), beta-human chorionic gonadotropin (β-hCG), gestational age at delivery, birth weight at delivery, and maternal diseases were obtained from the hospital's prenatal and neonatal screening systems (twin pregnancy was not included in the data on gestational age at delivery and the control group did not include data on maternal diseases.), and were analyzed using Kruskal-Wallis H test and Chi-square test. RESULTS Among the total of 63,883 subjects, 63,605 subjects were assigned to the control group, 197 subjects were assigned to the LFF group, and 81 subjects were assigned to the RLFF group. The median of BMI in the three groups was 22.43 kg/m2 (control), 25.71 kg/m2 (LFF), and 24.54 kg/m2 (RLFF). The median gestational age in the three groups was 130 days (control), 126 days (LFF), and 122/133 days (RLFF). The median maternal age in the three groups was 29 (control), 29 (LFF), and 33-years-old (RLFF). The proportion of twin pregnancies in the three groups was 3.3% (control), 10.7% (LFF), and 11.7% (RLFF). The proportion of IVF in the three groups was 4.7% (control), 11.7% (LFF), and 21.3% (RLFF). The factors significantly associated with LFF included BMI [2.18, (1.94, 2.45), p < 0.0001], gestational age [0.76, (0.67, 0.87), p < 0.0001], twin pregnancy [1.62, (1.02, 2.52), p = 0.0353], and IVF [2.68, (1.82, 3.86), p < 0.0001]. The factors associated with RLFF included maternal age [1.54, (1.17, 2.05), p = 0.0023] and IVF [2.55, (1.19, 5.54), p = 0.016]. Multiples of the median (MOM) value of β-hCG and pregnant persons' gestational age at delivery were significantly decreased in the LFF and RLFF groups compared to the control group. CONCLUSION According to our findings based on the OR value, factors associated strongly with LFF include a high BMI and the use of IVF. Factors associated less strongly with LFF include early gestational age and twin pregnancy, while advanced maternal age and IVF were independent risk factors for a second LFF result.
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Affiliation(s)
- Yun Pan
- The Central Laboratory of Birth Defects Prevention and Control, Women and Children's Hospital of Ningbo University, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Xiaoli Pan
- The Central Laboratory of Birth Defects Prevention and Control, Women and Children's Hospital of Ningbo University, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Danyan Zhuang
- The Central Laboratory of Birth Defects Prevention and Control, Women and Children's Hospital of Ningbo University, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Ying Zhou
- The Central Laboratory of Birth Defects Prevention and Control, Women and Children's Hospital of Ningbo University, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Jiangyang Xue
- The Central Laboratory of Birth Defects Prevention and Control, Women and Children's Hospital of Ningbo University, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Shanshan Wu
- Paediatric Surgery Center, Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Changshui Chen
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children's Hospital of Ningbo University, Ningbo, China
| | - Haibo Li
- The Central Laboratory of Birth Defects Prevention and Control, Women and Children's Hospital of Ningbo University, Ningbo, China
- Ningbo Key Laboratory for the Prevention and Treatment of Embryogenic Diseases, Women and Children's Hospital of Ningbo University, Ningbo, China
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Allen SK, Doyle S. Chapter 2: Non-invasive prenatal diagnosis. Best Pract Res Clin Obstet Gynaecol 2024; 97:102544. [PMID: 39255551 DOI: 10.1016/j.bpobgyn.2024.102544] [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: 06/04/2024] [Revised: 06/21/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024]
Abstract
Non-invasive prenatal diagnosis of monogenic disorders is becoming integrated into routine clinical care for many indications. This is carried out by testing cell-free DNA extracted from the plasma portion of a maternal blood sample. The cell-free DNA is low in concentration, and consists of a mixture of maternal and fetally-derived DNA which are not easy to separate. Methods used therefore need to be rapid, sensitive and specific, including real-time PCR, digital PCR and next generation sequencing with complex algorithms. Testing may be required for pregnancies with an increased chance of a monogenic disorder due to family history or carrier status, or where there are specific abnormalities identified by ultrasound scan. In these situations, testing is considered to be diagnostic and therefore does not require confirmation by invasive testing. With increased access to genomic technologies, and more diagnoses for rare disease patients, future demand for NIPD and possibilities during pregnancy will continue.
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Affiliation(s)
- Stephanie K Allen
- Birmingham Women's and Children's NHS Trust, Mindelsohn Way, Edgbaston, Birmingham, B15 2TG, UK.
| | - Samantha Doyle
- The Department of Perinatal Genetics, The National Maternity Hospital, Dublin, 2, Ireland; UCD Perinatal Research Centre, University College Dublin, National Maternity Hospital, Dublin, Ireland.
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Tung KTS, Tsang HW, Ngo U, Wong RS, Chow CHY, Tso WHY, Yam JCS, Chan GCF, Ip P. A systematic review on the applicability of cell-free DNA level as an obesity biomarker. Obes Rev 2024; 25:e13765. [PMID: 38770721 DOI: 10.1111/obr.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/19/2024] [Accepted: 04/06/2024] [Indexed: 05/22/2024]
Abstract
Obesity has become a global health concern in recent decades. Utilizing biomarkers presents a promising approach to comprehensively monitor the progress of obesity and its associated health conditions. This review aims to synthesize the available evidence on the correlation between cfDNA level and obesity and to provide insights into the applicability of using cfDNA level as a tool for monitoring progression of obesity. Searches were performed in PubMed and Embase on April 1, 2022. Data and other relevant information were extracted and compiled into a structured table for further analysis. Among 1170 articles screened, 11 articles were included in this review and assessed qualitatively. The results demonstrated that existing evidence mainly focused on three populations, including healthy individuals, cancer patients and pregnant women. Majority of the studies on healthy individuals identified a significant association between cfDNA level and body weight status but not among cancer patients. Varying results were observed among pregnant women at different gestational trimesters. Our review summarized some preliminary evidence on the association between cfDNA level and obesity. More cohort studies in larger scale with comprehensive assessment have to be conducted to examine the applicability of cfDNA as a biomarker for severity and disease progression of obesity.
