1
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Balaguer N, Rodrigo L, Mateu-Brull E, Campos-Galindo I, Castellón JA, Al-Asmar N, Rubio C, Milán M. Non-invasive cell-free DNA-based approach for the diagnosis of clinical miscarriage: A retrospective study. BJOG 2024; 131:213-221. [PMID: 37533357 DOI: 10.1111/1471-0528.17629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/05/2023] [Accepted: 07/21/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVE To evaluate cell-free DNA (cfDNA) testing as a non-invasive approach to detecting aneuploidies in clinical miscarriages. DESIGN A retrospective cohort study of women with pregnancy loss. SETTING Hospitals and genetic analysis laboratories. POPULATION OR SAMPLE Pregnancy losses in the period 2021-2022. METHODS Results derived from non-invasive cfDNA testing (Veriseq NIPT Solution V2) of maternal blood and invasive analysis of products of conception (POC) (Ion ReproSeq) compared in 120 women who suffered a miscarriage. MAIN OUTCOME MEASURES Concordance rate results, cfDNA testing performance, non-informative rate (NIR) and fetal fraction (FF). RESULTS We found no significant differences in the NIR between invasive (iPOC) and non-invasive (niPOC) analysis of POC (10.0% [12/120] versus 16.7% [20/120]). Of 120 samples, 90 provided an informative result in iPOC and niPOC groups (75%). cfDNA analysis correctly identified 74/87 (85.1%) samples (excluding triploidies). Sensitivity and specificity were 79.4% and 100%, respectively; all discordant cases were female. A binomial logistic model suggested fetal sex as the only variable influencing the concordance rate (P = 0.035). A Y-chromosome-based FF estimate allowed the optimal reclassification of cfDNA of non-informative male fetuses and a more accurate evaluation of cfDNA testing performance. The difference between the two FF estimates (native algorithm and Y-chromosome-based) suggests that female non-concordant cases may represent non-informative cases. CONCLUSIONS Cell-free DNA-based testing provides a non-invasive approach to determining the genetic cause of clinical miscarriage.
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Affiliation(s)
- Nuria Balaguer
- Prenatal Diagnosis Department, Igenomix Spain Lab S.L.U., Paterna, Spain
| | - Lorena Rodrigo
- Preimplantation Genetic Testing for Aneuploidies (PGT-A) Department, Igenomix Spain Lab S.L.U., Paterna, Spain
| | - Emilia Mateu-Brull
- Prenatal Diagnosis Department, Igenomix Spain Lab S.L.U., Paterna, Spain
| | - Inmaculada Campos-Galindo
- Preimplantation Genetic Testing for Aneuploidies (PGT-A) Department, Igenomix Spain Lab S.L.U., Paterna, Spain
| | | | | | - Carmen Rubio
- Research and Development Department, Igenomix Spain Lab S.L.U., Paterna, Spain
| | - Miguel Milán
- Prenatal Diagnosis Department, Igenomix Spain Lab S.L.U., Paterna, Spain
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2
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Moufarrej MN, Bianchi DW, Shaw GM, Stevenson DK, Quake SR. Noninvasive Prenatal Testing Using Circulating DNA and RNA: Advances, Challenges, and Possibilities. Annu Rev Biomed Data Sci 2023; 6:397-418. [PMID: 37196360 PMCID: PMC10528197 DOI: 10.1146/annurev-biodatasci-020722-094144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Prenatal screening using sequencing of circulating cell-free DNA has transformed obstetric care over the past decade and significantly reduced the number of invasive diagnostic procedures like amniocentesis for genetic disorders. Nonetheless, emergency care remains the only option for complications like preeclampsia and preterm birth, two of the most prevalent obstetrical syndromes. Advances in noninvasive prenatal testing expand the scope of precision medicine in obstetric care. In this review, we discuss advances, challenges, and possibilities toward the goal of providing proactive, personalized prenatal care. The highlighted advances focus mainly on cell-free nucleic acids; however, we also review research that uses signals from metabolomics, proteomics, intact cells, and the microbiome. We discuss ethical challenges in providing care. Finally, we look to future possibilities, including redefining disease taxonomy and moving from biomarker correlation to biological causation.
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Affiliation(s)
| | - Diana W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development and Section on Prenatal Genomics and Fetal Therapy, Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gary M Shaw
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - David K Stevenson
- Department of Pediatrics and March of Dimes Prematurity Research Center at Stanford University, Stanford University School of Medicine, Stanford, California, USA
| | - Stephen R Quake
- Department of Bioengineering and Department of Applied Physics, Stanford University, Stanford, California, USA
- Chan Zuckerberg Initiative, Redwood City, California, USA
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3
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Prensky L, Persson F. Apparent versus effective test performance: The importance of understanding and reviewing performance metrics. Prenat Diagn 2023; 43:1255-1258. [PMID: 37458530 DOI: 10.1002/pd.6408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
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4
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Saidel ML, Ananth U, Rose D, Farrell C. Non-Invasive prenatal testing with rolling circle amplification: Real-world clinical experience in a non-molecular laboratory. J Clin Lab Anal 2023; 37:e24870. [PMID: 36972484 PMCID: PMC10156098 DOI: 10.1002/jcla.24870] [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: 10/03/2022] [Revised: 02/17/2023] [Accepted: 03/08/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Non-invasive prenatal testing (NIPT) using cell-free DNA (cfDNA) circulating in maternal blood provides a sensitive and specific screening technique for common fetal aneuploidies, but the high cost and workflow complexity of conventional methodologies limit its widespread implementation. A unique rolling circle amplification methodology reduces cost and complexity, providing a promising alternative for increased global accessibility as a first-tier test. METHODS In this clinical study, 8160 pregnant women were screened on the Vanadis system for trisomies 13, 18, and 21, and positive results were compared to clinical outcomes where available. RESULTS The Vanadis system yielded a 0.07% no-call rate, a 98% overall sensitivity, and a specificity of over 99% based on available outcomes. CONCLUSION The Vanadis system provided a sensitive, specific, and cost-effective cfDNA assay for trisomies 13, 18, and 21, with good performance characteristics and low no-call rate, and it eliminated the need for either next-generation sequencing or polymerase chain reaction amplification.
