1
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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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2
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Gabrielli F, Papa FT, Di Pietro F, Paytuví-Gallart A, Julian D, Sanseverino W, Alfonsi C. MaterniCode: New Bioinformatic Pipeline to Detect Fetal Aneuploidies and Rearrangements Using Next-Generation Sequencing. Int J Genomics 2024; 2024:8859058. [PMID: 38962150 PMCID: PMC11221998 DOI: 10.1155/2024/8859058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 05/16/2024] [Accepted: 05/23/2024] [Indexed: 07/05/2024] Open
Abstract
Objective: The present study is aimed at introducing and evaluating MaterniCode, a state-of-the-art bioinformatic pipeline for noninvasive prenatal testing (NIPT) that leverages the Ion Torrent semiconductor sequencing platform. The initiative strives to revolutionize prenatal diagnostics by offering a rapid and cost-effective method without sacrificing accuracy. Methods: Two distinct bioinformatic strategies were employed for fetal sex determination, one of which achieved 100% accuracy. We analyzed 1225 maternal blood samples for fetal aneuploidies, benchmarking against the industry standard Illumina VeriSeq™ NIPT Solution v2. The capability of MaterniCode to detect and characterize complex chromosomal anomalies was also assessed. Results: MaterniCode achieved near-perfect accuracy in fetal sex determination through chromosome Y (chrY )-specific gene analysis, whereas the alternative method, employing the ratio of high-quality mapped reads on chrY relative to all reads, delivered 100% accuracy. For fetal aneuploidy detection, both the integrated WisecondorX and NIPTeR algorithms demonstrated a 100% sensitivity and specificity rate, consistent with Illumina VeriSeq™ NIPT Solution v2. The pipeline also successfully identified and precisely mapped significant chromosomal abnormalities, exemplified by a 2.4 Mb deletion on chromosome 13 and a 3 Mb duplication on chromosome 2. Conclusion: MaterniCode has proven to be an innovative and highly efficient tool in the domain of NIPT, demonstrating excellent sensitivity and specificity. Its robust capability to effectively detect a wide range of complex chromosomal aberrations, including rare and subtle variations, positions it as a promising and valuable addition to prenatal diagnostic technologies. This enhancement to diagnostic precision significantly aids clinicians in making informed decisions during pregnancy management.
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Affiliation(s)
- Federico Gabrielli
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | - Filomena Tiziana Papa
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | - Fabio Di Pietro
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
| | | | - Daniel Julian
- Sequentia Biotech SL, C/del Dr. Trueta, 179 08005, Barcelona, Spain
| | | | - Cinzia Alfonsi
- Biolab srl, Laboratorio di Genetica molecolare e Genomica 63100, Ascoli Piceno, Italy
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3
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Koukou Z, Panteris E, Manolakos E, Papadopoulos A, Papoulidis I, Relakis K, Sifakis S. Cell‑free fetal DNA at 11‑13 weeks of gestation is not altered in complicated pregnancies. Biomed Rep 2024; 20:69. [PMID: 38495346 PMCID: PMC10941718 DOI: 10.3892/br.2024.1757] [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: 06/19/2023] [Accepted: 12/13/2023] [Indexed: 03/19/2024] Open
Abstract
Non-invasive maternal cell-free fetal DNA (cffDNA) is a promising biomarker for screening common genetic syndromes. Alterations in the expression levels of cffDNA in the maternal circulation have been demonstrated in abnormal pregnancies. However, the results are conflicting. The present study aimed to investigate whether cffDNA levels are associated with pregnancy complications. The study group comprised pregnant women who presented with pregnancy complications, such as preterm birth, gestational hypertension, intrauterine growth retardation, gestational diabetes, polyhydramnios, oligohydramnios, vaginal bleeding and placental abruption. The control group comprised women who had a normal pregnancy course. Blood samples were obtained from 500 pregnant women between 11-13 weeks of gestation. cffDNA was amplified, sequenced and analyzed using the next-generation aneuploidy test of a Panorama-Natera kit. Nuchal translucency (NT) thickness as well as pregnancy associated plasma protein-A (PAPP-A) and β-human chorionic gonadotropin (β-hCG) levels were also assessed. Statistical analysis was performed in 494 out of the 500 samples collected with SPSS v.26 using non-parametric methods. The parameters were normalized by the multiples of median (MoM) method. The expression levels of PAPP-A, β-hCG, and the NT mean MoM values were significantly different between the study and control groups (P=0.005, P<0.001 and P=0.007, respectively). However, the expression levels of cffDNA and the mean MoM values were not significantly different between these two groups (P=0.687). The findings of the present study support the conclusion that cffDNA expression is not altered in a series of pregnancy complications. The prognostic value of cffDNA in predicting adverse pregnancy outcomes requires further investigation.
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Affiliation(s)
- Zoi Koukou
- School of Health Sciences, International Hellenic University (IHU), 57400 Thessaloniki, Greece
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, 71500 Heraklion, Greece
| | - Eleftherios Panteris
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Emmanouel Manolakos
- Access to Genome P.C., Clinical Laboratory Genetics, 11528 Thessaloniki, Greece
| | | | - Ioannis Papoulidis
- Access to Genome P.C., Clinical Laboratory Genetics, 11528 Thessaloniki, Greece
| | - Konstantinos Relakis
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, 71500 Heraklion, Greece
| | - Stavros Sifakis
- Department of Obstetrics and Gynecology, University Hospital of Heraklion, 71500 Heraklion, Greece
- Mitera Maternity Hospital, 71202 Heraklion, Greece
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4
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Wang Y, Qiu X, Chen S, Pan D, Hua R, Li S, Chen Y, Pan N, Cai X, Li J, Zhao X, Wang J, Jing R, Xiang G, Zhang Z, Huang HF, Xu C, Zhang J. Noninvasive Evaluation of Fetal Zygosity in Twin Pregnancies Involving a Binary Analysis of Single-Nucleotide Polymorphisms. J Mol Diagn 2023; 25:682-691. [PMID: 37599029 DOI: 10.1016/j.jmoldx.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 05/03/2023] [Accepted: 06/01/2023] [Indexed: 08/22/2023] Open
Abstract
Twin pregnancy constitutes significant risks for maternal and fetal health, which is usually detected by ultrasound examination at early gestation. However, the imaging-based approach may not accurately identify all twins confounded by practical or clinical variables. The analysis of fetal cell-free DNA in noninvasive prenatal screening assays can completement the ultrasound method for twin detection, which differentiates fraternal or identical twins based on their distinct genotypes. Here, a new noninvasive prenatal screening employing high-coverage next-generation sequencing for targeted nucleotide polymorphisms was developed for detection of zygosity and determination of fetal fraction in twin pregnancies. This method utilizes a binary analysis of both the number and allelic fraction of fetus-specific single-nucleotide polymorphisms to infer the zygosity. In 323 samples collected from 215 singleton, 90 dizygotic, and 18 monozygotic twin pregnancies, all 90 dizygotic twins were correctly detected, with a 100% sensitivity and a 100% specificity. In addition, this method can detect complex pregnancies, such as egg donors, contamination, and twins with complete hydatidiform mole. The fetus-specific fetal fraction change was monitored in nine dizygotic twin pregnancies, which demonstrated highly variable dynamics of fetal cell-free DNA turnover up to 7 weeks after twin reduction. Overall, this study provides a new noninvasive prenatal screening strategy for the accurate identification of twin zygosity and quantification of fetal fraction, which has important clinical implications for the management of twin pregnancies.
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Affiliation(s)
- Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Dong Pan
- Beijing BioBiggen Technology Co., Ltd., Beijing, China
| | - Renyi Hua
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd., Beijing, China
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd., Beijing, China
| | - Xin Zhao
- Beijing BioBiggen Technology Co., Ltd., Beijing, China
| | - Jing Wang
- Beijing BioBiggen Technology Co., Ltd., Beijing, China
| | - Ruilin Jing
- Beijing BioBiggen Technology Co., Ltd., Beijing, China
| | - Guangxin Xiang
- Beijing BioBiggen Technology Co., Ltd., Beijing, China; School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd., Beijing, China
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China; Beijing BioBiggen Technology Co., Ltd., Beijing, China.
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5
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Benn P, Cuckle H. Overview of Noninvasive Prenatal Testing (NIPT) for the Detection of Fetal Chromosome Abnormalities; Differences in Laboratory Methods and Scope of Testing. Clin Obstet Gynecol 2023; 66:536-556. [PMID: 37650667 DOI: 10.1097/grf.0000000000000803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Although nearly all noninvasive prenatal testing is currently based on analyzing circulating maternal cell-free DNA, the technical methods usedvary considerably. We review the different methods. Based on validation trials and clinical experience, there are mostly relatively small differences in screening performance for trisomies 21, 18, and 13 in singleton pregnancies. Recent reports show low no-call rates for all methods, diminishing its importance when choosing a laboratory. However, method can be an important consideration for twin pregnancies, screening for sex chromosome abnormalities, microdeletion syndromes, triploidy, molar pregnancies, rare autosomal trisomies, and segmental imbalances, and detecting maternal chromosome abnormalities.
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Affiliation(s)
- Peter Benn
- Department of Obstetrics and Gynecology, University of Connecticut Health Center, Farmington, Connecticut
| | - Howard Cuckle
- Department of Obstetrics and Gynecology, Faculty of Medicine, Tel Aviv University, Israel
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6
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Norton ME. Cell-free DNA Screening for Aneuploidy. Clin Obstet Gynecol 2023; 66:557-567. [PMID: 37650668 DOI: 10.1097/grf.0000000000000796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Cell-free DNA (cfDNA) screening has high detection for the common fetal autosomal aneuploidies, but is not diagnostic. The positive predictive value should be utilized in counseling after a positive cell-free DNA screen, and diagnostic testing should be offered for confirmation. cfDNA screening does not report a result in ~3% of cases; nonreportable results indicate an increased risk for aneuploidy and some adverse perinatal outcomes. False-positive cfDNA screening occurs due to confined placental mosaicism, maternal copy number variants, mosaicism, and cancer. Pretest education and counseling should be provided with emphasis on the potential benefits, risks, and limitations before cfDNA screening.