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Affiliation(s)
- Keith T S Tung
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Hing Wai Tsang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ulrike Ngo
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Rosa S Wong
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Special Education and Counselling (SEC), The Education University of Hong Kong, Hong Kong SAR, China
| | - Clare H Y Chow
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Winnie H Y Tso
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Jason C S Yam
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Godfrey C F Chan
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
| | - Patrick Ip
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Hong Kong SAR, China
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Benn P, Zhang J, Lyons D, Xu W, Leonard S, Demko Z. Accuracy of fetal fraction measurements in a single-nucleotide polymorphism-based noninvasive prenatal test. Prenat Diagn 2024. [PMID: 38991760 DOI: 10.1002/pd.6634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/30/2024] [Accepted: 07/03/2024] [Indexed: 07/13/2024]
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) for fetal aneuploidy relies on the analysis of fetoplacental cell-free DNA (cfDNA) found in maternal plasma. A minimum cfDNA fetal fraction (FF) is required for reliable test performance, but some methods may have suboptimal accuracy for FF measurement. This study investigated the accuracy of a single-nucleotide polymorphism- (SNP-) based NIPT method to assess FF. METHODS FF measurements using SNP-based NIPT in consecutive samples from singleton male pregnancies were compared with FF measured using a "gold standard" Y-chromosome method. RESULTS In a cohort of 106,846 samples, the SNP-based FF method showed a standard deviation (SD) of 0.42%. Compared to the Y chromosome FF method, a correlation coefficient, r, of 0.995, and bias of 0.17% were observed. The SD was not substantially different across specific FF ranges or for samples with high-risk NIPT results. CONCLUSIONS The SNP-based NIPT method estimates FF with good accuracy, with a SD three to eight times better than other NIPT methods (0.42% vs. 1.3%-3.4%). FF is an important quality control parameter and should be routinely reported as part of NIPT.
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Affiliation(s)
- Peter Benn
- University of Connecticut Health Center, Farmington, Connecticut, USA
| | | | | | - Wenbo Xu
- Natera, Inc., Austin, Texas, USA
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Claudel N, Barrois M, Vivanti AJ, Rosenblatt J, Salomon LJ, Jouannic JM, Picone O, Carbillon L, Vialard F, Launay E, Tsatsaris V, Curis E, El Khattabi L. Non-invasive cell-free DNA prenatal screening for trisomy 21 as part of primary screening strategy in twin pregnancy. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:807-814. [PMID: 37470702 DOI: 10.1002/uog.26311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 05/27/2023] [Accepted: 05/31/2023] [Indexed: 07/21/2023]
Abstract
OBJECTIVES The performance of non-invasive prenatal screening using cell-free DNA testing of maternal blood in twin pregnancy is underevaluated, while serum marker-based strategies yield poor results. This study aimed to assess the performance of non-invasive prenatal screening for trisomy 21 in twin pregnancy as a first-tier test. Secondary objectives were to assess its failure rate and factors associated with failure. METHODS This retrospective cohort study included twin pregnancies in which non-invasive prenatal screening using cell-free DNA was performed as the primary screening strategy between May 2017 and October 2019. We used the NIPT VeriSeq® test for in-vitro diagnosis and set a fetal fraction cut-off of 4% for monochorionic pregnancies and 8% for dichorionic ones. Clinical data and pregnancy outcome were collected from physicians or midwives via a questionnaire or were retrieved directly on-site. We calculated the performance of non-invasive cell-free DNA screening for trisomy 21, analyzed its failure rate and assessed potentially associated factors. RESULTS Among 1885 twin pregnancies with follow-up, there were six (0.32%) confirmed cases of trisomy 21. The sensitivity of non-invasive prenatal screening for trisomy 21 was 100% (95% CI, 54.1-100%) and the false-positive rate was 0.23% (95% CI, 0.06-0.59%). The primary failure rate was 4.6%, with 4.0% being due to insufficient fetal fraction. A successful result was obtained for 65.4% of women who underwent a new blood draw, reducing the overall failure rate to 2.8%. Maternal body mass index, gestational age at screening as well as chorionicity were significantly associated with the risk of failure. CONCLUSION This study provides further evidence of the high performance, at an extremely low false-positive rate, of non-invasive prenatal screening in twins as part of a primary screening strategy for trisomy 21. © 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)
- N Claudel
- Maternité Port Royal, AP-HP Hôpital Cochin, FHU Prema, Paris, France
- Université Paris Cité, Paris, France
- INSERM UMR_S1139, Paris, France
| | - M Barrois
- Maternité Port Royal, AP-HP Hôpital Cochin, FHU Prema, Paris, France
- Université Paris Cité, Paris, France
- INSERM UMR_S1139, Paris, France
| | - A J Vivanti
- Service de Gynécologie-Obstétrique, DMU Santé des Femmes et des Nouveau-nés, AP-HP Hôpital Antoine Béclère, Clamart, France
- Université Paris-Saclay, Orsay, France
| | - J Rosenblatt
- Service de Gynécologie-Obstétrique, AP-HP Hôpital Universitaire Robert-Debré, Paris, France
| | - L J Salomon
- Université Paris Cité, Paris, France
- Service de Gynécologie-Obstétrique, AP-HP Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - J-M Jouannic
- Département de Médecine Fœtale, Pôle ORIGYNE.6, AP-HP Hôpital Armand Trousseau, Paris, France
- Université Sorbonne Paris Cité, Paris, France
| | - O Picone
- Service de Gynécologie-Obstétrique, AP-HP Hôpital Louis Mourier, Colombes, France
- Université Paris Diderot, INSERM UMR1137, IAME, Paris, France
| | - L Carbillon
- Service de Gynécologie-Obstétrique, AP-HP Hôpital Jean-Verdier, Bondy, France
- Université Paris 13, Bobigny, France
| | - F Vialard
- Service de Cytogénétique, CHI Poissy-Saint Germain en Laye, Poissy, France
| | - E Launay
- Service de Cytogénétique et Biologie Cellulaire, CHU Rennes, Rennes, France
| | - V Tsatsaris
- UR 7537 BioSTM, UFR de Pharmacie, Faculté de Santé, Université Paris Cité, Paris, France
| | - E Curis
- UR 7537 BioSTM, UFR de Pharmacie, Faculté de Santé, Université Paris Cité, Paris, France
- Laboratoire d'Hématologie, Hôpital Lariboisière, AP-HP.nord, Paris, France
