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Faieta M, Falcone R, Duca S, Corsetti E, Giannico R, Gigante L, Diano L, Calugi G, Spinella F, Pizzuti F. Test performance and clinical utility of expanded non-invasive prenatal test: Experience on 71,883 unselected routine cases from one single center. Prenat Diagn 2024; 44:936-945. [PMID: 38686956 DOI: 10.1002/pd.6580] [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: 07/13/2023] [Revised: 02/29/2024] [Accepted: 04/08/2024] [Indexed: 05/02/2024]
Abstract
OBJECTIVE The balance between benefits and risks of discordant outcomes makes the Genome-Wide Non-Invasive Prenatal Test (GW-NIPT) controversial. This study aims to evaluate performance and clinical utility in a wide cohort of unselected clinical cases from a single center when a standardized protocol is applied and integrated with a secondary algorithm for data interpretation. METHOD In 2 years, over 70,000 pregnant patients underwent GW-NIPT for fetal common trisomies, sex chromosome aneuploidies, rare autosomal aneuploidies, segmental abnormalities (CNVs ≥ 7 Mb) and microdeletions (CNVs < 7 Mb). All samples were uniformly processed with Veriseq NIPT Solution v2 and analyzed using all data metrics along with a home-made algorithm for sequencing data analysis. Results were retrospectively reviewed for clinical outcomes. RESULTS Among 71,883 eligible cases including twin pregnancies, 1011 (1.4%) received a positive result and 781 were confirmed by invasive prenatal diagnosis. Clinical sensitivity ranged from 99.65% for common trisomy (T21, T18, T13) to 83.33% for microdeletions, while specificity remained high (99.98%) for each class of fetal abnormalities detected. CONCLUSIONS Integrating a standardized protocol with an internal algorithm allowed discordant results to be reduced, yielding high accuracy. Observed reliability in detecting genome-wide chromosomal conditions reinforced the expanded NIPT utility in clinical practice.
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Affiliation(s)
- Monica Faieta
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
| | - Rossella Falcone
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Sara Duca
- Department of NIPT, Eurofins Genoma Group, Rome, Italy
| | | | | | - Laura Gigante
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Laura Diano
- Department of Genetic Counselling, Eurofins Genoma Group, Rome, Italy
| | - Graziella Calugi
- Department of Research and Development, Eurofins Genoma Group, Rome, Italy
| | - Francesca Spinella
- Department of Research and Development, Eurofins Genoma Group, Rome, Italy
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Fortin O, Mulkey SB, Fraser JL. Advancing fetal diagnosis and prognostication using comprehensive prenatal phenotyping and genetic testing. Pediatr Res 2024:10.1038/s41390-024-03343-9. [PMID: 38937640 DOI: 10.1038/s41390-024-03343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Prenatal diagnoses of congenital malformations have increased significantly in recent years with use of high-resolution prenatal imaging. Despite more precise radiological diagnoses, discussions with expectant parents remain challenging because congenital malformations are associated with a wide spectrum of outcomes. Comprehensive prenatal genetic testing has become an essential tool that improves the accuracy of prognostication. Testing strategies include chromosomal microarray, exome sequencing, and genome sequencing. The diagnostic yield varies depending on the specific malformations, severity of the abnormalities, and multi-organ involvement. The utility of prenatal genetic diagnosis includes increased diagnostic clarity for clinicians and families, informed pregnancy decision-making, neonatal care planning, and reproductive planning. Turnaround time for results of comprehensive genetic testing remains a barrier, especially for parents that are decision-making, although this has improved over time. Uncertainty inherent to many genetic testing results is a challenge. Appropriate genetic counseling is essential for parents to understand the diagnosis and prognosis and to make informed decisions. Recent research has investigated the yield of exome or genome sequencing in structurally normal fetuses, both with non-invasive screening methods and invasive diagnostic testing; the prenatal diagnostic community must evaluate and analyze the significant ethical considerations associated with this practice prior to generalizing its use. IMPACT: Reviews available genetic testing options during the prenatal period in detail. Discusses the impact of prenatal genetic testing on care using case-based examples. Consolidates the current literature on the yield of genetic testing for prenatal diagnosis of congenital malformations.
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Affiliation(s)
- Olivier Fortin
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
| | - Sarah B Mulkey
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
- Department of Neurology and Rehabilitation Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jamie L Fraser
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA.
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA.
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
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Chen CP. Genetic counseling of non-invasive prenatal testing (NIPT) trisomy 7-positive pregnancies. Taiwan J Obstet Gynecol 2024; 63:293-296. [PMID: 38802190 DOI: 10.1016/j.tjog.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 05/29/2024] Open
Abstract
Trisomy 7 is the most common observed type of rare autosomal trisomies (RATs) detected at expanded genome-wide non-invasive prenatal testing (NIPT). Genetic counseling of NIPT trisomy 7-positive pregnancies remains to be not easy because the parents may worry about the likelihood of adverse pregnancy outcomes, fetal abnormality and the necessity of invasive procedures for confirmation of fetal mosaic trisomy 7 and uniparental disomy (UPD) 7. This review provides a comprehensive information on the update issues concerning genetic counseling of NIPT trisomy 7-positive pregnancies.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Medical Laboratory Science and Biotechnology, College of Medical and Health Science, Asia University, Taichung, Taiwan.
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Pan C, Li Z, Cheng G, Luo X, Nie F, Gao J, Yang P. Association between chromosome abnormities and prenatal diagnosis indicators screening in the second trimester of pregnancy. Medicine (Baltimore) 2023; 102:e34762. [PMID: 37657051 PMCID: PMC10476756 DOI: 10.1097/md.0000000000034762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/24/2023] [Indexed: 09/03/2023] Open
Abstract
This study aimed to explore the prenatal indicators in the second trimester of pregnancy and their association with chromosome abnormities (CA) to guide decisions toward invasive diagnostic procedures. Pregnant women who underwent prenatal screening and underwent amniocentesis in the second trimester in our Hospital between June 2017 and February 2019 were included in this retrospective cohort study. The reason for amniocentesis in prenatal screening and diagnoses was extracted from the charts. Finally, 3449 pregnant women were included. Of them, 181 were with CA confirmed by amniocentesis (i.e., the CA group), while 3268 were without CA (i.e., the non-CA group). Compared with the women in the non-CA group, those in the CA group were more likely to be older (30 [27,32] vs 29 [26,31], P < .001), had higher gestational weeks (20 [19,23] vs 19 [18,23], P = .008), an increased risk of advanced maternal age (AMA) (9.4% vs 2.2%, P < .001), had an increased risk of NIPT (IRN) (5.1% vs 1.9%, P < .001), had higher rates of a parental chromosome abnormality (PCA) (1.8% vs 0.9%, P = .002), and had increased risk of trisomy 21 (IRT21) (63.0% vs 45.3%, P < .001). AMA (OR = 4.22, 95% CI: 2.35-7.58, P < .001; AUC = 0.536), IRN (OR = 10.62, 95% CI: 6.66-16.94, P < .001; AUC = 0.589), PCA (OR = 4.77, 95% CI: 2.01-11.32, P < .001; AUC = 0.584), and IRT21 (OR = 0.67, 95% CI: 0.47-0.89, P = .008; AUC = 0.515) were independently associated with CA. AMA, IRN, IRT21, and PCA during the second trimester were independently associated with CA, but their predictive values for CA were relatively low. Combining those indicators may improve the predictive value.
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Affiliation(s)
- Ci Pan
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zilong Li
- Jinan Pediatric Research Institute, Qilu Children’s Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guomei Cheng
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaohua Luo
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Fufang Nie
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Gao
- Department of Ultrasound, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peifeng Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Clinical, Cytogenetic and Molecular Cytogenetic Outcomes of Cell-Free DNA Testing for Rare Chromosomal Anomalies. Genes (Basel) 2022; 13:genes13122389. [PMID: 36553656 PMCID: PMC9777917 DOI: 10.3390/genes13122389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
The scope of cell-free DNA (cfDNA) testing was expanded to the genome, which allowed screening for rare chromosome anomalies (RCAs). Since the efficiency of the test for RCAs remains below the common aneuploidies, there is a debate on the usage of expanded tests. This study focuses on the confirmatory and follow-up data of cases with positive cfDNA testing for RCAs and cases with screen-negative results in a series of 912 consecutive cases that underwent invasive testing following cfDNA testing. Chorion villus sampling (CVS), amniocentesis (AS), fetal blood sampling, and term placenta samples were investigated using classical cytogenetic and molecular cytogenetic techniques. Out of 593 screen-positive results, 504 (85%) were for common aneuploidies, 40 (6.7%) for rare autosomal trisomies (RATs), and 49 (8.3%) for structural chromosome anomalies (SAs). Of the screen-positives for RATs, 20 cases were evaluated only in fetal tissue, and confined placental mosaicism (CPM) could not be excluded. Among cases with definitive results (n = 20), the rates of true positives, placental mosaics, and false positives were 35%, 45%, and 10%, respectively. Among screen-positives for SAs, 32.7% were true positives. The confirmation rate was higher for duplications than deletions (58.3% vs. 29.4%). The rate of chromosomal abnormality was 10.9% in the group of 256 screen-negatives with pathological ultrasound findings. This study provides further data to assess the efficiency of expanded cfDNA testing for RATs and SAs. The test efficiency for cfDNA seems to be higher for duplications than for deletions, which is evidence of the role of expert ultrasound in identifying pregnancies at increased risk for chromosome anomalies, even in pregnancies with screen-negatives. Furthermore, we discussed the efficiency of CVS vs. AC in screen-positives for RATs.
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Hu R, Huang W, Zhou W, Luo X, Ren C, Huang H, Hou Y, Guo L, He W, Lu J. Phenotypic findings and pregnancy outcomes of fetal rare autosomal aneuploidies detected using chromosomal microarray analysis. Hum Genomics 2022; 16:64. [PMID: 36457118 PMCID: PMC9714082 DOI: 10.1186/s40246-022-00438-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Aneuploidies are the most common chromosomal abnormality and the main genetic cause of adverse pregnancy outcomes. Since numerous studies have focused on common trisomies, relatively little is known about the association between phenotypic findings and rare autosomal aneuploidies (RAAs). We conducted a retrospective study of 48,904 cases for chromosomal microarray analysis in a large tertiary referral center and reported the overall frequencies, clinical manifestations, and outcomes of prenatal RAAs. RESULTS A total of 90 RAAs were detected, of which 83 cases were mosaic trisomies and 7 were non-mosaic trisomies. Chromosomes 16, 22, and 9 were identified as the major chromosomes involving RAAs. The four predominant indications for prenatal diagnosis in our RAA cases were RAA-positive in noninvasive prenatal screening, advanced maternal age, ultrasound abnormalities, and high-risk for serum prenatal screening. Cardiovascular defects were the most frequently observed structural abnormalities, followed by musculoskeletal anomalies. Increased nuchal translucency and persistent left superior vena cava, the major soft marker abnormalities involved, were also observed in our RAA cases. Clinical outcomes were available for all RAAs, with 63 induced abortions and 27 live births recorded. CONCLUSIONS Variable phenotypes and outcomes were observed, which were highly heterogeneous in cases of prenatal RAAs. Thus, a cautious and comprehensive strategy should be implemented during prenatal counseling for RAAs.