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Affiliation(s)
- Matthew L Saidel
- Women's Health USA and Medical Director, Women's Health Connecticut, Rocky Hill, Connecticut, USA
| | - Uma Ananth
- Umagen LLC, Shrewsbury, Massachusetts, USA
| | - Donna Rose
- Women's Health Connecticut Laboratory, Rocky Hill, Connecticut, USA
| | - Cara Farrell
- Ancillary Growth Women's Health Connecticut, Rocky Hill, Connecticut, USA
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5
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Qi Z, Yu J. Synthesis of positive plasmas with known chromosomal abnormalities for validation of non-invasive prenatal screening. Front Genet 2023; 14:971087. [PMID: 36726805 PMCID: PMC9886268 DOI: 10.3389/fgene.2023.971087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Non-invasive prenatal screening (NIPS) is a DNA sequencing-based screening test for fetal aneuploidies and possibly other pathogenic genomic abnormalities, such as large deletions and duplications. Validation and quality assurance (QA) of this clinical test using plasmas with and without targeted chromosomal abnormalities from pregnant women as negative and positive controls are required. However, the positive plasma controls may not be available for many laboratories that are planning to establish NIPS. Limited synthetic positive plasmas are commercially available, but the types of abnormalities and the number/quantity of synthetic plasmas for each abnormality are insufficient to meet the minimal requirements for the initial validation. We report here a method of making synthetic positive plasmas by adding cell-free DNA (cfDNA) isolated from culture media of prenatal cells with chromosomal abnormalities to the plasmas from non-pregnant women. Thirty-eight positive plasmas with various chromosomal abnormalities, including autosomal and sex chromosomal aneuploidies, large deletions and duplications, were synthesized. The synthetic plasmas were characterized side-by-side with real positive plasmas from pregnant women and commercially available synthetic positive plasmas using the Illumina VeriSeq NIPT v2 system. All chromosomal abnormalities in the synthetic plasmas were correctly identified with the same testing sensitivity and specificity as in the real and commercial synthetic plasmas. The findings demonstrate that the synthetic positive plasmas are excellent alternatives of real positive plasmas for validation and QA of NIPS. The method described here is simple and straightforward, and can be readily used in clinical genetics laboratories with accessibility to prenatal cultures.
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6
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Xu C, Li J, Chen S, Cai X, Jing R, Qin X, Pan D, Zhao X, Ma D, Xu X, Liu X, Wang C, Yang B, Zhang L, Li S, Chen Y, Pan N, Tang P, Song J, Liu N, Zhang C, Zhang Z, Qiu X, Lu W, Ying C, Li X, Xu C, Wang Y, Wu Y, Huang HF, Zhang J. Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening. Cell Discov 2022; 8:109. [PMID: 36229437 PMCID: PMC9562363 DOI: 10.1038/s41421-022-00457-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Current non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed coordinative allele-aware target enrichment sequencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders.
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Affiliation(s)
- Chenming Xu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Ruilin Jing
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaomei Qin
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dong Pan
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xin Zhao
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Dongyang Ma
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiufeng Xu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiaojun Liu
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Can Wang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Bingxin Yang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lanlan Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yiyao Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Tang
- Jiaxing Maternity and Child Health Care Hospital, Jiaxing, Zhejiang, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, Hubei, China
| | - Chen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiwei Zhang
- Beijing BioBiggen Technology Co., Ltd, Beijing, China
| | - Xiang Qiu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Weiliang Lu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Congjian Xu
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanting Wu
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China. .,Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai, China.
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China. .,International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China. .,Beijing BioBiggen Technology Co., Ltd, Beijing, China.
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7
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Genovese G, Mello CJ, Loh PR, Handsaker RE, Kashin S, Whelan CW, Bayer-Zwirello LA, McCarroll SA. Chromosomal phase improves aneuploidy detection in non-invasive prenatal testing at low fetal DNA fractions. Sci Rep 2022; 12:12025. [PMID: 35835769 PMCID: PMC9283487 DOI: 10.1038/s41598-022-14049-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) to detect fetal aneuploidy by sequencing the cell-free DNA (cfDNA) in maternal plasma is being broadly adopted. To detect fetal aneuploidies from maternal plasma, where fetal DNA is mixed with far-larger amounts of maternal DNA, NIPT requires a minimum fraction of the circulating cfDNA to be of placental origin, a level which is usually attained beginning at 10 weeks gestational age. We present an approach that leverages the arrangement of alleles along homologous chromosomes—also known as chromosomal phase—to make NIPT analyses more conclusive. We validate our approach with in silico simulations, then re-analyze data from a pregnant mother who, due to a fetal DNA fraction of 3.4%, received an inconclusive aneuploidy determination through NIPT. We find that the presence of a trisomy 18 fetus can be conclusively inferred from the patient’s same molecular data when chromosomal phase is incorporated into the analysis. Key to the effectiveness of our approach is the ability of homologous chromosomes to act as natural controls for each other and the ability of chromosomal phase to integrate subtle quantitative signals across very many sequence variants. These results show that chromosomal phase increases the sensitivity of a common laboratory test, an idea that could also advance cfDNA analyses for cancer detection.
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Affiliation(s)
- Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Curtis J Mello
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Robert E Handsaker
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seva Kashin
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Christopher W Whelan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lucy A Bayer-Zwirello
- Steward St. Elizabeth's Medical Center, Tufts University School of Medicine, Boston, MA, 02135, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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8
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Shree R, Kolarova TR, MacKinnon HJ, Hedge JM, Vinopal E, Ma KK, Lockwood CM, Chandrasekaran S. Low fetal fraction in obese women at first trimester cell-free DNA based prenatal screening is not accompanied by differences in total cell-free DNA. Prenat Diagn 2021; 41:1277-1286. [PMID: 34297415 DOI: 10.1002/pd.6023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/26/2021] [Accepted: 07/10/2021] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Reasons for first trimester noninvasive prenatal screening (NIPS) test failure in obese women remain elusive. As dilution from maternal sources may be explanatory, we determined the relationship between obesity, fetal fraction (FF), and total cell-free DNA (cfDNA) using our NIPS platform. METHODS We assessed differences in first trimester (≤14 weeks) FF, indeterminate rate, and total cfDNA between obese (n = 518) and normal-weight women (n = 237) after exclusion of confounders (anticoagulation, autoimmunity, aneuploidy) and controlling for covariates. RESULTS Fetal fraction was lower, and the indeterminate rate higher, in obese compared to controls (9.2% ± 4.4 vs. 12.5% ± 4.5, p < 0.001 and 8.4 vs. 1.7%, p < 0.001, respectively), but total cfDNA was not different (92.0 vs. 82.1 pg/µl, p = 0.10). For each week, the FF remained lower in obese women (all p < 0.01) but did not increase across the first trimester for either group. Obesity increased the likelihood of indeterminate result (OR 6.1, 95% CI 2.5, 14.8; p < 0.001) and maternal body mass index correlated with FF (β -0.27, 95% CI -0.3, -0.22; p < 0.001), but not with total cfDNA (β 0.49, 95% CI -0.55, 1.53; p = 0.3). CONCLUSIONS First trimester obese women have persistently low FF and higher indeterminate rates, without differences in total cfDNA, suggesting placental-specific mechanisms versus dilution from maternal sources as a potential etiology.