| | - L El Khattabi
- Plateforme de Dépistage Prénatal Non Invasif par Analyse de l'ADN Libre Circulant, AP-HP, Hôpital Cochin and Université Paris Cité, Paris, France
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute (ICM), Inserm, CNRS, Hôpital Pitié Salpêtrière, Paris, France
- Unité de Génomique Chromosomique, Département de Génétique Médicale, APHP, Hôpitaux Armand Trousseau et Pitié-Salpêtrière, Paris Brain Institute - ICM, Sorbonne Université, Paris, France
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Shree R, MacKinnon HJ, Hannan J, Kolarova TR, Reichel J, Lockwood CM. Anticoagulation use is associated with lower fetal fraction and more indeterminate results. Am J Obstet Gynecol 2024; 230:95.e1-95.e10. [PMID: 37429430 PMCID: PMC10772208 DOI: 10.1016/j.ajog.2023.07.005] [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: 04/25/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Maternal anticoagulation use may increase indeterminate result rates on cell-free DNA-based screening, but existing studies are confounded by inclusion of individuals with autoimmune disease, which alone is associated with indeterminate results. Changes in chromosome level Z-scores are proposed by others as a reason for indeterminate results, but the etiology of this is uncertain. OBJECTIVE This study aimed to evaluate differences in fetal fraction, indeterminate result rate, and total cell-free DNA concentration in individuals on anticoagulation without autoimmune disease compared with controls undergoing noninvasive prenatal screening. Secondly, using a nested case-control design, we evaluated differences in fragment size, GC-content, and Z-scores to evaluate laboratory-level test characteristics. STUDY DESIGN This was a retrospective single-institution study of pregnant individuals undergoing cell-free DNA-based noninvasive prenatal screening using low-pass whole-genome sequencing between 2017 and 2021. Individuals with autoimmune disease, suspected aneuploidy, and cases where fetal fraction was not reported were excluded. Anticoagulation included heparin-derived products (unfractionated heparin, low-molecular-weight heparin), clopidogrel, and fondaparinux, with a separate group for those on aspirin alone. An indeterminate result was defined as fetal fraction <4%. We evaluated the association between maternal anticoagulation or aspirin use, and fetal fraction, indeterminate results, and total cell-free DNA concentration using univariate and multivariate analyses, controlling for body mass index, gestational age at sample collection, and fetal sex. For the anticoagulation cohort, we compared laboratory-level test characteristics among cases (on anticoagulation) and a subset of controls. Lastly, we evaluated for differences in chromosome level Z-scores among those on anticoagulation with and without indeterminate results. RESULTS A total of 1707 pregnant individuals met the inclusion criteria. Of those, 29 were on anticoagulation and 81 were on aspirin alone. For those on anticoagulation, the fetal fraction was significantly lower (9.3% vs 11.7%; P<.01), the indeterminate result rate was significantly higher (17.2% vs 2.7%; P<.001), and the total cell-free DNA concentration was significantly higher (218 pg/μL vs 83.7 pg/μL; P<.001). Among those on aspirin alone, the fetal fraction was lower (10.6% vs 11.8%; P=.04); however, there were no differences in the rate of indeterminate results (3.7% vs 2.7%; P=.57) or total cell-free DNA concentration (90.1 pg/μL vs 83.8 pg/μL; P=.31). After controlling for maternal body mass index, gestational age at sample collection, and fetal sex, anticoagulation was associated with an >8-fold increase in the likelihood of an indeterminate result (adjusted odds ratio, 8.7; 95% confidence interval, 3.1-24.9; P<.001), but not aspirin (adjusted odds ratio, 1.2; 95% confidence interval, 0.3-4.1; P=.8). Anticoagulation was not associated with appreciable differences in cell-free DNA fragment size or GC-content. Although differences in chromosome 13 Z-scores were observed, none were observed for chromosomes 18 or 21, and this difference did not contribute to the indeterminate result call. CONCLUSION In the absence of autoimmune disease, anticoagulation use, but not aspirin, is associated with lower fetal fraction, higher total cell-free DNA concentration, and higher rates of indeterminate results. Anticoagulation use was not accompanied by differences in cell-free DNA fragment size or GC-content. Statistical differences in chromosome level Z-scores did not clinically affect aneuploidy detection. This suggests a likely dilutional effect by anticoagulation on cell-free DNA-based noninvasive prenatal screening assays contributing to low fetal fraction and indeterminate results, and not laboratory or sequencing-level changes.
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Affiliation(s)
- Raj Shree
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA.
| | - Hayley J MacKinnon
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA
| | - Joely Hannan
- University of Washington School of Medicine, University of Washington, Seattle, WA
| | - Teodora R Kolarova
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA
| | - Jonathan Reichel
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
| | - Christina M Lockwood
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
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Pierre CC, Greene DN, Delaney S, Lockwood CM, Peck Palmer OM. Reconsidering the use of race adjustments in maternal serum screening. Am J Obstet Gynecol 2023; 229:522-525. [PMID: 37327981 DOI: 10.1016/j.ajog.2023.06.018] [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: 03/10/2023] [Revised: 06/09/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
The use of race in maternal serum screening is problematic because race is a social construct rather than a distinct biological classifier. Nevertheless, laboratories offering this testing are encouraged to use race-specific cutoff values for maternal serum screening biomarkers to determine the risk of fetal abnormalities. Large cohort studies examining racial differences in maternal serum screening biomarker concentrations have yielded conflicting results, which we postulate may be explained by genetic and socioeconomic differences between racial cohorts in different studies. We recommend that the use of race in maternal serum screening should be abandoned. Further research is needed to identify socioeconomic and environmental factors that contribute to differences in maternal serum screening biomarker concentrations observed between races. A better understanding of these factors may facilitate accurate race-agnostic risk estimates for aneuploidy and neural tube defects.