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Affiliation(s)
- Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California
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7
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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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8
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Zhao Q, Chen J, Ren L, Zhang H, Liu D, Xi X, Wu X, Fang C, Ye P, Zeng S, Zhong T. Two cases of placental trisomy 21 mosaicism causing false-negative NIPT results. Mol Cytogenet 2023; 16:16. [PMID: 37452352 PMCID: PMC10347865 DOI: 10.1186/s13039-023-00643-3] [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: 04/07/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) using cell-free DNA has been widely used for prenatal screening to detect the common fetal aneuploidies (such as trisomy 21, 18, and 13). NIPT has been shown to be highly sensitive and specific in previous studies, but false positives (FPs) and false negatives (FNs) occur. Although the prevalence of FN NIPT results for Down syndrome is rare, the impact on families and society is significant. CASE PRESENTATION This article described two cases of foetuses that tested "negative" for trisomy 21 by NIPT technology using the semiconductor sequencing platform. However, the fetal karyotypes of amniotic fluid were 46,XY, + 21 der(21;21)(q10;q10) and 47,XY, + 21 karyotypes, respectively. Placental biopsies confirmed that, in the first case, the chromosome 21 placenta chimerism ratio ranged from 13 to 88% with the 46,XX, + 21,der(21;21)(q10;q10)[86]/46,XX[14] karyotype of placental chorionic cells (middle of fetal-side placental tissue). However, in the second case, of all the placental biopsies, percentage of total chimerism was less than 30%; and placental biopsies taken at the middle of maternal side and middle of fetal side, also had variable trisomy 2 mosaicism levels of 10% and 8%, respectively. Ultimately, the pregnancies were interrupted at 30 gestational age (GA) and 27GA, respectively. CONCLUSIONS In this study, we present two cases of FN NIPT results that might have been caused by biological mechanisms, as opposed to poor quality, technical errors, or negligence. Clinical geneticists and their patients must understand that NIPT is a screening procedure.
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Affiliation(s)
- Qinfei Zhao
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Jing Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Ling Ren
- Department of Ultrasound, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Huijuan Zhang
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Dedong Liu
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Xuxiang Xi
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Xiangsheng Wu
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Chunyun Fang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Ping Ye
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Shaoying Zeng
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China.
| | - Tianyu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China.
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Cai M, Lin N, Chen X, Li Y, Lin M, Fu X, Huang H, He S, Xu L. Non-invasive prenatal testing for the diagnosis of congenital abnormalities: Insights from a large multicenter study in southern China. Braz J Med Biol Res 2023; 56:e12506. [PMID: 37377305 DOI: 10.1590/1414-431x2023e12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/04/2023] [Indexed: 06/29/2023] Open
Abstract
Although non-invasive prenatal testing (NIPT) is widely used to detect fetal abnormalities, the results of NIPT vary by population, and data for the screening efficiency of NIPT positive predictive value (PPV) from different populations is limited. Herein, we retrospectively analyzed the NIPT results in a large multicenter study involving 52,855 pregnant women. Depending on gestational age, amniotic fluid or umbilical cord blood was extracted for karyotype and/or chromosome microarray analysis (CMA) in NIPT-positive patients, and the PPV and follow-up data were evaluated to determine its clinical value. Among the 52,855 cases, 754 were NIPT-positive, with a positivity rate of 1.4%. Karyotype analysis and/or CMA confirmed 323 chromosomal abnormalities, with a PPV of 45.1%. PPV for trisomy 21 (T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosomal aneuploidies (SCAs), and copy number variations (CNVs) were 78.9, 35.3, 22.2, 36.9, and 32.9%, respectively. The PPVs for T21, T18, and T13 increased with age, whereas the PPVs for SCAs and CNVs had little correlation with age. The PPV was significantly higher in patients with advanced age and abnormal ultrasound. The NIPT results are affected by population characteristics. NIPT had a high PPV for T21 and a low PPV for T13 and T18, and screening for SCAs and CNVs showed clinical significance in southern China.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xianguo Fu
- Department of Prenatal Diagnosis, Ningde Municipal Hospital, Ningde Normal University, Ningde, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shuqiong He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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10
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Hui L, Ellis K, Mayen D, Pertile MD, Reimers R, Sun L, Vermeesch J, Vora NL, Chitty LS. Position statement from the International Society for Prenatal Diagnosis on the use of non-invasive prenatal testing for the detection of fetal chromosomal conditions in singleton pregnancies. Prenat Diagn 2023; 43:814-828. [PMID: 37076973 DOI: 10.1002/pd.6357] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/15/2023] [Indexed: 04/21/2023]
Abstract
Key points
What is already known about this topic?
In 2015, the International Society for Prenatal Diagnosis (ISPD) published its first position statement on the use of non‐invasive prenatal testing (NIPT) to screen for aneuploidy. Widespread uptake across the globe and subsequent published research has shed new light on test performance and implementation issues.
What does this study add?
This new position statement replaces the 2015 statement with updated information on the current technologies, clinical experience, and implementation practices.
As an international organization, ISPD recognizes that there are important population‐specific considerations in the organization of prenatal screening and diagnosis. These opinions are designed to apply to high income settings where prenatal screening for aneuploidy is an established part of antenatal care.
This position statement is not a clinical practice guideline but represents the consensus opinion of the current ISPD Board based on the current state of knowledge and clinical practice.
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Affiliation(s)
- Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia
- Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria, Australia
| | - Katie Ellis
- Illumina ANZ, Sydney, New South Wales, Australia
| | - Dora Mayen
- Genetics Clinic, Hospital Angeles Lomas, Estado de Mexico, Mexico
| | - Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Rebecca Reimers
- San Diego Perinatal Center, Rady Children's Hospital, San Diego, California, USA
- Scripps Research Institute, La Jolla, California, USA
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | | | - Neeta L Vora
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Division of Maternal Fetal Medicine, Chapel Hill, North Carolina, USA
| | - Lyn S Chitty
- Great Ormond Street NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
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11
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Goldring G, Trotter C, Meltzer JT, Souter V, Pais L, DiNonno W, Xu W, Weitzel JN, Vora NL. Maternal Malignancy After Atypical Findings on Single-Nucleotide Polymorphism-Based Prenatal Cell-Free DNA Screening. Obstet Gynecol 2023; 141:791-800. [PMID: 36897127 PMCID: PMC10026947 DOI: 10.1097/aog.0000000000005107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/15/2022] [Indexed: 03/11/2023]
Abstract
OBJECTIVE To evaluate the incidence and clinical outcomes of cell-free DNA results suspicious for maternal malignancy on prenatal cell-free DNA screening with single-nucleotide polymorphism (SNP)-based technology. METHODS This retrospective cohort study included data from SNP-based, noninvasive prenatal screening samples from a commercial laboratory from January 2015 to October 2021. Maternal plasma was screened for trisomy 21, 18, and 13; monosomy X; and triploidy. Cases were considered suspicious for maternal malignancy if retrospective bioinformatics and visual inspection of the SNP plot were suggestive of multiple maternal copy number variants across at least two of the tested chromosomes. Clinical follow-up on patients was obtained by contacting individual referring clinician offices by telephone, facsimile, or email. RESULTS A total of 2,004,428 noninvasive prenatal screening samples during the study period met criteria for inclusion in the analysis. Of these, 38 samples (0.002% or 1 in 52,748, 95% CI 1:74,539-1:38,430) had SNP-plot results that were suspicious for maternal malignancy. Maternal health outcomes were obtained in 30 of these patients (78.9%); eight were lost to follow-up. Maternal malignancy or suspected malignancy was identified in 66.7% (20/30) of the 30 patients with clinical follow-up provided by the clinic. The most common maternal malignancies were lymphoma (n=10), breast cancer (n=5), and colon cancer (n=3). CONCLUSION Results suspicious for maternal malignancy are rare with SNP-based noninvasive prenatal screening (1:53,000), but two thirds of patients who had a noninvasive prenatal screening result concerning for malignancy in this study had a cancer diagnosis. Investigation for malignancy should be recommended for all pregnant patients with this type of result. FUNDING SOURCE This study was funded by Natera, Inc.
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Affiliation(s)
- Georgina Goldring
- Natera, Inc., Austin, Texas; and the Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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12
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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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13
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Lee J, Lee SM, Ahn JM, Lee TR, Kim W, Cho EH, Ki CS. Development and performance evaluation of an artificial intelligence algorithm using cell-free DNA fragment distance for non-invasive prenatal testing (aiD-NIPT). Front Genet 2022; 13:999587. [DOI: 10.3389/fgene.2022.999587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/30/2022] Open
Abstract
With advances in next-generation sequencing technology, non-invasive prenatal testing (NIPT) has been widely implemented to detect fetal aneuploidies, including trisomy 21, 18, and 13 (T21, T18, and T13). Most NIPT methods use cell-free DNA (cfDNA) fragment count (FC) in maternal blood. In this study, we developed a novel NIPT method using cfDNA fragment distance (FD) and convolutional neural network-based artificial intelligence algorithm (aiD-NIPT). Four types of aiD-NIPT algorithm (mean, median, interquartile range, and its ensemble) were developed using 2,215 samples. In an analysis of 17,678 clinical samples, all algorithms showed >99.40% accuracy for T21/T18/T13, and the ensemble algorithm showed the best performance (sensitivity: 99.07%, positive predictive value (PPV): 88.43%); the FC-based conventional Z-score and normalized chromosomal value showed 98.15% sensitivity, with 40.77% and 36.81% PPV, respectively. In conclusion, FD-based aiD-NIPT was successfully developed, and it showed better performance than FC-based NIPT methods.
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14
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Kamath V, Chacko MP, Kamath MS. Non-invasive Prenatal Testing in Pregnancies Following Assisted Reproduction. Curr Genomics 2022; 23:326-336. [PMID: 36778193 PMCID: PMC9878858 DOI: 10.2174/1389202923666220518095758] [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: 12/23/2021] [Revised: 03/17/2022] [Accepted: 04/05/2022] [Indexed: 11/22/2022] Open
Abstract
In the decade since non-invasive prenatal testing (NIPT) was first implemented as a prenatal screening tool, it has gained recognition for its sensitivity and specificity in the detection of common aneuploidies. This review mainly focuses on the emerging role of NIPT in pregnancies following assisted reproductive technology (ART) in the light of current evidence and recommendations. It also deals with the challenges, shortcomings and interpretational difficulties related to NIPT in ART pregnancies, with particular emphasis on twin and vanishing twin pregnancies, which are widely regarded as the Achilles' heel of most pre-natal screening platforms. Future directions for exploration towards improving the performance and extending the scope of NIPT are also addressed.
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Affiliation(s)
- Vandana Kamath
- Department of Cytogenetics, Christian Medical College, Vellore 632004, India
| | - Mary Purna Chacko
- Department of Cytogenetics, Christian Medical College, Vellore 632004, India
| | - Mohan S. Kamath
- Department of Reproductive Medicine and Surgery, Christian Medical College, Vellore 632004, India,Address correspondence to this author at the Department of Reproductive Medicine and Surgery, Christian Medical College, Vellore, Tamil Nadu 632004, India; Tel: 91-416-2283301; E-mail:
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15
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Xu C, Li J, Chen S, Cai X, Jing R, Qin X, Pan D, Zhao X, Ma D, Xu X, Liu X, Wang C, Yang B, Zhang L, Li S, Chen Y, Pan N, Tang P, Song J, Liu N, Zhang C, Zhang Z, Qiu X, Lu W, Ying C, Li X, Xu C, Wang Y, Wu Y, Huang HF, Zhang J. Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening. Cell Discov 2022; 8:109. [PMID: 36229437 PMCID: PMC9562363 DOI: 10.1038/s41421-022-00457-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Current non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed coordinative allele-aware target enrichment sequencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders.
