1
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Bellair M, Amaral E, Ouren M, Roark C, Kim J, O'Connor A, Soriano A, Schindler ML, Wapner RJ, Stone JL, Tavella N, Merriam A, Perley L, Breman AM, Beaudet AL. Noninvasive single-cell-based prenatal genetic testing: A proof of concept clinical study. Prenat Diagn 2024; 44:304-316. [PMID: 38411249 DOI: 10.1002/pd.6529] [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: 08/16/2023] [Revised: 01/11/2024] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
OBJECTIVE To clinically assess a cell-based noninvasive prenatal genetic test using sequence-based copy number analysis of single trophoblasts from maternal blood. METHODS Blood was obtained from 401 (243 + 158) individuals (8-22 weeks) and shipped overnight. Red cells were lysed, and nucleated cells stained for cytokeratin (CK) and CD45 and enriched for positive CK staining. Automated scanning was used to identify and pick single CK+ /CD45- trophoblasts which were subjected to next-generation sequencing. RESULTS Blood was obtained from 243 pregnancies scheduled for CVS or amniocentesis. Luna results were normal for 160 singletons while 15 cases were abnormal (14 aneuploidy and one monozygotic twin with Williams syndrome deletion). The deletion was confirmed in both fetuses. Placental mosaicism occurred in 7 of 236 (3.0%) Luna cases and in 3 of 188 (1.6%) CVS cases (total 4.6%). No scorable trophoblasts were recovered in 32 of 236 usable samples. Additionally, 158 low-risk pregnancies not undergoing CVS/amniocentesis showed normal results in 133 cases. Seven had aneuploidy results, and there were three likely pathogenic deletions/duplications, including one15q11-q13 deletion. CONCLUSION Although the sample size is modest and statistically accurate measures of test performance are not possible, the Luna test detected aneuploidy and deletions/duplications based on concordance with CVS/amniocentesis.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ronald J Wapner
- Columbia University Irving Medical Center, New York, New York, USA
| | - Joanne L Stone
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicola Tavella
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Lauren Perley
- Yale School of Medicine, New Haven, Connecticut, USA
| | - Amy M Breman
- Indiana University School of Medicine, Indianapolis, Indiana, USA
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2
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Maktabi MA, Vossaert L, Van den Veyver IB. Cell-based Noninvasive Prenatal Testing (cbNIPT)-A Review on the Current Developments and Future Prospects. Clin Obstet Gynecol 2023; 66:636-648. [PMID: 37650673 PMCID: PMC10491429 DOI: 10.1097/grf.0000000000000798] [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] [Indexed: 09/01/2023]
Abstract
Considering the diagnostic limitations of cfDNA-based noninvasive prenatal testing (NIPT), scientists have long been interested in isolating and analyzing rare intact fetal and trophoblast cells from maternal blood or endocervical samples to diagnose fetal genetic conditions. These cells may be scarce and difficult to isolate, but they are a direct source of pure fetal genetic material. In this review, we summarize the history of cell-based NIPT, present an updated review on its current developments, evaluate its genetic diagnostic potential, and discuss its future prospects for clinical use.
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Affiliation(s)
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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3
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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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4
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Chang L, Jiao H, Chen J, Wu G, Liu P, Li R, Guo J, Long W, Tang X, Lu B, Xu H, Wu H. Single-cell whole-genome sequencing, haplotype analysis in prenatal diagnosis of monogenic diseases. Life Sci Alliance 2023; 6:e202201761. [PMID: 36810160 PMCID: PMC9947115 DOI: 10.26508/lsa.202201761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Monogenic inherited diseases are common causes of congenital disabilities, leading to severe economic and mental burdens on affected families. In our previous study, we demonstrated the validity of cell-based noninvasive prenatal testing (cbNIPT) in prenatal diagnosis by single-cell targeted sequencing. The present research further explored the feasibility of single-cell whole-genome sequencing (WGS) and haplotype analysis of various monogenic diseases with cbNIPT. Four families were recruited: one with inherited deafness, one with hemophilia, one with large vestibular aqueduct syndrome (LVAS), and one with no disease. Circulating trophoblast cells (cTBs) were obtained from maternal blood and analyzed by single-cell 15X WGS. Haplotype analysis showed that CFC178 (deafness family), CFC616 (hemophilia family), and CFC111 (LVAS family) inherited haplotypes from paternal and/or maternal pathogenic loci. Amniotic fluid or fetal villi samples from the deafness and hemophilia families confirmed these results. WGS performed better than targeted sequencing in genome coverage, allele dropout (ADO), and false-positive (FP) ratios. Our findings suggest that cbNIPT by WGS and haplotype analysis have great potential for use in prenatally diagnosing various monogenic diseases.
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Affiliation(s)
- Liang Chang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Haining Jiao
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiucheng Chen
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Guanlin Wu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Jianying Guo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Wenqing Long
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojian Tang
- Department of Obstetrics and Gynecology, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bingjie Lu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Haibin Xu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Han Wu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
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5
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Abstract
The options for prenatal genetic testing have evolved rapidly in the past decade, and advances in sequencing technology now allow genetic diagnoses to be made down to the single-base-pair level, even before the birth of the child. This offers women the opportunity to obtain information regarding the foetus, thereby empowering them to make informed decisions about their pregnancy. As genetic testing becomes increasingly available to women, clinician knowledge and awareness of the options available to women is of great importance. Additionally, comprehensive pretest and posttest genetic counselling about the advantages, pitfalls and limitations of genetic testing should be provided to all women. This review article aims to cover the range of genetic tests currently available in prenatal screening and diagnosis, their current applications and limitations in clinical practice as well as what the future holds for prenatal genetics.
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Affiliation(s)
- Karen Mei Xian Lim
- Department of Obstetrics and Gynaecology, National University Health System, Singapore
| | - Aniza Puteri Mahyuddin
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, National University Health System, Singapore,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Correspondence: A/Prof Mahesh Choolani, Head and Senior Consultant, Department of Obstetrics and Gynaecology, National University Health System, NUHS Tower Block, Level 12, 1E Kent Ridge Road, 119228, Singapore. E-mail:
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6
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Barrett AN, Huang Z, Aung S, Ho SSY, Roslan NS, Mahyuddin AP, Biswas A, Choolani M. Whole-Chromosome Karyotyping of Fetal Nucleated Red Blood Cells Using the Ion Proton Sequencing Platform. Genes (Basel) 2022; 13:genes13122257. [PMID: 36553524 PMCID: PMC9778445 DOI: 10.3390/genes13122257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/26/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
The current gold standard for the definitive diagnosis of fetal aneuploidy uses either chorionic villus sampling (CVS) or amniocentesis, both of which are which are invasive procedures carrying a procedure-related risk of miscarriage of up to 0.1-0.2%. Non-invasive prenatal diagnosis using fetal nucleated red blood cells (FNRBCs) isolated from maternal peripheral venous blood would remove this risk of miscarriage since these cells can be isolated from the mother's blood. We aimed to detect whole-chromosome aneuploidies from single nucleated fetal red blood cells using whole-genome amplification followed by massively parallel sequencing performed on a semiconductor sequencing platform. Twenty-six single cells were picked from the placental villi of twelve patients thought to have a normal fetal genotype and who were undergoing elective first-trimester surgical termination of pregnancy. Following karyotyping, it was subsequently found that two of these cases were also abnormal (one trisomy 15 and one mosaic genotype). One single cell from chorionic villus samples for two patients carrying a fetus with trisomy 21 and two single cells from women carrying fetuses with T18 were also picked. Pooled libraries were sequenced on the Ion Proton and data were analysed using Ion Reporter software. We correctly classified fetal genotype in all 24 normal cells, as well as the 2 T21 cells, the 2 T18 cells, and the two T15 cells. The two cells picked from the fetus with a mosaic result by CVS were classified as unaffected, suggesting that this was a case of confined placental mosaicism. Fetal sex was correctly assigned in all cases. We demonstrated that semiconductor sequencing using commercially available software for data analysis can be achieved for the non-invasive prenatal diagnosis of whole-chromosome aneuploidy with 100% accuracy.
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Affiliation(s)
- Angela N. Barrett
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Zhouwei Huang
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Sarah Aung
- iGene Laboratory Pte Ltd., 1 Science Park Road #04-10, The Capricorn, Singapore 117528, Singapore
| | - Sherry S. Y. Ho
- iGene Laboratory Pte Ltd., 1 Science Park Road #04-10, The Capricorn, Singapore 117528, Singapore
| | - Nur Syazana Roslan
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Aniza P. Mahyuddin
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Arijit Biswas
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
- Department of Obstetrics & Gynaecology, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
| | - Mahesh Choolani
- Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
- Department of Obstetrics & Gynaecology, National University Hospital, 1E Kent Ridge Road, NUHS Tower Block, Level 12, Singapore 119228, Singapore
- Correspondence:
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7
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Jeppesen LD, Hjortshøj TD, Hindkjær J, Hatt L, Petersen OB, Singh R, Schelde P, Andreasen L, Christensen R, Lildballe DL, Vogel I. Cell-Based NIPT Detects 47,XXY Genotype in a Twin Pregnancy. Front Genet 2022; 13:842092. [PMID: 35360877 PMCID: PMC8963804 DOI: 10.3389/fgene.2022.842092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The existing risk of procedure-related miscarriage following invasive sampling for prenatal diagnosis is higher for twin pregnancies and some women are reluctant to test these typically difficultly obtained pregnancies invasively. Therefore, there is a need for noninvasive testing options that can test twin pregnancies at an early gestational age and ideally test the twins individually.Case presentation: A pregnant woman opted for cell-based NIPT at GA 10 + 5. As cell-based NIPT is not established for use in twins, the test was provided in a research setting only, when an ultrasound scan showed that she carried dichorionic twins.Materials and Methods: Fifty mL of peripheral blood was sampled, and circulating fetal cells were enriched and isolated. Individual cells were subject to whole-genome amplification and STR analysis. Three fetal cells were analyzed by chromosomal microarray (aCGH).Results: We identified 20 fetal cells all sharing the same genetic profile, which increased the likelihood of monozygotic twins. aCGH of three fetal cells showed the presence of two X chromosomes and a gain of chromosome Y. CVS from both placentae confirmed the sex chromosomal anomaly, 47,XXY and that both fetuses were affected.Conclusion: NIPT options can provide valuable genetic information to twin pregnancies that help the couples in their decision-making on prenatal testing. Little has been published about the use of cell-based NIPT in twin pregnancies, but the method may offer the possibility to obtain individual cell-based NIPT results in dizygotic twins.