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Affiliation(s)
- Christina C Pierre
- Department of Pathology and Laboratory Medicine, Penn Medicine Lancaster General Health, Lancaster, PA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.
| | - Dina N Greene
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Shani Delaney
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of Washington, Seattle, WA
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Octavia M Peck Palmer
- Departments of Pathology and Clinical and Translational Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA
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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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9
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Zaki-Dizaji M, Shafiee A, Kohandel Gargari O, Fathi H, Heidary Z. Maternal and Fetal Factors Affecting Cell-Free Fetal DNA (cffDNA) Fraction: A Systematic Review. J Reprod Infertil 2023; 24:219-231. [PMID: 38164433 PMCID: PMC10757682 DOI: 10.18502/jri.v24i4.14149] [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: 05/06/2023] [Accepted: 08/07/2023] [Indexed: 01/03/2024] Open
Abstract
Background Cell-free fetal DNA (cffDNA) is a novel screening method for fetal aneuploidy that facilitated non-invasive prenatal testing (NIPT) through analysis of cffDNA in maternal plasma. However, despite increased sensitivity, it has a number of limitations that may complicate of its results interpretation. Therefore, elucidating factors affecting fetal fraction, as a critical limitation, guides its clinical application. Methods In this report, systematic search was carried out through PubMed, Web of Science, and Scopus databases until February 11, 2022 by using keywords consist of "noninvasive prenatal screening", "NIPT", "noninvasive prenatal", "cell free DNA" and "fetal fraction". The articles were screened for eligibility criteria before data extraction. Results A total of 39 eligible studies, most published between 2010 and 2020, were included. Based on the results of studies, a negative correlation between maternal age and BMI/body weight with fetal fraction was found. Furthermore, LDL, cholesterol, triglyceride level, metformin, heparin and enoxaparin therapy, hemoglobin-related hemoglobinopathies, and physical activity showed to have negative associations. Interestingly, it seems the ethnicity of patients from South and East Asia has a correlation with fetal fraction compared to Caucasians. Positive correlation was observed between gestational age, free β-hCG, PAPP-A, living in high altitude, and twin pregnancy. Conclusion Considering each factor, there was significant inconsistency and controversy regarding their impact on outcomes. Indeed, multiple factors can influence the accuracy of NIPS results, and it is worth noting that the impact of these factors may vary depending on the individual's ethnic background. Therefore, it is important to recognize that NIPS remains a screening test, and comprehensive pre- and post-NIPS counseling should be conducted as part of standard clinical practice.
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Affiliation(s)
- Majid Zaki-Dizaji
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Arman Shafiee
- Student Research Committee, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Omid Kohandel Gargari
- Student Research Committee, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Haniyeh Fathi
- Student Research Committee, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Zohreh Heidary
- Vali-E-Asr Reproductive Health Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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10
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Lannoo L, Van Camp J, Brison N, Parijs I, Vancoillie L, Van Den Bogaert K, Vermeesch JR, Devriendt K, Van Calsteren K. What helps define outcomes in persistent uninterpretable non-invasive prenatal testing: Maternal factors, fetal fraction or quality scores? Prenat Diagn 2023; 43:1333-1343. [PMID: 37592442 DOI: 10.1002/pd.6423] [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: 04/30/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/19/2023]
Abstract
OBJECTIVES To assess maternal characteristics and comorbidities in patients with persistent uninterpretable non-invasive prenatal testing (NIPT) and to evaluate the association with adverse pregnancy outcome in a general risk population. METHODS A retrospective cohort study (July 2017-December 2020) was conducted of patients with persistent uninterpretable NIPT samples. Maternal characteristics and pregnancy outcomes were compared with the general Belgian obstetric population. RESULTS Of the 148 patients with persistent uninterpretable NIPT, 37 cases were due to a low fetal fraction (LFF) and 111 due to a low quality score (LQS). Both groups (LFF, LQS) showed more obesity (60.6%, 42.4%), multiple pregnancies (18.9%, 4.5%) and more obstetrical complications. In the LQS group, a high rate of maternal auto-immune disorders (30.6%) was seen and hypertensive complications (17.6%), preterm birth (17.6%) and neonatal intensive care unit (NICU) admission (22%) were significantly increased. In the LFF group hypertensive complications (21.6%), gestational diabetes (20.6%), preterm birth (27%), SGA (25.6%), major congenital malformations (11.4%), c-section rate (51.4%) and NICU admission (34.9%) were significantly increased. Chromosomal abnormalities were not increased in both groups. CONCLUSIONS Patients with persistent uninterpretable NIPT have significantly more maternal obesity, comorbidities and adverse pregnancy outcome than the general population and should receive high-risk pregnancy care. Distinguishing between LFF and LQS optimizes counseling because maternal characteristics and pregnancy outcome differ between these groups.