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Affiliation(s)
- Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ruilin Jing
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dong Pan
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xin Zhao
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dongyang Ma
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiufeng Xu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaojun Liu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Can Wang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Tang
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Beijing BioBiggen Technology Co., Ltd, Beijing, China.
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16
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Wojas A, Martin KA, Koyen Malashevich A, Hashimoto K, Parmar S, White R, Demko Z, Billings P, Jelsema R, Rebarber A. Clinician-reported Chorionicity and Zygosity Assignment using single-nucleotide polymorphism-based cell-free DNA Lessons learned from 55,344 Twin Pregnancies. Prenat Diagn 2022; 42:1235-1241. [PMID: 35997139 PMCID: PMC9541063 DOI: 10.1002/pd.6218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/06/2022] [Accepted: 07/26/2022] [Indexed: 11/21/2022]
Abstract
Objective Prenatal chorionicity assessment relies on ultrasound, which can be confounded by many factors. Noninvasive assessment of zygosity is possible using single nucleotide polymorphism (SNP)‐based cell‐free DNA testing. Our objective was to determine the relationship between provider‐reported chorionicity and SNP‐cfDNA assignment of twin zygosity. Methods All twin pregnancy blood samples received by a reference laboratory between September 27, 2017 and September 8, 2021 were included. Chorionicity assignment was requested on the requisition, recorded as; monochorionic (MC), dichorionic, or “don't know”. SNP‐cfDNA zygosity results, monozygotic (MZ) or dizygotic (DZ), were correlated with chorionicity assignment. Results 59,471 twin samples (median gestational age = 12.0 weeks at draw) were received and analyzed; 55,344 (93.1%) received zygosity assignment. SNP‐cfDNA reported 16,673 (30.1%) MZ and 38,671 (69.9%) as DZ. Provider‐reported chorionicity was compared to the zygosity assignment for each case. Of 6283 provider‐reported MC twins, 318 (5.1%) were reported as DZ using SNP‐cfDNA. Conclusion(s) One in 20 suspected MC twin pregnancies were reported as DZ using SNP‐cfDNA. Approximately 30% of 55,344 twin pregnancies were found to be MZ, including cases where chorionicity was unknown. SNP‐cfDNA zygosity assessment is a useful adjunct assessment for twin pregnancies, particularly those reported as MC or without determined chorionicity. What's already known about the topic? The assignment of chorionicity early in pregnancy can improve perinatal outcomes of twin pregnancies. Prenatal assessment of chorionicity relies on ultrasound (US), and the accuracy of US can be confounded by many factors, including gestational age (GA) and operator experience. Noninvasive assessment of zygosity is now possible using single nucleotide polymorphism (SNP)‐based cell‐free DNA (cfDNA).
What does this study add? This is the first population‐based study describing the correlation between cfDNA assessment of zygosity and chorionicity. In 55,344 twin pregnancies, approximately 30% were found to be monozygotic (MZ), including cases where chorionicity was unknown. We found that one in 20 suspected monochorionic (MC) twin pregnancies were reported as dizygotic (DZ) twins (DZ) by SNP‐cfDNA testing. SNP‐cfDNA zygosity assessment is a useful adjunct assessment for twin pregnancies, particularly those reported as MC or without determined chorionicity.
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Affiliation(s)
- Anna Wojas
- Department of Obstetrics, Gynecology, and Reproductive Science, Mt. Sinai, New York, NY, USA
| | | | | | | | | | | | | | | | | | - Andrei Rebarber
- Department of Obstetrics, Gynecology, and Reproductive Science, Mt. Sinai, New York, NY, USA
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17
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Demko Z, Prigmore B, Benn P. A Critical Evaluation of Validation and Clinical Experience Studies in Non-Invasive Prenatal Testing for Trisomies 21, 18, and 13 and Monosomy X. J Clin Med 2022; 11:jcm11164760. [PMID: 36012999 PMCID: PMC9410356 DOI: 10.3390/jcm11164760] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) for trisomies 21, 18, 13 and monosomy X is widely utilized with massively parallel shotgun sequencing (MPSS), digital analysis of selected regions (DANSR), and single nucleotide polymorphism (SNP) analyses being the most widely reported methods. We searched the literature to find all NIPT clinical validation and clinical experience studies between January 2011 and January 2022. Meta-analyses were performed using bivariate random-effects and univariate regression models for estimating summary performance measures across studies. Bivariate meta-regression was performed to explore the influence of testing method and study design. Subgroup and sensitivity analyses evaluated factors that may have led to heterogeneity. Based on 55 validation studies, the detection rate (DR) was significantly higher for retrospective studies, while the false positive rate (FPR) was significantly lower for prospective studies. Comparing the performance of NIPT methods for trisomies 21, 18, and 13 combined, the SNP method had a higher DR and lower FPR than other methods, significantly so for MPSS, though not for DANSR. The performance of the different methods in the 84 clinical experience studies was consistent with validation studies. Clinical positive predictive values of all NIPT methods improved over the last decade. We conclude that all NIPT methods are highly effective for fetal aneuploidy screening, with performance differences across methodologies.
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Affiliation(s)
| | | | - Peter Benn
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
- Correspondence:
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18
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Genovese G, Mello CJ, Loh PR, Handsaker RE, Kashin S, Whelan CW, Bayer-Zwirello LA, McCarroll SA. Chromosomal phase improves aneuploidy detection in non-invasive prenatal testing at low fetal DNA fractions. Sci Rep 2022; 12:12025. [PMID: 35835769 PMCID: PMC9283487 DOI: 10.1038/s41598-022-14049-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) to detect fetal aneuploidy by sequencing the cell-free DNA (cfDNA) in maternal plasma is being broadly adopted. To detect fetal aneuploidies from maternal plasma, where fetal DNA is mixed with far-larger amounts of maternal DNA, NIPT requires a minimum fraction of the circulating cfDNA to be of placental origin, a level which is usually attained beginning at 10 weeks gestational age. We present an approach that leverages the arrangement of alleles along homologous chromosomes—also known as chromosomal phase—to make NIPT analyses more conclusive. We validate our approach with in silico simulations, then re-analyze data from a pregnant mother who, due to a fetal DNA fraction of 3.4%, received an inconclusive aneuploidy determination through NIPT. We find that the presence of a trisomy 18 fetus can be conclusively inferred from the patient’s same molecular data when chromosomal phase is incorporated into the analysis. Key to the effectiveness of our approach is the ability of homologous chromosomes to act as natural controls for each other and the ability of chromosomal phase to integrate subtle quantitative signals across very many sequence variants. These results show that chromosomal phase increases the sensitivity of a common laboratory test, an idea that could also advance cfDNA analyses for cancer detection.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Curtis J Mello
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seva Kashin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lucy A Bayer-Zwirello
- Steward St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA, 02135, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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19
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Kantor V, Jelsema R, Xu W, DiNonno W, Young K, Demko Z, Benn P. Non‐invasive prenatal screening for fetal triploidy using single nucleotide polymorphism (SNP)‐based testing: Differential Diagnosis And Clinical Management In Cases Showing An Extra Haplotype. Prenat Diagn 2022; 42:994-999. [PMID: 35574995 PMCID: PMC9539994 DOI: 10.1002/pd.6169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 12/02/2022]
Abstract
Objective An extra haplotype is infrequently encountered in single nucleotide polymorphism(SNP)‐based non‐invasive prenatal testing (NIPT) and is usually attributed to an undetected twin or triploidy. We reviewed a large series to establish relative frequencies of these outcomes and identify alternative causes. Methods In 515,804 women receiving NIPT from September 2017 through March 2019, all results with an extra haplotype were reviewed. Known viable and vanished twin pregnancies were excluded. For positive cases, pregnancy outcome information was sought. Results Of 1005 results with an extra haplotype (1 in 513), pregnancy outcome was available for 773 cases: 11% were confirmed or suspected triploidy; 65% to vanished twin; 10% with pregnancy loss. Rare explanations included complete mole, chimera, undisclosed donor egg pregnancy, maternal organ transplant and one instance of maternal neoplasm. Among triploid cases that were detected and independently confirmed, 23/27 (85%) were diandric. Conclusion SNP‐based NIPT, with detection of an extra haplotype, is 11% predictive of triploidy. For results with an extra haplotype, ultrasound is recommended to establish viability, evaluate for twins (viable or vanished), and detect findings consistent with triploidy. Review of patient history, serum screening, and ultrasound will reduce the number of CVS or amniocenteses necessary to confirm a diagnosis of triploidy.
What's already known about this topic?
Both digynic and diandric triploidy are occasionally seen in pregnancies but are extremely rare in live‐births In cell‐free DNA prenatal screening, the presence of an extra haplotype could be indicative of either twin pregnancy or triploidy
What does this study add?
