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Hammer C, Pierson S, Acevedo A, Goldberg J, Westover T, Chawla D, Mabey B, Muzzey D, Johansen Taber K. High positive predictive value 22q11.2 microdeletion screening by prenatal cell-free DNA testing that incorporates fetal fraction amplification. Prenat Diagn 2024; 44:925-935. [PMID: 38622914 DOI: 10.1002/pd.6562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVE 22q11.2 deletion syndrome (DS) is a serious condition with a range of features. The small microdeletion causing 22q11.2DS makes it technically challenging to detect using standard prenatal cfDNA screening. Here, we assess 22q11.2 microdeletion clinical performance by a prenatal cfDNA screen that incorporates fetal fraction (FF) amplification. METHODS The study cohort consisted of patients who received Prequel (Myriad Genetics, Inc.), a prenatal cfDNA screening that incorporates FF amplification, and met additional eligibility criteria. Pregnancy outcomes were obtained via a routine process for continuous quality improvement. Samples with diagnostic testing results were used to calculate positive predictive value (PPV). RESULTS 379,428 patients met study eligibility criteria, 76 of whom were screen-positive for a de novo 22q11.2 microdeletion. 22 (29.7%) had diagnostic testing results available, and all 22 cases were confirmed as true positives, for a PPV of 100% (95% CI 84.6%-100%). This performance was based on cases that ranged broadly across FF (5.9%-41.1%, mean 23.0%), body mass index (22.3-44.8, mean 29.9), and gestational age at testing (10.0w-34.6w, median 12.7w). Ultrasound findings in screen-positive pregnancies were consistent with those known to be associated with 22q11.2DS. CONCLUSION 22q11.2 microdeletion screening that incorporates FF amplification demonstrated high PPV across both general and high-risk population cohorts.
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Affiliation(s)
- Carly Hammer
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Summer Pierson
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Ashley Acevedo
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - James Goldberg
- Independent (unaffiliated), Washington, District of Columbia, USA
| | - Thomas Westover
- Maternal Fetal Medicine and Perinatal Genetics, Capital Health, Trenton, New Jersey, USA
| | - Devika Chawla
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Brent Mabey
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Dale Muzzey
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
| | - Katherine Johansen Taber
- Department of Research & Development, Myriad Genetics, Inc, South San Francisco, California, USA
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Arumugam S, Kalluri SS, Sharmila V, Mocherla A, Subbiah NK, Kulkarni JP, Ghoshal JA. Understanding the Awareness of Prenatal Genetic Screening Tests Among Pregnant Women in India: A Cross-Sectional Study. Cureus 2024; 16:e56932. [PMID: 38665723 PMCID: PMC11043792 DOI: 10.7759/cureus.56932] [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] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction Genetic disorders pose a significant health challenge in India, with chromosomal abnormalities ranking second only to congenital anomalies in terms of disease burden. Prenatal testing offers a crucial strategy for identifying and managing these disorders. However, the awareness and understanding of prenatal screening tests among pregnant women in India remain understudied. This study aims to fill this gap by investigating the awareness quotient of prenatal screening tests for genetic disorders among pregnant women in India. Methods A hospital-based cross-sectional study was conducted at the Genetics Unit, Department of Anatomy, and Department of Obstetrics and Gynecology, All India Institute of Medical Sciences, Mangalagiri. Ethical clearance was obtained, and data were collected using a self-administered questionnaire covering demographic characteristics and awareness assessment. Descriptive statistics, chi-square tests, and logistic regression analysis were employed for data analysis. Results Among the 200 pregnant women surveyed, the majority demonstrated inadequate awareness of prenatal screening tests for genetic disorders, with only 36.5% possessing adequate knowledge. Significant associations were found between awareness levels and factors such as age, trimester of pregnancy, and education level. Notably, awareness about non-invasive prenatal testing (NIPT) was notably low at 7%, indicating a need for targeted educational interventions. Comparison with international studies revealed varying levels of awareness across different populations, highlighting the influence of socio-cultural factors and healthcare systems. Conclusion This study underscores the need for improved awareness of prenatal screening tests among pregnant women in India. Addressing disparities in awareness, particularly among younger age groups and those with lower education levels, is crucial for informed decision-making in prenatal care. Targeted educational interventions can empower pregnant women to make informed choices, ultimately contributing to better maternal and child health outcomes. Further research should explore the effectiveness of such interventions in diverse settings to enhance prenatal care delivery.
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Affiliation(s)
- Sangeetha Arumugam
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Sri Sowmya Kalluri
- Obstetrics and Gynecology, All India Institute of Medical Sciences, Mangalagiri, IND
- Obstetrics and Gynecology, Siddhartha Medical College, Government General Hospital, Vijayawada, IND
| | - Vijayan Sharmila
- Obstetrics and Gynecology, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Akarsh Mocherla
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Nandha Kumar Subbiah
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Jyoti P Kulkarni
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
| | - Joy A Ghoshal
- Genetics Unit, Anatomy, All India Institute of Medical Sciences, Mangalagiri, IND
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Long S, O'Leary P, Dickinson JE. Western Australian women's expectations for expanded NIPT-An online survey regarding NIPT for single gene, recessive and chromosomal conditions. J Genet Couns 2023; 32:1047-1056. [PMID: 37096445 DOI: 10.1002/jgc4.1715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/16/2023] [Accepted: 03/20/2023] [Indexed: 04/26/2023]
Abstract
Prenatal screening has evolved rapidly following the introduction of non-invasive prenatal testing (NIPT), with screening now available for an increasing number of conditions. We explored the attitudes and expectations of women within the context of using NIPT to detect multiple different single gene and chromosome conditions during pregnancy. An online survey was used to assess these issues with a sample of 219 women from Western Australia. In our study, the majority of women (96%) support of the concept of expanded NIPT for single gene and chromosome conditions provided the test involves no risk to the pregnancy and can provide the parents with relevant medical information about the fetus at any stage of pregnancy. 80% believed that expanded NIPT for single gene and chromosome conditions should be available at any stage during pregnancy and 68% of women indicated that test cost would be a factor in determining their participation in testing. Under half (43%) of the women favored an option to terminate a pregnancy at any stage if the fetus had a medical condition that would interfere with day to day functioning. The majority (78%) of women believed that testing for multiple genetic conditions would provide reassurance and lead to the delivery of a healthy child.
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Affiliation(s)
- Sarah Long
- Genetic Services of Western Australia, King Edward Memorial Hospital for Women, Subiaco, Australia
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
| | - Peter O'Leary
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
- PathWest Laboratory Medicine, QE2 Medical Centre, Nedlands, Australia
| | - Jan E Dickinson
- Division of Obstetrics and Gynaecology, The University of Western Australia, Perth, Australia
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Battese Ellis K, Sathasivam N, Bonifacio M, Benzie R. Comparison of noninvasive prenatal screening with combined first-trimester screening as a frontline screening approach for common trisomies in a public hospital in Australia. Aust N Z J Obstet Gynaecol 2023; 63:666-672. [PMID: 36048565 DOI: 10.1111/ajo.13605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Combined first-trimester screening (cFTS) for fetal anomalies involves maternal serum screening for biochemical markers and measurement of the nuchal translucency (NT) by ultrasound. Noninvasive prenatal screening (NIPS) analyses cell-free DNA present in a maternal blood sample for presence of fetal chromosomal aneuploidies. AIMS To compare NIPS with cFTS as frontline screening in a public hospital in Australia. MATERIALS AND METHODS Women were offered NIPS in addition to the usual cFTS routinely offered to all women at a public hospital in NSW, Australia. The cFTS sample was collected at ten weeks' gestation and the NIPS sample at 12 weeks' gestation at the ultrasound appointment. RESULTS In a low-risk population of 997 women, frontline NIPS had a screen-positive rate of 0.5% (5/997) vs 4.2% (42/997) with cFTS. cFTS correctly identified one trisomy 21 case and one trisomy 18 case; however, there were two trisomy 18 false negatives. Of five positive NIPS calls, four were correctly identified as trisomy 21 (one) and trisomy 18 (three); there were no NIPS false negatives. Overall, the false-positive rate with NIPS was 0.1% vs 4.0% by cFTS. CONCLUSIONS The lower screen-positive rate with NIPS for common trisomies was a result of the significantly lower false-positive rate with NIPS. Consequently, NIPS as first-line screening, even if funded by the hospital, may provide cost savings. We believe NIPS should be used from ten weeks' gestation in conjunction with morphology ultrasound for routine first-trimester prenatal management.
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Affiliation(s)
| | - Nalayin Sathasivam
- Perinatal Ultrasound Unit, Nepean Hospital, Penrith, New South Wales, Australia
| | | | - Ronald Benzie
- Perinatal Ultrasound Unit, Nepean Hospital, Penrith, New South Wales, Australia
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Fiorentino D, Dar P. Prenatal Screening for Microdeletions and Rare Autosomal Aneuploidies. Clin Obstet Gynecol 2023; 66:579-594. [PMID: 37438896 DOI: 10.1097/grf.0000000000000799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Noninvasive prenatal screening with cell-free DNA is now considered a first-line screening for common aneuploidies. Advancements in existing laboratory techniques now allow to interrogate the entirety of the fetal genome, and many commercial laboratories have expanded their screening panels to include screening for rare autosomal aneuploidies and copy number variants. Here, we review the currently available data on the performance of fetal cell-free DNA to detect rare autosomal aneuploidies and copy number variants that are associated with clinically significant microdeletion and microduplication syndromes and the current position of medical societies on routine screening for these syndromes.
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Affiliation(s)
- Desiree Fiorentino
- Division of Fetal Medicine, Department of Obstetrics and Gynecology, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York
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Tian W, Yuan Y, Yuan E, Zhang L, Liu L, Li Y, Guo J, Cui X, Li P, Cui S. Evaluation of the clinical utility of extended non-invasive prenatal testing in the detection of chromosomal aneuploidy and microdeletion/microduplication. Eur J Med Res 2023; 28:304. [PMID: 37644576 PMCID: PMC10466692 DOI: 10.1186/s40001-023-01285-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND With the development of whole-genome sequencing technology, non-invasive prenatal testing (NIPT) has been applied gradually to screen chromosomal microdeletions and microduplications that cannot be detected by traditional karyotyping. However, in NIPT, some false positives and false negatives occur. This study aimed to investigate the applicability of extended NIPT (NIPT-PLUS) in the detection of chromosomal aneuploidy and microdeletion/microduplication syndrome (MMS). METHODS A total of 452 pregnancies that underwent prenatal diagnostic testing (amniocentesis or chorionic villus sampling) by chromosomal microarray analysis (CMA), were screened by NIPT-PLUS from the peripheral blood sample of the pregnant women. The results of the two tested items were compared and analysed. RESULTS Of the 452 cases, 335 (74.12%) had positive CMA results, and 117 (25.88%) had no abnormal results. A total of 86 cases of trisomy 21, 18 and 13 and sex chromosome aneuploidy (SCA) were detected by CMA and NIPT-PLUS, with a detection rate of 96.51% (83/86). Among them, the detection rates of T18, T13; 47, XXY; 47, XXX and 47 XYY were 100%, and the detection rates of T21 and 45 XO were 96.55% and 90%, respectively. The detection sensitivity of rare chromosomal trisomy (RAT) was 80% (4/5). The positive predictive values of NIPT-PLUS for chromosome aneuploidy T21, T18 and T13 and for SCA and RAT were 90.32%, 87.50%, 25.00%, 88.89% and 50%, respectively. A total of 249 cases (74.32%) of chromosomal MMS were detected by CMA. The detection rate of NIPT-PLUS was 63.86% (159/249), and 90 cases (36.14%) were missed. The larger the MMS fragment, the higher the NIPT-PLUS detection sensitivity. In addition, most small fragments were of maternal origin. CONCLUSION The comparison between the CMA and NIPT-PLUS techniques shows that NIPT-PLUS has high sensitivity for detecting chromosomal aneuploidy and chromosomal copy number variations (CNVs) with fragments > 5 M. However, the sensitivity of CNV for fragments < 5 M is low, and the missed detection rate is high. Additionally, confined placental mosaicism and foetal mosaicism are the key factors causing false negatives in NIPT-PLUS, while maternal chromosomal abnormalities and confined placental mosaicism are key contributors to false positives, so appropriate genetic counselling is especially important for pregnant women before and after NIPT-PLUS testing.