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Affiliation(s)
- Raj Shree
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Teodora R Kolarova
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Hayley J MacKinnon
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Jaclynne M Hedge
- School of Medicine, University of Washington, Seattle, Washington, USA
| | - Elena Vinopal
- School of Medicine, University of Washington, Seattle, Washington, USA
| | - Kimberly K Ma
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Suchitra Chandrasekaran
- Department of Obstetrics & Gynecology, Division of Maternal Fetal Medicine, University of Washington, Seattle, Washington, USA
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9
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Yaron Y, Borrell A. Reply: cfDNA testing in recurrent pregnancy loss: a new step in the right way but still raw for the clinical area. Hum Reprod 2021; 36:829-830. [PMID: 33378533 DOI: 10.1093/humrep/deaa360] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Antoni Borrell
- BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain.,Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
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10
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Yaron Y, Pauta M, Badenas C, Soler A, Borobio V, Illanes C, Paz-Y-Miño F, Martinez-Portilla R, Borrell A. Maternal plasma genome-wide cell-free DNA can detect fetal aneuploidy in early and recurrent pregnancy loss and can be used to direct further workup. Hum Reprod 2021; 35:1222-1229. [PMID: 32386059 PMCID: PMC7259365 DOI: 10.1093/humrep/deaa073] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 03/15/2020] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION Can maternal plasma cell-free DNA (cfDNA) detect chromosomal anomalies in early pregnancy loss (EPL) and recurrent pregnancy loss (RPL)? SUMMARY ANSWER Genome-wide cfDNA testing can serve as an alternative to cytogenetic analysis in products of conception (POCs) in RPLs and can guide further management. WHAT IS KNOWN ALREADY Random chromosomal anomalies are the single most common cause for EPL and RPL. Cytogenetic analysis in POCs may be used to direct management in RPL because the detection of random chromosomal anomalies can eliminate further unwarranted testing. STUDY DESIGN, SIZE, DURATION This was a prospective diagnostic test study from March 2018 to January 2019 of 109 patients experiencing pregnancy loss before 14 weeks gestation at a tertiary-care academic medical center. PARTICIPANTS/MATERIALS, SETTING, METHODS Blood samples were drawn for genome-wide cfDNA testing prior to chorionic villous sampling for cytogenetic analysis of POCs with both short-term cultures (STCs) and long-term cultures (LTCs). Final analysis included 86 patients with non-mosaic cytogenetic results in POCs and available cfDNA results. Aneuploidy detection rates by cfDNA testing and POC cytogenetic analysis were compared. The first 50 samples served as the Training Set to establish pregnancy loss-specific log-likelihood ratio (LLR) thresholds using receiver-operator characteristic (ROC)-like analyses. These were then used for the entire cohort. MAIN RESULTS AND THE ROLE OF CHANCE Seventy-eight samples (71.5%) had results available from both STC and LTC; 12 samples (11%) had a result from STC only, and 7 samples (6.4%) had a result from LTC only. A chromosomal anomaly was detected in 55/86 (64%). The rates of chromosomal anomalies were 61, 72, 73 and 44% in patients undergoing their first, second, third and ≥4th pregnancy losses, respectively. The median cfDNA fetal fraction was 5%. With standard LLR thresholds used for noninvasive prenatal screening, the sensitivity of cfDNA in detecting aneuploidy was 55% (30/55) and with a specificity of 100% (31/31). Using pregnancy loss-specific LLR thresholds, the sensitivity of cfDNA in detecting aneuploidy was 82% (45/55), with a specificity of 90% (28/31). The positive and negative likelihood ratios were 8.46 and 0.20, respectively. Fetal sex was correctly assigned in all cases. LIMITATIONS, REASONS FOR CAUTION Cases with a false-positive result by cfDNA analysis would not receive the indicated RPL workup. Specificity could be improved by using a fetal fraction (FF) cutoff of 4%, but this would result in exclusion of more than a quarter of cases. WIDER IMPLICATIONS OF THE FINDINGS cfDNA-based testing can serve as an alternative to POC cytogenetic analysis and can guide further RPL management: if cfDNA demonstrates aneuploidy, no further action is taken and if no abnormality is detected, the recommended RPL workup is performed. STUDY FUNDING/COMPETING INTEREST(S) Cell-free DNA testing was funded by Illumina, Inc., San Diego, CA. Y.Y. is a member of Illumina’s Clinical Expert Panel and has received travel grants. A.B. has received travel grants from Illumina. All authors have no competing interest to declare.
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Affiliation(s)
- Yuval Yaron
- Prenatal Genetic Diagnosis Unit, Genetic Institute, Sourasky Medical Center, Tel Aviv, Israel.,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Montse Pauta
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Celia Badenas
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Anna Soler
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Virginia Borobio
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Carmen Illanes
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | - Fernanda Paz-Y-Miño
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain
| | | | - Antoni Borrell
- Department of Maternal-Fetal Medicine, BCNatal, Hospital Clinic, Barcelona, Catalonia, Spain.,BCNatal, Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
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11
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Caldwell S, Almasri E, Schmidt L, Xu C, Dyr B, Wardrop J, Cacheris P. Not all low fetal fraction cell-free DNA screening failures are at increased risk for aneuploidy. Prenat Diagn 2021; 41:1372-1379. [PMID: 33682142 PMCID: PMC8596865 DOI: 10.1002/pd.5918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/11/2021] [Accepted: 01/31/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To evaluate cell-free DNA (cfDNA) redraws and pregnancy outcomes following low fetal fraction (FF) cfDNA failures, as it has been suggested that a failed cfDNA screen due to insufficient FF carries increased risk for fetal aneuploidy. METHODS Here >200,000 consecutive samples were reviewed and >1,100 patients were identified with a failed cfDNA due to low FF using genome-wide massively parallel sequencing. Redraw results following the initial low FF failure were analyzed, as well as pregnancy outcomes for patients with repeated low FF failure on redraw. RESULTS Upon redraw 84.2% of samples yielded a reportable result with no enrichment of aneuploidy observed (p = 0.332). Higher maternal weights and multifetal pregnancy rates were observed in samples with insufficient FF. In patients with repeated low FF failure on redraw, almost all pregnancies resulted in apparently healthy liveborns. CONCLUSION Insufficient FF was not an indicator of aneuploidy risk or adverse pregnancy outcomes in this study. Caution should be taken in generalizing aneuploidy risk to all low FF cfDNA failures. Redrawing may be an appropriate next step, as proceeding directly with diagnostic testing for aneuploidy may be unwarranted for most patients.