Outcomes for a large series of prenatal screening tests where an extra haplotype was identified in cell‐free DNA Complete moles, chimeras, transplantation, and donor egg are additional explanations for extra haplotypes We discuss prenatal management when an extra haplotype is observed in cell‐free DNA
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Affiliation(s)
| | | | | | | | | | | | - Peter Benn
- Department of Genetics and Genome Sciences UConn Health Farmington San Carlos CT USA
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20
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Kong L, Li S, Zhao Z, Feng J, Liu L, Tang W, Zhang H, Wu D, Sun L, Kong X. Noninvasive prenatal testing of Duchenne muscular dystrophy in a twin gestation. Prenat Diagn 2022; 42:518-523. [PMID: 35220584 DOI: 10.1002/pd.6124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/11/2022] [Accepted: 02/24/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Lingrong Kong
- Department of Fetal Medicine & Prenatal Diagnosis Center Shanghai First Maternity and Infant Hospital School of Medicine Tongji University Shanghai China
- Genetic and Prenatal Diagnosis Center Department of Obstetrics and Gynecology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Shaojun Li
- Celula (China) Medical Technology Co. Ltd. Chengdu 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
| | - Lina Liu
- 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
| | - Haichuan Zhang
- Celula (China) Medical Technology Co. Ltd. Chengdu China
| | - Di Wu
- Celula (China) Medical Technology Co. Ltd. Chengdu China
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center Shanghai First Maternity and Infant Hospital School of Medicine Tongji University Shanghai China
| | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center Department of Obstetrics and Gynecology The First Affiliated Hospital of Zhengzhou University Zhengzhou China
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21
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Dar P, Jacobsson B, Clifton R, Egbert M, Malone F, Wapner RJ, Roman AS, Khalil A, Faro R, Madankumar R, Edwards L, Strong N, Haeri S, Silver R, Vohra N, Hyett J, Demko Z, Martin K, Rabinowitz M, Flood K, Carlsson Y, Doulaveris G, Daly S, Hallingström M, MacPherson C, Kao C, Hakonarson H, Norton ME. Cell-free DNA screening for prenatal detection of 22q11.2 deletion syndrome. Am J Obstet Gynecol 2022; 227:79.e1-79.e11. [PMID: 35033576 DOI: 10.1016/j.ajog.2022.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Historically, prenatal screening has focused primarily on the detection of fetal aneuploidies. Cell-free DNA now enables noninvasive screening for subchromosomal copy number variants, including 22q11.2 deletion syndrome (or DiGeorge syndrome), which is the most common microdeletion and a leading cause of congenital heart defects and neurodevelopmental delay. Although smaller studies have demonstrated the feasibility of screening for 22q11.2 deletion syndrome, large cohort studies with confirmatory postnatal testing to assess test performance have not been reported. OBJECTIVE This study aimed to assess the performance of single-nucleotide polymorphism-based, prenatal cell-free DNA screening for detection of 22q11.2 deletion syndrome. STUDY DESIGN Patients who underwent single-nucleotide polymorphism-based prenatal cell-free DNA screening for 22q11.2 deletion syndrome were prospectively enrolled at 21 centers in 6 countries. Prenatal or newborn DNA samples were requested in all cases for genetic confirmation using chromosomal microarrays. The primary outcome was sensitivity, specificity, positive predictive value, and negative predictive value of cell-free DNA screening for the detection of all deletions, including the classical deletion and nested deletions that are ≥500 kb, in the 22q11.2 low-copy repeat A-D region. Secondary outcomes included the prevalence of 22q11.2 deletion syndrome and performance of an updated cell-free DNA algorithm that was evaluated with blinding to the pregnancy outcome. RESULTS Of the 20,887 women enrolled, a genetic outcome was available for 18,289 (87.6%). A total of 12 22q11.2 deletion syndrome cases were confirmed in the cohort, including 5 (41.7%) nested deletions, yielding a prevalence of 1 in 1524. In the total cohort, cell-free DNA screening identified 17,976 (98.3%) cases as low risk for 22q11.2 deletion syndrome and 38 (0.2%) cases as high risk; 275 (1.5%) cases were nonreportable. Overall, 9 of 12 cases of 22q11.2 were detected, yielding a sensitivity of 75.0% (95% confidence interval, 42.8-94.5); specificity of 99.84% (95% confidence interval, 99.77-99.89); positive predictive value of 23.7% (95% confidence interval, 11.44-40.24), and negative predictive value of 99.98% (95% confidence interval, 99.95-100). None of the cases with a nonreportable result was diagnosed with 22q11.2 deletion syndrome. The updated algorithm detected 10 of 12 cases (83.3%; 95% confidence interval, 51.6-97.9) with a lower false positive rate (0.05% vs 0.16%; P<.001) and a positive predictive value of 52.6% (10/19; 95% confidence interval, 28.9-75.6). CONCLUSION Noninvasive cell-free DNA prenatal screening for 22q11.2 deletion syndrome can detect most affected cases, including smaller nested deletions, with a low false positive rate.
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Affiliation(s)
- Pe'er Dar
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY.
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rebecca Clifton
- The Biostatistics Center, George Washington University, Rockville, MD
| | | | - Fergal Malone
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Ashley S Roman
- Department of Obstetrics and Gynecology, New York University Langone, New York, NY
| | - Asma Khalil
- Department of Obstetrics and Gynaecology, St George's Hospital, University of London, London, United Kingdom
| | - Revital Faro
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, NJ
| | - Rajeevi Madankumar
- Department of Obstetrics and Gynecology, Long Island Jewish Medical Center, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, NY
| | | | - Noel Strong
- Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sina Haeri
- Austin Maternal-Fetal Medicine, Austin, TX
| | - Robert Silver
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT
| | - Nidhi Vohra
- Department of Obstetrics and Gynecology, North Shore University Hospital, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Jon Hyett
- Department of Obstetrics and Gynecology, Royal Prince Alfred Hospital, University of Sydney, Camperdown, New South Wales, Australia
| | | | | | | | - Karen Flood
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ylva Carlsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Georgios Doulaveris
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY
| | - Sean Daly
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maria Hallingström
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Cora MacPherson
- The Biostatistics Center, George Washington University, Rockville, MD
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mary E Norton
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA
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22
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Yener C, Ates S. Evaluation of YouTube Videos as a Source of Information on Non-Invasive Prenatal Testing. EURASIAN JOURNAL OF FAMILY MEDICINE 2021. [DOI: 10.33880/ejfm.2021100403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Aim: Non-invasive prenatal testing is a method that determines the risk of a fetus being born with certain genetic abnormalities. In this study, we aimed to examine the quality of information on YouTube for non-invasive prenatal testing.
Methods: The term "Non-invasive prenatal testing" was entered in the YouTube search bar on May 1, 2021, and the top 50 YouTube videos of the non-invasive prenatal testing with the highest number of views were recorded after the exclusion of videos with a non-English language, videos repeated twice and irrelevant videos. Length of the videos, likes, and dislikes were recorded. Videos were evaluated by two obstetricians. A questionnaire consisting of 9 dichotomous questions was conducted to assess whether there was adequate information about non-invasive prenatal testing. In addition, video quality was evaluated with the Global Quality Scale, the Patient Education Materials Assessment Tool and the Journal of the American Medical Association Benchmark Criteria.
Results: The mean Global Quality Scale was 2.96±0.62. Most videos answered the question: ‘What is non-invasive prenatal testing?’ (94%), and ‘How is non-invasive prenatal testing done?’ (82%). However, there was a lack of information about the limitation of non-invasive prenatal testing in certain situations (only %16 of videos answered limitations of non-invasive prenatal testing). Three (6%) of the videos had misinformation. The mean Global Quality Scale was 2.96±0.62. The Patient Education Materials Assessment Tool mean value was 72% and 58% in terms of understandability and actionability, respectively. The mean Journal of the American Medical Association Benchmark Criteria score was found as 1.4±0.8.
Conclusion: The videos posted about non-invasive prenatal testing on YouTube were of poor-moderate quality. If the quality of the videos increases, patients can have sufficient and accurate information about non-invasive prenatal, especially during these pandemic days.
Keywords: health information, prenatal diagnosis, online systems
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Affiliation(s)
| | - Sinan Ates
- Trakya University Faculty of Medicine, Department of Obstetrics and Gynecology
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23
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Gao S. Noninvasive detection of fetal genetic variations through polymorphic site sequencing of maternal plasma DNA. J Gene Med 2021; 24:e3400. [PMID: 34850495 DOI: 10.1002/jgm.3400] [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: 08/24/2021] [Revised: 11/01/2021] [Accepted: 11/09/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) for common fetal aneuploidies has been widely adopted in clinical practice for its sensitivity and accuracy. However, detection of pathogenic copy number variations (pCNVs) or monogenic disorders (MDs) is inaccurate and not cost effective. Here we developed an assay, the noninvasive prenatal testing based on goodness-of-fit and graphical analysis of polymorphic sites (GGAP-NIPT), to simultaneously detect fetal aneuploidies, pCNVs, and MDs. METHODS Polymorphic sites were amplicon sequenced, followed by fetal fraction estimation using allelic reads counts and a robust linear regression model. The genotype of each polymorphic site or MD variant was then determined by allelic goodness-of-fit test or graphical analysis of its different alleles. Finally, aneuploidies and pCNVs were detected using collective goodness-of-fit test to select each best fit from all possible chromosomal models. RESULTS Of the simulated 1,692 chromosomes and 1,895 pCNVs, all normals and variants were correctly identified (accuracy 100%, sensitivity 100%, specificity 100%). Of the 713,320 simulated MD variants, more than 90% of the genotypes were determined correctly (accuracy: 98.3 ± 1.0%; sensitivity: 98.7 ± 1.96%; specificity: 99.7 ± 0.6%). The detection accuracies of three public MD datasets were 95.70%, 93.43%, and 96.83%. For an MD validation dataset, 75% detection accuracy was observed when a site with sample replicates was analyzed individually, and 100% accuracy was achieved when analyzed collectively. CONCLUSIONS Fetal aneuploidies, pCNVs, and MDs could be detected simultaneously and with high accuracy through amplicon sequencing of polymorphic and target sites, which showed the potential of extending NIPT to an expanded panel of genetic disorders.
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Affiliation(s)
- Song Gao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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24
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Ali TM, Mateu-Brull E, Balaguer N, Dantas C, Borges HR, de Oliveira MQG, Rodrigo L, Campos-Galindo I, Navarro R, Milán M. Inherited unbalanced reciprocal translocation with 3q duplication and 5p deletion in a foetus revealed by cell-free foetal DNA (cffDNA) testing: a case report. Eur J Med Res 2021; 26:64. [PMID: 34187576 PMCID: PMC8243479 DOI: 10.1186/s40001-021-00535-5] [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: 03/16/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
Background Since 2011, screening maternal blood for cell-free foetal DNA (cffDNA) fragments has offered a robust clinical tool to classify pregnancy as low or high-risk for Down, Edwards, and Patau syndromes. With recent advances in molecular biology and improvements in data analysis algorithms, the screening’s scope of analysis continues to expand. Indeed, screening now encompassess additional conditions, including aneuploidies for sex chromosomes, microdeletions and microduplications, rare autosomal trisomies, and, more recently, segmental deletions and duplications called copy number variations (CNVs). Yet, the ability to detect CNVs creates a new challenge for cffDNA analysis in couples in which one member carries a structural rearrangement such as a translocation or inversion. Case presentation We report a segmental duplication of the long arm of chromosome 3 and a segmental deletion of the short arm of chromosome 5 detected by cffDNA analysis in a 25-year-old pregnant woman. The blood sample was sequenced on a NextSeq 550 (Illumina) using the VeriSeq NIPT Solution v1 assay. G-band karyotyping in amniotic fluid only detected an abnormality in chromosome 5. Next-generation sequencing in amniocytes confirmed both abnormalities and identified breakpoints in 3q26.32q29 and 5p13.3p15. The foetus died at 21 weeks of gestation due to multiple abnormalities, and later G-band karyotyping in the parents revealed that the father was a carrier of a balanced reciprocal translocation [46,XY,t(3;5)(q26.2;p13)]. Maternal karyotype appeared normal. Conclusion This case provides evidence that extended cffDNA can detect, in addition to aneuploidies for whole chromosomes, large segmental aneuploidies. In some cases, this may indicate the presence of chromosomal rearrangements in a parent. Such abnormalities are outside the scope of standard cffDNA analysis targeting chromosomes 13, 18, 21, X, and Y, potentially leading to undiagnosed congenital conditions.
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Affiliation(s)
- Taccyanna M Ali
- Laboratório Igenomix, Laboratório de Genética E Medicina Reprodutiva, Sao Paulo, Sao Paulo, Brazil
| | - Emilia Mateu-Brull
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Nuria Balaguer
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Camila Dantas
- Laboratório Igenomix, Laboratório de Genética E Medicina Reprodutiva, Sao Paulo, Sao Paulo, Brazil
| | | | | | - Lorena Rodrigo
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Inmaculada Campos-Galindo
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Roser Navarro
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain
| | - Miguel Milán
- IGENOMIX Lab S.L.U., Parque tecnológico, Ronda Narciso Monturiol, 11B, Edificios Europark, 46980, Paterna, Valencia, Spain.