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Affiliation(s)
- Line Dahl Jeppesen
- ARCEDI, Vejle, Denmark
- Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- *Correspondence: Line Dahl Jeppesen,
| | - Tina Duelund Hjortshøj
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | | | | | - Olav Bjørn Petersen
- Center for Fetal Medicine, Department of Obstetrics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Lotte Andreasen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Christensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Dorte L. Lildballe
- Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark
| | - Ida Vogel
- Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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8
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Research Progress in Isolation and Enrichment of Fetal Cells from Maternal Blood. J CHEM-NY 2022. [DOI: 10.1155/2022/7131241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Prenatal diagnosis is an important means of early diagnosis of genetic diseases, which can effectively reduce the risk of birth defects. Free fetal cells, as a carrier of intact fetal genetic material, provide hope for the development of high-sensitivity and high-accuracy prenatal diagnosis technology. However, the number of fetal cells is small and it is difficult to apply clinically. In recent years, noninvasive prenatal diagnosis (NIPD) technology for fetal genetic material in maternal peripheral blood has developed rapidly, which makes it possible to diagnose genetic diseases by fetal cells in maternal peripheral blood. This article reviewed the current status of fetal cell separation and enrichment technology and its application in noninvasive prenatal diagnosis technology.
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9
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Wapner RJ, Norton ME. An Introduction: Prenatal Screening, Diagnosis, and Treatment of Single Gene Disorders. Clin Obstet Gynecol 2021; 64:852-860. [PMID: 34618720 DOI: 10.1097/grf.0000000000000660] [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: 11/25/2022]
Abstract
Increasing ability to diagnose fetal single gene disorders has changed the prenatal diagnostic paradigm. As fetal sequencing advances, the genomic information obtained can lead to improved prognostic counseling, and elucidation of recurrence risk and future prenatal diagnosis options. For some of these disorders, postnatal molecular therapy, including gene therapy, is available or being studied in clinical trials. Most of the initial research and clinical trials have involved children and adults, but there are potential benefits to treating conditions before birth. Many clinical studies are underway exploring the potential for in utero gene therapy.
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Affiliation(s)
- Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York
| | - Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California
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10
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Schobers G, Koeck R, Pellaers D, Stevens SJC, Macville MVE, Paulussen ADC, Coonen E, van den Wijngaard A, de Die-Smulders C, de Wert G, Brunner HG, Zamani Esteki M. Liquid biopsy: state of reproductive medicine and beyond. Hum Reprod 2021; 36:2824-2839. [PMID: 34562078 PMCID: PMC8523207 DOI: 10.1093/humrep/deab206] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/06/2021] [Indexed: 01/23/2023] Open
Abstract
Liquid biopsy is the process of sampling and analyzing body fluids, which enables non-invasive monitoring of complex biological systems in vivo. Liquid biopsy has myriad applications in health and disease as a wide variety of components, ranging from circulating cells to cell-free nucleic acid molecules, can be analyzed. Here, we review different components of liquid biopsy, survey state-of-the-art, non-invasive methods for detecting those components, demonstrate their clinical applications and discuss ethical considerations. Furthermore, we emphasize the importance of artificial intelligence in analyzing liquid biopsy data with the aim of developing ethically-responsible non-invasive technologies that can enhance individualized healthcare. While previous reviews have mainly focused on cancer, this review primarily highlights applications of liquid biopsy in reproductive medicine.
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Affiliation(s)
- Gaby Schobers
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rebekka Koeck
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Dominique Pellaers
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Merryn V E Macville
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Aimée D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Edith Coonen
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Center for Reproductive Medicine, Maastricht University Medical Centre+, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Christine de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Guido de Wert
- Faculty of Health, Medicine and Life Sciences, Department of Health, Ethics and Society, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
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11
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Sonek J, Muller R, Muller-Cohn J, Dickerson J, Garcia Lopez B, Barber-Singh J, Dufek D, Hiett AK, Buchanan P. Identification of fetal aneuploidy with dual-probe fluorescence in situ hybridization analysis in circulating trophoblasts after enrichment using a high-sensitivity microfluidic platform. Prenat Diagn 2021; 41:1701-1708. [PMID: 34582049 DOI: 10.1002/pd.6046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/08/2021] [Accepted: 09/09/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To evaluate a microfluidics-based positive selection technology for isolating circulating trophoblasts (CTs) from peripheral blood of women whose pregnancies are affected by aneuploidy and to evaluate fetal karyotype using fluorescence in situ hybridization (FISH). METHOD Ten 18-ml samples of peripheral blood were collected consecutively from pregnant women whose fetus was affected by aneuploidy. A preservation buffer was added, and the specimens were shipped overnight to the testing laboratory at ambient temperature. The specimen was infused into the fully automated microfluidics-based LiquidScan® instrument without pre-processing. This instrument contains microfluidic chips, which are coated with antibodies (anti-huEpCAM and a proprietary antibody mixture) specific to CT surface epitopes. FISH analysis was performed on the enriched cells. RESULTS Fetal aneuploidy evaluated included trisomy 21 (n = 3), trisomy 18 (n = 1), trisomy 13 (n = 1), monosomy X (n = 3), and triploidy (n = 1). CTs for analysis by FISH were identified in all samples. The average number of mononucleate cells per 1 ml of whole blood was 2.11 (range 0.38-4.63) overall and was 2.67 (range 1.13-4.63) using the proprietary combination of antibodies. FISH results were concordant with the aneuploidy based on other testing in all cases. Multinucleate cells were searched for and identified in the last seven samples (average number: 0.84/1 ml). CONCLUSIONS Our study demonstrates that the LiquidScan® , a high-sensitivity microfluidic platform, can enrich circulating trophoblasts (mononucleate and multinucleate). FISH can then be used to detect fetal aneuploidy.
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Affiliation(s)
- Jiri Sonek
- Department of Obstetrics and Gynecology, Wright State University, Dayton, Ohio, USA
| | - Rolf Muller
- BioFluidica, Inc., San Diego, California, USA
| | | | | | | | | | - Dylan Dufek
- BioFluidica, Inc., San Diego, California, USA
| | - Adam Kinney Hiett
- Department of Obstetrics and Gynecology, Wright State University, Dayton, Ohio, USA
| | - Philip Buchanan
- Department of Obstetrics and Gynecology, The George Washington University, Washington, DC, USA
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12
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Novel Approaches to an Integrated Route for Trisomy 21 Evaluation. Biomolecules 2021; 11:biom11091328. [PMID: 34572541 PMCID: PMC8465311 DOI: 10.3390/biom11091328] [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: 07/16/2021] [Revised: 08/16/2021] [Accepted: 09/06/2021] [Indexed: 12/31/2022] Open
Abstract
Trisomy 21 (T21) is one of the most commonly occurring genetic disorders, caused by the partial or complete triplication of chromosome 21. Despite the significant progress in the diagnostic tools applied for prenatal screening, commonly used methods are still imprecise and involve invasive diagnostic procedures that are related to a maternal risk of miscarriage. In this case, novel prenatal biomarkers are still being evaluated using highly specialized techniques, which could increase the diagnostic usefulness of biochemical prenatal screening for T21. From the other hand, the T21′s pathogenesis, caused by the improper division of genetic material, disrupting many metabolic pathways, could be further evaluated with the use of omics methods, which could result in bringing relevant insights for the evaluation of potential medical targets. Accordingly, a literature search was undertaken to collect novel information about prenatal screening for Down syndrome with the use of advanced technology, with a particular emphasis on the evaluation of novel screening biomarkers and the discovery of potential medical targets. These meta-analyses are focused on novel approaches designed with the use of omics techniques, representing the most rapidly developing and promising field in research today. Considering the limitations and progress of these methods, the use of omics techniques in evaluating T21 pathogenesis could bring beneficial results in prenatal screening, simultaneously uncovering novel potential medical targets.
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13
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Afshar Y, Dong J, Zhao P, Li L, Wang S, Zhang RY, Zhang C, Yin O, Han CS, Einerson BD, Gonzalez TL, Zhang H, Zhou A, Yang Z, Chou SJ, Sun N, Cheng J, Zhu H, Wang J, Zhang TX, Lee YT, Wang JJ, Teng PC, Yang P, Qi D, Zhao M, Sim MS, Zhe R, Goldstein JD, Williams J, Wang X, Zhang Q, Platt LD, Zou C, Pisarska MD, Tseng HR, Zhu Y. Circulating trophoblast cell clusters for early detection of placenta accreta spectrum disorders. Nat Commun 2021; 12:4408. [PMID: 34344888 PMCID: PMC8333096 DOI: 10.1038/s41467-021-24627-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 06/21/2021] [Indexed: 11/21/2022] Open
Abstract
Placenta accreta spectrum (PAS) is a high-risk obstetrical condition associated with significant morbidity and mortality. Current clinical screening modalities for PAS are not always conclusive. Here, we report a nanostructure-embedded microchip that efficiently enriches both single and clustered circulating trophoblasts (cTBs) from maternal blood for detecting PAS. We discover a uniquely high prevalence of cTB-clusters in PAS and subsequently optimize the device to preserve the intactness of these clusters. Our feasibility study on the enumeration of cTBs and cTB-clusters from 168 pregnant women demonstrates excellent diagnostic performance for distinguishing PAS from non-PAS. A logistic regression model is constructed using a training cohort and then cross-validated and tested using an independent cohort. The combined cTB assay achieves an Area Under ROC Curve of 0.942 (throughout gestation) and 0.924 (early gestation) for distinguishing PAS from non-PAS. Our assay holds the potential to improve current diagnostic modalities for the early detection of PAS. Placenta accreta spectrum (PAS) is a high-risk obstetrical complication associated with significant morbidity and mortality. Here the authors discover a uniquely high prevalence of circulating trophoblasts clusters in PAS and explore their diagnostic potential to augment current diagnostic modalities for the early detection of PAS.