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Affiliation(s)
- Samantha Caldwell
- Women's Health and Genetics, Laboratory Corporation of America, La Jolla, California, USA
| | - Eyad Almasri
- Women's Health and Genetics, Laboratory Corporation of America, La Jolla, California, USA
| | | | - Chen Xu
- Women's Health and Genetics, Laboratory Corporation of America, La Jolla, California, USA
| | - Brittany Dyr
- Women's Health and Genetics, Laboratory Corporation of America, La Jolla, California, USA
| | - Jenna Wardrop
- Women's Health and Genetics, Laboratory Corporation of America, La Jolla, California, USA
| | - Philip Cacheris
- Women's Health and Genetics, Laboratory Corporation of America, La Jolla, California, USA
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12
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Abstract
The American College of Obstetrics & Gynecology (ACOG) recommends offering aneuploidy screening to all pregnant women. Obesity and diabetes are not associated with an increased risk of aneuploidy; however, they can complicate and compromise testing options. As the prevalence of obesity and diabetes, or "diabesity" increases, counseling women regarding potential limitations in testing performance of aneuploidy screening is of paramount importance. This chapter reviews options for aneuploidy screening for women with diabesity including sonography/nuchal translucency, serum analyte screening, and cell-free DNA. Potential challenges associated with diagnostic testing with amniocentesis and chorionic villus sampling in women with obesity are also discussed.
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13
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Welker NC, Lee AK, Kjolby RAS, Wan HY, Theilmann MR, Jeon D, Goldberg JD, Haas KR, Muzzey D, Chu CS. High-throughput fetal fraction amplification increases analytical performance of noninvasive prenatal screening. Genet Med 2020; 23:443-450. [PMID: 33190143 PMCID: PMC7935715 DOI: 10.1038/s41436-020-01009-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 10/01/2020] [Accepted: 10/06/2020] [Indexed: 12/25/2022] Open
Abstract
Purpose The percentage of a maternal cell-free DNA (cfDNA) sample that is fetal-derived (the fetal fraction; FF) is a key driver of the sensitivity and specificity of noninvasive prenatal screening (NIPS). On certain NIPS platforms, >20% of women with high body mass index (and >5% overall) receive a test failure due to low FF (<4%). Methods A scalable fetal fraction amplification (FFA) technology was analytically validated on 1264 samples undergoing whole-genome sequencing (WGS)–based NIPS. All samples were tested with and without FFA. Results Zero samples had FF < 4% when screened with FFA, whereas 1 in 25 of these same patients had FF < 4% without FFA. The average increase in FF was 3.9-fold for samples with low FF (2.3-fold overall) and 99.8% had higher FF with FFA. For all abnormalities screened on NIPS, z-scores increased 2.2-fold on average in positive samples and remained unchanged in negative samples, powering an increase in NIPS sensitivity and specificity. Conclusion FFA transforms low-FF samples into high-FF samples. By combining FFA with WGS–based NIPS, a single round of NIPS can provide nearly all women with confident results about the broad range of potential fetal chromosomal abnormalities across the genome.
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Affiliation(s)
| | - Albert K Lee
- Myriad Women's Health, South San Francisco, CA, USA
| | | | - Helen Y Wan
- Myriad Women's Health, South San Francisco, CA, USA
| | | | - Diana Jeon
- Myriad Women's Health, South San Francisco, CA, USA
| | | | - Kevin R Haas
- Myriad Women's Health, South San Francisco, CA, USA
| | - Dale Muzzey
- Myriad Women's Health, South San Francisco, CA, USA.
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14
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Hancock S, Ben‐Shachar R, Adusei C, Oyolu CB, Evans EA, Kang HP, Haverty C, Muzzey D. Clinical experience across the fetal-fraction spectrum of a non-invasive prenatal screening approach with low test-failure rate. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2020; 56:422-430. [PMID: 31671482 PMCID: PMC7496885 DOI: 10.1002/uog.21904] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/08/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
OBJECTIVE To describe our clinical experience across the entire range of fetal-fraction (FF) measurements of a non-invasive prenatal screen (NIPS) that uses whole- genome sequencing (WGS). METHODS We analyzed retrospectively results from 58 105 singleton pregnancies that underwent NIPS on a customized WGS platform during an 8-month period and assessed clinical test performance for trisomy 21, trisomy 18 and trisomy 13. Pregnancy outcomes were sought for all screen-positive patients and for 18% of screen-negative patients. As differences in outcome-collection response rates could artificially impact test-performance calculations, we computed inferred sensitivity, specificity, positive predictive values (PPV) and negative predictive values adjusted for ascertainment bias. RESULTS The screening test yielded a result for 99.9% (n = 58 048) of patients, meaning that approximately 1 in 1000 patients received a test failure (i.e. test failure rate = 0.1%). Of pregnancies with a test result, 572 (1%) screened positive for one of the common aneuploidies (362 for trisomy 21, 142 for trisomy 18 and 68 for trisomy 13). Informative outcomes were received for 237 (41.4%) patients with a screen-positive result and 3258 (5.7%) of those with a screen-negative result. In the full cohort, inferred sensitivities for trisomy 21, trisomy 18 and trisomy 13 were 99.7%, 96.8% and 94.3%, respectively, and PPVs were 93.1%, 85.2% and 48.4%, respectively. If a FF threshold of 4% had been employed to guard against false negatives, calculated sensitivities for the three aneuploidies would not have changed significantly, yet, importantly, the overall test-failure rate would have increased to 6.6% (n = 3829), impacting 1 in 15 women. CONCLUSIONS Our clinical experience demonstrates that a customized WGS-based NIPS without a FF threshold achieves high accuracy while maintaining a low test-failure rate of 0.1%. As such, alternative strategies to ensure high accuracy of detection of common aneuploidies in samples with low FF (such as redraw after test failure, redrawing at a later gestational age, risk scoring based on FF) are not necessary for this screening approach. © 2019 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of the International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- S. Hancock
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - R. Ben‐Shachar
- Myriad Women's HealthSouth San FranciscoCAUSA