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Affiliation(s)
- Lore Lannoo
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Joke Van Camp
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - Nathalie Brison
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Ilse Parijs
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Leen Vancoillie
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Kristel Van Calsteren
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
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11
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Tian W, Yuan Y, Yuan E, Zhang L, Liu L, Li Y, Guo J, Cui X, Li P, Cui S. Evaluation of the clinical utility of extended non-invasive prenatal testing in the detection of chromosomal aneuploidy and microdeletion/microduplication. Eur J Med Res 2023; 28:304. [PMID: 37644576 PMCID: PMC10466692 DOI: 10.1186/s40001-023-01285-2] [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: 01/30/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND With the development of whole-genome sequencing technology, non-invasive prenatal testing (NIPT) has been applied gradually to screen chromosomal microdeletions and microduplications that cannot be detected by traditional karyotyping. However, in NIPT, some false positives and false negatives occur. This study aimed to investigate the applicability of extended NIPT (NIPT-PLUS) in the detection of chromosomal aneuploidy and microdeletion/microduplication syndrome (MMS). METHODS A total of 452 pregnancies that underwent prenatal diagnostic testing (amniocentesis or chorionic villus sampling) by chromosomal microarray analysis (CMA), were screened by NIPT-PLUS from the peripheral blood sample of the pregnant women. The results of the two tested items were compared and analysed. RESULTS Of the 452 cases, 335 (74.12%) had positive CMA results, and 117 (25.88%) had no abnormal results. A total of 86 cases of trisomy 21, 18 and 13 and sex chromosome aneuploidy (SCA) were detected by CMA and NIPT-PLUS, with a detection rate of 96.51% (83/86). Among them, the detection rates of T18, T13; 47, XXY; 47, XXX and 47 XYY were 100%, and the detection rates of T21 and 45 XO were 96.55% and 90%, respectively. The detection sensitivity of rare chromosomal trisomy (RAT) was 80% (4/5). The positive predictive values of NIPT-PLUS for chromosome aneuploidy T21, T18 and T13 and for SCA and RAT were 90.32%, 87.50%, 25.00%, 88.89% and 50%, respectively. A total of 249 cases (74.32%) of chromosomal MMS were detected by CMA. The detection rate of NIPT-PLUS was 63.86% (159/249), and 90 cases (36.14%) were missed. The larger the MMS fragment, the higher the NIPT-PLUS detection sensitivity. In addition, most small fragments were of maternal origin. CONCLUSION The comparison between the CMA and NIPT-PLUS techniques shows that NIPT-PLUS has high sensitivity for detecting chromosomal aneuploidy and chromosomal copy number variations (CNVs) with fragments > 5 M. However, the sensitivity of CNV for fragments < 5 M is low, and the missed detection rate is high. Additionally, confined placental mosaicism and foetal mosaicism are the key factors causing false negatives in NIPT-PLUS, while maternal chromosomal abnormalities and confined placental mosaicism are key contributors to false positives, so appropriate genetic counselling is especially important for pregnant women before and after NIPT-PLUS testing.
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Affiliation(s)
- Weifang Tian
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Yangyang Yuan
- Department of Medical Research Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Erfeng Yuan
- Department of Clinical Laboratory Science, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Linlin Zhang
- Department of Clinical Laboratory Science, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Ling Liu
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
- Perinatal Disease and Prevention of Birth Defects, Advanced Medical Center, Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Clinical Research Center for Perinatal Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ying Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Jing Guo
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Xueyin Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Pengyun Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Shihong Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China.
- Perinatal Disease and Prevention of Birth Defects, Advanced Medical Center, Zhengzhou University, Zhengzhou, 450052, China.
- Henan Provincial Clinical Research Center for Perinatal Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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12
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Hong K, Park HJ, Jang HY, Shim SH, Jang Y, Kim SH, Cha DH. A Novel Paradigm for Non-Invasive Prenatal Genetic Screening: Trophoblast Retrieval and Isolation from the Cervix (TRIC). Diagnostics (Basel) 2023; 13:2532. [PMID: 37568895 PMCID: PMC10417081 DOI: 10.3390/diagnostics13152532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
As the prevalence of pregnancies with advanced maternal age increases, the risk of fetal chromosomal abnormalities is on the rise. Therefore, prenatal genetic screening and diagnosis have become essential elements in contemporary obstetrical care. Trophoblast retrieval and isolation from the cervix (TRIC) is a non-invasive procedure that can be utilized for prenatal genetic diagnosis. The method involves the isolation of fetal cells (extravillous trophoblasts) by transcervical sampling; along with its non-invasiveness, TRIC exhibits many other advantages such as its usefulness in early pregnancy at 5 weeks of gestation, and no interference by various fetal and maternal factors. Moreover, the trophoblast yields from TRIC can provide valuable information about obstetrical complications related to abnormal placentation even before clinical symptoms arise. The standardization of this clinical tool is still under investigation, and the upcoming advancements in TRIC are expected to meet the increasing need for a safe and accurate option for prenatal diagnosis.
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Affiliation(s)
- Kirim Hong
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
| | - Hee Jin Park
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
| | - Hee Yeon Jang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (H.Y.J.); (S.H.S.)
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea; (H.Y.J.); (S.H.S.)
| | - Yoon Jang
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
| | - Soo Hyun Kim
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
| | - Dong Hyun Cha
- CHA Gangnam Medical Center, Department of Obstetrics and Gynecology, CHA University, Seoul 06125, Republic of Korea; (K.H.); (H.J.P.); (Y.J.)
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13
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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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14
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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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15
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Luo Y, Xu L, Ma Y, Yan X, Hou R, Huang Y, Liao X, Liu Y, Wang D, Jiang L, Chang Q. Association between the first and second trimester cell free DNA fetal fraction and spontaneous preterm birth. Expert Rev Mol Diagn 2023; 23:635-642. [PMID: 37249149 DOI: 10.1080/14737159.2023.2217331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/19/2023] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To evaluate whether the fetal fraction of cell-free DNA at the first and second trimesters is associated with spontaneous preterm birth. METHODS This was a retrospective cohort study with singleton pregnancies who underwent noninvasive prenatal testing. According to pregnancy outcome, eligible patients were divided into a delivery group ≥37 weeks of pregnancy (term group) and <37 weeks of pregnancy (spontaneous preterm group). Stepwise linear regression was used to identify maternal characteristics associated with the fetal fraction of cell-free DNA. Logistic regression analysis was performed to evaluate the association between the fetal fraction of cell-free DNA and spontaneous preterm birth, adjusted for confounding factors. RESULTS 14,020 cases were included in the study, 13292 cases (94.81%) in the term group and 728 cases (5.19%) in the spontaneous preterm group. The cell-free fraction of fetal DNA was inversely correlated with maternal age and body mass index. Positively correlated with gestational age, fertility, and assisted reproductive technology. After adjusting for the covariates, logistic regression analysis revealed no statistically significant association between the fetal fraction of cell-free DNA and spontaneous preterm birth. CONCLUSION In our original study, we found no association between the fetal fraction on NIPT and subsequent spontaneous preterm birth.