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Affiliation(s)
- Yalda Afshar
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jiantong Dong
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Pan Zhao
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong, China
| | - Lei Li
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Shan Wang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Ryan Y Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ceng Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ophelia Yin
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christina S Han
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Center for Fetal Medicine and Women's Ultrasound, Los Angeles, CA, USA
| | - Brett D Einerson
- Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, University of Utah Health, Salt Lake City, UT, USA
| | - Tania L Gonzalez
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Huirong Zhang
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong, China
| | - Anqi Zhou
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhuo Yang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shih-Jie Chou
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Na Sun
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ju Cheng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Henan Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jing Wang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tiffany X Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yi-Te Lee
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jasmine J Wang
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Pai-Chi Teng
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Peng Yang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dongping Qi
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Myung-Shin Sim
- Departments of Computational Medicine & Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ruilian Zhe
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong, China
| | - Jeffrey D Goldstein
- Department of Pathology and Laboratory Medicine, Ronald Reagan Medical Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - John Williams
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xietong Wang
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Qingying Zhang
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Obstetrics, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lawrence D Platt
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Center for Fetal Medicine and Women's Ultrasound, Los Angeles, CA, USA
| | - Chang Zou
- Clinical Medical Research Center, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong, China.
| | - Margareta D Pisarska
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Yazhen Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA.
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14
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Ito N, Tsukamoto K, Taniguchi K, Takahashi K, Okamoto A, Aoki H, Otera‐Takahashi Y, Kitagawa M, Ogata‐Kawata H, Morita H, Hata K, Nakabayashi K. Isolation and characterization of fetal nucleated red blood cells from maternal blood as a target for single cell sequencing-based non-invasive genetic testing. Reprod Med Biol 2021; 20:352-360. [PMID: 34262404 PMCID: PMC8254165 DOI: 10.1002/rmb2.12392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Although non-invasive prenatal testing (NIPT) based on cell-free DNA (cfDNA) in maternal plasma has been prevailing worldwide, low levels of fetal DNA fraction may lead to false-negative results. Since fetal cells in maternal blood provide a pure source of fetal genomic DNA, we aimed to establish a workflow to isolate and sequence fetal nucleated red blood cells (fNRBCs) individually as a target for NIPT. METHODS Using male-bearing pregnancy cases, we isolated fNRBCs individually from maternal blood by FACS, and obtained their genomic sequence data through PCR screening with a Y-chromosome marker and whole-genome amplification (WGA)-based whole-genome sequencing. RESULTS The PCR and WGA efficiencies of fNRBC candidates were consistently lower than those of control cells. Sequencing data analyses revealed that although the majority of the fNRBC candidates were confirmed to be of fetal origin, many of the WGA-based genomic libraries from fNRBCs were considered to have been amplified from a portion of genomic DNA. CONCLUSIONS We established a workflow to isolate and sequence fNRBCs individually. However, our results demonstrated that, to make cell-based NIPT targeting fNRBCs feasible, cell isolation procedures need to be further refined such that the nuclei of fNRBCs are kept intact.
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Affiliation(s)
- Noriko Ito
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
- Department of Pharmacotherapeutics, Course of Medical and Dental SciencesNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kazuhiro Tsukamoto
- Department of Pharmacotherapeutics, Course of Medical and Dental SciencesNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kosuke Taniguchi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Ken Takahashi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
- Department of Obstetrics and GynecologyThe Jikei University School of MedicineTokyoJapan
| | - Aikou Okamoto
- Department of Obstetrics and GynecologyThe Jikei University School of MedicineTokyoJapan
| | | | | | | | - Hiroko Ogata‐Kawata
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Hideaki Morita
- Department of Allergy and Clinical ImmunologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Kenichiro Hata
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Kazuhiko Nakabayashi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
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15
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Vossaert L, Chakchouk I, Zemet R, Van den Veyver IB. Overview and recent developments in cell-based noninvasive prenatal testing. Prenat Diagn 2021; 41:1202-1214. [PMID: 33974713 DOI: 10.1002/pd.5957] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022]
Abstract
Investigators have long been interested in the natural phenomenon of fetal and placental cell trafficking into the maternal circulation. The scarcity of these circulating cells makes their detection and isolation technically challenging. However, as a DNA source of fetal origin not mixed with maternal DNA, they have the potential of considerable benefit over circulating cell-free DNA-based noninvasive prenatal genetic testing (NIPT). Endocervical trophoblasts, which are less rare but more challenging to recover are also being investigated as an approach for cell-based NIPT. We review published studies from around the world describing both forms of cell-based NIPT and highlight the different approaches' advantages and drawbacks. We also offer guidance for developing a sound cell-based NIPT protocol.
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Affiliation(s)
- Liesbeth Vossaert
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Imen Chakchouk
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Roni Zemet
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ignatia B Van den Veyver
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA.,Pavillion for Women, Texas Children's Hospital, Houston, TX, USA
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16
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Zhang H, Yu X, Liu Y, Lin B, Jiang M, Song J, Di W, Zhu Z, Yang C. HUNTER-Chip: Bioinspired Hierarchically Aptamer Structure-Based Circulating Fetal Cell Isolation for Non-Invasive Prenatal Testing. Anal Chem 2021; 93:7235-7241. [PMID: 33949845 DOI: 10.1021/acs.analchem.1c00330] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Isolation and genetic analysis of circulating fetal cells from billions of maternal cells in peripheral blood are the cornerstone of fetal cell-based non-invasive prenatal testing. Inspired by the hierarchically multivalent architecture for enhanced capture of nature, an aptamer-based Hierarchically mUltivalent aNTibody mimic intERface (HUNTER) was designed with a tremendous avidity effect for highly efficient capture and non-destructive release of fetal cells. It was engineered by grafting Y-shaped DNA nanostructures to a linear polymer chain, creating a flexible polymer chain with bivalent aptamer side chains. This hierarchical arrangement of the aptamer ensures morphological complementarity, collective multiple-site interaction, and multivalent recognition between the aptamer and target cells. In combination with a deterministic lateral displacement (DLD)-patterned microdevice named as HUNTER-Chip, it achieves a binding affinity over 65-fold and a capture efficiency over 260%-fold due to the combination of hierarchically designed aptamers and frequent cell-ligand collision created by DLD. Moreover, a nuclease-assisted cell release strategy facilitates the release of fetal cells for gene analysis, such as fluorescence in situ hybridization. With the advantages of high affinity, excellent capture efficiency, and compatible downstream analysis, the HUNTER-Chip holds great potential for non-invasive prenatal diagnosis.
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Affiliation(s)
- Huimin Zhang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemical of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.,Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
| | - Xiyuan Yu
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemical of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yilong Liu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemical of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bingqian Lin
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemical of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Meng Jiang
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Juan Song
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemical of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wen Di
- Department of Obstetrics and Gynecology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai 200127, China
| | - Zhi Zhu
- MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemical of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.,MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, Key Laboratory for Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemical of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China.,Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen 361005, China
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17
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Zhuo X, Wang Q, Vossaert L, Salman R, Kim A, Van den Veyver I, Breman A, Beaudet A. Use of amplicon-based sequencing for testing fetal identity and monogenic traits with Single Circulating Trophoblast (SCT) as one form of cell-based NIPT. PLoS One 2021; 16:e0249695. [PMID: 33857205 PMCID: PMC8049273 DOI: 10.1371/journal.pone.0249695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 03/23/2021] [Indexed: 11/30/2022] Open
Abstract
A major challenge for cell-based non-invasive prenatal testing (NIPT) is to distinguish individual presumptive fetal cells from maternal cells in female pregnancies. We have sought a rapid, robust, versatile, and low-cost next-generation sequencing method to facilitate this process. Toward this goal, single isolated cells underwent whole genome amplification prior to genotyping. Multiple highly polymorphic genomic regions (including HLA-A and HLA-B) with 10-20 very informative single nucleotide polymorphisms (SNPs) within a 200 bp interval were amplified with a modified method based on other publications. To enhance the power of cell identification, approximately 40 Human Identification SNP (Applied Biosystems) test amplicons were also utilized. Using SNP results to compare to sex chromosome data from NGS as a reliable standard, the true positive rate for genotyping was 83.4%, true negative 6.6%, false positive 3.3%, and false negative 6.6%. These results would not be sufficient for clinical diagnosis, but they demonstrate the general validity of the approach and suggest that deeper genotyping of single cells could be completely reliable. A paternal DNA sample is not required using this method. The assay also successfully detected pathogenic variants causing Tay Sachs disease, cystic fibrosis, and hemoglobinopathies in single lymphoblastoid cells, and disease-causing variants in three cell-based NIPT cases. This method could be applicable for any monogenic diagnosis.