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25
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Schneider L, Tripathi A. Progress and Challenges in Laboratory-Based Diagnostic and Screening Approaches for Aneuploidy Detection during Pregnancy. SLAS Technol 2021; 26:425-440. [PMID: 34148381 DOI: 10.1177/24726303211021787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aneuploidy is caused by problems during cellular division and segregation errors during meiosis that lead to an abnormal number of chromosomes and initiate significant genetic abnormalities during pregnancy or the loss of a fetus due to miscarriage. Screening and diagnostic technologies have been developed to detect this genetic condition and provide parents with critical information about their unborn child. In this review, we highlight the complexities of aneuploidy as a disease as well as multiple technological advancements in testing that help to identify aneuploidy at various time points throughout pregnancy. We focus on aneuploidy diagnosis during preimplantation genetic testing that is performed during in vitro fertilization as well as prenatal screening and diagnosis during pregnancy. This review focuses on DNA-based analysis and laboratory techniques for aneuploidy detection through reviewing molecular- and engineering-based technical advancements. We also present key challenges in aneuploidy detection during pregnancy, including sample collection, mosaic embryos, economic factors, and the social implications of this testing. The goal of this review is to synthesize broad information about aneuploidy screening and diagnostic sample collection and analysis during pregnancy and discuss major challenges the field is still facing despite decades of advancements.
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Affiliation(s)
- Lindsay Schneider
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
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26
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Abstract
PURPOSE OF REVIEW Cell-free DNA-based noninvasive prenatal testing (cfDNA-based NIPT) using maternal blood is highly sensitive for detecting fetal trisomies. However, false-positive and false-negative results can occur, which prevents NIPT from being a diagnostic test. Fetoplacental mosaicism is one of the main reasons for discordant test results. It is therefore important to understand this phenomenon to enable more comprehensive and appropriate genetic counselling. The present review aims to summarize the current knowledge of fetoplacental mosaicism ascertained during cfDNA-based NIPT and refers to the development of recent analytical pipelines for its detection during pregnancy. RECENT FINDINGS Publications are emerging demonstrating that genome-wide approaches to analyzing cfDNA can detect chromosomal aneuploidy other than the common trisomies. Despite the high accuracy of current cfDNA-based NIPT, a substantial number of false-positive and false-negative test results remain. Biological causes, such as fetal or (confined) placental mosaicism have been identified using advanced bioinformatics algorithms. Fetoplacental mosaicism can occur as part of normal pregnancy development, hence clinical practice standards recommend confirmation of positive NIPT results with a diagnostic karyotype or microarray study. SUMMARY cfDNA-based NIPT for fetal chromosomal aneuploidies is not diagnostic because of false-positive and false-negative test results. Recently, novel algorithms have been described that identify pregnancies with an increased risk of fetoplacental mosaicism. Reporting the presence of fetoplacental mosaicism during pregnancy can influence risk estimation and improve genetic counseling.
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27
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Direct Assessment of Single-Cell DNA Using Crudely Purified Live Cells: A Proof of Concept for Noninvasive Prenatal Definitive Diagnosis. J Mol Diagn 2021; 22:132-140. [PMID: 32033633 DOI: 10.1016/j.jmoldx.2019.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 07/26/2019] [Accepted: 10/16/2019] [Indexed: 11/20/2022] Open
Abstract
Noninvasive testing techniques are often used for fetal diagnosis of genetic abnormalities but are limited by certain characteristics, including noninformative results. Thus, novel methods of noninvasive definitive diagnosis of fetal genetic abnormalities are needed. The aim of this study was to develop a single-cell DNA analysis method with high sensitivity and specificity that enables direct extraction of genetic information from live fetal cells in a crude mixture for simultaneous evaluation. Genomic DNA from circulating fetal CD45-CD14- cells, an extremely rare cell type, extracted from 10-mL samples of maternal peripheral blood, was extracted using a single-cell-based droplet digital (sc-dd) PCR system with a modified amount of polymerase. A hexachloro-6-carboxyfluorescein-labeled RPP30 probe was used as an internal control and a 6-carboxyfluorescein-labeled SRY probe as a target. The results indicated that no droplets generated with samples from pregnant women carrying female fetuses were positive for both probe signals, whereas droplets prepared with samples from pregnant women carrying male fetuses were positive for both probe signals. The latter was considered a direct assessment of genetic information from single circulating male fetal cells. Thus, the modified sc-ddPCR system allows the detection of genetic information from rare target cells in a crudely purified cell population. This research also serves as a proof of concept for noninvasive prenatal definitive diagnosis.
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28
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Deng C, Cheung SW, Liu H. Noninvasive prenatal screening for fetal sex chromosome aneuploidies. Expert Rev Mol Diagn 2021; 21:405-415. [PMID: 33787433 DOI: 10.1080/14737159.2021.1911651] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Sex chromosome aneuploidies (SCAs) are among the most common chromosome abnormalities observed in humans. Manifestations include low fertility, infertility, delayed language development, and dysfunction in motor development. Noninvasive prenatal screening (NIPS) based on cell-free fetal DNA from the peripheral blood of pregnant women is increasingly used for the screening of fetal chromosome abnormalities, including screening for fetal gender and fetal sex chromosome aneuploidy. A systematic review of the literature about NIPS for SCAs is needed. AREAS COVERED This review evaluated a vast array of published studies focusing on the clinical significance, detection methods, performance of NIPS for SCAs, and the management of positive SCA results following screening with the aim of facilitating a comprehensive and systematic understanding of NIPS for SCAs. EXPERT COMMENTARY Looking forward, NIPS is expected to become the primary screening test for common aneuploidies as well as other chromosome abnormalities, including some micro-deletions and micro-duplications, with the potential to transition from a screening test to a prenatal diagnosis method. Ultimately, the goal is to provide a safe and accurate method for increasing early diagnosis to improve long-term outcomes for the SCA patients and families by well- informed health care providers.
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Affiliation(s)
- Cechuan Deng
- Medical Genetics Department/Prenatal Diagnostic Center, 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
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hongqian Liu
- Medical Genetics Department/Prenatal Diagnostic Center, 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
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29
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Paul RS, Almokayad I, Collins A, Raj D, Jagadeesan M. Donor-derived Cell-free DNA: Advancing a Novel Assay to New Heights in Renal Transplantation. Transplant Direct 2021; 7:e664. [PMID: 33564715 PMCID: PMC7862009 DOI: 10.1097/txd.0000000000001098] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023] Open
Abstract
Despite advances in transplant immunosuppression, long-term renal allograft outcomes remain suboptimal because of the occurrence of rejection, recurrent disease, and interstitial fibrosis with tubular atrophy. This is largely due to limitations in our understanding of allogeneic processes coupled with inadequate surveillance strategies. The concept of donor-derived cell-free DNA as a signal of allograft stress has therefore rapidly been adopted as a noninvasive monitoring tool. Refining it for effective clinical use, however, remains an ongoing effort. Furthermore, its potential to unravel new insights in alloimmunity through novel molecular techniques is yet to be realized. This review herein summarizes current knowledge and active endeavors to optimize cell-free DNA-based diagnostic techniques for clinical use in kidney transplantation. In addition, the integration of DNA methylation and microRNA may unveil new epigenetic signatures of allograft health and is also explored in this report. Directing research initiatives toward these aspirations will not only improve diagnostic precision but may foster new paradigms in transplant immunobiology.
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Affiliation(s)
- Rohan S. Paul
- Division of Kidney Disease & Hypertension, George Washington University, Washington, DC
| | - Ismail Almokayad
- Division of Kidney Disease & Hypertension, George Washington University, Washington, DC
| | - Ashte Collins
- Division of Kidney Disease & Hypertension, George Washington University, Washington, DC
| | - Dominic Raj
- Division of Kidney Disease & Hypertension, George Washington University, Washington, DC
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30
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Alyafee Y, Al Tuwaijri A, Alam Q, Umair M, Haddad S, Alharbi M, Ballow M, Al Drees M, AlAbdulrahman A, Al Khaldi A, Alfadhel M. Next Generation Sequencing Based Non-invasive Prenatal Testing (NIPT): First Report From Saudi Arabia. Front Genet 2021; 12:630787. [PMID: 33613643 PMCID: PMC7889598 DOI: 10.3389/fgene.2021.630787] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/06/2021] [Indexed: 01/09/2023] Open
Abstract
Background: Non-invasive prenatal testing (NIPT) for aneuploidy in pregnant women screening has been recently established in Saudi Arabia. We aim from this study to report our experience in the implementation of this new technology in clinical practice and to assess factors influencing cell-free fetal (cffDNA) fraction and successful NIPT reporting. Methods: In total, 200 pregnant women were subjected to the NIPT test using standard methods. Next-generation sequencing (NGS) was used to analyze cffDNA in maternal plasma. Results: Out of the 200 NIPT cases, the average age of pregnant women was 35 ± 6 years (range: 21–48 years). The average cffDNA fraction of reported cases was 13.72% (range: 3–31%). Out of these 200 cases, 187 (93.5%) were at low risk, while 13 (6.5%) cases revealed high risk for aneuploidy. Among these chromosomal abnormalities, 7 (3.5%) cases of Down’s syndrome, 5 (2.5%) Edwards’ Syndrome, and only 1 case of (0.5%) Patau’s syndrome was observed. Out of the 13 high-risk cases, 2 (15.3%) were found in women below the age of 30. Conclusion: This is the first study reporting the successful implementation of an in-house NIPT screening service in Saudi Arabia. Our data showed high accuracy and sensitivity to detect high-risk cases indicating the usefulness of such a technique as an alternative to invasive testing and (hopefully) will change the common screening practice for pregnant women in Saudi Arabia.
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Affiliation(s)
- Yusra Alyafee
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abeer Al Tuwaijri
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Shahad Haddad
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mashael Alharbi
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Maryam Ballow
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mohammed Al Drees
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Abdulkareem AlAbdulrahman
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Aziza Al Khaldi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, King Abdul Aziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia.,Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children's Hospital, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, MNG-HA, Riyadh, Saudi Arabia
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31
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Choe SA, Seol HJ, Kwon JY, Park CW, Kim M, Lee JY, Kim MA, Hwang HS, Na S, Shim JY, Kim K, Ryu HM. Clinical Practice Guidelines for Prenatal Aneuploidy Screening and Diagnostic Testing from Korean Society of Maternal-Fetal Medicine: (1) Prenatal Aneuploidy Screening. J Korean Med Sci 2021; 36:e27. [PMID: 33496086 PMCID: PMC7834900 DOI: 10.3346/jkms.2021.36.e27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/11/2020] [Indexed: 01/06/2023] Open
Abstract
In 2019, the Korean Society of Maternal-Fetal Medicine developed the first Korean clinical practice guidelines for prenatal aneuploidy screening and diagnostic testing. These guidelines were developed by adapting established clinical practice guidelines in other countries that were searched systematically, and the guidelines aim to assist in decision making of healthcare providers providing prenatal care and to be used as a source for education and communication with pregnant women in Korea. This article delineates clinical practice guidelines specifically for maternal serum screening for fetal aneuploidy and cell-free DNA (cfDNA) screening. A total of 19 key questions (12 for maternal serum and 7 for cfDNA screening) were defined. The main recommendations are: 1) Pregnant women should be informed of common fetal aneuploidy that can be detected, risks for chromosomal abnormality according to the maternal age, detection rate and false positive rate for common fetal aneuploidy with each screening test, limitations, as well as the benefits and risks of invasive diagnostic testing, 2) It is ideal to give counseling about prenatal aneuploidy screening and diagnostic testing at the first prenatal visit, and counseling is recommended to be given early in pregnancy, 3) All pregnant women should be informed about maternal serum screening regardless of their age, 4) cfDNA screening can be used for the screening of trisomy 21, 18, 13 and sex-chromosome aneuploidy. It is not recommended for the screening of microdeletion, 5) The optimal timing of cfDNA screening is 10 weeks of gestation and beyond, and 6) cfDNA screening is not recommended for women with multiple gestations. The guideline was reviewed and approved by the Korean Academy of Medical Sciences.