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Affiliation(s)
- Weifang Tian
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Yangyang Yuan
- Department of Medical Research Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Erfeng Yuan
- Department of Clinical Laboratory Science, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Linlin Zhang
- Department of Clinical Laboratory Science, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, Zhengzhou, 450052, China
| | - Ling Liu
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
- Perinatal Disease and Prevention of Birth Defects, Advanced Medical Center, Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Clinical Research Center for Perinatal Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Ying Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Jing Guo
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Xueyin Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Pengyun Li
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China
| | - Shihong Cui
- Prenatal Diagnosis Center, The Third Affiliated Hospital of Zhengzhou University, Maternal and Child Health Hospital of Henan Province, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052, China.
- Perinatal Disease and Prevention of Birth Defects, Advanced Medical Center, Zhengzhou University, Zhengzhou, 450052, China.
- Henan Provincial Clinical Research Center for Perinatal Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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Tan P, Li D, Chang L, Shi J, Han Y, Zhang R, Li J. Evaluation of noninvasive prenatal screening for copy number variations among screening laboratories. Clin Biochem 2023; 118:110617. [PMID: 37507082 DOI: 10.1016/j.clinbiochem.2023.110617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 06/26/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
OBJECTIVE To evaluate the current situation of expanded noninvasive prenatal screening (NIPS) for copy number variations (CNVs) in laboratories in China, the National Center of Clinical Laboratories conducted an externalqualityassessment (EQA) program. METHODS The EQA panel consisted of 12 artificial samples associated with different syndromes, which were mixed with maternal plasma collected from pregnant women and enzyme-digested cell-free DNA (cfDNA) from cell lines with different fetal fractions (FFs) ranging from 5% to 15%. The panel was validated by next-generation sequencing and distributed to laboratories, along with questionnaires and case scenarios. RESULTS Sixty-nine laboratories participated in the EQA program, and 91.30% (63/69) of laboratories correctly identified all samples. A total of 7.25% (5/69) of the laboratories reported false-negative results, and 2.90% (2/69) of the laboratories reported unexpected CNVs. The correct rates of the 22q11.2 deletion syndrome, Cri-du-chat syndrome, 1p36 deletion syndrome and Angelman/Prader-Willi syndrome samples were 97.46%, 98.55%, 100%, and 100%, respectively. With the increase in the FF, deletion size, and read depth, the detection rate increased. For results reports, only five laboratories reported FF values, one laboratory reported the CNV classification type, and none reported sensitivity, specificity, positive predictive values, and negative predictive values. CONCLUSION The detection capabilities of NIPS for CNVs still need to be improved and standardized, and FF, deletion size, and read depth are factors that affect the detection rate.
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Affiliation(s)
- Ping Tan
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, P.R. China
| | - Dandan Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, P.R. China
| | - Lu Chang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, P.R. China
| | - Jiping Shi
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, P.R. China
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, P.R. China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, P.R. China.
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Cai M, Lin N, Chen X, Li Y, Lin M, Fu X, Huang H, He S, Xu L. Non-invasive prenatal testing for the diagnosis of congenital abnormalities: Insights from a large multicenter study in southern China. Braz J Med Biol Res 2023; 56:e12506. [PMID: 37377305 DOI: 10.1590/1414-431x2023e12506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 05/04/2023] [Indexed: 06/29/2023] Open
Abstract
Although non-invasive prenatal testing (NIPT) is widely used to detect fetal abnormalities, the results of NIPT vary by population, and data for the screening efficiency of NIPT positive predictive value (PPV) from different populations is limited. Herein, we retrospectively analyzed the NIPT results in a large multicenter study involving 52,855 pregnant women. Depending on gestational age, amniotic fluid or umbilical cord blood was extracted for karyotype and/or chromosome microarray analysis (CMA) in NIPT-positive patients, and the PPV and follow-up data were evaluated to determine its clinical value. Among the 52,855 cases, 754 were NIPT-positive, with a positivity rate of 1.4%. Karyotype analysis and/or CMA confirmed 323 chromosomal abnormalities, with a PPV of 45.1%. PPV for trisomy 21 (T21), trisomy 18 (T18), trisomy 13 (T13), sex chromosomal aneuploidies (SCAs), and copy number variations (CNVs) were 78.9, 35.3, 22.2, 36.9, and 32.9%, respectively. The PPVs for T21, T18, and T13 increased with age, whereas the PPVs for SCAs and CNVs had little correlation with age. The PPV was significantly higher in patients with advanced age and abnormal ultrasound. The NIPT results are affected by population characteristics. NIPT had a high PPV for T21 and a low PPV for T13 and T18, and screening for SCAs and CNVs showed clinical significance in southern China.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xuemei Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Min Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xianguo Fu
- Department of Prenatal Diagnosis, Ningde Municipal Hospital, Ningde Normal University, Ningde, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Shuqiong He
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Hui L, Ellis K, Mayen D, Pertile MD, Reimers R, Sun L, Vermeesch J, Vora NL, Chitty LS. Position statement from the International Society for Prenatal Diagnosis on the use of non-invasive prenatal testing for the detection of fetal chromosomal conditions in singleton pregnancies. Prenat Diagn 2023; 43:814-828. [PMID: 37076973 DOI: 10.1002/pd.6357] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/15/2023] [Indexed: 04/21/2023]
Abstract
Key points
What is already known about this topic?
In 2015, the International Society for Prenatal Diagnosis (ISPD) published its first position statement on the use of non‐invasive prenatal testing (NIPT) to screen for aneuploidy. Widespread uptake across the globe and subsequent published research has shed new light on test performance and implementation issues.
What does this study add?
This new position statement replaces the 2015 statement with updated information on the current technologies, clinical experience, and implementation practices.
As an international organization, ISPD recognizes that there are important population‐specific considerations in the organization of prenatal screening and diagnosis. These opinions are designed to apply to high income settings where prenatal screening for aneuploidy is an established part of antenatal care.
This position statement is not a clinical practice guideline but represents the consensus opinion of the current ISPD Board based on the current state of knowledge and clinical practice.
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Affiliation(s)
- Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia
- Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria, Australia
| | - Katie Ellis
- Illumina ANZ, Sydney, New South Wales, Australia
| | - Dora Mayen
- Genetics Clinic, Hospital Angeles Lomas, Estado de Mexico, Mexico
| | - Mark D Pertile
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia
| | - Rebecca Reimers
- San Diego Perinatal Center, Rady Children's Hospital, San Diego, California, USA
- Scripps Research Institute, La Jolla, California, USA
| | - Luming Sun
- Department of Fetal Medicine & Prenatal Diagnosis Center, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, China
| | | | - Neeta L Vora
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Division of Maternal Fetal Medicine, Chapel Hill, North Carolina, USA
| | - Lyn S Chitty
- Great Ormond Street NHS Foundation Trust, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
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Soster E, Dyr B, Rafalko J, Almasri E, Cacheris P. Positive cfDNA screening results for 22q11.2 deletion syndrome—Clinical and laboratory considerations. Front Genet 2023; 14:1146669. [PMID: 36968594 PMCID: PMC10036386 DOI: 10.3389/fgene.2023.1146669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Introduction: Non-invasive prenatal screening (NIPS) via cell-free DNA (cfDNA) screens for fetal chromosome disorders using maternal plasma, including 22q11.2 deletion syndrome (22q11.2DS). While it is the commonest microdeletion syndrome and has potential implications for perinatal management, prenatal screening for 22q11.2DS carries some inherent technical, biological, and counseling challenges, including varying deletion sizes/locations, maternal 22q11.2 deletions, confirmatory test choice, and variable phenotype.Materials and methods: This study addresses these considerations utilizing a retrospective cohort of 307 samples with screen-positive 22q11.2 NIPS results on a massively parallel sequencing (MPS) platform.Results: Approximately half of the cases reported ultrasound findings at some point during pregnancy. In 63.2% of cases with diagnostic testing, observed positive predictive values were 90.7%–99.4%. cfDNA identified deletions ranging from <1 Mb to 3.55 Mb, with significant differences in confirmed fetal versus maternal deletion sizes; estimated cfDNA deletion size was highly concordant with microarray findings. Mosaicism ratio proved useful in predicting the origin of a deletion (fetal versus maternal). Prediction of deletion size, location, and origin may help guide confirmatory testing.Discussion: The data shows that MPS-based NIPS can screen for 22q11.2DS with a high PPV, and that collaboration between the laboratory and clinicians allows consideration of additional metrics that may guide diagnostic testing and subsequent management.
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Affiliation(s)
- Erica Soster
- Labcorp, La Jolla, CA, United States
- *Correspondence: Erica Soster,
| | | | - Jill Rafalko
- Labcorp, La Jolla, CA, United States
- PetDx, The Center for Novel Therapeutics, La Jolla, CA, United States
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11
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Lüthgens K, Sinzel M, Kolar M, Kagan KO. Screen-positive rate in cell-free DNA screening for microdeletion 22q11.2. Prenat Diagn 2023; 43:288-293. [PMID: 36738442 DOI: 10.1002/pd.6328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To examine the impact of the fetal fraction (FF) on the screen-positive rate in screening for microdeletion 22q11.2. METHODS This study is based on samples that were analyzed using the Harmony® Prenatal Test (Roche Inc). The study cohort comprised samples from women with singleton pregnancies who were at least 16 years old and at least at 11 weeks' gestation. Logistic regression analysis was used to determine significant covariates that carry an impact on the screen-positive rate. RESULTS The study population consisted of 52,019 pregnancies, including 309 pregnancies with a high-risk result for microdeletion 22q11.2. Thus, the overall screen-positive rate was 0.59%. In the low-risk group, the FF was 10.1%, and in the high-risk group, it was 7.3%. Regression analysis indicated a strong correlation between the FF and the screen-positive rate. In the cases with an FF of <11.0%, the screen-positive rate was 0.92%, while it was 0.13% in the group with a higher FF. CONCLUSION The screen-positive rate depends on the FF. In order to keep the rate low, we recommend restricting the analysis to samples with a FF of 11% and more.
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Affiliation(s)
| | | | | | - Karl Oliver Kagan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
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12
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Raymond YC, Acreman ML, Bussolaro S, Mol BW, Fernando S, Menezes M, Da Silva Costa F, Fantasia I, Rolnik DL. The accuracy of cell-free DNA screening for fetal segmental copy number variants: A systematic review and meta-analysis. BJOG 2023; 130:549-559. [PMID: 36655363 DOI: 10.1111/1471-0528.17386] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 01/20/2023]
Abstract
BACKGROUND The performance of cell-free DNA (cfDNA) screening for microscopic copy number variants (CNVs) is unclear. OBJECTIVES This was a systematic review and meta-analysis to investigate the sensitivity, specificity and positive predictive value (PPV) of cfDNA screening for CNVs. SEARCH STRATEGY Articles published in EMBASE, PubMed or Web of Science before November 2022 were screened for inclusion. This protocol was registered with PROSPERO (23 March 2021, CRD42021250849) prior to initiation. SELECTION CRITERIA Articles published in English, detailing diagnostic outcomes for at least 10 high-risk CNV results with cfDNA were considered for inclusion. DATA COLLECTION AND ANALYSIS The PPV was calculated and pooled with random-effects models for double-arcsine transformed proportions, using cases with diagnostic confirmation. Overall sensitivity, specificity and a summary receiver-operating characteristics (ROC) curve were calculated using bivariate models. The risk of bias was assessed using QUADAS-2. MAIN RESULTS In all, 63 articles were included in the final analysis, detailing 1 591 459 cfDNA results. The pooled PPV was 37.5% (95% confidence interval [CI] 30.6-44.8), with substantial statistical heterogeneity (I2 = 93.9%). Bivariate meta-analysis estimated sensitivity and specificity to be 77.4% (95% CI 65.7-86.0) and 99.4% (95% CI 98.0-99.8), respectively, with an area under the summary ROC curve of 0.947 (95% CI 0.776-0.984). CONCLUSIONS Approximately one-third of women who screen high-risk for CNVs with cfDNA will have an affected fetus. This value is of importance for screening counselling.