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Affiliation(s)
- Xinming Zhuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Qun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Roseen Salman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Adriel Kim
- Graduate Program in Diagnostic Genetics, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Ignatia Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, United States of America
| | - Amy Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States of America
| | - Arthur Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
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18
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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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19
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Rezaei M, Radfar P, Winter M, McClements L, Thierry B, Warkiani ME. Simple-to-Operate Approach for Single Cell Analysis Using a Hydrophobic Surface and Nanosized Droplets. Anal Chem 2021; 93:4584-4592. [PMID: 33656329 DOI: 10.1021/acs.analchem.0c05026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microfluidics-based technologies for single-cell analysis are becoming increasingly important tools in biological studies. With the increasing sophistication of microfluidics, cellular barcoding techniques, and next-generation sequencing, a more detailed picture of cellular subtype is emerging. Unfortunately, the majority of the methods developed for single-cell analysis are high-throughput and not suitable for rare cell analysis as they require a high input cell number. Here, we report a low-cost and reproducible method for rare single-cell analysis using a highly hydrophobic surface and nanosized static droplets. Our method allows rapid and efficient on-chip single-cell lysis and subsequent collection of genetic materials in nanoliter droplets using a micromanipulator or a laboratory pipette before subsequent genetic analysis. We show precise isolation of single cancer cells with high purity using two different strategies (i- cytospin and ii- static droplet array) for subsequent RNA analysis using droplet digital polymerase chain reaction (PCR) and real-time PCR. Our highly controlled isolation method opens a new avenue for the study of subcellular functional mechanisms, enabling the identification of rare cells of potential functional or pathogenic consequence.
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Affiliation(s)
- Meysam Rezaei
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales, 2007, Australia.,Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia.,SUStech-UTS Joint Research Centre for Biomedical Materials and Devices, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China
| | - Payar Radfar
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales, 2007, Australia
| | - Marnie Winter
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, South Australia 5095, Australia
| | - Lana McClements
- School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, 2007, Australia
| | - Benjamin Thierry
- Future Industries Institute, University of South Australia, Mawson Lakes Campus, Adelaide, South Australia 5095, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, New South Wales, 2007, Australia.,Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, New South Wales 2007, Australia.,SUStech-UTS Joint Research Centre for Biomedical Materials and Devices, Southern University of Science and Technology, Shenzhen 518055, People's Republic of China.,Institute of Molecular Medicine, Sechenov University, Moscow 119991, Russia
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20
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Development of a Specific Monoclonal Antibody to Detect Male Cells Expressing the RPS4Y1 Protein. Int J Mol Sci 2021; 22:ijms22042001. [PMID: 33670450 PMCID: PMC7921920 DOI: 10.3390/ijms22042001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/24/2022] Open
Abstract
Hemophilia is an X-linked recessive bleeding disorder. In pregnant women carrier of hemophilia, the fetal sex can be determined by non-invasive analysis of fetal DNA circulating in the maternal blood. However, in case of a male fetus, conventional invasive procedures are required for the diagnosis of hemophilia. Fetal cells, circulating in the maternal bloodstream, are an ideal target for a safe non-invasive prenatal diagnosis. Nevertheless, the small number of cells and the lack of specific fetal markers have been the most limiting factors for their isolation. We aimed to develop monoclonal antibodies (mAbs) against the ribosomal protein RPS4Y1 expressed in male cells. By Western blotting, immunoprecipitation and immunofluorescence analyses performed on cell lysates from male human hepatoma (HepG2) and female human embryonic kidney (HEK293) we developed and characterized a specific monoclonal antibody against the native form of the male RPS4Y1 protein that can distinguish male from female cells. The availability of the RPS4Y1-targeting monoclonal antibody should facilitate the development of novel methods for the reliable isolation of male fetal cells from the maternal blood and their future use for non-invasive prenatal diagnosis of X-linked inherited disease such as hemophilia.
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21
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Bianchi DW, Khosrotehrani K, Way SS, MacKenzie TC, Bajema I, O'Donoghue K. Forever Connected: The Lifelong Biological Consequences of Fetomaternal and Maternofetal Microchimerism. Clin Chem 2020; 67:351-362. [PMID: 33417673 PMCID: PMC10072000 DOI: 10.1093/clinchem/hvaa304] [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: 08/29/2020] [Accepted: 10/28/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND Originally studied as a mechanism to understand eclampsia-related deaths during pregnancy, fetal cells in maternal blood have more recently garnered attention as a noninvasive source of fetal material for prenatal testing. In the 21st century, however, intact fetal cells have been largely supplanted by circulating cell-free placental DNA for aneuploidy screening. Instead, interest has pivoted to the ways in which fetal cells influence maternal biology. In parallel, an increasing appreciation of the consequences of maternal cells in the developing fetus has occurred. CONTENT In this review, we highlight the potential clinical applications and functional consequences of the bidirectional trafficking of intact cells between a pregnant woman and her fetus. Fetal cells play a potential role in the pathogenesis of maternal disease and tissue repair. Maternal cells play an essential role in educating the fetal immune system and as a factor in transplant acceptance. Naturally occurring maternal microchimerism is also being explored as a source of hematopoietic stem cells for transplant in fetal hematopoietic disorders. SUMMARY Future investigations in humans need to include complete pregnancy histories to understand maternal health and transplant success or failure. Animal models are useful to understand the mechanisms underlying fetal wound healing and/or repair associated with maternal injury and inflammation. The lifelong consequences of the exchange of cells between a mother and her child are profound and have many applications in development, health, and disease. This intricate exchange of genetically foreign cells creates a permanent connection that contributes to the survival of both individuals.
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Affiliation(s)
- Diana W Bianchi
- National Human Genome Research Institute and Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Kiarash Khosrotehrani
- Experimental Dermatology Group, The University of Queensland, UQ Diamantina Institute, Brisbane, Queensland, Australia
| | - Sing Sing Way
- Division of Infectious Diseases, Center for Inflammation and Tolerance, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Tippi C MacKenzie
- Center for Maternal-Fetal Precision Medicine and the Department of Surgery, University of California, San Francisco, CA, USA
| | - Ingeborg Bajema
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Keelin O'Donoghue
- Irish Centre for Maternal and Child Health (INFANT), University College Cork, Cork, Ireland
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22
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Wang Z, Cheng L, Sun Y, Wei X, Cai B, Liao L, Zhang Y, Zhao XZ. Enhanced Isolation of Fetal Nucleated Red Blood Cells by Enythrocyte-Leukocyte Hybrid Membrane-Coated Magnetic Nanoparticles for Noninvasive Pregnant Diagnostics. Anal Chem 2020; 93:1033-1042. [PMID: 33296189 DOI: 10.1021/acs.analchem.0c03933] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fetal nucleated red blood cells (fNRBCs) in maternal peripheral blood containing the whole genetic information of the fetus may serve for noninvasive pregnant diagnostics (NIPD). However, the fetal cell-based NIPD is seriously limited by the poor purity of the isolated fNRBCs. Recently, the biomimetic cell membrane-camouflaged nanoparticles containing outstanding features have been widely used to detect and isolate rare cells from the peripheral blood samples. In this work, enythrocyte (RBC) and leukocyte (WBC) membranes are fused and coated onto magnet nanoparticles and then modified with anti-CD147 to isolate fNRBCs from the maternal peripheral blood with significant efficiency (∼90%) and purity (∼87%) in simulated spiked blood samples. Further, fNRBCs were isolated and identified from a series of maternal peripheral blood samples coming from pregnant women of 11-13 gestational weeks, and different chromosomal aneuploidies were diagnosed using fNRBCs isolated from maternal blood in early pregnancy. Our strategy may offer additional opportunity to overcome the limitations of current cell-based NIPD platforms.
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Affiliation(s)
- Zixiang Wang
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lin Cheng
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yue Sun
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiaoyun Wei
- Key Laboratory of Medical Information and 3D Bioprinting of Zhejiang Province, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Bo Cai
- Research Center for Tissue Engineering and Regenerative Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Lei Liao
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yuanzhen Zhang
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xing-Zhong Zhao
- Key Laboratory of Artificial Micro- and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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23
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Jeppesen LD, Hatt L, Singh R, Ravn K, Kølvraa M, Schelde P, Uldbjerg N, Vogel I, Lildballe DL. Cell-based non-invasive prenatal diagnosis in a pregnancy at risk of cystic fibrosis. Prenat Diagn 2020; 41:234-240. [PMID: 33150588 DOI: 10.1002/pd.5861] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 11/12/2022]
Abstract
OBJECTIVE We aimed to develop cell-based NIPT for cystic fibrosis (CF) and test a pregnancy at risk of two common pathogenic variants. METHOD A pregnant woman carrying monozygotic twins opted for prenatal testing as she and her partner were heterozygote carriers of F508del (c.1521:1523del). The partner was also positive for the CFTR-related variant R117H (c.350G>A). Fetal trophoblasts from maternal blood were enriched and isolated using antibodies and a capillary-based cell-picking instrument. Multiplex PCR-based fragment length analysis was performed on the extracted fetal DNA for STR-genotyping, fetal gender and F508del variant status. The R117H variant status was tested using SNaPshot analysis. RESULTS The fetal origin of the isolated cells was verified by detection of two paternally inherited STR alleles and an Y chromosome marker, while no maternal DNA contamination was detected. The direct variant analysis detected F508del heterozygosity and the SNaPshot analysis for R117H detected only the normal allele. Thus, the results showed that the fetuses were healthy carriers of F508del, concordant with the findings of conventional prenatal testing. CONCLUSION Cell-based NIPT could accurately state the fetal variant status and distinguish fetal trophoblasts from maternal cells. In the future, cell-based NIPT may provide an accurate less invasive alternative to chorionic villous sampling.