- Myriad GeneticsSalt Lake CityUTUSA
| | - C. Adusei
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - C. B. Oyolu
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - E. A. Evans
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - H. P. Kang
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - C. Haverty
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - D. Muzzey
- Myriad Women's HealthSouth San FranciscoCAUSA
- Myriad GeneticsSalt Lake CityUTUSA
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15
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Hancock S, Ben‐Shachar R, Haverty C, Muzzey D. Reply. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2020; 56:472-473. [PMID: 32870590 PMCID: PMC7522669 DOI: 10.1002/uog.22105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- S. Hancock
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - R. Ben‐Shachar
- Myriad Women's HealthSouth San FranciscoCAUSA
- Myriad GeneticsSalt Lake CityUTUSA
| | - C. Haverty
- Myriad Women's HealthSouth San FranciscoCAUSA
| | - D. Muzzey
- Myriad Women's HealthSouth San FranciscoCAUSA
- Myriad GeneticsSalt Lake CityUTUSA
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16
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Oneda B, Sirleto P, Baldinger R, Taralczak M, Joset P, Zweier M, Niedrist D, Azzarello-Burri S, Britschgi C, Breymann C, Ochsenbein-Kölble N, Burkhardt T, Wisser J, Zimmermann R, Steindl K, Rauch A. Genome-wide non-invasive prenatal testing in single- and multiple-pregnancies at any risk: Identification of maternal polymorphisms to reduce the number of unnecessary invasive confirmation testing. Eur J Obstet Gynecol Reprod Biol 2020; 252:19-29. [PMID: 32619881 DOI: 10.1016/j.ejogrb.2020.05.070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Non-invasive prenatal testing by targeted or genome-wide copy number profiling (cnNIPT) has the potential to outperform standard NIPT targeting the common trisomies 13, 18, and 21, only. Nevertheless, prospective results and outcome data on cnNIPT are still scarce and there is increasing evidence for maternal copy number variants (CNVs) interfering with results of both, standard and cnNIPT. STUDY DESIGN We assessed the performance of cnNIPT in 3053 prospective and 116 retrospective cases with special consideration of maternal CNVs in singleton and multiple gestational pregnancies at any risk, as well as comprehensive follow-up. RESULTS A result was achieved in 2998 (98.2%) of total prospective cases (89.2% analyzed genome-wide). Confirmed fetal chromosomal abnormalities were detected in 45 (1.5%) cases, of which five (11%) would have remained undetected in standard NIPTs. Additionally, we observed 4 likely fetal trisomies without follow-up and a likely phenotype associated placental partial trisomy 16. Moreover, we observed clinically relevant confirmed maternal CNVs in 9 (0.3%) cases and likely maternal clonal hematopoiesis in 3 (0.1%). For common fetal trisomies we prospectively observed a very high sensitivity (100% [95% CI: 91.96-100%]) and specificity (>99.9% [95% CI: 99.8-100%]), and positive predictive value (PPV) (97.8% [95% CI: 86.1-99.7%]), but our retrospective control cases demonstrated that due to cases of fetal restricted mosaicism the true sensitivity of NIPT is lower. After showing that 97.3% of small CNVs prospectively observed in 8.3% of genome-wide tests were mostly benign maternal variants, sensitivity (75.0% [95% CI: 19.4%-99.4%]), specificity (99.7% [99.5%-99.9%]) and PPV (30.0% [14.5%-52.1%]) for relevant fetal CNVs were relatively high, too. Maternal autoimmune disorders and medication, such as dalteparin, seem to impair assay quality. CONCLUSION When maternal CNVs are recognized as such, cnNIPT showed a very high sensitivity, specificity and PPV for common trisomies in single and multiple pregnancies at any risk and very good values genome-wide. We found that the resolution for segmental aberrations is generally comparable to standard karyotyping, and exceeds the latter if the fetal fraction is above 10%, which allows detection of the 2.5 Mb 22q11.2 microdeletion associated with the velocardiofacial syndrome, even if the mother is not a carrier.
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Affiliation(s)
- Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.
| | - Pietro Sirleto
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Dunja Niedrist
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | | | - Christian Britschgi
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | | | - Nicole Ochsenbein-Kölble
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Tilo Burkhardt
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Josef Wisser
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Roland Zimmermann
- Division of Obstetrics, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
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17
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Tam JCW, Chan YM, Tsang SY, Yau CI, Yeung SY, Au KK, Chow CK. Noninvasive prenatal paternity testing by means of SNP-based targeted sequencing. Prenat Diagn 2020; 40:497-506. [PMID: 31674029 PMCID: PMC7154534 DOI: 10.1002/pd.5595] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/03/2019] [Accepted: 10/25/2019] [Indexed: 12/19/2022]
Abstract
Objective To develop a method for noninvasive prenatal paternity testing based on targeted sequencing of single nucleotide polymorphisms (SNPs). Method SNPs were selected based on population genetics data. Target‐SNPs in cell‐free DNA extracted from maternal blood (maternal cfDNA) were analyzed by targeted sequencing wherein target enrichment was based on multiplex amplification using QIAseq Targeted DNA Panels with Unique Molecular Identifiers. Fetal SNP genotypes were called using a novel bioinformatics algorithm, and the combined paternity indices (CPIs) and resultant paternity probabilities were calculated. Results Fetal SNP genotypes obtained from targeted sequencing of maternal cfDNA were 100% concordant with those from amniotic fluid‐derived fetal genomic DNA. From an initial panel of 356 target‐SNPs, an average of 148 were included in paternity calculations in 15 family trio cases, generating paternity probabilities of greater than 99.9999%. All paternity results were confirmed by short‐tandem‐repeat analysis. The high specificity of the methodology was validated by successful paternity discrimination between biological fathers and their siblings and by large separations between the CPIs calculated for the biological fathers and those for 60 unrelated men. Conclusion The novel method is highly effective, with substantial improvements over similar approaches in terms of reduced number of target‐SNPs, increased accuracy, and reduced costs.