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Affiliation(s)
- Yanmei Luo
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Liang Xu
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yongyi Ma
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xiaoli Yan
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Renke Hou
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yulin Huang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Xueqian Liao
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Yalan Liu
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Dan Wang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Lupin Jiang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Qing Chang
- Department of Gynecology and Obstetrics, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
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16
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Prior-de Castro C, Gómez-González C, Rodríguez-López R, Macher HC. Prenatal genetic diagnosis of monogenic diseases. ADVANCES IN LABORATORY MEDICINE 2023; 4:28-51. [PMID: 37359899 PMCID: PMC10197187 DOI: 10.1515/almed-2023-0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/04/2023] [Indexed: 06/28/2023]
Abstract
Prenatal genetic diagnosis of monogenic diseases is a process involving the use of a variety of molecular techniques for the molecular characterization of a potential monogenic disease in the fetus during pregnancy. Prenatal genetic diagnosis can be performed through invasive and non-invasive methods. A distinction must be made between "NIPD" (non-invasive prenatal diagnosis), which is considered to be diagnostic, from "NIPT" (non-invasive prenatal test), which is a screening test that requires subsequent confirmation by invasive methods. The different techniques currently available aim at detecting either, previously characterized pathogenic mutations in the family, the risk haplotype associated with the familial mutation, or potential pathogenic mutation(s) in a gene associated with a diagnostic suspicion. An overview is provided of relevant aspects of prenatal genetic diagnosis of monogenic diseases. The objective of this paper is to describe the main molecular techniques currently available and used in clinical practice. A description is provided of the indications, limitations and analytical recommendations regarding these techniques, and the standards governing genetic counseling. Continuous rapid advances in the clinical applications of genomics have provided increased access to comprehensive molecular characterization. Laboratories are struggling to keep in pace with technology developments.
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Affiliation(s)
| | | | - Raquel Rodríguez-López
- Laboratorio de Genética, Servicio Análisis Clínicos, Consorcio Hospital General Universitario, Valencia, Spain
| | - Hada C. Macher
- Departamento de Bioquímica Clínica, Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain
- Instituto de Investigaciones Biomédicas de Sevilla, IBIS, Universidad de Sevilla, Sevilla, Spain
| | - on behalf of the Prenatal Diagnosis Commission and the Genetics Commission of the Spanish Society of Laboratory Medicine
- Servicio de Genética, Hospital Universitario La Paz, Madrid, Spain
- Laboratorio de Genética, Servicio Análisis Clínicos, Consorcio Hospital General Universitario, Valencia, Spain
- Departamento de Bioquímica Clínica, Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain
- Instituto de Investigaciones Biomédicas de Sevilla, IBIS, Universidad de Sevilla, Sevilla, Spain
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17
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Shaw J, Scotchman E, Paternoster B, Ramos M, Nesbitt S, Sheppard S, Snowsill T, Chitty LS, Chandler N. Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches. Prenat Diagn 2023; 43:477-488. [PMID: 36760169 DOI: 10.1002/pd.6333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
OBJECTIVES To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches. METHODS Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses. RESULTS The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus. CONCLUSIONS ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.
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Affiliation(s)
- Joe Shaw
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Ben Paternoster
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Maureen Ramos
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sarah Nesbitt
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sophie Sheppard
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | | | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
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18
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Qiao L, Cao X, Tang H, Yu Z, Shi J, Xue Y, Wang T, Liang Y, Huang C, Wang J. White blood cell count affects fetal fraction and test failure rates in noninvasive prenatal screening. Front Med (Lausanne) 2023; 10:1088745. [PMID: 36817785 PMCID: PMC9932807 DOI: 10.3389/fmed.2023.1088745] [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: 11/03/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Objective To investigate the effects of white blood cell (WBC) count on fetal fraction (FF), which is an essential quality control for obtaining reliable results, and on the rate of screen failures in noninvasive prenatal screening (NIPS). Methods Noninvasive prenatal screening, serum lipid and liver enzyme level measurements, and WBC count were performed for 4,281 pregnancies with male fetuses. After adjusting for confounders, including the maternal characteristics and alanine aminotransferase (ALT) levels, the effect of WBC count on FF and test failure rate was measured by linear and logistic regression analyses. Results Fetal fraction was negatively associated with BMI, ALT, IVF conceptions, and WBC count and positively correlated with gestational age in the multivariate linear regression model. Moreover, WBC count was the most important factor affecting FF after BMI according to the standardization coefficient analysis. In the 4,281 pregnancy samples with male fetuses, FF decreased with WBC count from 11.45% at ≤8 to 9.02% at >12, and FF markedly decreased to 7.40% in pregnancies with a higher WBC count (>12) and higher BMI (≥25 kg/m2). Meanwhile, the test failure rates were significantly higher in the WBC count > 12 group (4.29%) than in the WBC count ≤ 8 group (0.89%). Notably, when the BMI of pregnancies with a WBC count of >12 was >25, the rate reached 7.53%. Subsequently, multivariate logistic regression analysis further confirmed that an increased BMI and WBC count were independently and significantly associated with the test failure rates. Conclusion An increased WBC count was associated with lower FF and higher test failure rates, suggesting that these important factors should be carefully considered during genetic counseling in pregnant women who decide to undergo blood collection or resampling.