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Affiliation(s)
- Line Dahl Jeppesen
- ARCEDI Biotech Aps, Vejle, Denmark.,Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark.,Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | | | | | | | | | - Niels Uldbjerg
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Aarhus, Denmark
| | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark.,Center for Fetal Diagnostics, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Dorte L Lildballe
- Department of Clinical Genetics, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
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24
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Chang L, Zhu X, Li R, Wu H, Chen W, Chen J, Liu H, Li S, Liu P. A novel method for noninvasive diagnosis of monogenic diseases from circulating fetal cells. Prenat Diagn 2020; 41:400-408. [PMID: 32673403 DOI: 10.1002/pd.5796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/16/2020] [Accepted: 07/13/2020] [Indexed: 01/10/2023]
Abstract
OBJECTIVE To establish a method for noninvasive fetal cell isolation from maternal blood and prenatal testing of monogenic diseases by a combination of direct sequencing and targeted NGS-based SNP haplotyping from single fetal cells. METHOD Peripheral blood of pregnant women in two families (congenital deafness and ichthyosis) was collected. After density-based separation and immunostaining with multiple biomarkers, candidate fetal cells were identified by high-throughput imagine analysis and picked up by automation. Individual fetal cells were subjected to STR-genotyping to identify their origin. Pathogenic mutations were identified by direct Sanger sequencing, and a combination of targeted NGS and SNP haplotyping using a custom panel. All the results were compared with amniotic fluid DNA. RESULTS Fetal trophoblasts were successfully harvested from maternal blood. STR-genotyping confirmed the fetal origin. Direct sequencing of pathogenic genetic mutations in fetal cells showed consistent results with amniotic fluid samples. For congenital deafness family, NGS-based SNP haplotyping also correctly identified the fetal haplotype. This single cell haplotyping method can be used to diagnose various genetic diseases. CONCLUSION We have established a method for noninvasive prenatal testing of monogenic diseases from circulating trophoblast cells. This cell-based NIPT can be further applied to the prenatal diagnosis of various monogenic diseases.
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Affiliation(s)
- Liang Chang
- Center for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynaecology, Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Xiaohui Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynaecology, Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Han Wu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Weijian Chen
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Jiucheng Chen
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Hu Liu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Shunjie Li
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynaecology, Peking University Third Hospital, Beijing, China.,National Clinical Research Center for Obstetrics and Gynaecology, Beijing, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
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25
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Non-invasive prenatal diagnosis and screening for monogenic disorders. Eur J Obstet Gynecol Reprod Biol 2020; 253:320-327. [PMID: 32907778 DOI: 10.1016/j.ejogrb.2020.08.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/20/2020] [Accepted: 08/06/2020] [Indexed: 02/07/2023]
Abstract
Cell-free fetal DNA (cffDNA) can be detected in the maternal circulation from 4 weeks gestation, and is present with cell-free maternal DNA at a level of between 5 % and 20 %. Cell-free DNA (cfDNA) can be extracted from a maternal blood sample and, although it is not possible to separate the fetal from the maternal cfDNA, it has enabled non-invasive prenatal diagnosis (NIPD) without the associated miscarriage risk that accompanies invasive testing. NIPD for monogenic diseases was first reported in 2000 and since then there have been many proof of principle studies showing how analysis of cfDNA can provide a definitive diagnosis early in pregnancy for a wide range of single gene diseases. Testing for a number of these diseases has been available in the UK National Health Service (NHS) since 2012. This review highlights the main techniques that are being used for NIPD and discusses the technical limitations of the methods, as well as the advances that are being made to overcome some of the issues. NIPD is technologically challenging for a number of reasons. Firstly, because it requires the detection of low level fetal variants in a high maternal background. For de novo and paternally-inherited variants this has been achieved through the use of techniques such as next-generation sequencing (NGS) and digital PCR to detect variants in the cffDNA that are not present in the maternal cfDNA. However, for maternally-inherited variants this is much more challenging and relies on dosage-based techniques to detect small differences in the levels of mutant and wild-type alleles. Alongside the technical advances that are making NIPD more widely available in both the public healthcare and commercial settings, it is crucial that we continue to monitor the social and ethical impact to ensure that patients are being offered safe and accurate testing.
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26
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Panchalee T, Vossaert L, Wang Q, Crovetti BR, McCombs AK, Wapner RJ, Van den Veyver IB, Beaudet AL. The effect of maternal body mass index and gestational age on circulating trophoblast yield in cell-based noninvasive prenatal testing. Prenat Diagn 2020; 40:1383-1389. [PMID: 32452065 DOI: 10.1002/pd.5755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To examine the effects of maternal body mass index (BMI) and gestational age (GA) on the number of single circulating trophoblasts (SCT). METHODS Maternal blood was collected in 20 to 40 mL. All singleton pregnant women at any gestation were recruited. Trophoblasts were recovered by immunomagnetic enrichment and stained for cytokeratin and CD45. Candidate trophoblasts were identified by fluorescence microscopy. RESULTS Blood samples were collected from 425 singleton pregnancies from April 2018 to December 2019. At least one candidate cell was identified in 88% (373/425). There was an inverse correlation between trophoblasts yield and increasing BMI (r = -0.19, P < .001). The mean ± SD number of trophoblasts/mL was 0.12 ± 0.22 in the underweight group (n = 5), 0.23 ± 0.25 in the normal weight (n = 169), 0.18 ± 0.19 in the overweight (n = 114), and 0.13 ± 0.15 in the obese (n = 109). Significantly more cells were identified in the normal weight than those in the obese (P = .001). In addition, the mean ± SD number of cells/mL was 0.21 ± 0.21 at GA of 10 to 14 weeks (n = 260), 0.14 ± 0.23 at GA ≥15 (n = 102) and 0.12 ± 0.12 at GA <10 (n = 63); P < .001. CONCLUSION The lower number of SCT was identified from the samples of women with a high BMI. Cell recovery for SCT testing seems optimal at GA of 10 to 14 weeks, but earlier and later testing is still possible.
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Affiliation(s)
- Tachjaree Panchalee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Qun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Anne K McCombs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York City, New York, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas, USA.,Department of Obstetrics and Gynecology, Texas Children's Hospital, Houston, Texas, USA
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27
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Dennis Lo YM. Screening of Fetal Chromosomal Aneuploidy by Noninvasive Prenatal Testing: From Innovation to Setting Public Health Agendas to Potential Impact on Other Fields. Clin Chem 2020; 66:25-28. [PMID: 31628140 DOI: 10.1373/clinchem.2019.303230] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/18/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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28
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Scotchman E, Chandler NJ, Mellis R, Chitty LS. Noninvasive Prenatal Diagnosis of Single-Gene Diseases: The Next Frontier. Clin Chem 2020; 66:53-60. [PMID: 31843868 DOI: 10.1373/clinchem.2019.304238] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 11/01/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Cell-free fetal DNA (cffDNA) is present in the maternal blood from around 4 weeks gestation and makes up 5%-20% of the total circulating cell-free DNA (cfDNA) in maternal plasma. Presence of cffDNA has allowed development of noninvasive prenatal diagnosis (NIPD) for single-gene disorders. This can be performed from 9 weeks gestation and offers a definitive diagnosis without the miscarriage risk associated with invasive procedures. One of the major challenges is distinguishing fetal mutations in the high background of maternal cfDNA, and research is currently focusing on the technological advances required to solve this problem. CONTENT Here, we review the literature to describe the current status of NIPD for monogenic disorders and discuss how the evolving methodologies and technologies are expected to impact this field in both the commercial and public healthcare setting. SUMMARY NIPD for single-gene diseases was first reported in 2000 and took 12 years to be approved for use in a public health service. Implementation has remained slow but is expected to increase as this testing becomes cheaper, faster, and more accurate. There are still many technical and analytical challenges ahead, and it is vital that discussions surrounding the ethical and social impact of NIPD take account of the considerations required to implement these services safely into the healthcare setting, while keeping up with the technological advances.
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Affiliation(s)
- Elizabeth Scotchman
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Natalie J Chandler
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Rhiannon Mellis
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Lyn S Chitty
- London North Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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29
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van de Looij A, Singh R, Hatt L, Ravn K, Jeppesen LD, Nicolaisen BH, Kølvraa M, Vogel I, Schelde P, Uldbjerg N. Do fetal extravillous trophoblasts circulate in maternal blood postpartum? Acta Obstet Gynecol Scand 2020; 99:751-756. [PMID: 32323316 PMCID: PMC7384123 DOI: 10.1111/aogs.13880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 02/01/2023]
Abstract
Introduction Circulating fetal extravillous trophoblasts may offer a superior alternative to cell‐free fetal DNA for noninvasive prenatal testing. Cells of fetal origin are a pure source of fetal genome; hence, unlike the cell‐free noninvasive prenatal test, the fetal cell‐based noninvasive prenatal test is not expected to be affected by maternal DNA. However, circulating fetal cells from previous pregnancies may lead to confounding results. Material and methods To study whether fetal trophoblast cells persist in maternal circulation postpartum, blood samples were collected from 11 women who had given birth to a boy, with blood sampling at 1‐3 days (W0), 4‐5 weeks (W4‐5), around 8 weeks (W8) and around 12 weeks (W12) postpartum. The existence of fetal extravillous trophoblasts was verified either by X and Y chromosome fluorescence in situ hybridization analysis or by short tandem repeat analysis. To exclude technological bias in isolating fetal cells, blood samples were also collected from 10 pregnant women between a gestational age of 10 and 14 weeks, the optimal time frame for cell‐based noninvasive prenatal test sampling. All the samples were processed according to protocols established by ARCEDI Biotech for fetal extravillous trophoblast enrichment and isolation. Results Fetal extravillous trophoblasts were found in all the 10 samples from pregnant women between a gestational age of 10 and 14 weeks. However, only 4 of 11 blood samples taken from women at 1‐3 days postpartum rendered fetal extravillous trophoblasts, and only 2 of 11 samples rendered fetal extravillous trophoblasts at 4 weeks postpartum. Conclusions In this preliminary dataset on few pregnancies, none of the samples rendered any fetal cells at or after 8 weeks postpartum, showing that cell‐based noninvasive prenatal testing based on fetal extravillous trophoblasts is unlikely to be influenced by circulating cells from previous pregnancies.