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Affiliation(s)
- Rong Hu
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Weiwei Huang
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Weining Zhou
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Xiaohui Luo
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Congmian Ren
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Huajie Huang
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Yaping Hou
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Li Guo
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Wei He
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
| | - Jian Lu
- grid.459579.30000 0004 0625 057XMedical Genetic Center, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400 Guangdong China ,grid.459579.30000 0004 0625 057XMaternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, 511400 China
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Dap M, Caffin L, Perdriolle-Galet E, Bonnet C, Morel O. Is Cell-free fetal DNA testing a safe option for women in a high-risk population after combined first-trimester testing? J Gynecol Obstet Hum Reprod 2022; 51:102329. [PMID: 35114410 DOI: 10.1016/j.jogoh.2022.102329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/23/2022] [Accepted: 01/30/2022] [Indexed: 11/16/2022]
Abstract
OBJECTIVES Our study aimed to examine the relevance of cell-free fetal DNA (cfDNA) testing on the screening of chromosomal defects and the issue of pregnancies in patients with a risk over 1:50 after the first-trimester combined test. METHODS This is a retrospective monocentric study. We included all consecutive patients with a singleton pregnancy between January 2015 and December 2020 attending our fetal medicine centre because the estimated risk for trisomy 21 after the first-trimester combined screening was over 1:50. The patients could either choose to have invasive testing or cell-free DNA testing. We collected data about the patient, the tests results (cfDNA, karyotype) and the pregnancy outcome (born alive, medical termination, miscarriage or intrauterine fetal death). RESULTS We included 98 patients with an estimated risk for trisomy 21 over 1:50. We found a total of 14 major chromosomal abnormalities (14/98; 14.3%), of which: thirteen trisomies 21 and one triploidy 69, XXY. A cfDNA testing was chosen by 34 (34/98; 34.7%) patients. Among the pathological results of invasive testing, 5 (5/64; 7.8%) couldn't be targeted by cfDNA testing. Two of them were placental mosaicism, one a triploidy 69, XXY, and two defects inherited from a parent and considered benign. There was no miscarriage linked to an invasive test in the population study. CONCLUSION In our monocentric cohort, a third of the patients choose cfDNA in a case of a risk over 1:50 after combined testing. Even if this cohort is too small to draw definitive conclusions, cfDNA could be safe in a high-risk population after combined testing. None of the chromosomal abnormalities found at the karyotype and non-detectable by cfDNA was a loss of information that impacted pregnancy follow-up. Further study could explore the input of Genome-Wide cfDNA and chromosomal micro-array in this population.
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Affiliation(s)
- Matthieu Dap
- Obstetrics and fetal medicine Unit, CHRU of Nancy, Nancy, France; Department of fetopathology and placental pathology, CHRU of Nancy, Nancy, France.
| | - Lucie Caffin
- Obstetrics and fetal medicine Unit, CHRU of Nancy, Nancy, France
| | | | - Céline Bonnet
- Department of Genetics, CHRU de Nancy, Vandœuvre-lès-Nancy, France
| | - Olivier Morel
- Obstetrics and fetal medicine Unit, CHRU of Nancy, Nancy, France; Inserm, Diagnostic and Interventional Adaptive Imaging, University of Lorraine, Nancy, France
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Goodman AM, Holden KA, Jeong AR, Kim L, Fitzgerald KD, Almasri E, McLennan G, Eisenberg M, Jahromi AH, Hoh C, Hurley M, Mulroney C, Tzachanis D, Ball ED, Jensen TJ, Kurzrock R. Assessing CAR T-Cell Therapy Response Using Genome-Wide Sequencing of Cell-Free DNA in Patients With B-Cell Lymphomas. Transplant Cell Ther 2021; 28:30.e1-30.e7. [PMID: 34655803 DOI: 10.1016/j.jtct.2021.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/09/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
Methods that enable monitoring of therapeutic efficacy of autologous chimeric antigen receptor (CAR) T-cell therapy will be clinically useful. The aim of this study is to demonstrate the feasibility of blood-derived cell-free DNA (cfDNA) to predict CAR T-cell therapy response in patients with refractory B-cell lymphomas. Whole blood was collected before and throughout CAR T-cell therapy until day 154. Low-coverage (∼0.4×), genome-wide cfDNA sequencing, similar to that established for noninvasive prenatal testing, was performed. The genomic instability number (GIN) was used to quantify plasma copy number alteration level. Twelve patients were enrolled. Seven (58%) patients achieved a complete response (CR); 2 (25%), a partial response. Median progression-free survival was 99 days; median overall survival was not reached (median follow-up, 247 days). Altogether, 127 blood samples were analyzed (median, 10 samples/patient [range 8-13]). All 5 patients who remained in CR at the time of last measurement had GIN <170 (threshold). Two patients who attained CR, but later relapsed, and all but one patient who had best response other than CR had last GIN measurement of >170. In 5 of 6 patients with relapsed or progressive disease, increasing GIN was observed before the diagnosis by imaging. The abundance of CAR T-cell construct (absolute number of construct copies relative to the number of human genome equivalents) also showed a trend to correlate with outcome (day 10, P = .052). These data describe a proof-of-concept for the use of multiple liquid biopsy technologies to monitor therapeutic response in B-cell lymphoma patients receiving CAR T-cell therapy.
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Affiliation(s)
- Aaron M Goodman
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California.
| | | | - Ah-Reum Jeong
- Department of Medicine, Division of Hematology/Oncology, University of California San Diego, La Jolla, California
| | - Lisa Kim
- Laboratory Corporation of America, San Diego, California
| | | | - Eyad Almasri
- Laboratory Corporation of America, San Diego, California
| | | | | | - Amin H Jahromi
- Department of Radiology, University of California San Diego, La Jolla, California
| | - Carl Hoh
- Department of Radiology, University of California San Diego, La Jolla, California
| | - Michael Hurley
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Carolyn Mulroney
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Dimitrios Tzachanis
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Edward D Ball
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Taylor J Jensen
- Laboratory Corporation of America, San Diego, California; Laboratory Corporation of America, Durham, North Carolina
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Ison HE, Griffin EL, Parrott A, Shikany AR, Meyers L, Thomas MJ, Syverson E, Demo EM, Fitzgerald KK, Fitzgerald-Butt S, Ziegler KL, Schartman AF, Stone KM, Helm BM. Genetic counseling for congenital heart disease - Practice resource of the national society of genetic counselors. J Genet Couns 2021; 31:9-33. [PMID: 34510635 DOI: 10.1002/jgc4.1498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 08/02/2021] [Accepted: 08/02/2021] [Indexed: 12/11/2022]
Abstract
Congenital heart disease (CHD) is an indication which spans multiple specialties across various genetic counseling practices. This practice resource aims to provide guidance on key considerations when approaching counseling for this particular indication while recognizing the rapidly changing landscape of knowledge within this domain. This resource was developed with consensus from a diverse group of certified genetic counselors utilizing literature relevant for CHD genetic counseling practice and is aimed at supporting genetic counselors who encounter this indication in their practice both pre- and postnatally.
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Affiliation(s)
- Hannah E Ison
- Stanford Center for Inherited Cardiovascular Disease, Stanford Health Care, Stanford, California, USA
| | - Emily L Griffin
- Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
| | | | - Amy R Shikany
- Cincinnati Children's Hospital Medical Center, The Heart Institute, Cincinnati, Ohio, USA
| | | | - Matthew J Thomas
- Department of Pediatrics, Division of Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Erin Syverson
- Department of Pediatrics, Division of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Erin M Demo
- Sibley Heart Center Cardiology at Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Kristi K Fitzgerald
- Nemours Cardiac Center, Alfred I. DuPont Hospital for Children, Wilmington, Delaware, USA
| | - Sara Fitzgerald-Butt
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | | | - Allison F Schartman
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, Indiana University Health, Indianapolis, Indiana, USA
| | - Kristyne M Stone
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, Indiana University Health, Indianapolis, Indiana, USA
| | - Benjamin M Helm
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Epidemiology, Indiana University Fairbanks School of Public Health, Indianapolis, Indiana, USA
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Soster E, Boomer T, Hicks S, Caldwell S, Dyr B, Chibuk J, Almasri E. Three years of clinical experience with a genome-wide cfDNA screening test for aneuploidies and copy-number variants. Genet Med 2021; 23:1349-1355. [PMID: 33731879 PMCID: PMC8257487 DOI: 10.1038/s41436-021-01135-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 11/11/2022] Open
Abstract
PURPOSE Pregnant women have unprecedented choices for prenatal screening and testing. Cell-free DNA (cfDNA) offers the option to screen for aneuploidy of all chromosomes and genome-wide copy-number variants (CNVs), expanding screening beyond the common trisomies ("traditional" cfDNA). We sought to review the utilization trends and clinical performance characteristics of a commercially available genome-wide cfDNA test, with a subset having available diagnostic testing outcomes. METHODS Retrospective analysis of 55,517 samples submitted for genome-wide cfDNA screening at a commercial laboratory, assessing indications, demographics, results, and performance. The cohort was broken into three "testing years"' to compare trends. RESULTS Indications shifted over time, with a decrease in referrals for ultrasound findings (22.0% to 12.0%) and an increase in no known high-risk indication (3.0% to 16.6%). Of the positive results, 25% would be missed with traditional cfDNA screening. High sensitivity and specificity were observed with a positive predictive value (PPV) of 72.6% for genome-wide CNVs and 22.4% for rare autosomal trisomies (RATs). CONCLUSION A broader patient population is utilizing genome-wide cfDNA, yet positivity rates and the contribution of genome-wide events have remained stable at approximately 5% and 25%, respectively. Test performance in a real-world clinical population shows high PPVs in those CNVs tested, with diagnostic outcomes in over 40% of positive cases.