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Affiliation(s)
- Yvette C Raymond
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia
| | - Melissa L Acreman
- Department of Obstetrics and Gynaecology, Ipswich Hospital, Ipswich, Queensland, Australia
| | - Sofia Bussolaro
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
| | - Ben W Mol
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Aberdeen Centre for Women's Health Research, University of Aberdeen, Aberdeen, UK
| | - Shavi Fernando
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's, Monash Health, Clayton, Victoria, Australia
| | - Melody Menezes
- Monash Ultrasound for Women, Melbourne, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Fabricio Da Silva Costa
- Maternal Fetal Medicine Unit, Gold Coast University Hospital, Gold Coast, Queensland, Australia.,School of Medicine, Griffith University, Gold Coast, Queensland, Australia
| | - Ilaria Fantasia
- Obstetrics & Gynaecology Unit, San Salvatore Hospital, L'Aquila, Italy
| | - Daniel Lorber Rolnik
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Victoria, Australia.,Monash Women's, Monash Health, Clayton, Victoria, Australia
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13
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Xiang J, Peng Z. Applications of Noninvasive Prenatal Testing for Subchromosomal Copy Number Variations Using Cell-Free DNA. Clin Lab Med 2022; 42:613-625. [PMID: 36368786 DOI: 10.1016/j.cll.2022.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jiale Xiang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyu Peng
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Yang L, Bu G, Ma Y, Zhao J, Rezak J, La X. Comparison of noninvasive prenatal screening for defined pathogenic microdeletion/microduplication syndromes and nonsyndromic copy number variations: a large multicenter study. J Comp Eff Res 2022; 11:1277-1291. [PMID: 36200453 DOI: 10.2217/cer-2022-0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background: This retrospective study assessed the precision of noninvasive prenatal testing (NIPT) in detecting microdeletion/microduplication syndromes (MMSs) and nonsyndromic copy number variations (CNVs). Methods: The study included 19,086 singleton pregnancies screened on NIPT using high-throughput sequencing. Pregnancies with CNVs on NIPT underwent amniocentesis for karyotyping and CNV sequencing (CNV-seq). We analyzed pathogenic MMSs and nonsyndromic CNVs separately, dividing the CNVs into subgroups based on fragment size and fetal ultrasound findings. Results: A total of 170 abnormalities were detected by NIPT, of which 113 (66.5%) underwent invasive testing. The positive predictive value (PPV) of CNV-seq for all types of CNV detected by NIPT was 35.4%, with PPVs of 61.5 and 27.6% for pathogenic MMSs and nonsyndromic CNVs, respectively. PPVs for NIPT showed different values depending on gestational characteristics, with the highest PPV for NIPT in the group with increased nuchal thickness (66.7%) and for the abnormal ultrasound group (57.1%). CNVs ≤5 Mb with normal ultrasound findings were generally associated with a healthy fetus. Conclusion: NIPT can detect chromosomal aberrations in the first trimester, with high performance for MMSs. However, due to the low PPV for nonsyndromic CNVs, and the good pregnancy outcome in most cases, the introduction of expanded NIPT would cause an increase in unnecessary invasive procedures and inappropriate terminations of pregnancy.
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Affiliation(s)
- Li Yang
- Department of Prenatal Diagnosis, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| | - Guosen Bu
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| | - Yuyu Ma
- State Key Laboratory of Pathogenesis, Prevention & Treatment of High Incidence Diseases in Central Asia, Clinical Laboratory Center, Tumor Hospital Affiliated to Xinjiang Medical University, Urumqi, Xinjiang, 830011, PR China
| | - Jing Zhao
- Department of Prenatal Diagnosis, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| | - Jiamilla Rezak
- Department of Prenatal Diagnosis, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
| | - Xiaolin La
- Department of Prenatal Diagnosis, Center for Reproductive Medicine, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830054, PR China
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15
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Xue H, Yu A, Lin M, Chen X, Guo Q, Xu L, Huang H. Efficiency of expanded noninvasive prenatal testing in the detection of fetal subchromosomal microdeletion and microduplication in a cohort of 31,256 single pregnancies. Sci Rep 2022; 12:19750. [PMID: 36396840 PMCID: PMC9672043 DOI: 10.1038/s41598-022-24337-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Noninvasive prenatal testing (NIPT) is widely used to screen for common fetal chromosomal aneuploidies. However, the ability of NIPT-Plus to detect copy number variation (CNV) is debatable. Accordingly, we assessed the efficiency of NIPT-Plus to detect clinically significant fetal CNV. We performed a prospective analysis of 31,260 singleton pregnancies, included from June 2017 to December 2020. Cell-free fetal DNA was directly sequenced using the semiconductor sequencing platform for women with high-risk CNV with clinically significant results. Fetal karyotyping and chromosomal microarray analysis (or next-generation sequencing) are recommended for invasive diagnostic procedures. Women at low risk with no other abnormal results continued their pregnancies. We analyzed the expanded NIPT results, diagnostic test results, and follow-up information to evaluate its performance in detecting fetal CNV. Of the 31,260 pregnant women who received NIPT-Plus, 31,256 cases were tested successfully, a high risk of clinically significant CNV was detected in 221 cases (0.71%); 18 women refused further diagnosis; 203 women underwent invasive prenatal diagnosis; and 78 true positive cases and 125 false positive cases, with an overall positive predictive value (PPV) of 38.42% and a false positive rate of 0.40%. For known microdeletion/microduplication syndromes (n = 27), the PPVs were 75% DiGeorge syndrome (DGS), 80% 22q11.22 microduplication, 50% Prader-Willi syndrome, and 50% cri-du-chat. For the remaining clinically significant fetal CNVs (n = 175), the combined PPVs were 46.5% (CNVs > 10 Mb) and 28.57% (CNVs ≤ 10 Mb). NIPT-Plus screening for CNV has certain clinical value. NIPT-Plus yielded relatively high PPVs for 22q11.2 microduplication syndrome and DGS, and low to moderate PPVs for other CNVs.
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Affiliation(s)
- Huili Xue
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Aili Yu
- grid.256112.30000 0004 1797 9307Reproductive Medicine Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Min Lin
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Xuemei Chen
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Qun Guo
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Liangpu Xu
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
| | - Hailong Huang
- grid.256112.30000 0004 1797 9307Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No. 18 Daoshan Road, Gulou District, Fuzhou City, 350001 Fujian Province China
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16
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Raymond YC, Fernando S, Menezes M, Meagher S, Mol BW, McLennan A, Scott F, Mizia K, Carey K, Fleming G, Rolnik DL. Cell-free DNA screening for rare autosomal trisomies and segmental chromosome imbalances. Prenat Diagn 2022; 42:1349-1357. [PMID: 36068932 PMCID: PMC9826090 DOI: 10.1002/pd.6233] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/02/2022] [Accepted: 08/26/2022] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To assess the outcomes of pregnancies at high-risk for rare autosomal trisomies (RATs) and segmental imbalances (SIs) on cell-free DNA (cfDNA) screening. METHOD A retrospective study of women who underwent cfDNA screening between September 2019 and July 2021 at three ultrasound services in Australia. Positive predictive values (PPVs) were calculated using fetal chromosomal analysis. RESULTS Among 23,857 women screened, there were 93 high-risk results for RATs (0.39%) and 82 for SIs (0.34%). The PPVs were 3.8% (3/78, 95% CI 0.8%-10.8%) for RATs and 19.1% (13/68, 95% CI 10.6%-30.5%) for SIs. If fetuses with structural anomalies were also counted as true-positive cases, the PPV for RATS increased to 8.5% (7/82, 95% CI 3.5%-16.8%). Among 85 discordant cases with birth outcomes available (65.4%), discordant positive RATs had a significantly higher proportion of infants born below the 10th and 3rd birthweight percentiles than expected (19.6% (p = 0.022) and 9.8% (p = 0.004), respectively), which was not observed in the SI group (2.9% < 10th (p = 0.168) and 0.0% <3rd (p = 0.305)). CONCLUSION The PPVs for SI and RAT results are low, except when a structural abnormality is also present. Discordant positive RATs are associated with growth restriction.
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Affiliation(s)
- Yvette C. Raymond
- Department of Obstetrics and GynecologyMonash UniversityClaytonVictoriaAustralia
| | - Shavi Fernando
- Department of Obstetrics and GynecologyMonash UniversityClaytonVictoriaAustralia,Monash Women'sMonash HealthClaytonVictoriaAustralia
| | - Melody Menezes
- Monash Ultrasound for WomenMelbourneVictoriaAustralia,Department of PediatricsThe University of MelbourneMelbourneVictoriaAustralia
| | - Simon Meagher
- Monash Ultrasound for WomenMelbourneVictoriaAustralia
| | - Ben W. Mol
- Department of Obstetrics and GynecologyMonash UniversityClaytonVictoriaAustralia,Monash Women'sMonash HealthClaytonVictoriaAustralia,Aberdeen Centre for Women's Health ResearchUniversity of AberdeenAberdeenUK
| | - Andrew McLennan
- Sydney Ultrasound for WomenSydneyNew South WalesAustralia,Discipline of Obstetrics, Gynaecology and NeonatologyThe University of SydneySydneyNew South WalesAustralia
| | - Fergus Scott
- Sydney Ultrasound for WomenSydneyNew South WalesAustralia,School of Women's and Children's HealthUniversity of New South WalesSydneyNew South WalesAustralia
| | - Karen Mizia
- Ultrasound CareSydneyNew South WalesAustralia,Australian National UniversityCanberraAustralia
| | - Karen Carey
- Sydney Ultrasound for WomenSydneyNew South WalesAustralia
| | | | - Daniel Lorber Rolnik
- Department of Obstetrics and GynecologyMonash UniversityClaytonVictoriaAustralia,Monash Women'sMonash HealthClaytonVictoriaAustralia
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17
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Kleinfinger P, Brechard M, Luscan A, Trost D, Boughalem A, Mylene Valduga, Serero DR S, Costa JM, Lohmann L. Case Report: How whole-genome sequencing-based cell-free DNA prenatal testing can help identify a marker mhromosome. Front Genet 2022; 13:926290. [PMID: 36226188 PMCID: PMC9549001 DOI: 10.3389/fgene.2022.926290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
A supernumerary marker chromosome (SMC) is a structurally abnormal chromosome that cannot be characterized by conventional banding cytogenetics. Marker chromosomes are present in 0.075% of prenatal cases. They are associated with variable phenotypes, ranging from normal to severely abnormal, and the prognosis is largely dependent on the results of further cytogenomic analysis. Here, we report the identification and characterization of a marker chromosome following prenatal screening in a 39-year-old pregnant patient. The patient had a normal first trimester ultrasound but was high-risk for fetal chromosome anomalies based on the results of maternal serum parameters. Chorionic villus sampling was performed, and analysis of chorionic villi revealed the presence of two identical marker chromosomes. In the interest of a rapid identification of the markers, we performed noninvasive prenatal testing (NIPT) together with chorionic villus sampling. A pericentromeric 29 Mb duplication of chromosome 20: dup (20) (p13q11.21) was identified and thereafter confirmed by targeted metaphasic FISH. Whole-genome sequencing-based NIPT was instrumental in rapid characterization of the SMCs and allowed us to obviate the need for multiple expensive and time-consuming FISH analyses.