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Affiliation(s)
- Seung Ah Choe
- Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea
| | - Hyun Joo Seol
- Department of Obstetrics and Gynecology, Kyung Hee University Hospital at Gangdong, Kyung Hee University College of Medicine, Seoul, Korea
| | - Ji Young Kwon
- Department of Obstetrics and Gynecology, College of Medicine,The Catholic University of Korea, Seoul, Korea
| | - Chan Wook Park
- Department of Obstetrics and Gynecology, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Minhyoung Kim
- Department of Obstetrics and Gynecology, MizMedi Hospital, Seoul, Korea
| | - Ji Yeon Lee
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Min A Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Institute of Women's Life Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Han Sung Hwang
- Department of Obstetrics and Gynecology, Research Institute of Medical Science, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, Korea
| | - Sunghun Na
- Department of Obstetrics and Gynecology, Kangwon National University Hospital, School of Medicine Kangwon National University, Chuncheon, Korea
| | - Jae Yoon Shim
- Mirae & Heemang Obstetrics and Gynecology Clinic, Seoul, Korea
| | | | - Hyun Mee Ryu
- Department of Obstetrics and Gynecology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea.
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Rabinowitz T, Deri-Rozov S, Shomron N. Improved noninvasive fetal variant calling using standardized benchmarking approaches. Comput Struct Biotechnol J 2020; 19:509-517. [PMID: 33510858 PMCID: PMC7809098 DOI: 10.1016/j.csbj.2020.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 11/28/2022] Open
Abstract
The technology of noninvasive prenatal testing (NIPT) enables risk-free detection of genetic conditions in the fetus, by analysis of cell-free DNA (cfDNA) in maternal blood. For chromosomal abnormalities, NIPT often effectively replaces invasive tests (e.g. amniocentesis), although it is considered as screening rather than diagnostics. Most recently, the NIPT has been applied to genome-wide, comprehensive genotyping of the fetus using cfDNA, i.e. identifying all its genetic variants and mutations. Previously, we suggested that NIPD should be treated as a special case of variant calling, and presented Hoobari, the first software tool for noninvasive fetal variant calling. Using a unique pipeline, we were able to comprehensively decipher the inheritance of SNPs and indels. A few caveats still exist in this pipeline. Performance was lower for indels and biparental loci (i.e. where both parents carry the same mutation), and performance was not uniform across the genome. Here we utilized standardized methods for benchmarking of variant calling pipelines and applied them to noninvasive fetal variant calling. By using the best performing pipeline and by focusing on coding regions, we showed that noninvasive fetal genotyping greatly improves performance, particularly in indels and biparental loci. These results emphasize the importance of using widely accepted concepts to describe the challenge of genome-wide NIPT of point mutations; and demonstrate a benchmarking process for the first time in this field. This study brings genome-wide and complete NIPD closer to the clinic; while potentially alleviating uncertainty and anxiety during pregnancy, and promoting informed choices among families and physicians.
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Affiliation(s)
- Tom Rabinowitz
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shira Deri-Rozov
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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Abstract
A high proportion of observed fetal sex discordances between single-nucleotide polymorphism–based noninvasive prenatal screening tests and prenatal or newborn examinations are attributable to disorders of sexual development. To assess the causes of reported discordance between noninvasive prenatal testing (NIPT) and ultrasound or other clinical information.
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Persico N, Boito S, Volpe P, Ischia B, Gentile M, Ronzoni L, De Robertis V, Fabietti I, Olivieri C, Periti E, Ficarella R, Silipigni R, Rembouskos G. Incidence of chromosomal abnormalities in fetuses with first trimester ultrasound anomalies and a low-risk cell-free DNA test for common trisomies. Prenat Diagn 2020; 40:1474-1481. [PMID: 33034897 DOI: 10.1002/pd.5799] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To examine the incidence and type of chromosomal abnormalities in fetuses with first trimester ultrasound anomalies and a low-risk cfDNA test for common trisomies. METHODS In 486 singleton pregnancies undergoing invasive testing after combined screening, a detailed first trimester ultrasound assessment was carried out and a maternal blood sample was sent for cfDNA analysis. Ultrasound and cfDNA data were analyzed in relation to fetal karyotype. RESULTS Invasive testing demonstrated a chromosomal abnormality in 157 (32.3%) of 486 fetuses. In 348 cases with a low-risk cfDNA test for common trisomies, NT ≥ 3.5 mm and/or a major structural defect were observed in 92 (26.4%) fetuses. A chromosomal abnormality was found in 17 (18.5%; 95%CI 10.55-26.41) of these pregnancies, including 1 (1.1%) case of trisomy 21 and 16 (17.4%) fetuses with abnormalities different from common trisomies. The respective incidence in the 256 cases with a low-risk cfDNA test result and no ultrasound anomalies was 2.3% (95% CI 0.49-4.20; n = 6). CONCLUSIONS In fetuses with first trimester ultrasound anomalies and a low-risk cfDNA result for trisomy 21, 18 and 13, diagnostic testing should be offered with the main objective to detect chromosomal abnormalities beyond common trisomies.
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Affiliation(s)
- Nicola Persico
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| | - Simona Boito
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Volpe
- Fetal Medicine Unit, Di Venere and Sarcone Hospitals, Bari, Italy
| | - Benedetta Ischia
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Luisa Ronzoni
- Medical Genetics Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Isabella Fabietti
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Enrico Periti
- Fetal Medicine Unit, Palagi Hospital, Florence, Italy
| | | | - Rosamaria Silipigni
- Laboratory of Medical Genetics, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
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Strategy for Use of Genome-Wide Non-Invasive Prenatal Testing for Rare Autosomal Aneuploidies and Unbalanced Structural Chromosomal Anomalies. J Clin Med 2020; 9:jcm9082466. [PMID: 32752152 PMCID: PMC7464024 DOI: 10.3390/jcm9082466] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/25/2020] [Accepted: 07/28/2020] [Indexed: 11/23/2022] Open
Abstract
Atypical fetal chromosomal anomalies are more frequent than previously recognized and can affect fetal development. We propose a screening strategy for a genome-wide non-invasive prenatal test (NIPT) to detect these atypical chromosomal anomalies (ACAs). Two sample cohorts were tested. Assay performances were determined using Cohort A, which consisted of 192 biobanked plasma samples—42 with ACAs, and 150 without. The rate of additional invasive diagnostic procedures was determined using Cohort B, which consisted of 3097 pregnant women referred for routine NIPT. Of the 192 samples in Cohort A, there were four initial test failures and six discordant calls; overall sensitivity was 88.1% (37/42; CI 75.00–94.81) and specificity was 99.3% (145/146; CI 96.22–99.88). In Cohort B, there were 90 first-pass failures (2.9%). The rate of positive results indicating an anomaly was 1.2% (36/3007) and 0.57% (17/3007) when limited to significant unbalanced chromosomal anomalies and trisomies 8, 9, 12, 14, 15, 16, and 22. These results show that genome-wide NIPT can screen for ACAs with an acceptable sensitivity and a small increase in invasive testing, particularly for women with increased risk following maternal serum screening and by limiting screening to structural anomalies and the most clinically meaningful trisomies.
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36
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Xu HH, Dai MZ, Wang K, Zhang Y, Pan FY, Shi WW. A rare Down syndrome foetus with de novo 21q;21q rearrangements causing false negative results in non-invasive prenatal testing: a case report. BMC Med Genomics 2020; 13:96. [PMID: 32631433 PMCID: PMC7339513 DOI: 10.1186/s12920-020-00751-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) has been established as a routine prenatal screening to assess the risk of common foetal aneuploidy disorder (trisomy 21, 18, and 13). NIPT has high sensitivity and high specificity, but false positive and false negative results still exist. False negative NIPT results involving Down syndrome are rare, but have a high clinical impact on families and society. CASE PRESENTATION We described a case of a foetus that tested "negative" for trisomy 21 (Z-score was 0.664) by NIPT based on the semiconductor sequencing platform (SSP). The foetal fraction of cell-free DNA was 16.9%; this percentage was much larger than the threshold of 4% for obtaining accurate NIPT results. However, postnatally, the newborn was diagnosed with Down syndrome with the 46,XY,der(21;21)(q10;q10),+ 21 karyotype. CONCLUSIONS We presented a case of false negative NIPT results, which may occur through biological mechanisms rather than poor quality, technical errors or negligence. It is imperative for clinical geneticists and their patients to understand that NIPT is still a screening test.
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Affiliation(s)
- Hui-Hui Xu
- Prenatal Diagnosis Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China. .,Medical Research Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China.
| | - Mei-Zhen Dai
- Prenatal Diagnosis Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China.,Medical Research Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China
| | - Kai Wang
- Prenatal Diagnosis Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China.,Department of Gynecology and Obstetrics, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China
| | - Yang Zhang
- Prenatal Diagnosis Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China.,Medical Research Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China
| | - Fei-Yan Pan
- Medical Research Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China
| | - Wei-Wu Shi
- Prenatal Diagnosis Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China. .,Medical Research Center, Taizhou Hospital, Wenzhou Medical University, Zhejiang, China.