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11
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Pertile MD, Flowers N, Vavrek D, Andrews D, Kalista T, Craig A, Deciu C, Duenwald S, Meier K, Bhatt S. Performance of a Paired-End Sequencing-Based Noninvasive Prenatal Screening Test in the Detection of Genome-Wide Fetal Chromosomal Anomalies. Clin Chem 2021; 67:1210-1219. [PMID: 34077512 DOI: 10.1093/clinchem/hvab067] [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] [Received: 12/15/2020] [Accepted: 04/13/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Noninvasive prenatal tests (NIPTs) detect fetal chromosomal anomalies with high clinical sensitivity and specificity. We examined the performance of a paired-end sequencing-based NIPT in the detection of genome-wide fetal chromosomal anomalies including common trisomies, sex chromosomal aneuploidies (SCA), rare autosomal aneuploidies (RAAs), and partial deletions/duplications ≥7 Mb. METHODS Frozen plasma samples from pregnant women were tested using the VeriSeq NIPT Solution v2 assay. All samples were previously tested with a laboratory-developed NIPT and had known clinical outcomes. Individuals performing the sequencing were blinded to clinical outcome data. Clinical sensitivity and specificity were determined for basic (chromosomes 21, 18, 13, X, and Y) and genome-wide screening modes. RESULTS Of 2335 samples that underwent genome-wide analysis, 28 did not meet QC requirements, resulting in a first-pass assay failure rate of 1.2%. Basic screening analysis, excluding known mosaics, correctly classified 130/130 trisomy 21 samples (sensitivity >99.9%, 95% confidence interval [CI] 97.1%-100%), 41/41 trisomy 18 samples (sensitivity >99.9%, 95% CI 91.4%-100%), and 26/26 trisomy 13 samples (sensitivity >99.9%, 95% CI 87.1%-100%) with 6 false-positive results; specificities ≥99.90% were reported for all 3 trisomies. Concordance for SCAs ranged from 90.5%-100%. Genome-wide screening analysis including known mosaics correctly classified 27/28 RAAs and 20/27 partial deletions/duplications with a specificity of 99.80% for both anomalies, and an overall genome-wide specificity for all anomalies of 99.34%. CONCLUSIONS The VeriSeq NIPT Solution v2 assay enables accurate identification of fetal aneuploidy, allowing detection of genome-wide fetal chromosomal anomalies with high clinical sensitivities and specificities and a low assay failure rate.Clinical Trial Notification [CTN] identification number [ID]: CT-2018-CTN-01585-1 v1, Protocol: NIPT T05 002.
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Affiliation(s)
- Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia
| | - Nicola Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Darcy Vavrek
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Daniel Andrews
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Tasha Kalista
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Andrew Craig
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Cosmin Deciu
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sven Duenwald
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Kristen Meier
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
| | - Sucheta Bhatt
- Departments of Bioinformatics, Biostatistics, Development, Medical Affairs, and Clinical Affairs, Illumina, Inc., San Diego, CA, USA
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12
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Gou L, Fang Y, Wang N, Zhang M, Liu T, Wang Y, Hu S, Zhang Y, Wu Q, Wang Y, Suo F, Gu M. Clinical management of pregnancies with positive screening results for rare autosomal aneuploidies at a single center. J Int Med Res 2021; 48:300060520966877. [PMID: 33167762 PMCID: PMC7658522 DOI: 10.1177/0300060520966877] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Objective To review our experiences on clinical management of pregnancies with positive noninvasive prenatal testing (NIPT) results for rare autosomal aneuploidies (RAAs) at a single center. Methods We performed a retrospective study and reviewed data from 18,016 pregnancies undergoing NIPT at a single center in China from March 2017 to February 2020. Depending on the patient’s choice, women with positive screening results for RAAs underwent chromosomal microarray analysis for invasive prenatal diagnosis. Results Thirty-three positive cases for RAAs were identified, with a positive screening rate of 0.18%. The most common RAA was trisomy 7 (33.3%), while trisomies for other chromosomes were less frequent. Monosomies involving chromosomes 16, 14, and 22 were observed. Twenty-eight cases of RAAs underwent invasive diagnosis. Abnormal pregnancy outcomes were observed in four cases, including true fetal mosaicism (n=1), partial uniparental disomy (n=1), miscarriage (n=1), and structural anomalies on ultrasound (n=1). Conclusions RAAs at NIPT might be associated with fetal uniparental disomy, mosaic aneuploidy, and poor pregnancy outcomes, but most positive cases have normal pregnancy outcomes. For RAAs, genetic counseling on the potential risks of abnormal NIPT results, as well as on benefits and limitations of invasive prenatal diagnosis, might help guide clinical management.
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Affiliation(s)
- Lingshan Gou
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yuan Fang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Na Wang
- DAAN Gene Co., Ltd. of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Man Zhang
- Zhejiang Biosan Biochemical Technologies Co., Ltd., Hangzhou, Zhejiang, China
| | - Tianya Liu
- Department of Pharmacy, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yi Wang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shunan Hu
- Office of Scientific Research & Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, Henan Province, China
| | - Yan Zhang
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qin Wu
- Zhejiang Biosan Biochemical Technologies Co., Ltd., Hangzhou, Zhejiang, China
| | - Yifan Wang
- Department of Ultrasound, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Feng Suo
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Maosheng Gu
- Center for Genetic Medicine, Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, Jiangsu, China
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13
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Chen Y, Lai Y, Xu F, Qin H, Tang Y, Huang X, Meng L, Su J, Sun W, Shen Y, Wei H. The application of expanded noninvasive prenatal screening for genome-wide chromosomal abnormalities and genetic counseling. J Matern Fetal Neonatal Med 2021; 34:2710-2716. [PMID: 33938369 DOI: 10.1080/14767058.2021.1907333] [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: 10/21/2022]
Abstract
OBJECTIVE To evaluate the clinical application of expanded noninvasive prenatal screening (eNIPS) for genome-wide large copy number variation (CNV), i.e. chromosomal deletion/duplication >5 Mb, and aneuploidy; also to provide practical information for counseling eNIPS positive cases. METHOD We recruited 34,620 women with singleton pregnancy for genome-wide cell-free plasma DNA sequencing. Screening positive cases were verified by karyotyping and/or SNP array. RESULT A total of 461 (1.33%) positive cases were identified through our cfDNA screening including 209 cases of common trisomies (0.60%), 124 cases of sex chromosomal abnormalities (SCA) (0.36%), 71 cases of other autosomal anueploidies (OAA) (0.21%), and 57 CNVs larger than 5 Mb (0.16%). The predictive positive values (PPV) were 70.06% in general for common trisomies with as high as 91.67% for Trisomy21 (T21), 40.22% in general for SCAs with as high as 100% for Jacob Syndrome (XYY). The PPV for OAAs was 5.45%, and T7/T8/T16/T22 were the most frequent OAAs (n = 15, 9, 9, 8, respectively). The PPV for CNVs larger than 5 Mb was 51.22% (n = 57) with the CNV mostly detected on Chr5/Chr4/Chr2/Chr7 (n = 10, 8, 5, 5, respectively). CONCLUSION The expanded NIPS had shown promising PPVs for CNVs (large than 5 Mb), SCAs and common trisomies, yet this method required higher efficacy in screening for OAAs. The post-test genetic counseling for expanded NIPS should be tailored to the types of positive cases and also address the origin of abnormal signals (fetal vs. maternal).
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Affiliation(s)
- Yun Chen
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Yunli Lai
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Fuben Xu
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Haisong Qin
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Yanqing Tang
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Xiaoshan Huang
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Lintao Meng
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Jiasun Su
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Weijia Sun
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
| | - Yiping Shen
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China.,Division of Genetics and Genomics, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hongwei Wei
- Genetic and Metabolic Central Laboratory, The Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Guangxi Birth Defects Prevention and Control Institute, Nanning, PR China
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14
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Utility of noninvasive genome-wide screening: a prospective cohort of obstetric patients undergoing diagnostic testing. Genet Med 2021; 23:1341-1348. [PMID: 33782554 DOI: 10.1038/s41436-021-01147-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Copy-number variant (CNV) assessment is recommended for patients undergoing prenatal diagnostic testing. Noninvasive screening tests have not been extensively validated for CNV detection. The objective of this study was to compare the ability of genome-wide noninvasive prenatal screening (NIPS) to chromosomal microarray to detect clinically significant findings. METHODS We prospectively enrolled 198 subjects at the time of consent for diagnostic prenatal testing. Genome-wide NIPS results were compared with diagnostic testing results to assess NIPS test performance (n = 160, 38 subjects without microarray results excluded). Cohen's kappa statistic was used to assess test agreement. RESULTS Genome-wide NIPS did not detect clinically significant chromosomal abnormalities at the same rate as diagnostic testing, κ = 0.75 (95% confidence interval [CI], 0.62-0.87). When excluding CNVs <7 Mb and findings outside the limits of genome-wide NIPS, test agreement improved, κ = 0.88 (0.79-0.97) driven by agreement for common aneuploidies (κ = 1.0). However, among patients with an abnormal fetal survey, agreement was only fair, κ = 0.38 (0.08-0.67). CONCLUSION While NIPS is an excellent screening test for common aneuploidies, genome-wide NIPS misses clinically significant findings detected on routine diagnostic testing. False positive and false negative cases highlight the importance of pretest counseling regarding NIPS limitations, especially in the setting of fetal anomalies.
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15
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Lai Y, Zhu X, He S, Dong Z, Tang Y, Xu F, Chen Y, Meng L, Tao Y, Yi S, Su J, Huang H, Luo J, Leung TY, Wei H. Performance of Cell-Free DNA Screening for Fetal Common Aneuploidies and Sex Chromosomal Abnormalities: A Prospective Study from a Less Developed Autonomous Region in Mainland China. Genes (Basel) 2021; 12:478. [PMID: 33806256 PMCID: PMC8067030 DOI: 10.3390/genes12040478] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/01/2021] [Accepted: 03/19/2021] [Indexed: 12/24/2022] Open
Abstract
To evaluate the performance of noninvasive prenatal screening (NIPS) in the detection of common aneuploidies in a population-based study, a total of 86,262 single pregnancies referred for NIPS were prospectively recruited. Among 86,193 pregnancies with reportable results, follow-up was successfully conducted in 1160 fetuses reported with a high-risk result by NIPS and 82,511 cases (95.7%) with a low-risk result. The screen-positive rate (SPR) of common aneuploidies and sex chromosome abnormalities (SCAs) provided by NIPS were 0.7% (586/83,671) and 0.6% (505/83,671), respectively. The positive predictive values (PPVs) for Trisomy 21, Trisomy 18, Trisomy 13 and SCAs were calculated as 89.7%, 84.0%, 52.6% and 38.0%, respectively. In addition, less rare chromosomal abnormalities, including copy number variants (CNVs), were detected, compared with those reported by NIPS with higher read-depth. Among these rare abnormalities, only 23.2% (13/56) were confirmed by prenatal diagnosis. In total, four common trisomy cases were found to be false negative, resulting in a rate of 0.48/10,000 (4/83,671). In summary, this study conducted in an underdeveloped region with limited support for the new technology development and lack of cost-effective prenatal testing demonstrates the importance of implementing routine aneuploidy screening in the public sector for providing early detection and precise prognostic information.
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Affiliation(s)
- Yunli Lai
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
| | - Xiaofan Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Genetics and Prenatal Diagnosis Center, The First Affiliation Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Sheng He
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Zirui Dong
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Yanqing Tang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Fuben Xu
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yun Chen
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Lintao Meng
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Yuli Tao
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Shang Yi
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jiasun Su
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Hongqian Huang
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Jingsi Luo
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Genetic and Metabolic Central Laboratory, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China; (X.Z.); (Z.D.); (T.Y.L.)
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518000, China
- The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Hongwei Wei
- Birth Defects Prevention and Control Institute of Guangxi Zhuang Autonomous Region, Nanning 530000, China; (Y.L.); (S.H.); (Y.T.); (F.X.); (Y.C.); (L.M.); (Y.T.); (S.Y.); (J.S.); (H.H.); (J.L.)