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18
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Zaninović L, Bašković M, Ježek D, Katušić Bojanac A. Validity and Utility of Non-Invasive Prenatal Testing for Copy Number Variations and Microdeletions: A Systematic Review. J Clin Med 2022; 11:jcm11123350. [PMID: 35743413 PMCID: PMC9224664 DOI: 10.3390/jcm11123350] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Valid data on prenatal cell-free DNA-based screening tests for copy number variations and microdeletions are still insufficient. We aimed to compare different methodological approaches concerning the achieved diagnostic accuracy measurements and positive predictive values. For this systematic review, we searched the Scopus and PubMed databases and backward citations for studies published between 2013 and 4 February 2022 and included articles reporting the analytical and clinical performance of cfDNA screening tests for CNVs and microdeletions. Of the 1810 articles identified, 32 met the criteria. The reported sensitivity of the applied tests ranged from 20% to 100%, the specificity from 81.62% to 100%, and the PPV from 3% to 100% for cases with diagnostic or clinical follow-up information. No confirmatory analysis was available in the majority of cases with negative screening results, and, therefore, the NPVs could not be determined. NIPT for CNVs and microdeletions should be used with caution and any developments regarding new technologies should undergo strict evaluation before their implementation into clinical practice. Indications for testing should be in correlation with the application guidelines issued by international organizations in the field of prenatal diagnostics.
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Affiliation(s)
- Luca Zaninović
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10 000 Zagreb, Croatia
| | - Marko Bašković
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Children’s Hospital Zagreb, Ulica Vjekoslava Klaića 16, 10 000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-3636-379
| | - Davor Ježek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Department of Histology and Embryology, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia
- Department of Transfusion Medicine and Transplantation Biology, University Hospital Centre Zagreb, Kišpatićeva 12, 10 000 Zagreb, Croatia
| | - Ana Katušić Bojanac
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia; (L.Z.); (D.J.); (A.K.B.)
- Department of Medical Biology, School of Medicine, University of Zagreb, Šalata 3, 10 000 Zagreb, Croatia
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19
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Chen Y, Lu L, Zhang Y, Wang F, Ni Y, Wang Q, Ying C. Clinical application of expanded noninvasive prenatal testing for fetal chromosome abnormalities in a cohort of 39,580 pregnancies. Am J Med Genet A 2022; 188:1426-1434. [PMID: 35107205 DOI: 10.1002/ajmg.a.62657] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/02/2022] [Accepted: 01/06/2022] [Indexed: 11/07/2022]
Abstract
The aim of this study was to determine the predictive value of expanded noninvasive prenatal testing (NIPT-plus) for fetal chromosome abnormalities in the second trimester (12-26 weeks). We conducted a retrospective cohort study of 39,580 pregnancies with NIPT-plus. Screening positive cases were diagnosed with karyotyping and single-nucleotide polymorphism array analysis (SNP array)/copy number variation sequencing (CNV-seq) with follow-up. The positive predictive values (PPVs) of trisomy 21, 18, and 13 (T21, T18, and T13), sex chromosome aneuploidies (SCAs), and microdeletion and microduplication syndromes (MMS) by NIPT-plus were recorded. We assessed the predictive value of NIPT-plus based on maternal age and conventional indications. Of 39,580 pregnancies with NIPT-plus, 511 (1.3%) had prenatal screening positive results of fetal chromosome abnormality, of which 87.7% (448/511) had invasive prenatal diagnosis. NIPT-plus performed better in predicting fetal SCAs and chromosome aneuploidies for pregnancies with advanced maternal age (AMA) than young maternal age (YMA). Besides, the PPVs of T21, T13, and chromosome aneuploidies showed an upward trend when comparison was based on maternal age in 5-year subintervals. The termination rates of 45,X, 47,XXX, 47,XXY, and 47,XYY were 100% (11/11), 20.0% (3/15), 91.7% (22/24), and 7.1% (1/14) with postnatal follow-up. Last but not least, the PPV for MMS is 41.7% (30/72), which may have a positive correlation between the size of CNVs. Pregnant women with screen-positive results for common trisomies (T13, T18, and T21) were more willing to conduct invasive prenatal diagnosis compared to those with positive results for SCAs or MMS. However, the current study demonstrated SCAs and MMS had the lowest PPV. This highlights the importance of confirmatory prenatal diagnosis in those patients and the potential impact on genetic counseling and informative decision-making.
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Affiliation(s)
- Yisheng Chen
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Loukaiyi Lu
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Ying Zhang
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Feifei Wang
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yinghua Ni
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Qiang Wang
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Chunmei Ying
- Department of Laboratory Medicine, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
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20
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Dar P, Jacobsson B, Clifton R, Egbert M, Malone F, Wapner RJ, Roman AS, Khalil A, Faro R, Madankumar R, Edwards L, Strong N, Haeri S, Silver R, Vohra N, Hyett J, Demko Z, Martin K, Rabinowitz M, Flood K, Carlsson Y, Doulaveris G, Daly S, Hallingström M, MacPherson C, Kao C, Hakonarson H, Norton ME. Cell-free DNA screening for prenatal detection of 22q11.2 deletion syndrome. Am J Obstet Gynecol 2022; 227:79.e1-79.e11. [PMID: 35033576 DOI: 10.1016/j.ajog.2022.01.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/03/2022] [Accepted: 01/05/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Historically, prenatal screening has focused primarily on the detection of fetal aneuploidies. Cell-free DNA now enables noninvasive screening for subchromosomal copy number variants, including 22q11.2 deletion syndrome (or DiGeorge syndrome), which is the most common microdeletion and a leading cause of congenital heart defects and neurodevelopmental delay. Although smaller studies have demonstrated the feasibility of screening for 22q11.2 deletion syndrome, large cohort studies with confirmatory postnatal testing to assess test performance have not been reported. OBJECTIVE This study aimed to assess the performance of single-nucleotide polymorphism-based, prenatal cell-free DNA screening for detection of 22q11.2 deletion syndrome. STUDY DESIGN Patients who underwent single-nucleotide polymorphism-based prenatal cell-free DNA screening for 22q11.2 deletion syndrome were prospectively enrolled at 21 centers in 6 countries. Prenatal or newborn DNA samples were requested in all cases for genetic confirmation using chromosomal microarrays. The primary outcome was sensitivity, specificity, positive predictive value, and negative predictive value of cell-free DNA screening for the detection of all deletions, including the classical deletion and nested deletions that are ≥500 kb, in the 22q11.2 low-copy repeat A-D region. Secondary outcomes included the prevalence of 22q11.2 deletion syndrome and performance of an updated cell-free DNA algorithm that was evaluated with blinding to the pregnancy outcome. RESULTS Of the 20,887 women enrolled, a genetic outcome was available for 18,289 (87.6%). A total of 12 22q11.2 deletion syndrome cases were confirmed in the cohort, including 5 (41.7%) nested deletions, yielding a prevalence of 1 in 1524. In the total cohort, cell-free DNA screening identified 17,976 (98.3%) cases as low risk for 22q11.2 deletion syndrome and 38 (0.2%) cases as high risk; 275 (1.5%) cases were nonreportable. Overall, 9 of 12 cases of 22q11.2 were detected, yielding a sensitivity of 75.0% (95% confidence interval, 42.8-94.5); specificity of 99.84% (95% confidence interval, 99.77-99.89); positive predictive value of 23.7% (95% confidence interval, 11.44-40.24), and negative predictive value of 99.98% (95% confidence interval, 99.95-100). None of the cases with a nonreportable result was diagnosed with 22q11.2 deletion syndrome. The updated algorithm detected 10 of 12 cases (83.3%; 95% confidence interval, 51.6-97.9) with a lower false positive rate (0.05% vs 0.16%; P<.001) and a positive predictive value of 52.6% (10/19; 95% confidence interval, 28.9-75.6). CONCLUSION Noninvasive cell-free DNA prenatal screening for 22q11.2 deletion syndrome can detect most affected cases, including smaller nested deletions, with a low false positive rate.
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Affiliation(s)
- Pe'er Dar
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY.
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Rebecca Clifton
- The Biostatistics Center, George Washington University, Rockville, MD
| | | | - Fergal Malone
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, NY
| | - Ashley S Roman
- Department of Obstetrics and Gynecology, New York University Langone, New York, NY
| | - Asma Khalil
- Department of Obstetrics and Gynaecology, St George's Hospital, University of London, London, United Kingdom
| | - Revital Faro
- Department of Obstetrics and Gynecology, Saint Peter's University Hospital, New Brunswick, NJ
| | - Rajeevi Madankumar
- Department of Obstetrics and Gynecology, Long Island Jewish Medical Center, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New Hyde Park, NY
| | | | - Noel Strong
- Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sina Haeri
- Austin Maternal-Fetal Medicine, Austin, TX
| | - Robert Silver
- Department of Obstetrics and Gynecology, University of Utah, Salt Lake City, UT
| | - Nidhi Vohra
- Department of Obstetrics and Gynecology, North Shore University Hospital, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY
| | - Jon Hyett
- Department of Obstetrics and Gynecology, Royal Prince Alfred Hospital, University of Sydney, Camperdown, New South Wales, Australia
| | | | | | | | - Karen Flood
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ylva Carlsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Georgios Doulaveris
- Department of Obstetrics and Gynecology and Women's Health, Montefiore Medical Center, Albert Einstein College of Medicine, New York, NY
| | - Sean Daly
- Department of Obstetrics and Gynecology, Rotunda Hospital, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Maria Hallingström
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Cora MacPherson
- The Biostatistics Center, George Washington University, Rockville, MD
| | - Charlly Kao
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Mary E Norton
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA
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21
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Clinical utility of expanded NIPT for chromosomal abnormalities and etiology analysis of cytogenetic discrepancies cases. J Assist Reprod Genet 2022; 39:267-279. [PMID: 35000096 PMCID: PMC8866633 DOI: 10.1007/s10815-021-02351-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/29/2021] [Indexed: 01/03/2023] Open
Abstract
PURPOSE This study is to assess the performance of expanded noninvasive prenatal testing (NIPT) in detecting chromosome aneuploidies and chromosome copy number variants (CNVs), and elucidate the discordant cases between NIPT and fetal karyotype. METHODS A total of 2139 single pregnancies have been recruited and sequenced with expanded NIPT. Karyotype analysis and CNV sequencing (CNV-seq) of amniotic fluid were performed in 22 of 23 high-risk, three low-risk NIPT pregnant women with abnormal ultrasound findings in the follow-up, and three non-reportable NIPT pregnant women. The genetic investigation of discordant results between NIPT and amniocytes in three cases was proceeded. Placental samples, fetal samples from the limb, hip, umbilical cord, and maternal peripheral blood leukocytes were collected for CNV-Seq. RESULTS Expanded NIPT revealed a total of 23 positive pregnancies and yielded the overall positive predictive value (PPV) 65.2%. For T21, T18, and XXY, all the PPV was 100% respectively. For CNVs > 10 Mb and 5-10 Mb, the PPV was 42.8% and 16.7%, respectively. The genetic investigation of placental and fetal samples indicated different levels of placental and fetal mosaicism contributing to two of three verified discordant results. CONCLUSIONS The results showed that screening for CNVs with expanded NIPT is promising although the accuracy rate remains insufficient. The different occurring time of mitotic non-disjunction of different chromosome in early development of embryo results in varying levels of chromosomal mosaicism in different placental and fetal tissues. The result highlights the significance of comprehensive cytogenetic validation of placental and fetal specimens with an inconsistent NIPT results.
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22
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Yang J, Chen M, Shen W, Wu H, Shou J, Sun J, Wu W. Knowledge, attitudes, and practices of healthcare professionals working in prenatal diagnosis toward expanded non-invasive prenatal testing in China. Prenat Diagn 2021; 42:3-14. [PMID: 34888898 DOI: 10.1002/pd.6075] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 11/12/2022]
Abstract
OBJECTIVES To investigate the knowledge, attitudes, and practices of healthcare professionals (HCPs) working in prenatal diagnosis toward expanded non-invasive prenatal testing (NIPT) in China. METHODS We conducted a national online survey among HCPs working in prenatal diagnosis, including specialists in prenatal diagnosis and foetal medicine, obstetricians and gynaecologists, nurses in obstetrics and gynaecology, obstetric ultrasound doctors, and technicians in prenatal diagnosis laboratories. A total of 1882 questionnaires were collected, among which 1822 questionnaires met the research criteria and were included in the analysis. RESULTS More than 99% of all participants opted for NIPT for trisomies 21, 18, and 13. The rates of support for expanded NIPT for sex chromosome aneuploidies, rare autosomal trisomies, microdeletions and microduplications, and single-gene disorders were 93.9%, 88.6%, 89.4%, and 86.8%, respectively. Specialists in prenatal diagnosis and foetal medicine had greater knowledge but were less likely to support expanded NIPT compared to other participants. Knowledge increased with educational level, whereas support for expanded NIPT decreased with educational level. CONCLUSIONS More than 80% of HCPs working in prenatal diagnosis in China expressed support for expanding NIPT to conditions other than common trisomies. The degree of knowledge was negatively associated with the rate of support.