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NIPT Technique Based on the Use of Long Chimeric DNA Reads. Genes (Basel) 2020; 11:genes11060590. [PMID: 32466452 PMCID: PMC7349339 DOI: 10.3390/genes11060590] [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: 04/21/2020] [Revised: 05/15/2020] [Accepted: 05/21/2020] [Indexed: 11/17/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) for aneuploidy on Chromosomes 21 (T21), 18 (T18) and 13 (T13) is actively used in clinical practice around the world. One of the limitations of the wider implementation of this test is the high cost of the analysis itself, as high-throughput sequencing is still relatively expensive. At the same time, there is an increasing trend in the length of reads yielded by sequencers. Since extracellular DNA is short, in the order of 140–160 bp, it is not possible to effectively use long reads. The authors used high-performance sequencing of cell-free DNA (cfDNA) libraries that went through additional stages of enzymatic fragmentation and random ligation of the resulting products to create long chimeric reads. The authors used a controlled set of samples to analyze a set of cfDNA samples from pregnant women with a high risk of fetus aneuploidy according to the results of the first trimester screening and confirmed by invasive karyotyping of the fetus using laboratory and analytical approaches developed by the authors. They evaluated the sensitivity, specificity, PPV (positive predictive value), and NPV (negative predictive value) of the results. The authors developed a technique for constructing long chimeric reads from short cfDNA fragments and validated the test using a control set of extracellular DNA samples obtained from pregnant women. The obtained sensitivity and specificity parameters of the NIPT developed by the authors corresponded to the approaches proposed earlier (99.93% and 99.14% for T21; 100% and 98.34% for T18; 100% and 99.17% for T13, respectively).
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38
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Ultra-high throughput single-cell analysis of proteins and RNAs by split-pool synthesis. Commun Biol 2020; 3:213. [PMID: 32382044 PMCID: PMC7205613 DOI: 10.1038/s42003-020-0896-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 03/04/2020] [Indexed: 12/11/2022] Open
Abstract
Single-cell omics provide insight into cellular heterogeneity and function. Recent technological advances have accelerated single-cell analyses, but workflows remain expensive and complex. We present a method enabling simultaneous, ultra-high throughput single-cell barcoding of millions of cells for targeted analysis of proteins and RNAs. Quantum barcoding (QBC) avoids isolation of single cells by building cell-specific oligo barcodes dynamically within each cell. With minimal instrumentation (four 96-well plates and a multichannel pipette), cell-specific codes are added to each tagged molecule within cells through sequential rounds of classical split-pool synthesis. Here we show the utility of this technology in mouse and human model systems for as many as 50 antibodies to targeted proteins and, separately, >70 targeted RNA regions. We demonstrate that this method can be applied to multi-modal protein and RNA analyses. It can be scaled by expansion of the split-pool process and effectively renders sequencing instruments as versatile multi-parameter flow cytometers. Maeve O’Huallachain et al. report a method that enables simultaneous, ultra-high throughput single-cell barcoding for targeted single-cell protein and RNA analysis. They show the utility of their method in analyses of mRNA and protein expression in human and mouse cells.
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Panchalee T, Poungvarin N, Amornrit W, Pooliam J, Taluengjit P, Wataganara T. Clinical performance of DNA-based prenatal screening using single-nucleotide polymorphisms approach in Thai women with singleton pregnancy. Mol Genet Genomic Med 2020; 8:e1256. [PMID: 32329244 PMCID: PMC7336763 DOI: 10.1002/mgg3.1256] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/22/2020] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Background To review the performance of noninvasive prenatal screening (NIPS) using targeted single‐nucleotide polymorphisms (SNPs) approach in mixed‐risk Thai women. Methods Retrospective analysis of data for detection of trisomy 21 (T21), 18 (T18), 13 (T13), monosomy X (XO), other sex chromosome aneuploidies (SCA), and triploidy/vanishing twins (VT) from a single commercial laboratory. Results Mean (±SD) gestational age and maternal weight were 13.2 (±2.1) weeks and 125.7 (±22.4) pounds, respectively (n = 8,572). From 462/8,572 (5.4%) no‐calls; 1/462 (0.2%) was uninformative SNPs, and 1/462 chose amniocentesis. Redraw settled 323/460 (70%) samples with low fetal fraction (FF); and 8,434/8,572 (98.4%) were finally reportable, with 131 high risks (1.6%). The median (min‐max) FF of reportable (n = 8,434) and unreportable samples (n = 137) samples were 10.5% (2.6–37.9) and 3.8% (1–14.1), respectively (p < .05). Fetal karyotypes were available in 106/131 (80.9%) and 52/138 (37.7%) high risk and repeated no‐calls, respectively. The positive predictive values (PPVs) for T21 (n = 47), T18 (n = 15), T13 (n = 7), XO (n = 8), other SCA (n = 7), and triploidy/VT were 94%, 100%, 58.3%, 66.7%, 70%, and 57.1%, respectively. None of repeated no‐calls had aneuploidies. Conclusion SNP‐based NIPS has high PPVs for T21 and T18. Although the proprietary SNPs library is not population‐specific, uninformative SNPs are uncommon.
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Affiliation(s)
- Tachjaree Panchalee
- Department of Obstetrics and Gynecology, Mahidol University, Bangkok, Thailand
| | | | | | - Julaporn Pooliam
- Division of Clinical Epidemiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Tuangsit Wataganara
- Department of Obstetrics and Gynecology, Mahidol University, Bangkok, Thailand
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40
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Yuan Y, Chai X, Liu N, Gu B, Li S, Gao Y, Zhou L, Liu Q, Yang F, Liu J, Qiu J, Zhang J, Hou Y, Cen M, Tian Z, Tang W, Zhang H, Chen F, Yin Y, Wang W. FF-QuantSC: accurate quantification of fetal fraction by a neural network model. Mol Genet Genomic Med 2020; 8:e1232. [PMID: 32281746 PMCID: PMC7284026 DOI: 10.1002/mgg3.1232] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) is one of the most commonly employed clinical measures for screening of fetal aneuploidy. Fetal Fraction (ff) has been demonstrated to be one of the key factors affecting the performance of NIPT. Accurate quantification of ff plays vital role in NIPT. METHODS In this study, we present a new approach, the accurate Quantification of Fetal Fraction with Shallow-Coverage sequencing of maternal plasma DNA (FF-QuantSC), for the estimation of ff in NIPT. The method employs neural network model and utilizes differential genomic patterns between fetal and maternal genomes to quantify ff. RESULTS Our results show that the predicted ff by FF-QuantSC exhibit high correlation with the Y chromosome-based method on male pregnancies, and achieves the highest accuracy compared with other ff estimation approaches. We also demonstrate that the model generates statistically similar results on both male and female pregnancies. CONCLUSION FF-QuantSC achieves high accuracy in ff quantification. The method is suitable for application in both male and female pregnancies. Since the method does not require additional information upon NIPT routines, it can be easily incorporated into current NIPT settings without causing extra costs. We believe that FF-QuantSC shall provide valuable additions to NIPT.
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Affiliation(s)
- Yuying Yuan
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Xianghua Chai
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Na Liu
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Bida Gu
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | | | - Ya Gao
- BGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
| | - Lijun Zhou
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Qiang Liu
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Fan Yang
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Jingjuan Liu
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Jiao Qiu
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Jinjin Zhang
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Yumei Hou
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Miaolan Cen
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Zhongming Tian
- Tianjin Medical LaboratoryBGI‐TianjinBGI‐ShenzhenTianjinChina
| | - Weijiang Tang
- BGI‐Wuhan Clinical LaboratoriesBGI‐ShenzhenWuhanChina
| | - Hongyun Zhang
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | | | - Ye Yin
- BGI GenomicsBGI‐ShenzhenShenzhenChina
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Gammon BL, Jaramillo C, Riggan KA, Allyse M. Decisional regret in women receiving high risk or inconclusive prenatal cell-free DNA screening results. J Matern Fetal Neonatal Med 2020; 33:1412-1418. [PMID: 30269633 PMCID: PMC10694839 DOI: 10.1080/14767058.2018.1519541] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Objectives: This study examined the experiences of women receiving high-risk cell-free DNA (cfDNA) screening results, with particular focus on decisional satisfaction after receiving high-risk, false, or inconclusive results. It is already known that cell-free DNA screening is rapidly expanding in the clinical practice. A growing number of women are offered cfDNA screening for an increasingly broad range of chromosomal and microdeletion syndromes. However, research shows that the very low false positive rate attributed to cfDNA screening for trisomy 21 does not apply to other conditions.Methods: As a part of the larger study on patient experiences, 40 semistructured telephone interviews were conducted with women who were, or had recently been, pregnant and received high-risk (n = 15), false positive/negative (n = 20), or inconclusive (n = 5) results from cfDNA screening.Results: One third of participants would not elect to have cfDNA screening in a future pregnancy, and another third would only have the screen under particular circumstances or if the scope of the panel was limited. Many women reported feeling misled by the information they received prior to accepting cfDNA screening or receiving their results.Conclusions: Study participants described issues with the clinical dialog when cfDNA screening is offered; when results are returned; and problems with the availability of information about the existence of false positives. These reports suggest that inadequate pretest discussion contributes to women's experience of decisional regret after receiving high-risk, false positive, or inconclusive results. Given the confusion about cfDNA screening accuracy, the prevalence of follow-up invasive tests, and the number of women who reported that they regretted choosing cfDNA screening, the mode of offering cfDNA should be reassessed.
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Affiliation(s)
- Betsy L. Gammon
- Mayo Clinic, Biomedical Ethics Program, Rochester, MN, USA
- University of Virginia School of Medicine, Charlottesville, VA, USA
| | | | | | - Megan Allyse
- Mayo Clinic, Biomedical Ethics Program, Rochester, MN, USA
- Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, USA
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42
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Dengu F. Next-generation sequencing methods to detect donor-derived cell-free DNA after transplantation. Transplant Rev (Orlando) 2020; 34:100542. [PMID: 32265093 DOI: 10.1016/j.trre.2020.100542] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/18/2020] [Accepted: 02/24/2020] [Indexed: 12/30/2022]
Abstract
Following the initial technical challenge of implanting an organ, maintaining the organ against a vast array of pathologies for years to come, remains a colossal challenge for all clinicians working in transplantation. Drug toxicity, opportunistic infection, primary disease recurrence, and the constant battle against organ rejection are all differentials that are considered when graft dysfunction is observed, promoting a lifetime of laborious surveillance. Cell free DNA (cfDNA) since its discovery in 1948 has made an impactful change in transplantation. A growing body of evidence in transplantation (109 manuscripts from 55 studies) shows the promise of this tool as an early and accurate detection of allograft injury rejection as well the benefit to rule out injury as part of screening and routine monitoring. With next generation sequencing rapidly becoming the standard of care in quantifying DNA, understanding this science in the context of transplantation is critical to ensure studies, outcomes and care is improved.
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Affiliation(s)
- Fungai Dengu
- Nuffield Department of Surgical Sciences, University of Oxford, United Kingdom.