- Guangxi Clinical Research Center for Fetal Diseases, Nanning 530000, China
- Department of Obstetrics and Gynaecology, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530000, China
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16
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Rafalko J, Caldwell S, Soster E, Almasri E, McLennan G, Liu T, Weinblatt V, Cacheris P, McCullough R. Application of mosaicism ratio to multifetal gestations. PLoS One 2021; 16:e0248467. [PMID: 33711042 PMCID: PMC7954340 DOI: 10.1371/journal.pone.0248467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/28/2021] [Indexed: 12/02/2022] Open
Abstract
Mosaicism ratio, or MR, is a laboratory metric that can be calculated using massively parallel sequencing data from cell-free DNA (cfDNA) screening. MR compares the amount of cfDNA present from a particular chromosome or chromosomal region to the overall fetal fraction of the specimen. In singleton gestations, MR may be used to refine the positive predictive value of an abnormal cfDNA screening result by identifying cases that could be impacted by various biological factors, such as placental mosaicism or prior co-twin demise. The current study was designed to examine the behavior of mosaicism ratio (MR) in multifetal gestations. Multifetal cfDNA specimens with positive results for trisomies 21, 18, or 13 and confirmed diagnostic outcomes were compiled to examine MR of the aneuploid chromosome based on the number of affected fetuses/placentas. A second multifetal cohort was assembled to analyze the MR of the Y chromosome in cases with at least one male fetus. For aneuploid cases, the average MR of affected singletons (used as a biological proxy for two affected twins) was significantly higher than the average MR for twins in which one fetus was affected. The average MR of the aneuploid chromosome for one affected twin was 52%, 42%, and 48% of that of singleton gestations for trisomy 21, 18, and 13 cases, respectively. MR cutoffs of 0.7 for trisomy 21, and 0.5 for trisomies 18 and 13 may help predict whether one versus both twins are affected with aneuploidy when clinical concern arises. For male cases, the Y MR of XX/XY gestations was 48% of the Y MR for XY/XY gestations. Using a Y MR cutoff of 0.8 allowed determination of XX/XY versus XY/XY gestations with 92.3-94.9% accuracy. Based on the data presented, MR may have utility in the analysis and interpretation of cfDNA data from multifetal gestations.
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Affiliation(s)
- Jill Rafalko
- Laboratory Corporation of America, La Jolla, California, United States of America
| | - Samantha Caldwell
- Laboratory Corporation of America, La Jolla, California, United States of America
| | - Erica Soster
- Laboratory Corporation of America, La Jolla, California, United States of America
| | - Eyad Almasri
- Laboratory Corporation of America, La Jolla, California, United States of America
| | - Graham McLennan
- Laboratory Corporation of America, La Jolla, California, United States of America
| | - Tong Liu
- Laboratory Corporation of America, La Jolla, California, United States of America
| | - Vivian Weinblatt
- Laboratory Corporation of America, La Jolla, California, United States of America
| | - Philip Cacheris
- Laboratory Corporation of America, La Jolla, California, United States of America
| | - Ron McCullough
- Laboratory Corporation of America, La Jolla, California, United States of America
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17
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Rodríguez J, Avila J, Rolfo C, Ruíz-Patiño A, Russo A, Ricaurte L, Ordóñez-Reyes C, Arrieta O, Zatarain-Barrón ZL, Recondo G, Cardona AF. When Tissue is an Issue the Liquid Biopsy is Nonissue: A Review. Oncol Ther 2021; 9:89-110. [PMID: 33689160 PMCID: PMC8140006 DOI: 10.1007/s40487-021-00144-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/11/2021] [Indexed: 02/07/2023] Open
Abstract
Precision medicine has impacted the field of medical oncology by introducing personalized therapies, improving all measurable outcomes. This field, in turn, has expanded to obtaining and analyzing a vast and ever-increasing amount of genomic information. One technique currently applied is the liquid biopsy, which consists of detecting and isolating DNA and exosomes in cancer patients. Newly developed techniques have made it possible to use the liquid biopsy in a wide range of settings. However, challenges regarding the validation of its clinical utility exist because of a lack of standardization across different techniques and tumor types, confounder genomic information, lack of appropriate clinical trial designs, and a non-measured, and therefore not estimated, economic impact on population health. Nowadays, liquid biopsy is not routinely used, but ongoing research is increasing its popularity, and a new era in oncology is developing. Therefore, it is essential to have an in-depth understanding of the liquid biopsy technique. In this review, we summarize the leading techniques and liquid biopsy applications in cancer.
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Affiliation(s)
- July Rodríguez
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Jenny Avila
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Christian Rolfo
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alejandro Ruíz-Patiño
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia
| | - Alessandro Russo
- Medical Oncology Unit A.O. Papardo and Department of Human Pathology, University of Messina, Messina, Italy
| | - Luisa Ricaurte
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia
- Pathology Department, Mayo Clinic, Rochester, MN, USA
| | | | - Oscar Arrieta
- Thoracic Oncology Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | - Gonzalo Recondo
- Thoracic Oncology Section, Centro de Educación Médica e Investigaciones Clínicas (CEMIC), Buenos Aires, Argentina
| | - Andrés F Cardona
- Foundation for Clinical and Applied Cancer Research (FICMAC), Bogota, Colombia.
- Molecular Oncology and Biology Systems Research Group (Fox-G/ONCOLGroup), Universidad El Bosque, Bogota, Colombia.
- Clinical and Traslational Oncology Group, Clinica del Country, Bogota, Colombia.
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18
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Zhu X, Chen M, Wang H, Guo Y, Chau MHK, Yan H, Cao Y, Kwok YKY, Chen J, Hui ASY, Zhang R, Meng Z, Zhu Y, Leung TY, Xiong L, Kong X, Choy KW. Clinical utility of expanded non-invasive prenatal screening and chromosomal microarray analysis in high-risk pregnancy. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:459-465. [PMID: 32198896 DOI: 10.1002/uog.22021] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/27/2020] [Accepted: 03/13/2020] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To evaluate the utility of expanded non-invasive prenatal screening (NIPS), compared with chromosomal microarray analysis (CMA), for the detection of chromosomal abnormalities in high-risk pregnancies. METHODS This was a multicenter retrospective study of singleton pregnancies at high risk for chromosomal abnormality. Patients who underwent expanded NIPS and CMA sequentially during pregnancy from 2015 to 2019 were included in the analysis. Pregnancies with a positive result for sex chromosome aneuploidy were excluded as the full details could not be retrieved. The utility of expanded NIPS and CMA for detection of chromosomal abnormalities in this cohort was compared by assessing the concordance between the results. RESULTS Of the 774 included high-risk pregnancies, 550 (71.1%) had a positive NIPS result, while a positive CMA result was detected in 308 (39.8%) cases. The rate of full or partial concordance between NIPS and CMA was 82.2%, 59.6% and 25.0% for trisomies 21, 18 and 13, respectively. For rare aneuploidies and segmental imbalances, NIPS and CMA results were fully or partially concordant in 7.5% and 33.3% of cases, respectively. Copy-number variants < 5 Mb were detected more often by CMA, with an incidence of 7.9% (61/774) compared with 3.1% (24/774) by NIPS. A genetic aberration was detected by CMA in 1 in 17 (5.8%) high-risk pregnancies that had a negative or non-reportable NIPS result. CONCLUSION CMA allows for comprehensive detection of genome-wide chromosomal abnormalities in high-risk pregnancies. CMA should be offered instead of expanded NIPS for high-risk pregnancies. Copyright © 2020 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- X Zhu
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - M Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - H Wang
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Y Guo
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - M H K Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - H Yan
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Y Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Y K Y Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - J Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - A S Y Hui
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - R Zhang
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Z Meng
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - Y Zhu
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - T Y Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - L Xiong
- Department of Central Laboratory, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Guangdong, China
| | - X Kong
- Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - K W Choy
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, SAR, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- The Chinese University of Hong Kong, Baylor College of Medicine Joint Center for Medical Genetics, The Chinese University of Hong Kong, Hong Kong, SAR, China
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Clinical Significance of Non-Invasive Prenatal Screening for Trisomy 7: Cohort Study and Literature Review. Genes (Basel) 2020; 12:genes12010011. [PMID: 33374124 PMCID: PMC7824243 DOI: 10.3390/genes12010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/09/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022] Open
Abstract
Trisomy 7 is the most frequently observed type of rare autosomal trisomies in genome-wide non-invasive prenatal screening (NIPS). Currently, the clinical significance of trisomy 7 NIPS-positive results is still unknown. We reviewed two independent cohorts from two laboratories where similar NIPS metrics were applied. A total of 70,441 singleton cases who underwent genome-wide NIPS were analyzed, among which 39 pregnancies were positive for trisomy 7, yielding a screen-positive rate of 0.055% (39/70,441). There were 28 cases with invasive testing results available; the positive predictive value (PPV) was 3.6% (1/28). We then searched the published NIPS studies to generate a large cohort of 437,873 pregnancies and identified 247 cases (0.056%) that were screened positive for trisomy 7. The overall PPV was 3.4% (4/118) in the combined data. The presence of uniparental disomy 7 was not detected in the NIPS trisomy 7-positive pregnancies with normal fetal karyotype. Among the 85 cases with pregnancy outcome available in combined data, 88.2% were normal live births, 14.1% had intrauterine growth restriction, preterm birth or low birth weight, 3.5% presented with ultrasound abnormality, and no fetal loss was observed. Our data provide valuable information for counseling and management of trisomy 7-positive NIPS pregnancies.
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Abstract
For decades, prenatal testing has been offered to evaluate pregnancies for genetic conditions. In recent years, the number of testing options and range of testing capabilities has dramatically increased. Because of the risks associated with invasive diagnostic testing, research has focused on the detection of genetic conditions through screening technologies such as cell-free DNA. Screening for aneuploidy, copy number variants, and monogenic disorders is clinically available using a sample of maternal blood, but limited data exist on the accuracy of some of these testing options. Additional research is needed to examine the accuracy and utility of screening for increasingly rare conditions. As the breadth of prenatal genetic testing options continues to expand, patients, clinical providers, laboratories, and researchers need to find collaborative means to validate and introduce new testing technologies responsibly. Adequate validation of prenatal tests and effective integration of emerging technologies into prenatal care will become even more important once prenatal treatments for genetic conditions become available.