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Affiliation(s)
- Jing Yang
- Department of Obstetrics, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Min Chen
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Shen
- Department of Obstetrics, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Heli Wu
- Department of Obstetrics, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jian Shou
- Department of Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Jimei Sun
- Department of Obstetrics and Gynecology, Department of Fetal Medicine and Prenatal Diagnosis, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wenyan Wu
- BGI Guangzhou Medical Institute Company Limited, Guangzhou, Guangdong, China
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Duan HL, Li J, Wang WJ, Cram DS, Liu W, Cao PX, Zhu XY, Hu YL. Cell-free DNA test for pathogenic copy number variations: A retrospective study. Taiwan J Obstet Gynecol 2021; 60:1066-1071. [PMID: 34794739 DOI: 10.1016/j.tjog.2021.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2020] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVE To evaluate the detection rate (DR) by prenatal cell-free DNA test for pathogenic copy number variations (CNVs)>2 Mb among pregnancies with fetal ultrasound abnormalities. MATERIALS AND METHODS This was a retrospective study on 29 pregnant women with fetuses diagnosed as microdeletion/microduplication syndromes by prenatal chromosome microarray analysis (CMA). Cell-free DNA from the maternal plasma was sequenced on the NextSeq CN500 sequencer. The quality standard of unique map reads in a single sample was greater than 10 M and only gains and losses of more than 2 Mb were reported. RESULTS A total of 24 CNVs were identified by cell-free DNA test among the 21 fetuses with pathogenic CNVs identified by prenatal CMA, including 20 consistent CNVs and 4 inconsistent CNVs. Overall, the DR of cell-free DNA test for pathogenic CNVs >2 Mb was 69%. Microdeletions or microduplications at 22q11.2 were the most common CNVs, with a DR of 4/5 (80%) and 3/4 (75%) respectively. CONCLUSION Cell-free DNA test exhibited a moderate DR for pathogenic CNVs >2 Mb among fetuses with ultrasound abnormalities. Cell-free DNA test could provide an opportunity for early screening before the appearance of abnormalities on fetal ultrasound, while further clinical data and cost-effectiveness assessment are needed.
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Affiliation(s)
- Hong-Lei Duan
- Department of Obstetrics and Gynecology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jie Li
- Department of Obstetrics and Gynecology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Wan-Jun Wang
- Department of Obstetrics and Gynecology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | | | - Wei Liu
- Department of Obstetrics and Gynecology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Pei-Xuan Cao
- Department of Obstetrics and Gynecology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xiang-Yu Zhu
- Department of Obstetrics and Gynecology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Ya-Li Hu
- Department of Obstetrics and Gynecology, Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China.
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24
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Bevilacqua E, Jani JC, Chaoui R, Suk EA, Palma‐Dias R, Ko T, Warsof S, Stokowski R, Jones KJ, Grati FR, Schmid M. Performance of a targeted cell-free DNA prenatal test for 22q11.2 deletion in a large clinical cohort. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:597-602. [PMID: 34090308 PMCID: PMC8518527 DOI: 10.1002/uog.23699] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/10/2021] [Accepted: 05/21/2021] [Indexed: 05/17/2023]
Abstract
OBJECTIVE 22q11.2 deletion is more common than trisomies 18 and 13 combined, yet no routine approach to prenatal screening for this microdeletion has been established. This study evaluated the clinical sensitivity and specificity of a targeted cell-free DNA (cfDNA) test to screen for fetal 22q11.2 deletion in a large cohort, using blinded analysis of prospectively enrolled pregnancies and stored clinical samples. METHODS In order to ensure that the analysis included a meaningful number of cases with fetal 22q11.2 deletion, maternal plasma samples were obtained by prospective, multicenter enrolment of pregnancies with a fetal cardiac abnormality and from stored clinical samples from a research sample bank. Fetal genetic status, as evaluated by microarray analysis, karyotyping with fluorescence in-situ hybridization or a comparable test, was available for all cases. Samples were processed as described previously for the Harmony prenatal test, with the addition of DANSR (Digital Analysis of Selected Regions) assays targeting the 3.0-Mb region of 22q11.2 associated with 22q11.2 deletion syndrome. Operators were blinded to fetal genetic status. Sensitivity and specificity of the cfDNA test for 22q11.2 deletion were calculated based on concordance between the cfDNA result and fetal genotype. RESULTS The final study group consisted of 735 clinical samples, including 358 from prospectively enrolled pregnancies and 377 stored clinical samples. Of 46 maternal plasma samples from pregnancies with a 22q11.2 deletion, ranging in size from 1.25 to 3.25 Mb, 32 had a cfDNA result indicating a high probability of 22q11.2 deletion (sensitivity, 69.6% (95% CI, 55.2-80.9%)). All 689 maternal plasma samples without a 22q11.2 deletion were classified correctly by the cfDNA test as having no evidence of a 22q11.2 deletion (specificity, 100% (95% CI, 99.5-100%)). CONCLUSIONS The results of this large-scale prospective clinical evaluation of the sensitivity and specificity of a targeted cfDNA test for fetal 22q11.2 deletion demonstrate that this test can detect the common and smaller, nested 22q11.2 deletions with a low (0-0.5%) false-positive rate. Although the positive predictive value (PPV) observed in this study population was 100%, the expected PPV in the general pregnant population is estimated to be 12.2% at 99.5% specificity and 41.1% at 99.9% specificity. The use of this cfDNA test to screen for 22q11.2 deletion could enhance identification of pregnancies at risk for 22q11.2 deletion syndrome without significantly increasing the likelihood of maternal anxiety and unnecessary invasive procedures related to a false-positive result. © 2021 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- E. Bevilacqua
- Department of Obstetrics and Gynecology, University Hospital BrugmannUniversité Libre de BruxellesBrusselsBelgium
| | - J. C. Jani
- Department of Obstetrics and Gynecology, University Hospital BrugmannUniversité Libre de BruxellesBrusselsBelgium
| | - R. Chaoui
- Prenatal Diagnosis and Human GeneticsBerlinGermany
| | - E.‐K. A. Suk
- Prenatal Diagnosis and Human GeneticsBerlinGermany
| | - R. Palma‐Dias
- The Royal Women's HospitalUniversity of MelbourneParkvilleVICAustralia
| | - T.‐M. Ko
- Genephile Bioscience Laboratory, Ko's Obstetrics & Gynecology ClinicTaipei CityTaiwan
| | - S. Warsof
- Eastern Virginia Medical SchoolNorfolkVAUSA
| | | | - K. J. Jones
- Roche Sequencing Solutions, Inc.San JoseCAUSA
| | - F. R. Grati
- TOMA Advanced Biomedical Assays S.p.A, Impact Lab.Busto ArsizioItaly
| | - M. Schmid
- Roche Sequencing Solutions, Inc.San JoseCAUSA
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25
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Lin TY, Hsieh TT, Cheng PJ, Hung TH, Chan KS, Tsai C, Shaw SW. Taiwanese Clinical Experience with Noninvasive Prenatal Testing for DiGeorge Syndrome. Fetal Diagn Ther 2021; 48:672-677. [PMID: 34569534 DOI: 10.1159/000519057] [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: 03/09/2021] [Accepted: 08/16/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVE DiGeorge syndrome (DGS) is associated with microdeletions of chromosome 22q11. It is the second most common cause of congenital heart disease and is an important consideration whenever a conotruncal cardiac anomaly is identified. The availability of noninvasive prenatal testing (NIPT) is altering the practice of prenatal genetics and maternal-fetal medicine, resulting in a decline in invasive testing. Antenatal ultrasound and other biomarkers have their own limitation. NIPT was proposed to screen DGS with cell-free DNA in Taiwan. Here, we present our experience of prenatal diagnosis of DGS in our center. METHODS This was a retrospective study between November 1, 2019, and August 31, 2020, in Taiwan. Data were collected from 7,826 pregnant women self-referred for DGS screening with massive parallel shotgun sequencing-based NIPT. High-risk cases subsequently received amniocentesis for array comparative genomic hybridization (aCGH) to confirm the diagnosis. Characteristics of pregnancies were documented when participants received the test. Report of NIPT was completed 2 weeks after the test. Follow-up on high-risk cases was completed by telephone interview on January 30, 2021. RESULTS Thirteen cases showed high risk by NIPT, and 7 cases were confirmed by aCGH. The sensitivity and specificity were 100% (95% confidence interval [CI] 64.57-100.00%) and 99.92% (95% CI 99.83-99.96%). The prevalence of DGS was 1 in 1,118 pregnancies. The positive predictive rate was 53.85% (95% CI 29.14-76.79%). One true positive (TP) showed US anomaly, and 5 TPs selected termination. DISCUSSION/CONCLUSION NIPT demonstrated good performance in DGS screening. Detection of 22q11.2 deletion could be combined with routine screening to facilitate proper intervention.
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Affiliation(s)
- Tzu-Yi Lin
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - T'sang-T'ang Hsieh
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Po-Jen Cheng
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Tai-Ho Hung
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Kok-Seong Chan
- Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan
| | | | - Steven W Shaw
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Obstetrics and Gynecology, Taipei Chang Gung Memorial Hospital, Taipei, Taiwan.,Prenatal Cell and Gene Therapy Group, Institute for Women's Health University College London, London, United Kingdom
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26
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Shi P, Wang Y, Liang H, Hou Y, Chen D, Zhao G, Dai P, Xia Y, Feng Y, Cram DS, Kong X. The potential of expanded noninvasive prenatal screening for detection of microdeletion and microduplication syndromes. Prenat Diagn 2021; 41:1332-1342. [PMID: 34181751 DOI: 10.1002/pd.6002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 11/10/2022]
Abstract
OBJECTIVES To evaluate the clinical potential of a higher resolution noninvasive prenatal screening (NIPS-Plus) test for detection of microdeletion/microduplication syndromes (MMS) in addition to common aneuploidies. METHODS In a multicenter prospective study, 37,002 pregnant women with unremarkable first-trimester ultrasound scans had a NIPS-Plus test. Ultrasound screen positive women were not included in this study. RESULTS Of 36,970 ultrasound negative women there were 291 NIPS-Plus screen positive results indicating 237 aneuploidies and 54 MMS. Following amniocentesis, 171 (72%) were confirmed as genuine, comprising 3 T13s, 10 T18s, 61 T21s, 70 SCAs and 27 MMS. The PPV for MMS with unremarkable ultrasound findings was 50%. Routine clinical examination of children born from NIPS-Plus negative pregnancies revealed no obvious signs of chromosome disease syndromes at one year of age. CONCLUSIONS NIPS-Plus has the potential for clinical utility not only for routine aneuploid screening but also for MMS that do not show overt signs during early pregnancy ultrasound screening. We suggest that ultrasound with NIPS-Plus in combination with appropriate counselling could be considered as a comprehensive first-tier prenatal screening approach for all pregnant women.