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Affiliation(s)
| | - Yee Man Chan
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Shui Ying Tsang
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Chung In Yau
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Shuk Ying Yeung
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Ka Ki Au
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
| | - Chun Kin Chow
- Department of R&D, Medtimes Medical Group Limited, Kwai Chung, Hong Kong
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18
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Muzzey D, Goldberg JD, Haverty C. Noninvasive prenatal screening for patients with high body mass index: Evaluating the impact of a customized whole genome sequencing workflow on sensitivity and residual risk. Prenat Diagn 2019; 40:333-341. [PMID: 31697845 PMCID: PMC7065115 DOI: 10.1002/pd.5603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/27/2019] [Accepted: 10/15/2019] [Indexed: 12/20/2022]
Abstract
Objective Women with high body mass index (BMI) tend to have reduced fetal fraction (FF) during cell‐free DNA‐based noninvasive prenatal screening (NIPS), causing test failure rates up to 24.3% and prompting guidelines that recommend aneuploidy screening other than NIPS for patients with significant obesity. Because alternatives to NIPS are only preferable if they perform better, we compared the respective sensitivities at different BMI levels of traditional aneuploidy screening and a customized whole‐genome sequencing NIPS. Method The relationship between FF, aneuploidy, and BMI was quantified from 58 105 patients screened with a customized NIPS that does not fail samples because of low FF alone. Expected analytical sensitivity as a function of aneuploidy and BMI (eg, trisomy 18 sensitivity when BMI = 35) was determined by scaling the BMI‐ and aneuploidy‐specific FF distribution by the FF‐ and aneuploidy‐specific sensitivity calculated from empirically informed simulations. Results Across all classes of obesity and assuming zero FF‐related test failures, analytical sensitivity for the investigated NIPS exceeded that of traditional aneuploidy screening for trisomies 13, 18, and 21. Conclusion Relative to traditional aneuploidy screening, a customized NIPS with high accuracy at low FF and a low test‐failure rate is a superior screening option for women with high BMI. What's already known about this topic?
Women with high body mass index (BMI) often receive a test failure on noninvasive prenatal screening (NIPS) because of low fetal fraction (FF). The American College of Medical Genetics and Genomics recommends offering traditional aneuploidy screening to patients with “significant obesity.” NIPS offerings differ in their efficacy at low FF.
What does this study add?
Irrespective of BMI and without FF‐based test failures, it is possible for a customized NIPS to provide all women with accurate prenatal screening.
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Affiliation(s)
- Dale Muzzey
- Myriad Women's Health, South San Francisco, CA, USA.,Myriad Genetics, Salt Lake City, UT, USA
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19
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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: 70] [Impact Index Per Article: 14.0] [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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20
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Hopkins MK, Dugoff L, Durnwald C, Havrilesky LJ, Dotters-Katz S. Cell-free DNA for Down syndrome screening in obese women: Is it a cost-effective strategy? Prenat Diagn 2019; 40:173-178. [PMID: 31803969 DOI: 10.1002/pd.5605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/22/2019] [Accepted: 10/27/2019] [Indexed: 01/19/2023]
Abstract
OBJECTIVE Determine cost differences between cell-free DNA (cfDNA) and serum integrated screening (INT) in obese women given the limitations of aneuploidy screening in this population. METHODS Using a decision-analytic model, we estimated the cost-effectiveness of trisomy 21 screening in class III obese women using cfDNA compared with INT. Primary outcomes of the model were cost, number of unnecessary invasive tests, procedure-related fetal losses, and missed cases of trisomy 21. RESULTS In base case, the mean cost of cfDNA was $498 greater than INT ($1399 vs $901). cfDNA resulted in lower probabilities of unnecessary invasive testing (2.9% vs 3.5%), procedure-related loss (0.015% vs 0.019%), and missed cases of T21 (0.00013% vs 0.02%). cfDNA cost $87 485 per unnecessary invasive test avoided, $11 million per procedure-related fetal loss avoided, and $2.2 million per missed case of T21 avoided. In sensitivity analysis, when the probability of insufficient fetal fraction is assumed to be >25%, cfDNA is both costlier than INT and results in more unnecessary invasive testing (a dominated strategy). CONCLUSION When the probability of insufficient fetal fraction more than 25% (a maternal weight of ≥300 lbs), cfDNA is costlier and results in more unnecessary invasive testing than INT.
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Affiliation(s)
- Maeve K Hopkins
- Division of Maternal and Fetal Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Lorraine Dugoff
- Division of Maternal and Fetal Medicine and Reproductive Genetics, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Celeste Durnwald
- Division of Maternal and Fetal Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA
| | - Laura J Havrilesky
- Division of Gynecologic Oncology, Duke University Medical Center, Durham, NC
| | - Sarah Dotters-Katz
- Division of Maternal and Fetal Medicine, Duke University Medical Center, Durham, NC
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21
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Putra M, Idler J, Patek K, Contos G, Walker C, Olson D, Hicks MA, Chaperon J, Korzeniewski SJ, Patwardhan SC, Sokol RJ. The association of HBB-related significant hemoglobinopathies and low fetal fraction on noninvasive prenatal screening for fetal aneuploidy. J Matern Fetal Neonatal Med 2019; 34:3657-3661. [PMID: 31736384 DOI: 10.1080/14767058.2019.1689558] [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: 10/25/2022]
Abstract
Objectives: HBB-related significant hemoglobinopathies have been anecdotally associated with low fetal fraction on noninvasive prenatal screening (NIPS). We sought to compare the difference in fetal fraction using NIPS in women with HBB-related significant hemoglobinopathies (HSH) and women with normal hemoglobin.Study design: This is a retrospective case-control study. Cases were women with a diagnosis of HSH using NIPS from a commercial laboratory. The comparison group was women with hemoglobin AA from a tertiary care center database. We tested for differences in median fetal fraction using quantile regression analysis, adjusting for maternal body weight and gestational age.Results: This study includes 35 women with clinically significant HSH and a comparison group of 636 women with hemoglobin AA. Adjusting for gestational age and body weight, the median fetal fraction was 4.1 point lower in the HSH than in the comparison group (β - 4.1; 95% -5.7 to -2.5, p < .05). The rate of no-calls due to low fetal fraction was significantly higher in the clinically significant HSH group than in the comparison group [HSH: n = 9/35, 25.7% versus comparison: n = 32/636, 5.0% (p < .001)].Conclusion: Women with HSH were more likely to have a lower fetal fraction and ultimately a five-fold higher no-call rate. What's already known about this topic?Low fetal fraction is one of the most common causes of no-call result in noninvasive prenatal screeningHigh maternal weight, early gestational age and fetal aneuploidies are associated with low fetal fraction What does this study add?HBB-related significant hemoglobinopathies are associated with low fetal fractionReduction in fetal fraction due to HBB-related significant hemoglobinopathies may also result in higher no-call rate.