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Affiliation(s)
- Blair Stevens
- McGovern Medical School at UTHealth in Houston, Department of Obstetrics, Gynecology and Reproductive Sciences, Houston, Texas 77030, USA
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21
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Abstract
Prenatal testing for chromosomal abnormalities is designed to provide an accurate assessment of a patient's risk of carrying a fetus with a chromosomal disorder. A wide variety of prenatal screening and diagnostic tests are available; each offers varying levels of information and performance, and each has relative advantages and limitations. When considering screening test characteristics, no one test is superior in all circumstances, which results in the need for nuanced, patient-centered counseling from the obstetric care professional and complex decision making by the patient. Each patient should be counseled in each pregnancy about options for testing for fetal chromosomal abnormalities. It is important that obstetric care professionals be prepared to discuss not only the risk of fetal chromosomal abnormalities but also the relative benefits and limitations of the available screening and diagnostic tests. Testing for chromosomal abnormalities should be an informed patient choice based on provision of adequate and accurate information, the patient's clinical context, accessible health care resources, values, interests, and goals. All patients should be offered both screening and diagnostic tests, and all patients have the right to accept or decline testing after counseling.The purpose of this Practice Bulletin is to provide current information regarding the available screening test options available for fetal chromosomal abnormalities and to review their benefits, performance characteristics, and limitations. For information regarding prenatal diagnostic testing for genetic disorders, refer to Practice Bulletin No. 162, Prenatal Diagnostic Testing for Genetic Disorders. For additional information regarding counseling about genetic testing and communicating test results, refer to Committee Opinion No. 693, Counseling About Genetic Testing and Communication of Genetic Test Results. For information regarding carrier screening for genetic conditions, refer to Committee Opinion No. 690, Carrier Screening in the Age of Genomic Medicine and Committee Opinion No. 691, Carrier Screening for Genetic Conditions. This Practice Bulletin has been revised to further clarify methods of screening for fetal chromosomal abnormalities, including expanded information regarding the use of cell-free DNA in all patients regardless of maternal age or baseline risk, and to add guidance related to patient counseling.
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22
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Rafalko JM, Caldwell S, Tynan J, Almasri E, Weinblatt V, McCullough R. Impact of mosaicism ratio on positive predictive value of cfDNA screening. Prenat Diagn 2020; 41:28-34. [PMID: 33151555 PMCID: PMC7894494 DOI: 10.1002/pd.5863] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/25/2020] [Accepted: 10/01/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To examine the relationship between the fraction of cell-free DNA (cfDNA) affected by aneuploidy compared to the overall fetal fraction of a prenatal screening specimen and its effect on positive predictive value (PPV). METHOD CfDNA specimens positive for trisomy 13, 18, and 21 with diagnostic outcomes were analysed over a 22-month period in one clinical laboratory. For each positive specimen, a "mosaicism ratio" (MR) was calculated by dividing the fraction of cfDNA affected by aneuploidy by the overall fetal fraction of the specimen. PPVs were calculated and analyzed based on various MR ranges. RESULTS Trisomy 13 was the aneuploidy most commonly seen in mosaic form, followed by trisomy 18 and trisomy 21. Significant differences in positive predictive values were noted for all three trisomies between samples with an MR in the "mosaic" versus "non-mosaic" range, as well as between results classified as "low-mosaic" versus "high-mosaic." CONCLUSION PPVs may be influenced, in part, by the mosaicism ratio associated with a particular result. The data generated from this study may be useful in providing more personalized risk assessments for patients with positive cfDNA screening results.
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Affiliation(s)
- Jill M Rafalko
- Laboratory Corporation of America Holdings, Integrated Genetics, Westborough, Massachusetts, USA
| | - Samantha Caldwell
- Laboratory Corporation of America Holdings, Sequenom Center for Molecular Medicine, LLC, San Diego, California, USA
| | - John Tynan
- Laboratory Corporation of America Holdings, Sequenom Center for Molecular Medicine, LLC, San Diego, California, USA
| | - Eyad Almasri
- Laboratory Corporation of America Holdings, Sequenom Center for Molecular Medicine, LLC, San Diego, California, USA
| | - Vivian Weinblatt
- Laboratory Corporation of America Holdings, Integrated Genetics, Westborough, Massachusetts, USA
| | - Ron McCullough
- Laboratory Corporation of America Holdings, Sequenom Center for Molecular Medicine, LLC, San Diego, California, USA
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23
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Lu W, Huang T, Wang XR, Zhou JH, Yuan HZ, Yang Y, Huang TT, Liu DP, Liu YQ. Next-generation sequencing: a follow-up of 36,913 singleton pregnancies with noninvasive prenatal testing in central China. J Assist Reprod Genet 2020; 37:3143-3150. [PMID: 33094428 PMCID: PMC7714822 DOI: 10.1007/s10815-020-01977-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/12/2020] [Indexed: 12/18/2022] Open
Abstract
PURPOSE To evaluate the noninvasive prenatal testing (NIPT) results of 36,913 cases in Jiangxi province of central China and explore its application value in prenatal screening and diagnosis. METHODS This retrospective analysis included 36,913 singleton pregnant women who underwent NIPT because of moderate-/high-risk pregnancy or voluntary requirements between January 2017 and December 2019 in our hospital. Chromosomal abnormalities such as trisomies 21, 18, and 13 (T21, T18, T13) and sex chromosome aneuploidies (SCAs) were judged by standard Z-score analysis. Positive NIPT results were confirmed by amniocentesis and karyotyping. Pregnancy outcomes were followed up via telephone interview. RESULTS A total of 1.01% (371/36,913) positive cases were detected by NIPT, comprising 137, 46, 31, and 157 cases of T21, T18, T13, and SCAs, respectively. A total of 116 of T21, 27 of T18, 13 of T13, and 51 of SCAs were confirmed to be true positive; all normal cases that had been followed up were verified to be true negative. The NIPT sensitivity in T21, T18, T13, and SCAs was 100.00% individually, whereas the specificity was 99.94% (36,488/36,509), 99.95% (36,579/36,598), 99.95% (36,594/36,612), and 99.72% (36,472/36,574), respectively. Furthermore, the negative predictive values of T21, T18, T13, and SCAs were all 100%, while the positive predictive values were 84.67%, 58.70%, 41.94%, and 33.33%, respectively. CONCLUSION NIPT is highly sensitive and has a low false positive rate in testing clinically significant fetal aneuploidies of general reproductive women. However, this technique cannot substitute for amniocentesis and karyotyping, and detailed genetic counseling is also essential for the high-risk group of NIPT.
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Affiliation(s)
- Wan Lu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ting Huang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Xin-Rong Wang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ji-Hui Zhou
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Hui-Zhen Yuan
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Yan Yang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Ting-Ting Huang
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Dan-Ping Liu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China
| | - Yan-Qiu Liu
- Prenatal Diagnosis Center, Jiangxi Maternal and Child Health Hospital, Nanchang, 330006, Jiangxi, China.
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24
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Gašperšič J, Videtič Paska A. Potential of modern circulating cell-free DNA diagnostic tools for detection of specific tumour cells in clinical practice. Biochem Med (Zagreb) 2020; 30:030504. [PMID: 32774122 PMCID: PMC7394254 DOI: 10.11613/bm.2020.030504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022] Open
Abstract
Personalized medicine is a developing field of medicine that has gained in importance in recent decades. New diagnostic tests based on the analysis of circulating cell-free DNA (cfDNA) were developed as a tool of diagnosing different cancer types. By detecting the subpopulation of mutated DNA from cancer cells, it is possible to detect the presence of a specific tumour in early stages of the disease. Mutation analysis is performed by quantitative polymerase chain reaction (qPCR) or the next generation sequencing (NGS), however, cfDNA protocols need to be modified carefully in preanalytical, analytical, and postanalytical stages. To further improve treatment of cancer the Food and Drug Administration approved more than 20 companion diagnostic tests that combine cancer drugs with highly efficient genetic diagnostic tools. Tools detect mutations in the DNA originating from cancer cells directly through the subpopulation of cfDNA, the circular tumour DNA (ctDNA) analysis or with visualization of cells through intracellular DNA probes. A large number of ctDNA tests in clinical studies demonstrate the importance of new findings in the field of cancer diagnosis. We describe the innovations in personalized medicine: techniques for detecting ctDNA and genomic DNA (gDNA) mutations approved Food and Drug Administration companion genetic diagnostics, candidate genes for assembling the cancer NGS panels, and a brief mention of the multitude of cfDNA currently in clinical trials. Additionally, an overview of the development steps of the diagnostic tools will refresh and expand the knowledge of clinics and geneticists for research opportunities beyond the development phases.
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Affiliation(s)
- Jernej Gašperšič
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alja Videtič Paska
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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25
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Flowers NJ, Burgess T, Giouzeppos O, Shi G, Love CJ, Hunt CE, Scarff KL, Archibald AD, Pertile MD. Genome-wide noninvasive prenatal screening for carriers of balanced reciprocal translocations. Genet Med 2020; 22:1944-1955. [PMID: 32807973 DOI: 10.1038/s41436-020-0930-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Balanced reciprocal translocation carriers are at increased risk of producing gametes with unbalanced forms of the translocation leading to miscarriage, fetal anomalies, and birth defects. We sought to determine if genome-wide cell-free DNA based noninvasive prenatal screening (gw-NIPS) could provide an alternative to prenatal diagnosis for carriers of these chromosomal rearrangements. METHODS This pilot series comprises a retrospective analysis of gw-NIPS and clinical outcome data from 42 singleton pregnancies where one parent carried a balanced reciprocal translocation. Gw-NIPS was performed between August 2015 and March 2018. Inclusion criteria required at least one translocation segment to be ≥15 Mb in size. RESULTS Forty samples (95%) returned an informative result; 7 pregnancies (17.5%) were high risk for an unbalanced translocation and confirmed after diagnostic testing. The remaining 33 informative samples were low risk and confirmed after diagnostic testing or normal newborn physical exam. Test sensitivity of 100% (95% confidence interval [CI]: 64.6-100%) and specificity of 100% (95% CI: 89.6-100%) were observed for this pilot series. CONCLUSION We demonstrate that gw-NIPS is a potential option for a majority of reciprocal translocation carriers. Further confirmation of this methodology could lead to adoption of this noninvasive alternative.
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Affiliation(s)
- Nicola Jane Flowers
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Trent Burgess
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Olivia Giouzeppos
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Grace Shi
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clare Jane Love
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Clare Elizabeth Hunt
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Katrina Louise Scarff
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Alison Dalton Archibald
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Mark Domenic Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia. .,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia.
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26
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Yan H, Zhu X, Chen J, Cao Y, Kwok YKY, Chen Z, Leung TY, Chen M, Choy KW. Noninvasive prenatal sequencing for multiple Mendelian monogenic disorders among fetuses with skeletal dysplasia or increased nuchal translucency. Prenat Diagn 2020; 40:1459-1465. [PMID: 32668031 DOI: 10.1002/pd.5792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/19/2020] [Accepted: 07/12/2020] [Indexed: 01/05/2023]
Abstract
OBJECTIVES To evaluate the performance of noninvasive prenatal sequencing for multiple Mendelian monogenic disorders (NIPS-M) among fetuses with skeletal abnormalities or increased nuchal translucency (NT). METHODS Pregnancies with fetal skeletal abnormalities or increased NT (≥3.0 mm) observed by ultrasonography were recruited between October 2017 and March 2019. Parental blood from 13 couples were collected for NIPS-M testing reported. All the NIPS-M results were followed up by invasive diagnostic testing or neonatal examination. RESULTS Among the 13 cases, 8 (61.5%) yielded positive results for pathogenic variants in the FGFR3, COL1A1, RAF1, PTPN11 and SOS1 genes by NIPS-M. One case was excluded for further analysis due to insufficient fetal DNA (<4.5%). De novo mutations were reported in six of the eight positive cases (75%). The other two were inconclusive as the pathogenic variants were detected in both plasma and genomic DNA of the mothers. The sensitivity of NIPS-M was 100%. CONCLUSIONS Our pilot study demonstrates that NIPS-M is an accurate approach for detection of multiple monogenic disorders among fetuses with skeletal abnormalities or increased NT. It serves as an alternative and highly sensitive method to provide valuable molecular information for these groups of women who are reluctant to undergo invasive procedure.