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43
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Recent Advances in the Noninvasive Prenatal Testing for Chromosomal Abnormalities Using Maternal Plasma DNA. JOURNAL OF FETAL MEDICINE 2020. [DOI: 10.1007/s40556-019-00229-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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44
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Porreco RP, Burson C, Bao L, Haag M. Monozygosity by cell-free DNA screening in a dichorionic twin pregnancy with discordant fetal sex: Informed antenatal and postnatal care. Prenat Diagn 2020; 40:758-760. [PMID: 31916615 DOI: 10.1002/pd.5640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/17/2019] [Accepted: 12/22/2019] [Indexed: 11/06/2022]
Affiliation(s)
| | - Catherine Burson
- Center for Maternal Fetal Health, Rocky Mountain Hospital for Children, Denver, Colorado
| | - Liming Bao
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado
| | - Mary Haag
- Colorado Genetics Laboratory, Department of Pathology, University of Colorado School of Medicine, Aurora, Colorado
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Tam JCW, Chan YM, Tsang SY, Yau CI, Yeung SY, Au KK, Chow CK. Noninvasive prenatal paternity testing by means of SNP-based targeted sequencing. Prenat Diagn 2020; 40:497-506. [PMID: 31674029 PMCID: PMC7154534 DOI: 10.1002/pd.5595] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022]
Abstract
Objective To develop a method for noninvasive prenatal paternity testing based on targeted sequencing of single nucleotide polymorphisms (SNPs). Method SNPs were selected based on population genetics data. Target‐SNPs in cell‐free DNA extracted from maternal blood (maternal cfDNA) were analyzed by targeted sequencing wherein target enrichment was based on multiplex amplification using QIAseq Targeted DNA Panels with Unique Molecular Identifiers. Fetal SNP genotypes were called using a novel bioinformatics algorithm, and the combined paternity indices (CPIs) and resultant paternity probabilities were calculated. Results Fetal SNP genotypes obtained from targeted sequencing of maternal cfDNA were 100% concordant with those from amniotic fluid‐derived fetal genomic DNA. From an initial panel of 356 target‐SNPs, an average of 148 were included in paternity calculations in 15 family trio cases, generating paternity probabilities of greater than 99.9999%. All paternity results were confirmed by short‐tandem‐repeat analysis. The high specificity of the methodology was validated by successful paternity discrimination between biological fathers and their siblings and by large separations between the CPIs calculated for the biological fathers and those for 60 unrelated men. Conclusion The novel method is highly effective, with substantial improvements over similar approaches in terms of reduced number of target‐SNPs, increased accuracy, and reduced costs.
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Affiliation(s)
| | - Yee Man Chan
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Shui Ying Tsang
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Chung In Yau
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Shuk Ying Yeung
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Ka Ki Au
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Chun Kin Chow
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
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Genomic Medicine-Progress, Pitfalls, and Promise. Cell 2020; 177:45-57. [PMID: 30901547 DOI: 10.1016/j.cell.2019.02.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 02/07/2023]
Abstract
In the wake of the Human Genome Project (HGP), strong expectations were set for the timeline and impact of genomics on medicine-an anticipated transformation in the diagnosis, treatment, and prevention of disease. In this Perspective, we take stock of the nascent field of genomic medicine. In what areas, if any, is genomics delivering on this promise, or is the path to success clear? Where are we falling short, and why? What have been the unanticipated developments? Overall, we argue that the optimism surrounding the transformational potential of genomics on medicine remains justified, albeit with a considerably different form and timescale than originally projected. We also argue that the field needs to pivot back to basics, as understanding the entirety of the genotype-to-phenotype equation is a likely prerequisite for delivering on the full potential of the human genome to advance the human condition.
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Pan M, Yang D, He Y, Han J, Zhen L, Yang YD, Li DZ. Early prenatal detection of triploidy: a 9-year experience in mainland China. J Matern Fetal Neonatal Med 2019; 34:4072-4076. [PMID: 31852294 DOI: 10.1080/14767058.2019.1702963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Objective: In this study, we report the indications for prenatal cytogenetic diagnosis of triploid cases, in an attempt to identify clues to early diagnosis.Study design: This was a retrospective analysis of prenatal cases of triploidy during a 9-year period at mainland China. Clinical data were reviewed for these cases, including maternal demographics, indications for invasive testing, fetal ultrasound findings, and pregnancy outcomes.Results: A total of 22 singleton pregnancies affected with triploid fetuses were detected. The fetal karyotype included 69,XXX (72.7%) and 69,XXY (27.3%). Eighteen cases were identified by the first trimester screening program. One case was missed by maternal cell-free DNA testing, but detected by second trimester anatomy scan. Three cases escaped the first trimester screening and were detected by second trimester anatomy scan.Conclusions: The present study demonstrates that most triploid cases can be diagnosed prenatally during the first trimester. The early asymmetrical fetal growth restriction, structural anomalies, and extremely high risk serum screening result for trisomy 21 or 18 should alert the physicians to the investigation of triploidy.Key Message: Ultrasound-based first-trimester screening plays a major role in early diagnosis of fetal triploidy. Future replacement of routine first-trimester screening by cell-DNA testing might miss the chance of early diagnosis and management of triploid pregnancies.
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Affiliation(s)
- Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Dan Yang
- Capitalbio Genomics Co., Ltd, Dongguan, China
| | - Yi He
- Prenatal Diagnosis Center, Dongguan Women and Children Healthcare Hospital, Dongguan, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Li Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yan-Dong Yang
- Department of Ultrasound, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Dong-Zhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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Ioannides M, Achilleos A, Kyriakou S, Kypri E, Loizides C, Tsangaras K, Constantinou L, Koumbaris G, Patsalis PC. Development of a new methylation-based fetal fraction estimation assay using multiplex ddPCR. Mol Genet Genomic Med 2019; 8:e1094. [PMID: 31821748 PMCID: PMC7005606 DOI: 10.1002/mgg3.1094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/17/2019] [Indexed: 01/12/2023] Open
Abstract
Background Non‐invasive prenatal testing (NIPT) for fetal aneuploidies has rapidly been incorporated into clinical practice. Current NGS‐based methods can reliably detect fetal aneuploidies non‐invasively with fetal fraction of at least 4%. Inaccurate fetal fraction assessment can compromise the accuracy of the test as affected samples with low fetal fraction have an increased risk for misdiagnosis. Using a novel set of fetal‐specific differentially methylated regions (DMRs) and methylation sensitive restriction digestion (MSRD), we developed a multiplex ddPCR assay for accurate detection of fetal fraction in maternal plasma. Methods We initially performed MSRD followed by methylation DNA immunoprecipitation (MeDIP) and NGS on fetal and non‐pregnant female tissues to identify fetal‐specific DMRs. DMRs with the highest methylation difference between the two tissues were selected for fetal fraction estimation employing MSRD and multiplex ddPCR. Chromosome Y multiplex ddPCR assay (YMM) was used as a reference standard, to develop our fetal fraction estimation model in male pregnancy samples. Additional 123 samples were tested to examine whether the model is sex dependent and/or ploidy dependent. Results In all, 93 DMRs were identified of which seven were selected for fetal fraction estimation. Statistical analysis resulted in the final model which included four DMRs (FFMM). High correlation with YMM‐based fetal fractions was observed using 85 male pregnancies (r = 0.86 95% CI: 0.80–0.91). The model was confirmed using an independent set of 53 male pregnancies. Conclusion By employing a set of well‐characterized DMRs, we developed a SNP‐, sex‐ and ploidy‐independent methylation‐based multiplex ddPCR assay for accurate fetal fraction estimation.
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Altuğ Y, Liang N, Ram R, Ravi H, Ahmed E, Brevnov M, Swenerton RK, Zimmermann B, Malhotra M, Demko ZP, Billings PR, Ryan A. Analytical Validation of a Single-nucleotide Polymorphism-based Donor-derived Cell-free DNA Assay for Detecting Rejection in Kidney Transplant Patients. Transplantation 2019; 103:2657-2665. [PMID: 30801536 PMCID: PMC6867667 DOI: 10.1097/tp.0000000000002665] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 01/23/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Early detection of rejection in kidney transplant recipients holds the promise to improve clinical outcomes. Development and implementation of more accurate, noninvasive methods to detect allograft rejection remain an ongoing challenge. The limitations of existing allograft surveillance methods present an opportunity for donor-derived cell-free DNA (dd-cfDNA), which can accurately and rapidly differentiate patients with allograft rejection from patients with stable organ function. METHODS This study evaluated the analytical performance of a massively multiplexed polymerase chain reaction assay that targets 13 962 single-nucleotide polymorphisms, characterized and validated using 66 unique samples with 1064 replicates, including cell line-derived reference samples, plasma-derived mixtures, and transplant patient samples. The dd-cfDNA fraction was quantified in both related and unrelated donor-recipient pairs. RESULTS The dd-cfDNA assay showed a limit of blank of 0.11%, a limit of detection and limit of quantitation of 0.15% for unrelated donors, and limit of blank of 0.23%, a limit of detection and limit of quantitation of 0.29% for related donors. All other metrics (linearity, accuracy, and precision) were observed to be equivalent between unrelated and related donors. The measurement precision of coefficient of variation was 1.8% (repeatability, 0.6% dd-cfDNA) and was <5% for all the different reproducibility measures. CONCLUSIONS This study validates the performance of a single-nucleotide polymorphism-based massively multiplexed polymerase chain reaction assay to detect the dd-cfDNA fraction with improved precision over currently available tests, regardless of donor-recipient relationships.
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First Trimester Screening for Fetal Aneuploidies Using Placental Growth Factor: The Great Obstetrical Syndrome (GOS) Study. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2019; 40:1044-1049. [PMID: 30103877 DOI: 10.1016/j.jogc.2017.11.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/16/2017] [Accepted: 11/16/2017] [Indexed: 11/20/2022]
Abstract
OBJECTIVE This study sought to estimate the ability of first trimester maternal serum placental growth factor (PlGF) to identify fetal aneuploidies. METHODS A prospective cohort study of singleton pregnancy at 11 to 13 weeks was conducted. Maternal serum PlGF concentration was measured using BRAHMS PlGF plus KRYPTOR automated assays (Thermo Scientific BRAHMS, Hennigsdorf, Germany). PlGF and nuchal translucency were log-transformed and reported as multiples of the median (MoM) adjusted for crown-rump length. Detection rates were calculated using receiver-operator characteristic curves. RESULTS The study observed 21 cases of fetal aneuploidies (0.4%) out of 4765 participants. Trisomy 21 (13 cases; 0.85 MoM; interquartile range [IQR] 0.80-0.93), trisomy 18 (two cases; 0.77 MoM; IQR 0.66-0.87) and trisomy 13 (two cases; 0.68 MoM; IQR 0.61-0.75) were associated with low PlGF concentrations. The low PlGF values observed in the cases of monosomy X (two cases; 0.85 MoM; IQR 0.82-0.88, P = 0.05), triploidy (0.78 MoM, P = 0.11), and 47,XX,i(22)(p10) (0.18 MoM, P = 0.08) were not statistically different from the controls. A model including maternal age, nuchal translucency, and PlGF could have identified all (95% CI 83%-100%) cases of trisomy 21 and six of the other fetal aneuploidies (75%) at a false-positive rate of 9%. CONCLUSION Low first trimester PlGF is associated with an increased risk of fetal aneuploidy. PlGF combined with first trimester ultrasound (nuchal translucency, uterine artery Doppler, and early fetal anatomy) could identify not only women at high risk for preeclampsia, but also fetuses at high risk of aneuploidy for optimal further testing (non-invasive testing for common aneuploidy screening or chorionic villus sampling for full screening and diagnosis).
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