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Affiliation(s)
- Panlai Shi
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuan Wang
- Berry Genomics Corporation, Beijing, China
| | | | - Yaqin Hou
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Duo Chen
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ganye Zhao
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Peng Dai
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanjie Xia
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yin Feng
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | | | - Xiangdong Kong
- Genetic and Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Gou L, Suo F, Wang Y, Wang N, Wu Q, Hu S, Wang P, Gu L, Zhang M, Wang C, Zhang Y, Yin X, Zhang P, Xu J, Wang X, Gu M. Clinical value for the detection of fetal chromosomal deletions/duplications by noninvasive prenatal testing in clinical practice. Mol Genet Genomic Med 2021; 9:e1687. [PMID: 33951332 PMCID: PMC8222853 DOI: 10.1002/mgg3.1687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 03/04/2021] [Accepted: 03/23/2021] [Indexed: 01/13/2023] Open
Abstract
Objective This study was to report the experiences on the clinical value of noninvasive prenatal testing (NIPT) for the screening of fetal chromosomal deletions/duplications. Methods We performed a retrospective analysis of a cohort of 20,439 pregnancies undergoing NIPT from March 2017 to September 2020 at a single center. Patients with positive NIPT results for fetal chromosomal deletions or duplications had options of invasive diagnostic testing or no further testing. The data were complied from all cases with positive NIPT results for chromosomal deletions/duplications. The positive predictive value (PPV) was calculated from tabulated data. Results In this cohort, positive NIPT results for fetal chromosomal deletions/duplications were found in 60 pregnant women. Of the positive samples, further invasive testing was performed in 39 cases, in which 9 cases were found to be true positive. The overall PPV for chromosomal deletions/duplications was 23.1%. In addition, fetal structural anomaly was found by ultrasound examination in three cases, in which the chromosomal deletions/duplications of three cases were not verified. Moreover, an unexpected pathogenic 8p23.3 deletion was identified by invasive testing in 1 fetus with a false positive NIPT screen for 3q27.3q29 duplication. Conclusions In summary, positive NIPT results of chromosomal deletions/duplications were not uncommon in clinical practice, whereas the PPV for the testing was low. Hence, potential risks and high percentage of false positives for these abnormal NIPT results might be informed to pregnant women before the choice made of invasive testing.
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Affiliation(s)
- Lingshan Gou
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Feng Suo
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yi Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Na Wang
- Department of Technology, Suzhou Beikang Medical Device Co. Ltd., Suzhou, China
| | - Qin Wu
- Zhejiang Biosan Biochemical Technologies Co. Ltd., Hangzhou, 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, China
| | - Peng Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Lize Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Man Zhang
- Zhejiang Biosan Biochemical Technologies Co. Ltd., Hangzhou, China
| | - Chuanxia Wang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Yan Zhang
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Xin Yin
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
| | - Peng Zhang
- Shenzhen Longgang Institute of Stomatology, Shenzhen Longgang E.N.T. Hospital, Shenzhen, China
| | - Jian Xu
- Shenzhen Longgang Institute of Stomatology, Shenzhen Longgang E.N.T. Hospital, Shenzhen, China
| | - Xingqi Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu Province, School of Life Science, Jiangsu Normal University, Xuzhou, China
| | - Maosheng Gu
- Center for Genetic Medicine, Xuzhou Maternity and Child Health Care Hospital Affiliated to Xuzhou Medical University, Xuzhou, China
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Christiaens L, Chitty LS, Langlois S. Current controversies in prenatal diagnosis: Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered. Prenat Diagn 2021; 41:1316-1323. [PMID: 33829520 DOI: 10.1002/pd.5943] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 11/11/2022]
Abstract
Non-invasive prenatal testing (NIPT) based on analysis of cell free DNA circulating in the maternal plasma has been available clinically to screen for chromosomal abnormalities since 2011. There is significant evidence to suggest that NIPT has revolutionised prenatal screening for the common trisomies 13, 18, and 21. However, the evidence in favour of its extended use to screen for conditions other than these trisomies remains a topic of debate with no national or international organisation supporting clinical implementation for these indications. In the debate presented here - "Expanded NIPT that includes conditions other than trisomies 13, 18, and 21 should be offered" - we will see the pros and cons of screening for a wider range of chromosomal problems. The discussion presented swung the vote from 65% in favour and 35% against before the arguments were voiced to 41% in favour and 59% against. This significant swing in the vote indicates that the majority of our community feel more evidence is required before clinical implementation of extended NIPT.
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Affiliation(s)
- Lieve Christiaens
- Illumina Inc., San Diego, California, USA.,University Hospital of Utrecht, Utrecht, Netherlands
| | - Lyn S Chitty
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,The UCL Great Ormond Street Institute of Child Health, London, UK
| | - Sylvie Langlois
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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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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Bedei I, Wolter A, Weber A, Signore F, Axt-Fliedner R. Chances and Challenges of New Genetic Screening Technologies (NIPT) in Prenatal Medicine from a Clinical Perspective: A Narrative Review. Genes (Basel) 2021; 12:501. [PMID: 33805390 PMCID: PMC8065512 DOI: 10.3390/genes12040501] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
In 1959, 63 years after the death of John Langdon Down, Jérôme Lejeune discovered trisomy 21 as the genetic reason for Down syndrome. Screening for Down syndrome has been applied since the 1960s by using maternal age as the risk parameter. Since then, several advances have been made. First trimester screening, combining maternal age, maternal serum parameters and ultrasound findings, emerged in the 1990s with a detection rate (DR) of around 90-95% and a false positive rate (FPR) of around 5%, also looking for trisomy 13 and 18. With the development of high-resolution ultrasound, around 50% of fetal anomalies are now detected in the first trimester. Non-invasive prenatal testing (NIPT) for trisomy 21, 13 and 18 is a highly efficient screening method and has been applied as a first-line or a contingent screening approach all over the world since 2012, in some countries without a systematic screening program. Concomitant with the rise in technology, the possibility of screening for other genetic conditions by analysis of cfDNA, such as sex chromosome anomalies (SCAs), rare autosomal anomalies (RATs) and microdeletions and duplications, is offered by different providers to an often not preselected population of pregnant women. Most of the research in the field is done by commercial providers, and some of the tests are on the market without validated data on test performance. This raises difficulties in the counseling process and makes it nearly impossible to obtain informed consent. In parallel with the advent of new screening technologies, an expansion of diagnostic methods has begun to be applied after invasive procedures. The karyotype has been the gold standard for decades. Chromosomal microarrays (CMAs) able to detect deletions and duplications on a submicroscopic level have replaced the conventional karyotyping in many countries. Sequencing methods such as whole exome sequencing (WES) and whole genome sequencing (WGS) tremendously amplify the diagnostic yield in fetuses with ultrasound anomalies.
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Affiliation(s)
- Ivonne Bedei
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
| | - Aline Wolter
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
| | - Axel Weber
- Institute of Human Genetics, Justus Liebig University Giessen, 35392 Giessen, Germany;
| | - Fabrizio Signore
- Department of Obstetrics and Gynecology, Opedale S. Eugenio, 00144 Rome, Italy;
| | - Roland Axt-Fliedner
- Department of Prenatal Medicine and Fetal Therapy, Justus Liebig University Giessen, 35392 Giessen, Germany; (A.W.); (R.A.-F.)
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31
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Familiari A, Boito S, Rembouskos G, Ischia B, Accurti V, Fabietti I, Volpe P, Persico N. Cell-free DNA analysis of maternal blood in prenatal screening for chromosomal microdeletions and microduplications: a systematic review. Prenat Diagn 2021; 41:1324-1331. [PMID: 33710639 DOI: 10.1002/pd.5928] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIM OF THE STUDY Scientific Societies do not recommend the use of cell-free DNA (cfDNA) testing as a first-tier screening for microdeletion and microduplication syndromes (MMs). The aim of this study was to review the current available literature on the performance of cell-free DNA as a screening for MMs. METHODS Medline, Embase and the Cochrane Library were searched electronically from 2000 to January 2020 and articles reporting the diagnostic performance of cfDNA screening for MMs in large (>5000 cases) series were included. Between-study heterogeneity and random effect model for screen positive rate (SPR), false positive rate (FPR) and positive predictive value (PPV) were calculated. RESULTS We identified 42 papers, seven included, for a total of 474,189 pregnancies and 210 cases of MMs. Diagnostic verification of positive cases was available overall in 486 (71.68 %) of 678 cases. The weighted pooled SPR, FPR and PPV were 0.19% (95% CI = 0.09-0.33), 0.07 (95% CI = 0.02-0.15) and 44.1 (95% CI = 31.49-63.07). In conclusion, the pooled PPV of cfDNA testing in screening for MMs was about 40%, ranging from 29% to 91%, for an overall FPR <0.1%. CONCLUSIONS No confirmatory analysis was available in cases that did not undergo invasive testing, which were the vast majority of cases with a negative test, and therefore, the DR and the negative predictive value cannot be determined.
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Affiliation(s)
- Alessandra Familiari
- High Risk Pregnancy Unit, Children and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Simona Boito
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | | | - Benedetta Ischia
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Veronica Accurti
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Isabella Fabietti
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Paolo Volpe
- Fetal Medicine Unit, Di Venere and Sarcone Hospitals, Bari, Italy
| | - Nicola Persico
- Fetal Medicine and Surgery Service, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Clinical Science and Community Health, University of Milan, Italy
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Chitty LS, Ghidini A, Deprest J, Van Mieghem T, Levy B, Hui L, Bianchi DW. Right or wrong? Looking through the retrospectoscope to analyse predictions made a decade ago in prenatal diagnosis and fetal surgery. Prenat Diagn 2020; 40:1627-1635. [PMID: 33231306 DOI: 10.1002/pd.5870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,UCL Great Ormond Street Institute of Child Health, London, UK
| | - Alessandro Ghidini
- Department of Obstetrics and Gynecology, Georgetown University Hospital, Washington, DC.,Antenatal Testing Center, Inova Alexandria Hospital, Alexandria, VA
| | - Jan Deprest
- Department of Obstetrics and Gynaecology, University of Leuven, Leuven, Belgium and the Institute for Women's Health, UCL, London
| | - Tim Van Mieghem
- Fetal Medicine Unit and Ontario Fetal Centre, Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Brynn Levy
- Division of Personalized Genomic Medicine, Columbia University Medical Center & the New York Presbyterian Hospital, New York, New York, USA
| | - Lisa Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Victoria, Australia.,Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Murdoch Children's Research Institute, Parkville, Victoria, Australia.,The Northern Hospital, Epping, Victoria, Australia
| | - Diana W Bianchi
- Division of Prenatal Genomics and Fetal Therapy, Medical Genomics and Metabolic Genetics Branch, National Human Genome Institute, National Human Genome Institute, National Institutes of Health, Bethesda, Maryland, USA
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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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34
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Identification of copy number variants by NGS-based NIPT at low sequencing depth. Eur J Obstet Gynecol Reprod Biol 2020; 256:297-301. [PMID: 33310305 DOI: 10.1016/j.ejogrb.2020.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/20/2020] [Accepted: 11/06/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To explore the clinical utility of detecting chromosome copy number variants (CNVs) in the fetus by noninvasive prenatal testing (NIPT) using the low-pass whole-genome sequencing. METHODS Eight hundred and seventy-three singleton pregnancies with chromosomal microarray analysis (CMA) available between January 2017 to December 2019 and stored enough plasma sample for NIPT testing were included in this study. The CMA results show that forty-eight pregnancies with CNVs and eight hundred and twenty-five pregnancies are normal. Each pregnancy's plasma sample was blindly tested with NIPT at a depth of 0.51-1.19x for CNVs detection. The performance of the NIPT method for CNVs detection compared with the CMA method is evaluated. RESULTS A total of fifty-two CNVs ranging from 0.1-47.3 Mb identified in forty-eight samples were identified by NIPT, of which thirty-four CNVs were consistent with CMA results. Additionally, eighteen CNVs were missed by NIPT. The overall sensitivity and specificity for the detection of CNVs were 65.38% (95% CI: 51.76%-76.89%) and 97.45% (95% CI: 96.12%-98.35%), respectively. However, for the detection of CNVs larger than 2 Mb and CNVs less than 2Mb, the sensitivities were 81.58% (95% CI: 66.27%-91.09%) and 21.43% (95% CI: 6.84%-48.32%), respectively. CONCLUSION Our study demonstrated that the NIPT might be an alternative method for screening CNVs comparable with other studies. However, CNVs less than 2Mb in length shows poor sensitivity by NIPT. Noninvasive CNVs detection based on the NIPT method still needs more clinical validation studies and technical improvement to achieve clinically acceptable accuracy.