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Affiliation(s)
- Longwei Qiao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - XiaoJu Cao
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Haoyu Tang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zheng Yu
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jingye Shi
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ying Xue
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ting Wang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yuting Liang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
| | - Chao Huang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
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Deng C, Liu J, Liu S, Liu H, Bai T, Jing X, Xia T, Liu Y, Cheng J, Wei X, Xing L, Luo Y, Zhou Q, Zhu Q, Liu S. Maternal and fetal factors influencing fetal fraction: A retrospective analysis of 153,306 pregnant women undergoing noninvasive prenatal screening. Front Pediatr 2023; 11:1066178. [PMID: 37114008 PMCID: PMC10126334 DOI: 10.3389/fped.2023.1066178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
Background Genetic factors are important causes of birth defects. Noninvasive prenatal screening (NIPS) is widely used for prenatal screening of trisomy 21, trisomy 18, and trisomy 13, which are the three most common fetal aneuploidies. Fetal fraction refers to the proportion of cell-free fetal DNA in maternal plasma, which can influence the accuracy of NIPS. Elucidating the factors that influence fetal fraction can provide guidance for the interpretation of NIPS results and genetic counseling. However, there is currently no broad consensus on the known factors that influence fetal fraction. Objective The study aimed to explore the maternal and fetal factors influencing fetal fraction. Methods A total of 153,306 singleton pregnant women who underwent NIPS were included. Data on gestational age; maternal age; body mass index (BMI); z-scores for chromosomes 21, 18, and 13; and fetal fraction in NIPS were collected from the study population, and the relationships between fetal fraction and these factors were examined. The relationship between fetal fraction and different fetal trisomy types was also analyzed. Results The results showed that the median gestational age, maternal age, and BMI of the pregnant women were 18 (16, 20) weeks, 29 (25, 32) years, and 22.19 (20.40, 24.24) kg/m2, respectively. The median fetal fraction was 11.62 (8.96, 14.7)%. Fetal fraction increased with gestational age and decreased with maternal age and BMI (P < 0.001). Fetal fraction of fetuses with trisomies 21, 18, and 13 was similar to that of the NIPS-negative group. The z-scores of pregnant women with trisomy 21 and 18 fetuses were positively correlated with fetal fraction, but not with that of the trisomy 13 cases. Conclusions The factors that influence fetal fraction need to be taken into consideration before NIPS for quality control and after NIPS for result interpretation.
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Affiliation(s)
- Cechuan Deng
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jianlong Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Sha Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hongqian Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Ting Bai
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiaosha Jing
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Tianyu Xia
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yunyun Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Jing Cheng
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiang Wei
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Lingling Xing
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yuan Luo
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Quanfang Zhou
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Qian Zhu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- Correspondence: Qian Zhu Shanling Liu
| | - Shanling Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
- Correspondence: Qian Zhu Shanling Liu
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Mousavi S, Shokri Z, Bastani P, Ghojazadeh M, Riahifar S, Nateghian H. Factors affecting low fetal fraction in fetal screening with cell-free DNA in pregnant women: a systematic review and meta-analysis. BMC Pregnancy Childbirth 2022; 22:918. [PMID: 36482322 PMCID: PMC9733315 DOI: 10.1186/s12884-022-05224-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Cell-Free DNA (cfDNA) is a non-invasive perinatal test (NIPT) used to assess fetal anomalies. The ability to detect fetal chromosomal aneuploidies is directly related to a sample's fetal to total DNA fraction, known as the fetal fraction (FF). The minimum FF is considered 4%, and the test result below 4% is uncertain due to low fetal fraction (LFF). This study aimed to conduct a systematic review and a meta-analysis to determine the possible factors affecting LFF in cfDNA testing for fetal screening. METHODS PubMed, Web of Science, Google Scholar, Since Direct, Scopus, CINHAL, Cochrane Library, and Persian databases, including Scientific Information Database, Irandoc, and Magiran were searched for studies investigating factors affecting LFF in cfDNA testing from 2000 until the end of 2021. Gathered data were analyzed using Comprehensive Meta-Analysis (CMA) software version 3.3.070. The quality of the included studies was assessed using the Joanna Briggs Institute Critical Appraisal of Cohort Studies tool. RESULTS Thirteen articles related to the topic were included, and seven related articles were reviewed for meta-analysis. The other six were reviewed qualitatively. Four factors were identified that might have a potential effect on the LFF, of which only gestational age had a significant association with LFF (Pooled mean difference= -1.111, SE = 0.515, 95% CI= -2.121, -0.101, (P-value < 0.05)). Maternal age (P-value = 0.573), maternal weight (P-value = 0.113), and Body Mass Index (P-value = 0.104) had no statically significant effect. The effect size was pooled by mean difference and 95% confidence interval. CONCLUSION Lower gestational age is significantly associated with LFF. Thus, this factor can be considered when interpreting prenatal cfDNA screening tests.
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Affiliation(s)
- Sanaz Mousavi
- grid.412888.f0000 0001 2174 8913Department of Gynecology and Obstetrics, Al-Zahra Hospital, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ziba Shokri
- grid.412888.f0000 0001 2174 8913Department of Gynecology and Obstetrics, Al-Zahra Hospital, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parvin Bastani
- grid.412888.f0000 0001 2174 8913Department of Gynecology and Obstetrics, Al-Zahra Hospital, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Ghojazadeh
- grid.412888.f0000 0001 2174 8913Research Center for Evidence‑Based Medicine, Iranian EBM Centre: A Joanna Briggs Institute Affiliated Group, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sevda Riahifar
- grid.411746.10000 0004 4911 7066Department of Biostatistics, Faculty of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Hooman Nateghian
- grid.412888.f0000 0001 2174 8913Research Center for Evidence‑Based Medicine, Iranian EBM Centre: A Joanna Briggs Institute Affiliated Group, Tabriz University of Medical Sciences, Tabriz, Iran
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21
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Yang SY, Kang KM, Kim SY, Lim SY, Jang HY, Hong K, Cha DH, Shim SH, Joung JG. Combined Model-Based Prediction for Non-Invasive Prenatal Screening. Int J Mol Sci 2022; 23:ijms232314990. [PMID: 36499318 PMCID: PMC9737181 DOI: 10.3390/ijms232314990] [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: 11/01/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022] Open
Abstract
The risk of chromosomal abnormalities in the child increases with increasing maternal age. Although non-invasive prenatal testing (NIPT) is a safe and effective prenatal screening method, the accuracy of the test results needs to be improved owing to various testing conditions. We attempted to achieve a more accurate and robust prediction of chromosomal abnormalities by combining multiple methods. Here, three different methods, namely standard Z-score, normalized chromosome value, and within-sample reference bin, were used for 1698 reference and 109 test samples of whole-genome sequencing. The logistic regression model combining the three methods achieved a higher accuracy than any single method. In conclusion, the proposed method offers a promising approach for increasing the reliability of NIPT.