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Affiliation(s)
- Anne van de Looij
- Department of Women's Disease and Birth, Aarhus University Hospital, Aarhus, Denmark
| | | | | | | | | | | | | | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | | | - Niels Uldbjerg
- Department of Women's Disease and Birth, Aarhus University Hospital, Aarhus, Denmark
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30
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Gur O, Chang CL, Jain R, Zhong Y, Savran CA. High-purity isolation of rare single cells from blood using a tiered microchip system. PLoS One 2020; 15:e0229949. [PMID: 32182245 PMCID: PMC7077832 DOI: 10.1371/journal.pone.0229949] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 02/18/2020] [Indexed: 11/19/2022] Open
Abstract
We present a two-tiered microchip system to capture and retrieve rare cells from blood samples with high purity. The first module of the system is a high throughput microfluidic interface that is used to immunomagnetically isolate targeted rare cells from whole blood, and discard > 99.999% of the unwanted leukocytes. The second module is a microwell array that furthers the purification by magnetically guiding each cell into a separate well concurrently, and allows individual retrieval of each cell. We demonstrate the design of the system as well as its characterization by experiments using model cell lines that represent circulating fetal trophoblasts. Our results show that single cells can be retrieved with efficiencies and purities as high as 100% within 145 mins.
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Affiliation(s)
- Onur Gur
- School of Electrical Engineering, Purdue University, West Lafayette, IN, United States of America
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, United States of America
| | - Chun-Li Chang
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, United States of America
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, United States of America
| | - Rohil Jain
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, United States of America
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, United States of America
| | - Yuan Zhong
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, United States of America
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, United States of America
| | - Cagri A. Savran
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN, United States of America
- School of Mechanical Engineering, Purdue University, West Lafayette, IN, United States of America
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31
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Wapner RJ, Van den Veyver IB, Beaudet AL. Obituary: Laird Jackson. Prenat Diagn 2020. [DOI: 10.1002/pd.5647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ronald J. Wapner
- Department of Obstetrics and GynecologyColumbia University Irving Medical Center
- New York City NY
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and GynecologyBaylor College of Medicine Houston TX
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston TX
| | - Arthur L. Beaudet
- Department of Molecular and Human GeneticsBaylor College of Medicine Houston TX
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32
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Dong J, Chen JF, Smalley M, Zhao M, Ke Z, Zhu Y, Tseng HR. Nanostructured Substrates for Detection and Characterization of Circulating Rare Cells: From Materials Research to Clinical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1903663. [PMID: 31566837 PMCID: PMC6946854 DOI: 10.1002/adma.201903663] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/02/2019] [Indexed: 05/03/2023]
Abstract
Circulating rare cells in the blood are of great significance for both materials research and clinical applications. For example, circulating tumor cells (CTCs) have been demonstrated as useful biomarkers for "liquid biopsy" of the tumor. Circulating fetal nucleated cells (CFNCs) have shown potential in noninvasive prenatal diagnostics. However, it is technically challenging to detect and isolate circulating rare cells due to their extremely low abundance compared to hematologic cells. Nanostructured substrates offer a unique solution to address these challenges by providing local topographic interactions to strengthen cell adhesion and large surface areas for grafting capture agents, resulting in improved cell capture efficiency, purity, sensitivity, and reproducibility. In addition, rare-cell retrieval strategies, including stimulus-responsiveness and additive reagent-triggered release on different nanostructured substrates, allow for on-demand retrieval of the captured CTCs/CFNCs with high cell viability and molecular integrity. Several nanostructured substrate-enabled CTC/CFNC assays are observed maturing from enumeration and subclassification to molecular analyses. These can one day become powerful tools in disease diagnosis, prognostic prediction, and dynamic monitoring of therapeutic response-paving the way for personalized medical care.
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Affiliation(s)
- Jiantong Dong
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Jie-Fu Chen
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Matthew Smalley
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, P. R. China
| | - Zunfu Ke
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P. R. China
| | - Yazhen Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
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33
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Vossaert L, Wang Q, Salman R, McCombs AK, Patel V, Qu C, Mancini MA, Edwards DP, Malovannaya A, Liu P, Shaw CA, Levy B, Wapner RJ, Bi W, Breman AM, Van den Veyver IB, Beaudet AL. Validation Studies for Single Circulating Trophoblast Genetic Testing as a Form of Noninvasive Prenatal Diagnosis. Am J Hum Genet 2019; 105:1262-1273. [PMID: 31785788 PMCID: PMC6904821 DOI: 10.1016/j.ajhg.2019.11.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/03/2019] [Indexed: 02/07/2023] Open
Abstract
It has long been appreciated that genetic analysis of fetal or trophoblast cells in maternal blood could revolutionize prenatal diagnosis. We implemented a protocol for single circulating trophoblast (SCT) testing using positive selection by magnetic-activated cell sorting and single-cell low-coverage whole-genome sequencing to detect fetal aneuploidies and copy-number variants (CNVs) at ∼1 Mb resolution. In 95 validation cases, we identified on average 0.20 putative trophoblasts/mL, of which 55% were of high quality and scorable for both aneuploidy and CNVs. We emphasize the importance of analyzing individual cells because some cells are apoptotic, in S-phase, or otherwise of poor quality. When two or more high-quality trophoblast cells were available for singleton pregnancies, there was complete concordance between all trophoblasts unless there was evidence of confined placental mosaicism. SCT results were highly concordant with available clinical data from chorionic villus sampling (CVS) or amniocentesis procedures. Although determining the exact sensitivity and specificity will require more data, this study further supports the potential for SCT testing to become a diagnostic prenatal test.
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Affiliation(s)
- Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roseen Salman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne K McCombs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dean P Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Ronald J Wapner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York City, NY 10032, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy M Breman
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ignatia B Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
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A Rapid Method for Label-Free Enrichment of Rare Trophoblast Cells from Cervical Samples. Sci Rep 2019; 9:12115. [PMID: 31431640 PMCID: PMC6702343 DOI: 10.1038/s41598-019-48346-3] [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: 01/14/2019] [Accepted: 07/19/2019] [Indexed: 12/11/2022] Open
Abstract
Extravillous trophoblasts (EVTs) have the potential to provide the entire fetal genome for prenatal testing. Previous studies have demonstrated the presence of EVTs in the cervical canal and the ability to retrieve a small quantity of these cells by cervical sampling. However, these small quantities of trophoblasts are far outnumbered by the population of cervical cells in the sample, making isolation of the trophoblasts challenging. We have developed a method to enrich trophoblast cells from a cervical sample using differential settling of the cells in polystyrene wells. We tested the addition of small quantities of JEG-3 trophoblast cell line cells into clinical samples from standard Pap tests taken at 5 to 20 weeks of gestation to determine the optimal work flow. We observed that a 4 min incubation in the capture wells led to a maximum in JEG-3 cell settling on the surface (71 ± 10% of the initial amount added) with the removal of 91 ± 3% of the cervical cell population, leading to a 700% enrichment in JEG-3 cells. We hypothesized that settling of mucus in the cervical sample affects the separation. Finally, we performed a proof-of-concept study using our work flow and CyteFinder cell picking to verify enrichment and pick individual JEG-3 and trophoblast cells free of cervical cells. Ultimately, this work provides a rapid, facile, and cost-effective method for enriching native trophoblasts from cervical samples for use in subsequent non-invasive prenatal testing using methods including single cell picking.
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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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Pin-Jung C, Pai-Chi T, Zhu Y, Jen Jan Y, Smalley M, Afshar Y, Li-Ching C, Pisarska MD, Hsian-Rong T. Noninvasive Prenatal Diagnostics: Recent Developments Using Circulating Fetal Nucleated Cells. CURRENT OBSTETRICS AND GYNECOLOGY REPORTS 2019; 8:1-8. [PMID: 31565541 PMCID: PMC6764767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to highlight recent research advances in noninvasive prenatal diagnostic methods. RECENT FINDINGS Recent studies developing noninvasive prenatal diagnostic (NIPD) methods have been focused on either fetal nucleated red blood cells (fNRBCs) or circulating trophoblasts (cTBs). Enriched cTBs were successfully utilized for whole genome profiling and short tandem repeat (STR) identification to confirm feto-maternal relationship. However, further analysis of isolated fNRBCs remains confined to examining fetal cytogenetics. SUMMARY Invasive prenatal diagnostic procedures, amniocentesis and chorionic villus sampling, are the gold standard for the diagnosis of fetal chromosomal abnormalities and genetic disorders. Meanwhile, noninvasive techniques of analyzing circulating cell-free fetal DNA (cffDNA) have been limited to screening tools and are highly fragmented and confounded by maternal DNA. By detecting circulating fetal nucleated cells (CFNCs) we are able to noninvasively confirm fetal chromosomal abnormalities, truly realizing the concept of "noninvasive prenatal diagnostics". The primary technical challenge is the enrichment of the low abundance of CFNCs in maternal peripheral blood. For any cell-based NIPD method, both fetal whole genome profiling and confirmation of the feto-parental relationship are essential. This has been successfully performed using enriched and isolated cTBs, making cTB a better candidate for NIPD. cTB enumeration also correlates with abnormal fetal or placental development. On the other hand, downstream analysis of fNRBCs remains limited to examining fetal sex and aneuploidies. Furthermore, trophoblast-based NIPD via an endocervical sample is also promising because of reduced dilution from hematologic cells.