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Affiliation(s)
- Huanchen Yan
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China
| | - Xiaofan Zhu
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Jingsi Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China
| | - Ye Cao
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yvonne Ka Yin Kwok
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zihan Chen
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Tak Yeung Leung
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Min Chen
- Department of Fetal Medicine and Prenatal Diagnosis, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Obstetrics & Gynecology Institute of Guangzhou, Guangzhou, China
| | - Kwong Wai Choy
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China.,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
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27
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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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28
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Vervecken E, Blaumeiser B, Vanderheyden T, Hauspy J, Janssens K. Terminal deletion of chromosome 13 in a fetus with normal NIPT: The added value of invasive prenatal diagnosis in the NIPT era. Clin Case Rep 2020; 8:1461-1466. [PMID: 32884775 PMCID: PMC7455455 DOI: 10.1002/ccr3.2889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/29/2020] [Indexed: 12/14/2022] Open
Abstract
In the age of noninvasive prenatal testing, there is still an important role for invasive prenatal diagnosis, even for chromosomes 13, 18, and 21.
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Affiliation(s)
- Evy Vervecken
- Department of Obstetrics and GynaecologyGZA HospitalsSt. AugustinusWilrijkBelgium
| | - Bettina Blaumeiser
- Center of Medical GeneticsUniversity Hospital and University of AntwerpAntwerpBelgium
| | - Tina Vanderheyden
- Department of Obstetrics and GynaecologyGZA HospitalsSt. AugustinusWilrijkBelgium
| | - Jan Hauspy
- Department of Obstetrics and GynaecologyGZA HospitalsSt. AugustinusWilrijkBelgium
| | - Katrien Janssens
- Center of Medical GeneticsUniversity Hospital and University of AntwerpAntwerpBelgium
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29
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Lalonde E, Rentas S, Lin F, Dulik MC, Skraban CM, Spinner NB. Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution. Front Pediatr 2020; 8:373. [PMID: 32733828 PMCID: PMC7360789 DOI: 10.3389/fped.2020.00373] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
Powerful, recent advances in technologies to analyze the genome have had a profound impact on the practice of medical genetics, both in the laboratory and in the clinic. Increasing utilization of genome-wide testing such as chromosomal microarray analysis and exome sequencing have lead a shift toward a "genotype-first" approach. Numerous techniques are now available to diagnose a particular syndrome or phenotype, and while traditional techniques remain efficient tools in certain situations, higher-throughput technologies have become the de facto laboratory tool for diagnosis of most conditions. However, selecting the right assay or technology is challenging, and the wrong choice may lead to prolonged time to diagnosis, or even a missed diagnosis. In this review, we will discuss current core technologies for the diagnosis of classic genetic disorders to shed light on the benefits and disadvantages of these strategies, including diagnostic efficiency, variant interpretation, and secondary findings. Finally, we review upcoming technologies posed to impart further changes in the field of genetic diagnostics as we move toward "genome-first" practice.
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Affiliation(s)
- Emilie Lalonde
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Stefan Rentas
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Fumin Lin
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Matthew C. Dulik
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Cara M. Skraban
- Division of Human Genetics, Department of Pediatrics, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
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A retrospective analysis the clinic data and follow-up of non-invasive prenatal test in detection of fetal chromosomal aneuploidy in more than 40,000 cases in a single prenatal diagnosis center. Eur J Med Genet 2020; 63:104001. [PMID: 32622960 DOI: 10.1016/j.ejmg.2020.104001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 03/22/2020] [Accepted: 06/28/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To evaluate the efficacy of non-invasive prenatal test (NIPT) in the detection of chromosomal aneuploidy according to the follow-up information from a single prenatal diagnosis center. METHODS A total of 40,311 cases were retrospectively reviewed. The screening was performed using a BGI protocol, pre-test and post-test genetic counseling was provided, and the pregnancy outcomes were recorded. The results of NIPT and clinical follow-up data were analyzed together with the pregnancy outcomes, confirmatory testing results, and ultrasound findings. RESULTS Of the 40,311cases were includes in the study, successful follow-up was conducted in 468 (1.16%) cases with high risk, 225 (0.56%) cases with rare autosomal trisomy (RAT) and copy number variation (CNV). 39,572 (98.17%) cases with low risk and 623 (1.57%) cases of which were confirmed with adverse pregnancy outcomes. 46 (0.1%) cases with failed tests. Among them, 398 (84.7%) cases with high-risk results chose invasive testing, revealing 198 true positive cases. In cases with RAT and CNV results, 189 cases underwent invasive testing, revealing 5 cases RAT and 4 pathogenic CNVs. CONCLUSIONS NIPT appears to be effective in detecting the fetal chromosomal aneuploidies T21, T18 and SCAs, but it exist false positive/negative cases, unconfirmed high-risk cfDNA results, and the high false positive rate in cases with RAT and CNV results implied the limitations of this screening method. Our study showed the importance to associate cfDNA screening results with clinical follow-up data and provided information that may help with result interpretation, genetic counseling and the decision making in clinic.
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Samura O. Update on noninvasive prenatal testing: A review based on current worldwide research. J Obstet Gynaecol Res 2020; 46:1246-1254. [PMID: 32558079 DOI: 10.1111/jog.14268] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/11/2020] [Indexed: 12/25/2022]
Abstract
Eight years have passed since noninvasive prenatal testing (NIPT) was clinically evaluated and data on NIPT for trisomy 21, 18 and 13 were collected. The data revealed that NIPT is more accurate than conventional first-trimester screening. However, there is still insufficient data regarding the clinical use of NIPT results in detecting sex chromosome aneuploidies or whole-genome regions. NIPT is already being used as a clinical screening method globally. However, it is an unconfirmed diagnostic test and the results must be interpreted with caution as they may yield false negatives, false positives or inconclusive results. Therefore, the aim of this review is to highlight the current status of information, including the different methodologies, shortcomings and implications, regarding NIPT after its adoption worldwide. It is important to include genetic counseling when implementing NIPT. Going forward, the knowledge obtained to date, including the associated shortcomings, must be considered in evaluating the effectiveness of NIPT in detecting genetic abnormalities.
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Affiliation(s)
- Osamu Samura
- Department of Obstetrics and Gynecology, Jikei University School of Medicine, Tokyo, Japan
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Oneda B, Sirleto P, Baldinger R, Taralczak M, Joset P, Zweier M, Niedrist D, Azzarello-Burri S, Britschgi C, Breymann C, Ochsenbein-Kölble N, Burkhardt T, Wisser J, Zimmermann R, Steindl K, Rauch A. Genome-wide non-invasive prenatal testing in single- and multiple-pregnancies at any risk: Identification of maternal polymorphisms to reduce the number of unnecessary invasive confirmation testing. Eur J Obstet Gynecol Reprod Biol 2020; 252:19-29. [PMID: 32619881 DOI: 10.1016/j.ejogrb.2020.05.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Non-invasive prenatal testing by targeted or genome-wide copy number profiling (cnNIPT) has the potential to outperform standard NIPT targeting the common trisomies 13, 18, and 21, only. Nevertheless, prospective results and outcome data on cnNIPT are still scarce and there is increasing evidence for maternal copy number variants (CNVs) interfering with results of both, standard and cnNIPT. STUDY DESIGN We assessed the performance of cnNIPT in 3053 prospective and 116 retrospective cases with special consideration of maternal CNVs in singleton and multiple gestational pregnancies at any risk, as well as comprehensive follow-up. RESULTS A result was achieved in 2998 (98.2%) of total prospective cases (89.2% analyzed genome-wide). Confirmed fetal chromosomal abnormalities were detected in 45 (1.5%) cases, of which five (11%) would have remained undetected in standard NIPTs. Additionally, we observed 4 likely fetal trisomies without follow-up and a likely phenotype associated placental partial trisomy 16. Moreover, we observed clinically relevant confirmed maternal CNVs in 9 (0.3%) cases and likely maternal clonal hematopoiesis in 3 (0.1%). For common fetal trisomies we prospectively observed a very high sensitivity (100% [95% CI: 91.96-100%]) and specificity (>99.9% [95% CI: 99.8-100%]), and positive predictive value (PPV) (97.8% [95% CI: 86.1-99.7%]), but our retrospective control cases demonstrated that due to cases of fetal restricted mosaicism the true sensitivity of NIPT is lower. After showing that 97.3% of small CNVs prospectively observed in 8.3% of genome-wide tests were mostly benign maternal variants, sensitivity (75.0% [95% CI: 19.4%-99.4%]), specificity (99.7% [99.5%-99.9%]) and PPV (30.0% [14.5%-52.1%]) for relevant fetal CNVs were relatively high, too. Maternal autoimmune disorders and medication, such as dalteparin, seem to impair assay quality. CONCLUSION When maternal CNVs are recognized as such, cnNIPT showed a very high sensitivity, specificity and PPV for common trisomies in single and multiple pregnancies at any risk and very good values genome-wide. We found that the resolution for segmental aberrations is generally comparable to standard karyotyping, and exceeds the latter if the fetal fraction is above 10%, which allows detection of the 2.5 Mb 22q11.2 microdeletion associated with the velocardiofacial syndrome, even if the mother is not a carrier.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.