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Affiliation(s)
- So-Yun Yang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Kyung Min Kang
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
| | - Sook-Young Kim
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam 13488, Republic of Korea
| | - Seo Young Lim
- Department of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea
| | - Hee Yeon Jang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
| | - Kirim Hong
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Dong Hyun Cha
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, CHA University, Seoul 06135, Republic of Korea
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- Center for Genome Diagnostics, CHA Biotech Inc., Seoul 06135, Republic of Korea
- Correspondence: (S.H.S.); (J.-G.J.); Tel.: +82-31-881-7182 (J.-G.J.); +82-31-881-7148 (S.H.S.)
| | - Je-Gun Joung
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam 13488, Republic of Korea
- Institute for Biomedical Informatics, CHA University School of Medicine, CHA University, Seongnam 13488, Republic of Korea
- Correspondence: (S.H.S.); (J.-G.J.); Tel.: +82-31-881-7182 (J.-G.J.); +82-31-881-7148 (S.H.S.)
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22
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Hanson B, Scotchman E, Chitty LS, Chandler NJ. Non-invasive prenatal diagnosis (NIPD): how analysis of cell-free DNA in maternal plasma has changed prenatal diagnosis for monogenic disorders. Clin Sci (Lond) 2022; 136:1615-1629. [PMID: 36383187 PMCID: PMC9670272 DOI: 10.1042/cs20210380] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 07/30/2023]
Abstract
Cell-free fetal DNA (cffDNA) is released into the maternal circulation from trophoblastic cells during pregnancy, is detectable from 4 weeks and is representative of the entire fetal genome. The presence of this cffDNA in the maternal bloodstream has enabled clinical implementation of non-invasive prenatal diagnosis (NIPD) for monogenic disorders. Detection of paternally inherited and de novo mutations is relatively straightforward, and several methods have been developed for clinical use, including quantitative polymerase chain reaction (qPCR), and PCR followed by restriction enzyme digest (PCR-RED) or next-generation sequencing (NGS). A greater challenge has been in the detection of maternally inherited variants owing to the high background of maternal cell-free DNA (cfDNA). Molecular counting techniques have been developed to measure subtle changes in allele frequency. For instance, relative haplotype dosage analysis (RHDO), which uses single nucleotide polymorphisms (SNPs) for phasing of high- and low-risk alleles, is clinically available for several monogenic disorders. A major drawback is that RHDO requires samples from both parents and an affected or unaffected proband, therefore alternative methods, such as proband-free RHDO and relative mutation dosage (RMD), are being investigated. cffDNA was thought to exist only as short fragments (<500 bp); however, long-read sequencing technologies have recently revealed a range of sizes up to ∼23 kb. cffDNA also carries a specific placental epigenetic mark, and so fragmentomics and epigenetics are of interest for targeted enrichment of cffDNA. Cell-based NIPD approaches are also currently under investigation as a means to obtain a pure source of intact fetal genomic DNA.
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Affiliation(s)
- Britt Hanson
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
| | - Lyn S. Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
- Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, U.K
| | - Natalie J. Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, U.K
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Jiang Y, Zhang Y, Yang Q, Zeng D, Zhao K, Ma X, Yin W. The association between fetal fraction and pregnancy-related complications among Chinese population. PLoS One 2022; 17:e0271219. [PMID: 35819933 PMCID: PMC9275705 DOI: 10.1371/journal.pone.0271219] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/25/2022] [Indexed: 11/18/2022] Open
Abstract
To examine the association of fetal fraction with a wide spectrum of pregnancy-related complications among Chinese population, we carried out a single-institution retrospective cohort study of women with negative Noninvasive prenatal testing (NIPT) results and singleton pregnancies between May 2018 and May 2020. Indicators of pregnancy-related complications were examined individually, including preterm birth, low birth weight, hypertensive disorders of pregnancy, gestational diabetes, oligohydramnios and intrahepatic cholestasis. We evaluated disease odds ratios (ORs) and 95% confidence intervals (CIs), after controlling for potential confounders including body mass index (BMI), maternal age and gestational week at NIPT. A total of 3534 women were included in our analyses. Women with fetal fraction<15.15% had increased risk of gestational hypertension (OR 4.41, CI [1.65, 12.45]) and oligohydramnios (OR 2.26, CI [1.33, 3.80]) compared to women with fetal fraction≥15.15%. No significant associations with fetal fraction were found for preterm birth, low birth weight, gestational diabetes, and intrahepatic cholestasis. In Summary, fetal fraction is inversely associated with the risk of gestational hypertension and oligohydramnios.
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Affiliation(s)
- Yan Jiang
- Department of Obstetrics, Mianyang People’s Hospital, Mianyang, Sichuan, China
| | | | - Qin Yang
- Department of Clinical Laboratory, Mianyang People’s Hospital, Mianyang, Sichuan, China
| | - Dan Zeng
- Chengdu CapitalBio Technology Co., Ltd., Chengdu, Sichuan, China
| | | | - Xin Ma
- GenomCan Inc., Chengdu, Sichuan, China
- Department of Statistics, Stanford University, Stanford, CA, United States of America
- * E-mail: (XM); (WY)
| | - Wei Yin
- Department of Obstetrics, Mianyang People’s Hospital, Mianyang, Sichuan, China
- * E-mail: (XM); (WY)
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