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Affiliation(s)
- Chen Pin-Jung
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, Crump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA, USA
| | - Teng Pai-Chi
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, Crump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yazhen Zhu
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, Crump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yu Jen Jan
- Urologic Oncology Program and Uro-Oncology Research Laboratories, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, Los Angeles, CA, USA
| | - Matthew Smalley
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, Crump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yalda Afshar
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Chen Li-Ching
- Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, Taiwan
| | - Margareta D. Pisarska
- Division of Maternal Fetal Medicine, Department of Obstetrics and Gynecology, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tseng Hsian-Rong
- Department of Molecular and Medical Pharmacology, California NanoSystems Institute, Crump Institute for Molecular Imaging, University of California, Los Angeles, Los Angeles, CA, USA
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A Silicon-based Coral-like Nanostructured Microfluidics to Isolate Rare Cells in Human Circulation: Validation by SK-BR-3 Cancer Cell Line and Its Utility in Circulating Fetal Nucleated Red Blood Cells. MICROMACHINES 2019; 10:mi10020132. [PMID: 30781548 PMCID: PMC6413103 DOI: 10.3390/mi10020132] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Abstract
Circulating fetal cells (CFCs) in maternal blood are rare but have a strong potential to be the target for noninvasive prenatal diagnosis (NIPD). "Cell RevealTM system" is a silicon-based microfluidic platform capable to capture rare cell populations in human circulation. The platform is recently optimized to enhance the capture efficiency and system automation. In this study, spiking tests of SK-BR-3 breast cancer cells were used for the evaluation of capture efficiency. Then, peripheral bloods from 14 pregnant women whose fetuses have evidenced non-maternal genomic markers (e.g., de novo pathogenic copy number changes) were tested for the capture of circulating fetal nucleated red blood cells (fnRBCs). Captured cells were subjected to fluorescent in situ hybridization (FISH) on chip or recovered by an automated cell picker for molecular genetic analyses. The capture rate for the spiking tests is estimated as 88.1%. For the prenatal study, 2⁻71 fnRBCs were successfully captured from 2 mL of maternal blood in all pregnant women. The captured fnRBCs were verified to be from fetal origin. Our results demonstrated that the Cell RevealTM system has a high capture efficiency and can be used for fnRBC capture that is feasible for the genetic diagnosis of fetuses without invasive procedures.
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38
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Noninvasive Prenatal Diagnostics: Recent Developments Using Circulating Fetal Nucleated Cells. CURRENT OBSTETRICS AND GYNECOLOGY REPORTS 2019. [DOI: 10.1007/s13669-019-0254-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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39
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Rezaei M, Winter M, Zander-Fox D, Whitehead C, Liebelt J, Warkiani ME, Hardy T, Thierry B. A Reappraisal of Circulating Fetal Cell Noninvasive Prenatal Testing. Trends Biotechnol 2018; 37:632-644. [PMID: 30501925 DOI: 10.1016/j.tibtech.2018.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 01/09/2023]
Abstract
New tools for higher-resolution fetal genome analysis including microarray and next-generation sequencing have revolutionized prenatal screening. This article provides commentary on this rapidly advancing field and a future perspective emphasizing circulating fetal cell (CFC) utility. Despite the tremendous technological challenges associated with their reliable and cost-effective isolation from maternal blood, CFCs have a strong potential to bridge the gap between the diagnostic sensitivity of invasive procedures and the desirable noninvasive nature of cell-free fetal DNA (cffDNA). Considering the rapid advances in both rare cell isolation and low-input DNA analysis, we argue here that CFC-based noninvasive prenatal testing is poised to be implemented clinically in the near future.
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Affiliation(s)
- Meysam Rezaei
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; Joint first authors. https://twitter.com/@CBNSSA
| | - Marnie Winter
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; Joint first authors. https://twitter.com/@CBNSSA
| | | | - Clare Whitehead
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Ultimo NSW 2007, Australia; Institute of Molecular Medicine, Sechenov First Moscow State University, Moscow 119991, Russia
| | - Tristan Hardy
- SA Pathology, Adelaide, Australia; Repromed, Dulwich, South Australia, Australia.
| | - Benjamin Thierry
- Future Industries Institute and ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Mawson Lakes Campus, Mawson Lakes, South Australia, Australia; http://bionanoengineering.com/. https://twitter.com/@CBNSSA
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40
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Lemaire CA, Liu SZ, Wilkerson CL, Ramani VC, Barzanian NA, Huang KW, Che J, Chiu MW, Vuppalapaty M, Dimmick AM, Carlo DD, Kochersperger ML, Crouse SC, Jeffrey SS, Englert RF, Hengstler S, Renier C, Sollier-Christen E. Fast and Label-Free Isolation of Circulating Tumor Cells from Blood: From a Research Microfluidic Platform to an Automated Fluidic Instrument, VTX-1 Liquid Biopsy System. SLAS Technol 2018; 23:16-29. [PMID: 29355087 DOI: 10.1177/2472630317738698] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Tumor tissue biopsies are invasive, costly, and collect a limited cell population not completely reflective of patient cancer cell diversity. Circulating tumor cells (CTCs) can be isolated from a simple blood draw and may be representative of the diverse biology from multiple tumor sites. The VTX-1 Liquid Biopsy System was designed to automate the isolation of clinically relevant CTC populations, making the CTCs available for easy analysis. We present here the transition from a cutting-edge microfluidic innovation in the lab to a commercial, automated system for isolating CTCs directly from whole blood. As the technology evolved into a commercial system, flexible polydimethylsiloxane microfluidic chips were replaced by rigid poly(methyl methacrylate) chips for a 2.2-fold increase in cell recovery. Automating the fluidic processing with the VTX-1 further improved cancer cell recovery by nearly 1.4-fold, with a 2.8-fold decrease in contaminating white blood cells and overall improved reproducibility. Two isolation protocols were optimized that favor either the cancer cell recovery (up to 71.6% recovery) or sample purity (≤100 white blood cells/mL). The VTX-1's performance was further tested with three different spiked breast or lung cancer cell lines, with 69.0% to 79.5% cell recovery. Finally, several cancer research applications are presented using the commercial VTX-1 system.
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Affiliation(s)
| | - Sean Z Liu
- 1 Vortex Biosciences Inc., Menlo Park, CA, USA
| | | | - Vishnu C Ramani
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - James Che
- 1 Vortex Biosciences Inc., Menlo Park, CA, USA
| | | | | | | | - Dino Di Carlo
- 3 Department of Bioengineering, Department of Mechanical and Aerospace Engineering, California NanoSystems Institute, and Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA
| | | | | | - Stefanie S Jeffrey
- 2 Department of Surgery, Stanford University School of Medicine, Stanford, CA, USA
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Vossaert L, Wang Q, Salman R, Zhuo X, Qu C, Henke D, Seubert R, Chow J, U'ren L, Enright B, Stilwell J, Kaldjian E, Yang Y, Shaw C, Levy B, Wapner R, Breman A, Van den Veyver I, Beaudet A. Reliable detection of subchromosomal deletions and duplications using cell-based noninvasive prenatal testing. Prenat Diagn 2018; 38:1069-1078. [PMID: 30357877 PMCID: PMC6587831 DOI: 10.1002/pd.5377] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 09/04/2018] [Accepted: 10/13/2018] [Indexed: 12/19/2022]
Abstract
Objective To gather additional data on the ability to detect subchromosomal abnormalities of various sizes in single fetal cells isolated from maternal blood, using low‐coverage shotgun next‐generation sequencing for cell‐based noninvasive prenatal testing (NIPT). Method Fetal trophoblasts were recovered from approximately 30 mL of maternal blood using maternal white blood cell depletion, density‐based cell separation, immunofluorescence staining, and high‐resolution scanning. These trophoblastic cells were picked as single cells and underwent whole genome amplification for subsequent genome‐wide copy number analysis and genotyping to confirm the fetal origin of the cells. Results Applying our fetal cell isolation method to a series of 125 maternal blood samples, we detected on average 4.17 putative fetal cells/sample. The series included 15 cases with clinically diagnosed fetal aneuploidies and five cases with subchromosomal abnormalities. This method was capable of detecting findings that were 1 to 2 Mb in size, and all were concordant with the microarray or karyotype data obtained on a fetal sample. A minority of fetal cells showed evidence of genome degradation likely related to apoptosis. Conclusion We demonstrate that this cell‐based NIPT method has the capacity to reliably diagnose fetal chromosomal abnormalities down to 1 to 2 Mb in size. What is already known about this topic?
Fetal trophoblastic cells can be isolated from maternal blood and be used for the detection of fetal aneuploidies and copy number variants. The data on the detection of subchromosomal deletions and duplications is currently limited.
What does this study add?
Cell‐based NIPT can be used for the detection of copy number abnormalities of greater than or equal to 1 Mb in the fetus by low‐coverage next‐generation sequencing after single cell whole genome amplification. Data are provided here for five cases in which different subchromosomal deletions and duplications ranging from 1.2 to 18.9 Mb were detected in single cells.
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Affiliation(s)
- Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Qun Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Roseen Salman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Xinming Zhuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chunjing Qu
- Baylor Genetics Laboratory, Houston, TX, USA
| | - David Henke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | | | | | - Jackie Stilwell
- RareCyte Inc., Seattle, WA, USA.,Immune Design, Seattle, WA, USA
| | | | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Brynn Levy
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ignatia Van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Arthur Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Shinde P, Mohan L, Kumar A, Dey K, Maddi A, Patananan AN, Tseng FG, Chang HY, Nagai M, Santra TS. Current Trends of Microfluidic Single-Cell Technologies. Int J Mol Sci 2018; 19:E3143. [PMID: 30322072 PMCID: PMC6213733 DOI: 10.3390/ijms19103143] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023] Open
Abstract
The investigation of human disease mechanisms is difficult due to the heterogeneity in gene expression and the physiological state of cells in a given population. In comparison to bulk cell measurements, single-cell measurement technologies can provide a better understanding of the interactions among molecules, organelles, cells, and the microenvironment, which can aid in the development of therapeutics and diagnostic tools. In recent years, single-cell technologies have become increasingly robust and accessible, although limitations exist. In this review, we describe the recent advances in single-cell technologies and their applications in single-cell manipulation, diagnosis, and therapeutics development.
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Affiliation(s)
- Pallavi Shinde
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Loganathan Mohan
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Amogh Kumar
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Koyel Dey
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Anjali Maddi
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
| | - Alexander N Patananan
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095, USA.
| | - Fan-Gang Tseng
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu City 30071, Taiwan.
| | - Hwan-You Chang
- Department of Medical Science, National Tsing Hua University, Hsinchu City 30071, Taiwan.
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, Toyohashi 441-8580, Japan.
| | - Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India.