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Affiliation(s)
- Manesha Putra
- Department of Reproductive Biology, Division of Maternal-Fetal Medicine, MetroHealth Medical Center, Cleveland, OH, USA.,University Hospitals Cleveland Medical Center, Cleveland, OH, USA.,Case Western Reserve University, Cleveland, OH, USA
| | - Jay Idler
- Detroit Medical Center, Detroit, MI, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - Kara Patek
- Detroit Medical Center, Detroit, MI, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - George Contos
- Detroit Medical Center, Detroit, MI, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - Christopher Walker
- Detroit Medical Center, Detroit, MI, USA.,Wayne State University School of Medicine, Detroit, MI, USA
| | - Danielle Olson
- Department of Reproductive Biology, Division of Maternal-Fetal Medicine, MetroHealth Medical Center, Cleveland, OH, USA.,Case Western Reserve University, Cleveland, OH, USA
| | | | | | | | | | - Robert J Sokol
- Wayne State University School of Medicine, Detroit, MI, USA
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22
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Influence of Body Mass Index on Fetal Fraction Increase With Gestation and Cell-Free DNA Test Failure. Obstet Gynecol 2019; 132:436-443. [PMID: 29995742 DOI: 10.1097/aog.0000000000002752] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To assess the influence of body mass index (BMI) on fetal fraction increase with gestational age and on the rates of test failure. METHODS We performed a cross-sectional study of consecutive singleton pregnancies in which cell-free DNA screening for fetal aneuploidies was performed from 10 weeks of gestation, between May 2013 and January 2018, at two fetal medicine clinics in Australia using one of two different platforms. Maternal characteristics, fetal fraction, and failure after a first attempt ("no-call") and after resampling ("test failure") were recorded. Body mass index was classified as normal (BMI less than 25.0), overweight (BMI 25.0-29.9), obesity class I (BMI 30.0-34.9), and obesity classes II and III (BMI 35.0 or greater). Fetal fraction and proportions of no-call results and test failure were compared between the groups. RESULTS Of 14,223 singleton pregnancies included, 8,583 (60.3%) were screened with platform A and 5,640 (39.7%) with platform B. Median fetal fraction values were lower, and no-call and failure rates were higher in increased BMI groups across both platforms (P<.001 in both). When compared with women with normal BMIs, women with BMIs of 35 or greater had a significantly smaller increase in fetal fraction (0.1 vs 0.3 units/wk, P<.001, in both platforms). In this subgroup, when compared with women with normal BMIs, the odds ratios for a no-call result were 22.0 (95% CI 13.8-35.3, 16.6% vs 0.9%) and 8.0 (95% CI 4.1-15.6, 7.8% vs 1.0%) and for a failed test were 25.0 (95% CI 11.2-55.7, 6.4% vs 0.3%) and 5.8 (95% CI 2.0-17.3, 2.7% vs 0.5%) using platforms A and B, respectively. CONCLUSION The increase in fetal fraction throughout gestation in women with BMIs of 35 or above is minimal. Postponing the test is unlikely to reduce test failure rates in this population.
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Belandres D, Shamonki M, Arrach N. Current status of spent embryo media research for preimplantation genetic testing. J Assist Reprod Genet 2019; 36:819-826. [PMID: 30895497 DOI: 10.1007/s10815-019-01437-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
In recent years, a growing body of literature has emerged investigating the clinical utility of spent embryo media (SEM) for preimplantation genetic testing for aneuploidy (PGT-A) (Hammond et al. in Fertil Steril. 107(1):220-8, 2017; Xu et al. in Proc Natl Acad Sci USA. 113(42):11907-12, 2016; Shamonki et al. in Fertil Steril. 106(6):1312-8, 2016; Feichtinger et al. in Reprod BioMed Online. 34(6):583-9, 2017; Vera-Rodriguez et al. in Hum Reprod. 33(4):745-56, 2018; Kuznyetsov et al. in PLoS One. 13(5):e0197262, 2018; Ho et al. in Fertil Steril. 110(3):467-75, 2018; Capalbo et al. in Fertil Steril. 110(5):870-9, 2018). Most of these studies have reported moderate success rates, suggesting the need for improvements in sensitivity and specificity. The concordance between spent media and embryo biopsy or whole embryo was reported to be between 30.4 and 90%, with 50-70% correlation being the most representative (Xu et al. in Proc Natl Acad Sci USA. 113(42):11907-12, 2016; Shamonki et al. in Fertil Steril. 106(6):1312-8, 2016; Feichtinger et al. in Reprod BioMed Online. 34(6):583-9, 2017; Vera-Rodriguez et al. in Hum Reprod. 33(4):745-56, 2018; Kuznyetsov et al. in PLoS One. 13(5):e0197262, 2018; Ho et al. in Fertil Steril. 110(3):467-75, 2018). Here, we will analyze all spent media testing strategies including SEM collection methods, whole genome amplification (WGA) strategies, chromosome copy number detection, and bioinformatics analysis tools. We will propose improvements to further increase the accuracy and sensitivity of the assay before bringing PGT-A with SEM into the clinical sphere.
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Affiliation(s)
- Denice Belandres
- Progenesis Inc., 4150 Regents Park Row, Suite 245, La Jolla, CA, 92037, USA
| | - Mousa Shamonki
- Fertility and Surgical Associates of California, 325 Rolling Oaks Drive, Suite 110, Thousand Oaks, CA, 91361, USA.,University of California, Los Angeles, CA, 90095, USA
| | - Nabil Arrach
- Progenesis Inc., 4150 Regents Park Row, Suite 245, La Jolla, CA, 92037, USA.