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35
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Nunley PB, Hashmi SS, Johnson A, Ashfaq M, Farach LS, Singletary CN, Stevens BK. Exploring the predicted yield of prenatal testing by evaluating a postnatal population with structural abnormalities using a novel mathematical model. Prenat Diagn 2020; 41:354-361. [PMID: 33128384 DOI: 10.1002/pd.5858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 08/29/2020] [Accepted: 10/19/2020] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To determine the yield of prenatal testing and screening options after identification of fetal structural abnormalities using a novel mathematical model. METHOD A retrospective chart review was conducted to collect structural abnormality and genetic testing data on infants who were evaluated postnatally by a medical geneticist. A novel mathematical model was used to determine and compare the predicted diagnostic yields of prenatal testing and screening options. RESULTS Over a quarter of patients with at least one structural abnormality (28.1%, n = 222) had a genetic aberration identified that explained their phenotype. Chromosomal microarray (CMA) had the highest predicted diagnostic yield (26.8%, P < .001). Karyotype (20.8%) had similar yields as genome wide NIPT (21.2%, P = .859) and NIPT with select copy number variants (CNVs) (17.9%, P = .184). Among individuals with an isolated structural abnormality, whole exome sequencing (25.9%) and CMA (14.9%) had the highest predicted yields. CONCLUSION This study introduces a novel mathematical model for predicting the potential yield of prenatal testing and screening options. This study provides further evidence that CMA has the highest predicted diagnostic yield in cases with structural abnormalities. Screening with expanded NIPT options shows potential for patients who decline invasive testing, but only in the setting of adequate pre-test counseling.
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Affiliation(s)
- Peyton B Nunley
- Department of Obstetrics and Gynecology, University of South Carolina School of Medicine, Columbia, South Carolina, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Syed S Hashmi
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Anthony Johnson
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Myla Ashfaq
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Laura S Farach
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Claire N Singletary
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Blair K Stevens
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, Texas, USA
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Wu X, Li Y, Xie X, Su L, Cai M, Lin N, Du S, Xu L, Huang H. Clinical Review of Noninvasive Prenatal Testing: Experience from 551 Pregnancies with Noninvasive Prenatal Testing-Positive Results in a Tertiary Referral Center. J Mol Diagn 2020; 22:1469-1475. [PMID: 33069877 DOI: 10.1016/j.jmoldx.2020.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/15/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
A total of 551 pregnancies with positive results for noninvasive prenatal testing (NIPT) using traditional karyotyping and chromosomal microarray analysis were analyzed. Confirmatory results, positive predictive values, etiology exploration of false-positive results, and pregnancy outcomes were recorded. The study demonstrated that NIPT performed better in predicting trisomy 21 and trisomy 18 for pregnancies with advanced maternal age than for pregnancies with young maternal age; as for trisomy 13 and sex chromosomal aneuploidy (SCA) prediction, there was no significant difference between the two groups. The positive predictive values for trisomy 21, trisomy 18, trisomy 13, and SCA showed no significant upward trend when compared based on specific age categories (an interval of 5 years), which suggested that NIPT-positive result deserves equal attention from both providers and patients regardless of maternal age. In addition, the termination rates of 45,X, 47,XXY, 47,XXX, and 47,XYY were 100% (2/2), 92.9% (26/28), 33.3% (5/15), and 9.5% (2/21), respectively, which demonstrated that the decision-making regarding pregnancies varied greatly according to the types of SCAs, and further reinforce the importance of confirmatory prenatal diagnosis. The current study also supported the viewpoint that confined placental mosaicism and maternal mosaicism were the important etiology of false-positive results.
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Affiliation(s)
- Xiaoqing Wu
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Ying Li
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Xiaorui Xie
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Linjuan Su
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Meiying Cai
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Na Lin
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Shengrong Du
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China
| | - Liangpu Xu
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China.
| | - Hailong Huang
- Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Prenatal Diagnosis Center of Fujian Provincial Maternity and Children Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou City, China.
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Kagan KO, Hoopmann M, Pfaff T, Prodan N, Wagner P, Schmid M, Dufke A, Mau-Holzmann U, Brucker S, Marcato L, Malvestiti B, Grati FR. First Trimester Screening for Common Trisomies and Microdeletion 22q11.2 Syndrome Using Cell-Free DNA: A Prospective Clinical Study. Fetal Diagn Ther 2020; 47:841-852. [PMID: 32877902 DOI: 10.1159/000510069] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/08/2020] [Indexed: 11/19/2022]
Abstract
OBJECTIVES The aims of the study were to assess the false-positive and uninformative test rate with first trimester cell-free DNA (cfDNA) screening for common trisomies and microdeletion 22q11.2 (22q11.2DS) and to examine women's attitudes toward such an approach. METHODS This is a prospective study at the Prenatal Medicine Department of the University of Tübingen, Germany, at 11-13 weeks. In all pregnancies, a detailed ultrasound examination was carried out, followed by a cfDNA analysis for common trisomies and 22q11.2DS. In cases where the cfDNA analysis indicated 22q11.2DS, invasive prenatal diagnostic testing and parental testing were performed. After delivery, a detailed neonatal clinical examination was carried out including further genetic testing. Prior to counselling about the study, we asked the pregnant women who were potentially eligible for the study to anonymously report on their knowledge about 22q11.2DS. RESULTS A total of 1,127 pregnancies were included in the final analysis of the study. The first cfDNA test was uninformative in 15 (1.33%) pregnancies. In 10 (0.89%) cases, the test remained uninformative, even after the second blood sample. There were 3 (0.27%) cases with a positive cfDNA test for 22q11.2DS. In all, 983 women returned the anonymous questionnaire prior to study participation. Only 80 (8.1%) women responded that they felt familiar or very familiar with 22q11.2DS. CONCLUSION The addition of 22q11.2DS in first trimester cfDNA screening for common trisomies is feasible. The uninformative test rate for common trisomies and 22q11.2DS is 0.9%, and the false-positive rate for 22q11.2DS is 0.3%. Awareness and education around 22q11.2DS should be improved.
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Affiliation(s)
- Karl Oliver Kagan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany,
| | - Markus Hoopmann
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Theresa Pfaff
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Natalia Prodan
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Philipp Wagner
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Maximilian Schmid
- Roche Sequencing Solutions Inc., Ariosa Diagnostics Inc., San Jose, California, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Ulrike Mau-Holzmann
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Sara Brucker
- Department of Women's Health, University Women's Hospital, Tuebingen, Germany
| | - Livia Marcato
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
| | - Barbara Malvestiti
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
| | - Francesca Romana Grati
- Research and Development, Cytogenetics and Medical Genetics Unit, TOMA Advanced Biomedical Assays S.p.A., Impact Lab Group, Busto Arsizio, Italy
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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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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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Luo Y, Lin J, Sun Y, Qian Y, Wang L, Chen M, Dong M, Jin F. Non-invasive prenatal screening for Emanuel syndrome. Mol Cytogenet 2020; 13:9. [PMID: 32158503 PMCID: PMC7057502 DOI: 10.1186/s13039-020-0476-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/07/2020] [Indexed: 12/27/2022] Open
Abstract
Objective The aim of this study was to validate the results of two Emanuel syndromes detected by non-invasive prenatal screening (NIPS) screening using invasive methods, providing clinical performance of NIPS on chromosome microduplication detection. Methods NIPS was performed to diagnose the Emanuel syndrome. Amniocentesis or cordocentesis was performed to confirm the positive screening result of Emanuel syndrome cases. Fetal sample was detected by karyotyping, fluorescence in situ hybridization (FISH), and single nucleotide polymorphism array (SNP Array). Parental karyotyping and FISH were also carried out. Results Two cases with chromosomal abnormalities of 11q23.3q25 and 22q11.1q11.21 were found by NIPS. Chromosomal karyotyping showed that the two fetuses each have a small supernumerary marker chromosome (sSMC), SNP Array further demonstrated double duplications approximately 18 Mb in 11q23.3q25 and 3 Mb in 22q11.1q11.21. FISH confirmed that the small supernumerary marker chromosome (sSMC) was ish der(22)t(11;22) (TUPLE1+, ARSA-). Ultrasound scan and MRI showed some structure malformations in two fetuses. The two mothers were found to be a balanced carrier: 46,XX, t(11;22)(q23.3;q11.2). Conclusion NIPS could effectively identify Emanuel syndrome, which may indicate risks of a parent being a balanced rearrangement carrier. The followed confirmation test for positive sample is necessary and ensures the accuracy of the diagnosis.
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Affiliation(s)
- Yuqin Luo
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Jie Lin
- 2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Yixi Sun
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Yeqing Qian
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Liya Wang
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Min Chen
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Minyue Dong
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China
| | - Fan Jin
- 1Department of Reproductive Genetics, Women's Hospital,School of Medicine, Zhejiang University, 1 Xueshi Road, Hangzhou, 310006 Zhejiang China.,2Ministry of Education, Key Laboratory of Reproductive Genetics (Zhejiang University), Hangzhou, People's Republic of China.,3Centre of Reproductive Medicine, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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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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Du Q, de la Morena MT, van Oers NSC. The Genetics and Epigenetics of 22q11.2 Deletion Syndrome. Front Genet 2020; 10:1365. [PMID: 32117416 PMCID: PMC7016268 DOI: 10.3389/fgene.2019.01365] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
Chromosome 22q11.2 deletion syndrome (22q11.2del) is a complex, multi-organ disorder noted for its varying severity and penetrance among those affected. The clinical problems comprise congenital malformations; cardiac problems including outflow tract defects, hypoplasia of the thymus, hypoparathyroidism, and/or dysmorphic facial features. Additional clinical issues that can appear over time are autoimmunity, renal insufficiency, developmental delay, malignancy and neurological manifestations such as schizophrenia. The majority of individuals with 22q11.2del have a 3 Mb deletion of DNA on chromosome 22, leading to a haploinsufficiency of ~106 genes, which comprise coding RNAs, noncoding RNAs, and pseudogenes. The consequent haploinsufficiency of many of the coding genes are well described, including the key roles of T-box Transcription Factor 1 (TBX1) and DiGeorge Critical Region 8 (DGCR8) in the clinical phenotypes. However, the haploinsufficiency of these genes alone cannot account for the tremendous variation in the severity and penetrance of the clinical complications among those affected. Recent RNA and DNA sequencing approaches are uncovering novel genetic and epigenetic differences among 22q11.2del patients that can influence disease severity. In this review, the role of coding and non-coding genes, including microRNAs (miRNA) and long noncoding RNAs (lncRNAs), will be discussed in relation to their bearing on 22q11.2del with an emphasis on TBX1.
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Affiliation(s)
- Qiumei Du
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - M. Teresa de la Morena
- Department of Pediatrics, The University of Washington and Seattle Children’s Hospital, Seattle, WA, United States
| | - Nicolai S. C. van Oers
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, TX, United States
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Hui L, Bianchi DW. Fetal fraction and noninvasive prenatal testing: What clinicians need to know. Prenat Diagn 2019; 40:155-163. [PMID: 31821597 PMCID: PMC10040212 DOI: 10.1002/pd.5620] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/15/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022]
Abstract
The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal testing (NIPT) results. Clinicians need to understand the biological influences on FF to be able to provide optimal post-test counseling and clinical management. There are many different technologies available for the measurement of FF. Clinicians do not need to know the details behind the bioinformatics algorithms of FF measurements, but they do need to appreciate the significant variations between the different sequencing technologies used by different laboratories. There is no universal FF threshold that is applicable across all platforms and there have not been any differences demonstrated in NIPT performance by sequencing platform or method of FF calculation. Importantly, while FF should be routinely measured, there is not yet a consensus as to whether it should be routinely reported to the clinician. The clinician should know what to expect from a standard test report and whether reasons for failed NIPT results are revealed. Emerging solutions to the challenges of samples with low FF should reduce rates of failed NIPT in the future. In the meantime, having a "plan B" prepared for those patients for whom NIPT is unsuccessful is essential in today's clinical practice.