| | - Pietro Sirleto
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Dunja Niedrist
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Christian Britschgi
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | | | - Nicole Ochsenbein-Kölble
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Tilo Burkhardt
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Josef Wisser
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Roland Zimmermann
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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Current Status of Noninvasive Prenatal Testing and Counselling Considerations: An Indian Perspective. JOURNAL OF FETAL MEDICINE 2020. [DOI: 10.1007/s40556-019-00228-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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van der Meij KR, Sistermans EA, Macville MV, Stevens SJ, Bax CJ, Bekker MN, Bilardo CM, Boon EM, Boter M, Diderich KE, de Die-Smulders CE, Duin LK, Faas BH, Feenstra I, Haak MC, Hoffer MJ, den Hollander NS, Hollink IH, Jehee FS, Knapen MF, Kooper AJ, van Langen IM, Lichtenbelt KD, Linskens IH, van Maarle MC, Oepkes D, Pieters MJ, Schuring-Blom GH, Sikkel E, Sikkema-Raddatz B, Smeets DF, Srebniak MI, Suijkerbuijk RF, Tan-Sindhunata GM, van der Ven AJE, van Zelderen-Bhola SL, Henneman L, Galjaard RJH, Van Opstal D, Weiss MM. TRIDENT-2: National Implementation of Genome-wide Non-invasive Prenatal Testing as a First-Tier Screening Test in the Netherlands. Am J Hum Genet 2019; 105:1091-1101. [PMID: 31708118 DOI: 10.1016/j.ajhg.2019.10.005] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/02/2019] [Indexed: 12/30/2022] Open
Abstract
The Netherlands launched a nationwide implementation study on non-invasive prenatal testing (NIPT) as a first-tier test offered to all pregnant women. This started on April 1, 2017 as the TRIDENT-2 study, licensed by the Dutch Ministry of Health. In the first year, NIPT was performed in 73,239 pregnancies (42% of all pregnancies), 7,239 (4%) chose first-trimester combined testing, and 54% did not participate. The number of trisomies 21 (239, 0.33%), 18 (49, 0.07%), and 13 (55, 0.08%) found in this study is comparable to earlier studies, but the Positive Predictive Values (PPV)-96% for trisomy 21, 98% for trisomy 18, and 53% for trisomy 13-were higher than expected. Findings other than trisomy 21, 18, or 13 were reported on request of the pregnant women; 78% of women chose to have these reported. The number of additional findings was 207 (0.36%); these included other trisomies (101, 0.18%, PPV 6%, many of the remaining 94% of cases are likely confined placental mosaics and possibly clinically significant), structural chromosomal aberrations (95, 0.16%, PPV 32%,) and complex abnormal profiles indicative of maternal malignancies (11, 0.02%, PPV 64%). The implementation of genome-wide NIPT is under debate because the benefits of detecting other fetal chromosomal aberrations must be balanced against the risks of discordant positives, parental anxiety, and a potential increase in (invasive) diagnostic procedures. Our first-year data, including clinical data and laboratory follow-up data, will fuel this debate. Furthermore, we describe how NIPT can successfully be embedded into a national screening program with a single chain for prenatal care including counseling, testing, and follow-up.
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He Y, Liu YH, Xie RG, Liu SA, Li DZ. Rare autosomal trisomies on non-invasive prenatal testing: not as adverse as expected. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 54:838-839. [PMID: 30887590 DOI: 10.1002/uog.20264] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Affiliation(s)
- Y He
- Prenatal Diagnosis Unit, Dongguan Women and Children, Healthcare Hospital, Dongguan, Guangdong, China
| | - Y-H Liu
- Prenatal Diagnosis Unit, Dongguan Women and Children, Healthcare Hospital, Dongguan, Guangdong, China
| | - R-G Xie
- Prenatal Diagnosis Unit, Dongguan Women and Children, Healthcare Hospital, Dongguan, Guangdong, China
| | - S-A Liu
- Prenatal Diagnosis Unit, Dongguan Women and Children, Healthcare Hospital, Dongguan, Guangdong, China
| | - D-Z Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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Benn P, Malvestiti F, Grimi B, Maggi F, Simoni G, Grati FR. Rare autosomal trisomies: comparison of detection through cell-free DNA analysis and direct chromosome preparation of chorionic villus samples. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 54:458-467. [PMID: 31237735 DOI: 10.1002/uog.20383] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/24/2019] [Accepted: 06/15/2019] [Indexed: 06/09/2023]
Abstract
OBJECTIVE Direct chromosome preparations of chorionic villus samples (CVS) and cell-free DNA (cfDNA) testing both involve analysis of the trophoblastic cell lineage. The aim of this study was to compare the spectrum of rare autosomal trisomies (RATs) detected by these two approaches and assess the available information on their clinical significance. METHODS Data from 10 reports on genome-wide cfDNA testing were pooled to determine which chromosomes were most frequently involved in RAT-positive cases, and pregnancy outcome information was reviewed. CVS information was obtained from an updated database of 76 102 consecutive CVS analyses performed over a period of 18 years at TOMA laboratory, in which trophoblastic and mesenchymal layers were analyzed and amniotic fluid cell analysis was recommended for RAT-positive cases. Chromosomes involved and presence of confined placental mosaicism, true fetal mosaicism and uniparental disomy (UPD) for imprinted chromosomes were assessed. Also evaluated were the frequency and types of RATs in products of conception. RESULTS RATs were present in 634 of 196 662 (0.32%) cfDNA samples and 237 of 57 539 (0.41%) CVS trophoblast samples (P < 0.01). The frequency of RATs varied over 8-fold between the cfDNA reports. Confirmation of abnormality through amniocentesis was more likely when RATs were ascertained through cfDNA (14 of 151; 9.3%) than through CVS trophoblasts (seven of 237; 3.0%) (P < 0.01). In cfDNA-ascertained cases, trisomies 15, 16 and 22, which are associated with fetal loss, were identified proportionately more often. Of 151 cases with RAT identified by cfDNA and outcome information available, 41.1% resulted in normal live birth; 27.2% in fetal loss; 7.3% had phenotypic abnormality detected through ultrasound or other follow-up evaluation; 2.0% had a clinically significant UPD; and 14.6% had fetal growth restriction or low birth weight. All autosomes were involved in trisomies in products of conception; the most common RATs detected were trisomies 16, 22 and 15 with a frequency of > 9% each. CONCLUSIONS Although there are strong parallels between RATs ascertained through cfDNA analysis and direct chromosome preparation of CVS, caution is needed in applying conclusions from CVS analysis to cfDNA testing, and vice versa. RATs identified through genome-wide cfDNA tests have uncertain risks for fetal loss, growth restriction or fetal abnormality. Copyright © 2019 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- P Benn
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - F Malvestiti
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
| | - B Grimi
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
| | - F Maggi
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
| | - G Simoni
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
| | - F R Grati
- Unit of Research and Development, Cytogenetics and Medical Genetics, TOMA, Advanced Biomedical Assays S.p.A., Busto Arsizio, Varese, Italy
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Shi J, Zhang R, Li J, Zhang R. Novel perspectives in fetal biomarker implementation for the noninvasive prenatal testing. Crit Rev Clin Lab Sci 2019; 56:374-392. [PMID: 31290367 DOI: 10.1080/10408363.2019.1631749] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Noninvasive prenatal testing (NIPT) utilizes cell-free fetal DNA (cffDNA) present in maternal peripheral blood to detect chromosomal abnormalities. The detection of 21-trisomy, 18-trisomy, and 13-trisomy in the fetus has become a common screening method during pregnancy and has been widely applied in routine clinical testing because of its analytical and clinical validity. Currently, noninvasive prenatal testing involving copy number variations (CNVs) and other frequent single-gene disorders is being widely studied, and it plays an important and indispensable role in prenatal detection. The multiple approaches that have been reported and validated by various laboratories have different merits and limitations. Their clinical validity, utility, and application vary with different diseases. This review summarizes the principles, methods, advantages, and limitations of noninvasive prenatal testing for the detection of aneuploidy, CNVs and single-gene disorders. Before implementation of NIPT into clinical practice, a list of criteria that the application must meet is crucial. Essential parameters such as clinical sensitivity, clinical specificity, positive predictive value (PPV) and negative predictive value (NPV) are required to properly evaluate the clinical validity and utility of NIPT. We then discuss and analyze these clinical parameters and clinical application guidelines, providing physicians and scientists with feasible strategies and the latest research information.
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Affiliation(s)
- Jiping Shi
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Runling Zhang
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Graduate School, Chinese Academy of Medical Sciences, Peking Union Medical College , Beijing , China
| | - Jinming Li
- National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
| | - Rui Zhang
- Peking University Fifth School of Clinical Medicine, National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,National Center for Clinical Laboratories, National Center of Gerontology, Beijing Hospital , Beijing , China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital , Beijing , China
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38
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Di Renzo GC, Bartha JL, Bilardo CM. Expanding the indications for cell-free DNA in the maternal circulation: clinical considerations and implications. Am J Obstet Gynecol 2019; 220:537-542. [PMID: 30639383 DOI: 10.1016/j.ajog.2019.01.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 12/30/2018] [Accepted: 01/04/2019] [Indexed: 12/26/2022]
Abstract
Noninvasive prenatal testing for fetal aneuploidy using cell-free DNA has been widely integrated into routine obstetrical care. The scope of cell-free DNA testing has expanded from trisomies 21, 18, and 13 to include sex chromosome conditions, panels of specific microdeletions, and more recently genome-wide copy number variants and rare autosomal trisomies. Because the technical ability to test for a condition does not necessarily correspond with a clinical benefit to a population or to individual pregnant women, the benefits and harms of screening programs must be carefully weighed before implementation. Application of the World Health Organization criteria to cell-free DNA screening is informative when considering implementation of expanded cell-free DNA test menus. Most microdeletions and duplications are rare to the point that the prevalence has not even been defined and their natural history cannot be reliably predicted in the prenatal period. At the current time, scientific evidence regarding clinical performance of expanded cell-free DNA panels is lacking. Expanded cell-free DNA menus therefore create a dilemma for diagnosis, treatment, and counseling of patients. The clinical utility of expanding cell-free DNA testing to include panels of microdeletions and genome-wide assessment of large chromosomal imbalances has yet to be demonstrated; as such, the clinical implementation of this testing is premature.
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Abstract
All patients should be offered prenatal screening and diagnosis. Testing options depend on many factors, including patient age, family history, and patient preference. Options are rapidly changing with emerging technology. Aneuploidy screening options include ultrasound, maternal analytes, and cell-free DNA. Prenatal chromosomal microarray is the recommended diagnostic test for patients with anomalies visualized on prenatal ultrasound. Prenatal whole exome sequencing is clinically available but is limited by challenges with counseling, interpretation, and turn-around time. Future technologies are emerging and may soon allow for translation of prenatal diagnosis to in utero therapy.
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Ravegnini G, Sammarini G, Serrano C, Nannini M, Pantaleo MA, Hrelia P, Angelini S. Clinical relevance of circulating molecules in cancer: focus on gastrointestinal stromal tumors. Ther Adv Med Oncol 2019; 11:1758835919831902. [PMID: 30854029 PMCID: PMC6399766 DOI: 10.1177/1758835919831902] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/30/2018] [Indexed: 12/12/2022] Open
Abstract
In recent years, growing research interest has focused on the so-called liquid biopsy. A simple blood test offers access to a plethora of information, which might be extremely helpful in understanding or characterizing specific diseases. Blood contains different molecules, of which circulating free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs) and extracellular vesicles (EVs) are the most relevant. Conceivably, these molecules have the potential for tumor diagnosis, monitoring tumor evolution, and evaluating treatment response and pharmacological resistance. This review aims to present a state-of-the-art of recent advances in circulating DNA and circulating RNA in gastrointestinal stromal tumors (GISTs). To date, progress in liquid biopsy has been scarce in GISTs due to several issues correlated with the nature of the pathology. Namely, heterogeneity in primary and secondary mutations in key driver genes has greatly slowed the development and application in GISTs, unlike in other tumor types in which liquid biopsy has already been translated into clinical practice. However, meaningful novel data have shown in recent years a significant clinical potential of ctDNA, CTCs, EVs and circulating RNA in GISTs.