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Fleiss B, Wong F, Brownfoot F, Shearer IK, Baud O, Walker DW, Gressens P, Tolcos M. Knowledge Gaps and Emerging Research Areas in Intrauterine Growth Restriction-Associated Brain Injury. Front Endocrinol (Lausanne) 2019; 10:188. [PMID: 30984110 PMCID: PMC6449431 DOI: 10.3389/fendo.2019.00188] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/06/2019] [Indexed: 12/16/2022] Open
Abstract
Intrauterine growth restriction (IUGR) is a complex global healthcare issue. Concerted research and clinical efforts have improved our knowledge of the neurodevelopmental sequelae of IUGR which has raised the profile of this complex problem. Nevertheless, there is still a lack of therapies to prevent the substantial rates of fetal demise or the constellation of permanent neurological deficits that arise from IUGR. The purpose of this article is to highlight the clinical and translational gaps in our knowledge that hamper our collective efforts to improve the neurological sequelae of IUGR. Also, we draw attention to cutting-edge tools and techniques that can provide novel insights into this disorder, and technologies that offer the potential for better drug design and delivery. We cover topics including: how we can improve our use of crib-side monitoring options, what we still need to know about inflammation in IUGR, the necessity for more human post-mortem studies, lessons from improved integrated histology-imaging analyses regarding the cell-specific nature of magnetic resonance imaging (MRI) signals, options to improve risk stratification with genomic analysis, and treatments mediated by nanoparticle delivery which are designed to modify specific cell functions.
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Affiliation(s)
- Bobbi Fleiss
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
- NeuroDiderot, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, St Thomas' Hospital, London, United Kingdom
- *Correspondence: Bobbi Fleiss
| | - Flora Wong
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Paediatrics, Monash University, Clayton, VIC, Australia
- Monash Newborn, Monash Children's Hospital, Clayton, VIC, Australia
| | - Fiona Brownfoot
- Translational Obstetrics Group, Department of Obstetrics and Gynaecology, Mercy Hospital for Women, University of Melbourne, Heidelberg, VIC, Australia
| | - Isabelle K. Shearer
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Olivier Baud
- NeuroDiderot, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Division of Neonatal Intensive Care, University Hospitals of Geneva, Children's Hospital, University of Geneva, Geneva, Switzerland
| | - David W. Walker
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Pierre Gressens
- NeuroDiderot, INSERM, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
- Centre for the Developing Brain, School of Biomedical Engineering and Imaging Sciences, King's College London, St Thomas' Hospital, London, United Kingdom
- PremUP, Paris, France
| | - Mary Tolcos
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
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25
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Noninvasive paternal exclusion testing for cystic fibrosis in the first five to eight weeks of gestation. Sci Rep 2018; 8:15941. [PMID: 30374031 PMCID: PMC6205998 DOI: 10.1038/s41598-018-34396-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/16/2018] [Indexed: 12/23/2022] Open
Abstract
Prenatal genetic testing is not generally applicable to the very early stages of pregnancy (prior to week 8 gestation), a time period that is crucial to pregnant couples with high risk for transmission of genetic disease to their fetus. Therefore, we developed a new ultra-sensitive targeted next generation sequencing method for noninvasive haplotype-based paternal allele exclusion testing of the cystic fibrosis-associated gene, CFTR. This new method was compared to a conventional library prep and sequencing analysis method and all test results were validated by amniotic fluid testing at later stages of pregnancy. Out of 7 enrolled couples, who provided at least two blood samples (at least one week apart) for noninvasive CFTR testing, a result was obtained for 6 fetuses. Using the new hypersensitive method, all six couples (100%) received a correct diagnosis for the paternal allele as opposed to 3/6 (50%) when tested with the conventional strategy. Among 4 couples who provided just one early pregnancy blood draw for analysis, diagnosis was possible in one fetus, but only using the ultra-sensitive method. Thus, we describe a novel noninvasive CFTR screening method which demonstrates unprecedented fetal allele typing accuracy in the earliest stages of pregnancy.
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26
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Chesnais V, Ott A, Chaplais E, Gabillard S, Pallares D, Vauloup-Fellous C, Benachi A, Costa JM, Ginoux E. Using massively parallel shotgun sequencing of maternal plasmatic cell-free DNA for cytomegalovirus DNA detection during pregnancy: a proof of concept study. Sci Rep 2018; 8:4321. [PMID: 29531245 PMCID: PMC5847603 DOI: 10.1038/s41598-018-22414-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/22/2018] [Indexed: 12/29/2022] Open
Abstract
Human cytomegalovirus (HCMV) primary infections of pregnant women can lead to congenital infections of the fetus that could have severe impacts on the health of the newborn. Recent studies have shown that 10-100 billion DNA fragments per milliliter of plasma are circulating cell-free. The study of this DNA has rapidly expanding applications to non-invasive prenatal testing (NIPT). In this study, we have shown that we can detect viral specific reads in the massively parallel shotgun sequencing (MPSS) NIPT data. We have also observed a strong correlation between the viral load of calibration samples and the number of reads aligned on the reference genome. Based on these observations we have constructed a statistical model able to quantify the viral load of patient samples. We propose to use this new method to detect and quantify circulating DNA virus like HCMV during pregnancy using the same sequencing results as NIPT data. This method could be used to improve the NIPT diagnosis.
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Affiliation(s)
| | | | | | | | | | - Christelle Vauloup-Fellous
- AP-HP, Hôpital Paul Brousse, Groupe Hospitalier Universitaire Paris-Sud, Virologie, Université Paris-Sud, INSERM U1193, Villejuif, France
| | - Alexandra Benachi
- AP-HP, Hôpital Antoine Béclère, Service de Gynécologie-Obstétrique et Médecine de la Reproduction, Université Paris-Sud, Clamart, France
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Ryan A, Martin KA. Comment on "Noninvasive prenatal screening at low fetal fraction: comparing whole-genome sequencing and single-nucleotide polymorphism methods". Prenat Diagn 2017; 37:725-726. [PMID: 28675625 PMCID: PMC5575504 DOI: 10.1002/pd.5072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/03/2017] [Accepted: 05/06/2017] [Indexed: 01/05/2023]
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28
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Muzzey D, Haverty C, Evans EA, Goldberg JD. Response to "Noninvasive prenatal screening at low fetal fraction: comparing whole-genome sequencing and single-nucleotide polymorphism methods". Prenat Diagn 2017; 37:727-728. [PMID: 28675624 PMCID: PMC5811916 DOI: 10.1002/pd.5071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 05/13/2017] [Indexed: 11/11/2022]
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