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Affiliation(s)
- Lisa Hui
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia.,Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria, Australia
| | - Diana W Bianchi
- Prenatal Genomics and Therapy Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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Guseh SH. Noninvasive prenatal testing: from aneuploidy to single genes. Hum Genet 2019; 139:1141-1148. [PMID: 31555907 DOI: 10.1007/s00439-019-02061-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 09/04/2019] [Indexed: 12/16/2022]
Abstract
Noninvasive prenatal testing has undergone rapid advances in the last few years. Although researchers have long known about circulating pregnancy-based cell-free fragments of DNA in maternal plasma, it was the introduction of massively parallel sequencing that allowed noninvasive prenatal testing to become a widely used clinical test. This review will begin with an in-depth analysis of the use of noninvasive prenatal testing for aneuploidy, including common causes for inaccurate and/or discordant results. It will also review the ongoing expansion of noninvasive prenatal testing to include copy number variants and select single-gene disorders. Finally, integrated throughout the review is a comparison of noninvasive prenatal testing to more traditional screening methods along with some medical and ethical implications of the widespread use of this new technology.
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Affiliation(s)
- Stephanie H Guseh
- Division of Maternal-Fetal Medicine, Obstetrics and Gynecology, Harvard Medical School, Brigham and Women's Hospital, 75 Francis St, Boston, MA, USA.
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Factors Associated With Informative Redraw After an Initial No Result in Noninvasive Prenatal Testing. Obstet Gynecol 2019; 132:428-435. [PMID: 29995728 DOI: 10.1097/aog.0000000000002728] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Noninvasive prenatal testing (NIPT) sometimes fails to provide a test result, usually as a result of low cell-free DNA fetal fraction. We investigated how initial fetal fraction, maternal weight, gestational age, and time between blood sampling contribute to obtaining an informative result when a redraw is performed. METHODS We performed a retrospective data review of NIPT samples received between January and October 2016 by a commercial laboratory, where the initial blood draw did not yield a result and a second sample was drawn between 5 and 28 days after the initial sampling. We included cases with fetal fraction less than 2.8% (the threshold for "no result" in this laboratory) and those with higher fetal fraction but where the NIPT results could not be interpreted with high confidence. RESULTS For 4,018 cases in which a redraw was recommended, a result was obtained for the second sample in 2,835 cases (70.6%) (95% CI 69.1-72.0%). For the 2,959 cases with insufficient fetal fraction, there was a result for the second sample in 1,861 cases (62.9%) (95% CI 61.1-64.6%). For this subset, the average increase in fetal fraction was 1.2% with an average interval between draws of 14 days. Informative redraw rate was strongly dependent on maternal weight and fetal fraction measured at the first draw. Gestational age was not an important determinant. Informative redraw rate increased rapidly over the first 8 days after the initial draw and more slowly thereafter. CONCLUSION Based on fetal fraction in the initial sample, maternal weight, and interval between blood draws, women can be provided with a personalized estimate of their likelihood of a result on redraw. This should aid in the counseling of women faced with the choice of reattempting NIPT, conventional screening, or an invasive diagnostic test.
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Porreco RP, Sekedat M, Bombard A, Garite TJ, Maurel K, Marusiak B, Adair D, Bleich A, Combs CA, Kramer W, Longo S, Nageotte M, Samuel A, Vanderhoeven J, Buis J, Jacobs KB, Stoerker J. Evaluation of a novel screening method for fetal aneuploidy using cell-free DNA in maternal plasma. J Med Screen 2019; 27:1-8. [PMID: 31510865 DOI: 10.1177/0969141319873682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Objective To evaluate the test performance of a novel sequencing technology using molecular inversion probes applied to cell-free DNA screening for fetal aneuploidy. Methods Two cohorts were included in the evaluation; a risk-based cohort of women receiving diagnostic testing in the first and second trimesters was combined with stored samples from pregnancies with fetuses known to be aneuploid or euploid. All samples were blinded to testing personnel before being analyzed, and validation occurred after the study closed and results were merged. Results Using the new sequencing technology, 1414 samples were analyzed. The findings showed sensitivities and specificities for the common trisomies and the sex chromosome aneuploidies at >99% (Trisomy 21 sensitivity 99.2 CI 95.6–99.2; specificity 99.9 CI 99.6–99.9). Positive predictive values among the trisomies varied from 85.2% (Trisomy 18) to 99.0% (Trisomy 21), reflecting their prevalence rates in the study. Comparisons with a meta-analysis of recent cell-free DNA screening publications demonstrated equivalent test performance. Conclusion This new technology demonstrates equivalent test performance compared with alternative sequencing approaches, and demonstrates that each chromosome can be successfully interrogated using a single probe.
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Affiliation(s)
| | | | | | | | - Kimberly Maurel
- Center for Research, Education, Quality, and Safety (CREQS), Obstetrix Medical Group, an affiliate of Mednax, Inc., Fountain Valley, CA, USA
| | - Barbara Marusiak
- Center for Research, Education, Quality, and Safety (CREQS), Obstetrix Medical Group, an affiliate of Mednax Inc., Phoenix, AZ, USA
| | - David Adair
- Regional Obstetrical Consultants, Chattanooga, TN, USA
| | - April Bleich
- Maternal Fetal Medicine, Obstetrix Medical Group of Texas, Fort Worth, TX, USA
| | - C Andrew Combs
- Obstetrix Medical Group of California, Campbell, CA, USA
| | - Wayne Kramer
- Obstetrix Medical Group of Rockville, Rockville, MD, USA
| | | | - Michael Nageotte
- Long Beach Memorial Medical Ctr, Women's Hospital, Long Beach, CA, USA
| | - Amber Samuel
- Obstetrix Medical Group of Houston, The Woodlands, TX, USA
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Avram CM, Shaffer BL, Sparks TN, Allen AJ, Caughey AB. Cell-free fetal DNA screening for detection of microdeletion syndromes: a cost-effectiveness analysis. J Matern Fetal Neonatal Med 2019; 34:1732-1740. [PMID: 31327283 DOI: 10.1080/14767058.2019.1647161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Fetuses with genetic copy number variants are poorly detected through traditional prenatal screening. Microdeletions and duplications are clearly identified with diagnostic testing through chromosomal microarray, and screening of a select number of microdeletions has become available with cell-free DNA (cfDNA). Our study compares the costs and outcomes of cfDNA for five pathogenic microdeletions and aneuploidy to cfDNA for aneuploidy alone in conjunction with ultrasound. METHODS A decision-analytic model was constructed using TreeAge software to compare cfDNA with microdeletions versus traditional cfDNA in a theoretical cohort of 4,000,000 pregnancies that would also be screened with ultrasound. Probabilities, costs, and utilities were derived from literature. The primary outcomes were the incremental cost per quality-adjusted life-year (QALY), terminations, and procedure-related losses. Because the microdeletion results are available, but not reported, on all cfDNA testing we set the incremental cost of the cfDNA microdeletion screening test to zero at baseline and varied the cost in sensitivity analysis. RESULTS Screening with cfDNA for microdeletions among all pregnant women would result in 83 fewer anomalous neonates compared to traditional cfDNA with ultrasound. This reduction is due to increased diagnosis and termination of fetuses with microdeletions in this group. Routine use of cfDNA with microdeletions resulted in more procedure-related losses. cfDNA with microdeletions would improve effectiveness by 977 QALYs and decrease costs by $90,991,784. When we varied the specificity of the screening test, we found that it remained cost-effective down to a specificity of 91%. With a threshold of $100,000/QALY, microdeletion screening is cost-effective to an incremental increase in cost over cfDNA for aneuploidy alone of $47.10. CONCLUSION For detection of fetal subchromosomal abnormalities, use of cfDNA with microdeletions is a cost-effective strategy compared to cfDNA for aneuploidy alone in conjunction with ultrasound. Cell-free DNA for microdeletions is not currently recommended as routine screening for low-risk obstetric populations by the American College of Obstetrics and Gynecologists or the Society for Maternal-Fetal Medicine. The test characteristics of cfDNA with microdeletions require greater examination before being routinely recommended.
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Affiliation(s)
- Carmen M Avram
- Department of Obstetrics and Gynecology, Oregon Health & Sciences University, Portland, OR, USA
| | - Brian L Shaffer
- Department of Obstetrics and Gynecology, Oregon Health & Sciences University, Portland, OR, USA
| | - Teresa N Sparks
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Univeristy of California San Francisco, San Francisco, CA, USA
| | - Allison J Allen
- Department of Obstetrics and Gynecology, Oregon Health & Sciences University, Portland, OR, USA
| | - Aaron B Caughey
- Department of Obstetrics and Gynecology, Oregon Health & Sciences University, Portland, OR, USA
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Petracchi F, Sisterna S, Igarzabal L, Wilkins-Haug L. Fetal cardiac abnormalities: Genetic etiologies to be considered. Prenat Diagn 2019; 39:758-780. [PMID: 31087396 DOI: 10.1002/pd.5480] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/16/2019] [Accepted: 04/27/2019] [Indexed: 12/21/2022]
Abstract
Congenital heart diseases are a common prenatal finding. The prenatal identification of an associated genetic syndrome or a major extracardiac anomaly helps to understand the etiopathogenic diagnosis. Besides, it also assesses the prognosis, management, and familial recurrence risk while strongly influences parental decision to choose termination of pregnancy or postnatal care. This review article describes the most common genetic diagnoses associated with a prenatal finding of a congenital heart disease and a suggested diagnostic process.
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Affiliation(s)
- Florencia Petracchi
- Sección Genética Departamento de Ginecología y Obstetricia, CEMIC Instituto Universitario, Buenos Aires, Argentina
| | - Silvina Sisterna
- Sección Genética Departamento de Ginecología y Obstetricia, CEMIC Instituto Universitario, Buenos Aires, Argentina
| | - Laura Igarzabal
- Sección Genética Departamento de Ginecología y Obstetricia, CEMIC Instituto Universitario, Buenos Aires, Argentina
| | - Louise Wilkins-Haug
- Harvard Medical School Department of Obstetrics, Gynecology and Reproductive Medicine Division Chief Maternal Fetal Medicine and Reproductive Genetics, Brigham and Women's Hospital, Boston, MA
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Audibert F, De Bie I, Johnson JA, Okun N, Wilson RD, Armour C, Chitayat D, Kim R. No. 348-Joint SOGC-CCMG Guideline: Update on Prenatal Screening for Fetal Aneuploidy, Fetal Anomalies, and Adverse Pregnancy Outcomes. JOURNAL OF OBSTETRICS AND GYNAECOLOGY CANADA 2019; 39:805-817. [PMID: 28859766 DOI: 10.1016/j.jogc.2017.01.032] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To review the available prenatal screening options in light of the recent technical advances and to provide an update of previous guidelines in the field of prenatal screening. INTENDED USERS Health care providers involved in prenatal screening, including general practitioners, obstetricians, midwives, maternal fetal medicine specialists, geneticists, and radiologists. TARGET POPULATION All pregnant women receiving counselling and providing informed consent for prenatal screening. EVIDENCE Published literature was retrieved through searches of Medline, PubMed, and the Cochrane Library in and prior to March 2016 using an appropriate controlled vocabulary (prenatal diagnosis, amniocentesis, chorionic villi sampling, non-invasive prenatal screening) and key words (prenatal screening, prenatal genetic counselling). Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies written in English and published from January 1985 to May 2016. Searches were updated on a regular basis and incorporated in the guideline. Grey (unpublished) literature was identified through searching the websites of health technology assessment and health technology-related agencies, clinical practice guideline collections, clinical trial registries, and national and international medical speciality societies. GUIDELINE UPDATE Evidence will be reviewed 5 years after publication to determine whether all or part of the guideline should be updated. However, if important new evidence is published prior to the 5-year cycle, the review process may be accelerated for a more rapid update of some recommendations.
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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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