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Affiliation(s)
- Gloria Ravegnini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Sammarini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - César Serrano
- Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Margherita Nannini
- Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Maria A Pantaleo
- Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Sabrina Angelini
- Department of Pharmacy and Biotechnology, Via Irnerio 48, 40126 Bologna, Italy
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Wilkins-Haug L, Zhang C, Cerveira E, Ryan M, Mil-Homens A, Zhu Q, Reddi H, Lee C, Bianchi DW. Biological explanations for discordant noninvasive prenatal test results: Preliminary data and lessons learned. Prenat Diagn 2019; 38:445-458. [PMID: 29633279 DOI: 10.1002/pd.5260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Maternal plasma cell-free DNA (cfDNA) analysis is a powerful screening tool for Down syndrome. In a pilot series, we examined biologic causes of discordance between the cfDNA test results and the fetal karyotype. We also explored the feasibility of obtaining trio biospecimens by using parental engagement. METHODS A convenience sample of women with discordant cfDNA results were recruited by their care providers. We provided shipping materials and instructions for biospecimen collection. Maternal, newborn, and placental samples were examined with droplet digital PCR. RESULTS Thirteen of 15 women successfully had biospecimens obtained remotely. High-quality DNA was extracted in 12 of 13 women. Presumed biologic etiologies for discordance were identified in 7 of 12 women: 3 cases from additional clinical review (male renal transplant, vanishing twin, and colon cancer) and 4 cases from additional laboratory investigation using droplet digital PCR (3 with confined placental mosaicism and 1 with true fetal mosaicism). CONCLUSIONS Understanding the biology behind cfDNA-fetal karyotype discordancy is useful for follow-up clinical care. Our study suggests that most cases could be resolved by using a trio biospecimen protocol and parental involvement. To improve accuracy, additional sequencing of biospecimens will be required.
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Affiliation(s)
- Louise Wilkins-Haug
- Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mallory Ryan
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Adam Mil-Homens
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Honey Reddi
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Diana W Bianchi
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA.,Prenatal Genomics and Therapy Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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Jensen TJ, Goodman AM, Kato S, Ellison CK, Daniels GA, Kim L, Nakashe P, McCarthy E, Mazloom AR, McLennan G, Grosu DS, Ehrich M, Kurzrock R. Genome-Wide Sequencing of Cell-Free DNA Identifies Copy-Number Alterations That Can Be Used for Monitoring Response to Immunotherapy in Cancer Patients. Mol Cancer Ther 2018; 18:448-458. [DOI: 10.1158/1535-7163.mct-18-0535] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/05/2018] [Accepted: 11/26/2018] [Indexed: 11/16/2022]
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Kaseniit KE, Hogan GJ, D'Auria KM, Haverty C, Muzzey D. Strategies to minimize false positives and interpret novel microdeletions based on maternal copy-number variants in 87,000 noninvasive prenatal screens. BMC Med Genomics 2018; 11:90. [PMID: 30340588 PMCID: PMC6194617 DOI: 10.1186/s12920-018-0410-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/01/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Noninvasive prenatal screening (NIPS) of common aneuploidies using cell-free DNA from maternal plasma is part of routine prenatal care and is widely used in both high-risk and low-risk patient populations. High specificity is needed for clinically acceptable positive predictive values. Maternal copy-number variants (mCNVs) have been reported as a source of false-positive aneuploidy results that compromises specificity. METHODS We surveyed the mCNV landscape in 87,255 patients undergoing NIPS. We evaluated both previously reported and novel algorithmic strategies for mitigating the effects of mCNVs on the screen's specificity. Further, we analyzed the frequency, length, and positional distribution of CNVs in our large dataset to investigate the curation of novel fetal microdeletions, which can be identified by NIPS but are challenging to interpret clinically. RESULTS mCNVs are common, with 65% of expecting mothers harboring an autosomal CNV spanning more than 200 kb, underscoring the need for robust NIPS analysis strategies. By analyzing empirical and simulated data, we found that general, outlier-robust strategies reduce the rate of mCNV-caused false positives but not as appreciably as algorithms specifically designed to account for mCNVs. We demonstrate that large-scale tabulation of CNVs identified via routine NIPS could be clinically useful: together with the gene density of a putative microdeletion region, we show that the region's relative tolerance to duplications versus deletions may aid the interpretation of microdeletion pathogenicity. CONCLUSIONS Our study thoroughly investigates a common source of NIPS false positives and demonstrates how to bypass its corrupting effects. Our findings offer insight into the interpretation of NIPS results and inform the design of NIPS algorithms suitable for use in screening in the general obstetric population.
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Affiliation(s)
- Kristjan Eerik Kaseniit
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Gregory J Hogan
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Kevin M D'Auria
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Carrie Haverty
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA
| | - Dale Muzzey
- Myriad Women's Health (previously Counsyl), 180 Kimball Way, South San Francisco, CA, 94080, USA.
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Liang D, Lin Y, Qiao F, Li H, Wang Y, Zhang J, Liu A, Ji X, Ma D, Jiang T, Hu P, Xu Z. Perinatal outcomes following cell-free DNA screening in >32 000 women: Clinical follow-up data from a single tertiary center. Prenat Diagn 2018; 38:755-764. [PMID: 29966040 DOI: 10.1002/pd.5328] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/24/2018] [Accepted: 06/25/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Dong Liang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Ying Lin
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Fengchang Qiao
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Hang Li
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Yan Wang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Jingjing Zhang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - An Liu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Xiuqing Ji
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Dingyuan Ma
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Tao Jiang
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Ping Hu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
| | - Zhengfeng Xu
- State Key Laboratory of Reproductive Medicine, Department of Prenatal Diagnosis; The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital; Nanjing Jiangsu Province 210004 China
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Pertile MD, Halks-Miller M, Flowers N, Barbacioru C, Kinnings SL, Vavrek D, Seltzer WK, Bianchi DW. Rare autosomal trisomies, revealed by maternal plasma DNA sequencing, suggest increased risk of feto-placental disease. Sci Transl Med 2018; 9:9/405/eaan1240. [PMID: 28855395 PMCID: PMC10040211 DOI: 10.1126/scitranslmed.aan1240] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 06/22/2017] [Accepted: 08/10/2017] [Indexed: 12/13/2022]
Abstract
Whole-genome sequencing (WGS) of maternal plasma cell-free DNA (cfDNA) can potentially evaluate all 24 chromosomes to identify abnormalities of the placenta, fetus, or pregnant woman. Current bioinformatics algorithms typically only report on chromosomes 21, 18, 13, X, and Y; sequencing results from other chromosomes may be masked. We hypothesized that by systematically analyzing WGS data from all chromosomes, we could identify rare autosomal trisomies (RATs) to improve understanding of feto-placental biology. We analyzed two independent cohorts from clinical laboratories, both of which used a similar quality control parameter, normalized chromosome denominator quality. The entire data set included 89,817 samples. Samples flagged for analysis and classified as abnormal were 328 of 72,932 (0.45%) and 71 of 16,885 (0.42%) in cohorts 1 and 2, respectively. Clinical outcome data were available for 57 of 71 (80%) of abnormal cases in cohort 2. Visual analysis of WGS data demonstrated RATs, copy number variants, and extensive genome-wide imbalances. Trisomies 7, 15, 16, and 22 were the most frequently observed RATs in both cohorts. Cytogenetic or pregnancy outcome data were available in 52 of 60 (87%) of cases with RATs in cohort 2. Cases with RATs detected were associated with miscarriage, true fetal mosaicism, and confirmed or suspected uniparental disomy. Comparing the trisomic fraction with the fetal fraction allowed estimation of possible mosaicism. Analysis and reporting of aneuploidies in all chromosomes can clarify cases in which cfDNA findings on selected "target" chromosomes (21, 18, and 13) are discordant with the fetal karyotype and may identify pregnancies at risk of miscarriage and other complications.
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Affiliation(s)
- Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Victoria 3052, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria 3010, Australia
| | | | - Nicola Flowers
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Victoria 3052, Australia
| | | | | | | | | | - Diana W Bianchi
- Tufts Medical Center and Tufts University School of Medicine, Boston, MA 02111, USA. .,National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Chen F, Liu P, Gu Y, Zhu Z, Nanisetti A, Lan Z, Huang Z, Liu JS, Kang X, Deng Y, Luo L, Jiang D, Qiu Y, Pan J, Xia J, Xiong K, Liu C, Xie L, Shi Q, Li J, Zhang X, Wang W, Drmanac S, Bolund L, Jiang H, Drmanac R, Xu X. Isolation and whole genome sequencing of fetal cells from maternal blood towards the ultimate non-invasive prenatal testing. Prenat Diagn 2017; 37:1311-1321. [DOI: 10.1002/pd.5186] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Fang Chen
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen; DK-2100 Copenhagen Denmark
| | - Ping Liu
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Ying Gu
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Zhu Zhu
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Amulya Nanisetti
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Zhangzhang Lan
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Zhiwei Huang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Jia Sophie Liu
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Xiongbin Kang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Yuqing Deng
- PEKING University Shenzhen Hospital; Shenzhen China
| | - Liqiong Luo
- Shenzhen Longhua New District People's Hospital, Affiliated Hospital Southern Medical University; Guangzhou China
| | - Dan Jiang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Yong Qiu
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Jianchang Pan
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Jun Xia
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Ken Xiong
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Chao Liu
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Lin Xie
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Qianyu Shi
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Jing Li
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Xiuqing Zhang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Wei Wang
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Snezana Drmanac
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Lars Bolund
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen; DK-2100 Copenhagen Denmark
- Department of Biomedicine, Aarhus University; Aarhus Denmark
| | - Hui Jiang
- BGI-Shenzhen; Shenzhen 518083 PR China
- MGI, BGI-Shenzhen; Shenzhen 518083 China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
| | - Radoje Drmanac
- BGI-Shenzhen; Shenzhen 518083 PR China
- Complete Genomics, Inc.; 2904 Orchard Parkway San Jose CA 95134 USA
| | - Xun Xu
- BGI-Shenzhen; Shenzhen 518083 PR China
- China National GeneBank, BGI-Shenzhen; Shenzhen 518120 China
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Fiorentino F, Bono S, Pizzuti F, Duca S, Polverari A, Faieta M, Baldi M, Diano L, Spinella F. Author's reply to Grati and Benn. Prenat Diagn 2017; 37:1053-1054. [DOI: 10.1002/pd.5136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/02/2017] [Indexed: 11/09/2022]
Affiliation(s)
| | - Sara Bono
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | | | - Sara Duca
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | | | - Monica Faieta
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | - Marina Baldi
- GENOMA - Molecular Genetics Laboratories; Rome Italy
| | - Laura Diano
- GENOMA - Molecular Genetics Laboratories; Rome Italy
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Genome-wide cell free fetal DNA screening spots variations standard screening doesn't: Diagnostic testing data needed to validate results and prove accuracy. Am J Med Genet A 2017; 173:2573-2574. [PMID: 28921852 DOI: 10.1002/ajmg.a.38482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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