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Kaldjian EP, Ramirez AB, Sun Y, Campton DE, Werbin JL, Varshavskaya P, Quarre S, George T, Madan A, Blau CA, Seubert R. The RareCyte® platform for next-generation analysis of circulating tumor cells. Cytometry A 2018; 93:1220-1225. [PMID: 30277660 PMCID: PMC6586054 DOI: 10.1002/cyto.a.23619] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/22/2018] [Accepted: 08/31/2018] [Indexed: 01/09/2023]
Abstract
Circulating tumor cells (CTCs) can reliably be identified in cancer patients and are associated with clinical outcome. Next-generation "liquid biopsy" technologies will expand CTC diagnostic investigation to include phenotypic characterization and single-cell molecular analysis. We describe here a rare cell analysis platform designed to comprehensively collect and identify CTCs, enable multi-parameter assessment of individual CTCs, and retrieve single cells for molecular analysis. The platform has the following four integrated components: 1) density-based separation of the CTC-containing blood fraction and sample deposition onto microscope slides; 2) automated multiparameter fluorescence staining; 3) image scanning, analysis, and review; and 4) mechanical CTC retrieval. The open platform utilizes six fluorescence channels, of which four channels are used to identify CTC and two channels are available for investigational biomarkers; a prototype assay that allows three investigational biomarker channels has been developed. Single-cell retrieval from fixed slides is compatible with whole genome amplification methods for genomic analysis. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
| | | | - Yao Sun
- RareCyte, Inc., Seattle, Washington, USA
| | | | | | | | | | - Tad George
- RareCyte, Inc., Seattle, Washington, USA
| | - Anup Madan
- Covance Genomics, Redmond, Washington, USA
| | - C Anthony Blau
- Center for Cancer Innovation, University of Washington, Seattle, Washington, USA
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Abstract
Prenatal whole exome sequencing (WES) has the potential to increase the ability to provide more diagnostic capabilities in fetuses with sonographic abnormalities, which would then improve the ability to counsel families. It is also often the first step in improving the path toward informed diagnosis and treatment, which is especially important in the era of advancing in utero fetal therapy. This article discusses the current literature regarding prenatal WES, clinical indications for WES, challenges with interpretation/counseling (variants of unknown significance), research priorities, ethical issues, and potential future advances.
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Affiliation(s)
- Angie C Jelin
- Division of Maternal-Fetal Medicine, Department of Gynecology and Obstetrics, Johns Hopkins School of Medicine, 500 North Wolfe Street, Phipps 222, Baltimore, MD 21218, USA
| | - Neeta Vora
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, 3010 Old Clinic Building/Cb# 7516, Chapel Hill, NC 27599, USA.
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45
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Mellis R, Chandler N, Chitty LS. Next-generation sequencing and the impact on prenatal diagnosis. Expert Rev Mol Diagn 2018; 18:689-699. [PMID: 29962246 DOI: 10.1080/14737159.2018.1493924] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION The advent of affordable and rapid next-generation sequencing has been transformative for prenatal diagnosis. Sequencing of cell-free DNA in maternal plasma has enabled the development of not only a highly sensitive screening test for fetal aneuploidies, but now definitive noninvasive prenatal diagnosis for monogenic disorders at an early gestation. Sequencing of fetal exomes offers broad diagnostic capability for pregnancies with unexpected fetal anomalies, improving the yield and accuracy of diagnoses and allowing better counseling for parents. The challenge now is to translate these approaches into mainstream use in the clinic. Areas covered: Here, the authors review the current literature to describe the technologies available and how these have evolved. The opportunities and challenges at hand, including considerations for service delivery, counseling, and development of ethical guidelines, are discussed. Expert commentary: As technology continues to advance, future developments may be toward noninvasive fetal whole exome or whole genome sequencing and a universal method for noninvasive prenatal diagnosis without the need to sequence both parents or an affected proband. Expansion of cell-free fetal DNA analysis to include the transcriptome and the methylome is likely to yield clinical benefits for monitoring other pregnancy-related pathologies such as preeclampsia and intrauterine growth restriction.
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Affiliation(s)
- Rhiannon Mellis
- a Genetics and Genomic Medicine , Great Ormond Street NHS Foundation Trust , London , UK
| | - Natalie Chandler
- b North Thames NHS Regional Genetics Service , Great Ormond Street NHS Foundation Trust , London , UK
| | - Lyn S Chitty
- a Genetics and Genomic Medicine , Great Ormond Street NHS Foundation Trust , London , UK.,c Genetics and Genomic Medicine , UCL Great Ormond Street Institute of Child Health , London , UK
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Marie R, Pødenphant M, Koprowska K, Bærlocher L, Vulders RCM, Wilding J, Ashley N, McGowan SJ, van Strijp D, van Hemert F, Olesen T, Agersnap N, Bilenberg B, Sabatel C, Schira J, Kristensen A, Bodmer W, van der Zaag PJ, Mir KU. Sequencing of human genomes extracted from single cancer cells isolated in a valveless microfluidic device. LAB ON A CHIP 2018; 18:1891-1902. [PMID: 29873383 DOI: 10.1039/c8lc00169c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sequencing the genomes of individual cells enables the direct determination of genetic heterogeneity amongst cells within a population. We have developed an injection-moulded valveless microfluidic device in which single cells from colorectal cancer derived cell lines (LS174T, LS180 and RKO) and fresh colorectal tumors have been individually trapped, their genomes extracted and prepared for sequencing using multiple displacement amplification (MDA). Ninety nine percent of the DNA sequences obtained mapped to a reference human genome, indicating that there was effectively no contamination of these samples from non-human sources. In addition, most of the reads are correctly paired, with a low percentage of singletons (0.17 ± 0.06%) and we obtain genome coverages approaching 90%. To achieve this high quality, our device design and process shows that amplification can be conducted in microliter volumes as long as the lysis is in sub-nanoliter volumes. Our data thus demonstrates that high quality whole genome sequencing of single cells can be achieved using a relatively simple, inexpensive and scalable device. Detection of genetic heterogeneity at the single cell level, as we have demonstrated for freshly obtained single cancer cells, could soon become available as a clinical tool to precisely match treatment with the properties of a patient's own tumor.
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Affiliation(s)
- Rodolphe Marie
- Department for Micro and Nanotechnology, Technical University of Denmark, Ørsteds Plads Building 345C, 2800 Kgs. Lyngby, Denmark.
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Stilwell JL, Varshavskaya P, Werbin JL, Nordberg JJ, Ramirez AB, Quarre S, Tzucker J, Chow J, Enright B, Kaldjian EP. RareCyte ® CTC Analysis Step 3: Using the CytePicker ® Module for Individual Cell Retrieval and Subsequent Whole Genome Amplification of Circulating Tumor Cells for Genomic Analysis. Methods Mol Biol 2018; 1634:181-192. [PMID: 28819851 DOI: 10.1007/978-1-4939-7144-2_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The CytePicker module built into the RareCyte CyteFinder instrument allows researchers to easily retrieve individual cells from microscope slides for genomic analyses, including array CGH, targeted sequencing, and next-generation sequencing. Here, we describe the semiautomated retrieval of CTCs from the blood processed by AccuCyte (see Chapter 13) and amplification of genomic DNA so that molecular analysis can be performed.
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Affiliation(s)
| | | | | | | | | | - Steve Quarre
- RareCyte, Inc., 312 Dexter Ave. N, Seattle, WA, 98109, USA
| | - Jay Tzucker
- RareCyte, Inc., 312 Dexter Ave. N, Seattle, WA, 98109, USA
| | - Jennifer Chow
- RareCyte, Inc., 312 Dexter Ave. N, Seattle, WA, 98109, USA
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Beyond screening for chromosomal abnormalities: Advances in non-invasive diagnosis of single gene disorders and fetal exome sequencing. Semin Fetal Neonatal Med 2018; 23:94-101. [PMID: 29305293 DOI: 10.1016/j.siny.2017.12.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Emerging genomic technologies, largely based around next generation sequencing (NGS), are offering new promise for safer prenatal genetic diagnosis. These innovative approaches will improve screening for fetal aneuploidy, allow definitive non-invasive prenatal diagnosis (NIPD) of single gene disorders at an early gestational stage without the need for invasive testing, and improve our ability to detect monogenic disorders as the aetiology of fetal abnormalities. This presents clinicians and scientists with novel challenges as well as opportunities. In addition, the transformation of prenatal genetic testing arising from the introduction of whole genome, exome and targeted NGS produces unprecedented volumes of data requiring complex analysis and interpretation. Now translating these technologies to the clinic has become the goal of clinical genomics, transforming modern healthcare and personalized medicine. The achievement of this goal requires the most progressive technological tools for rapid high-throughput data generation at an affordable cost. Furthermore, as larger proportions of patients with genetic disease are identified we must be ready to offer appropriate genetic counselling to families and potential parents. In addition, the identification of novel treatment targets will continue to be explored, which is likely to introduce ethical considerations, particularly if genome editing techniques are included in these targeted treatments and transferred into mainstream personalized healthcare. Here we review the impact of NGS technology to analyse cell-free DNA (cfDNA) in maternal plasma to deliver NIPD for monogenic disorders and allow more comprehensive investigation of the abnormal fetus through the use of exome sequencing.
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Deleye L, Vander Plaetsen AS, Weymaere J, Deforce D, Van Nieuwerburgh F. Short Tandem Repeat analysis after Whole Genome Amplification of single B-lymphoblastoid cells. Sci Rep 2018; 8:1255. [PMID: 29352241 PMCID: PMC5775416 DOI: 10.1038/s41598-018-19509-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 01/02/2018] [Indexed: 11/30/2022] Open
Abstract
To allow multiple genetic analyses on a single cell, whole genome amplification (WGA) is required. Unfortunately, studies comparing different WGA methods for downstream human identification Short Tandem Repeat (STR) analysis remain absent. Therefore, the aim of this work was to assess the performance of four commercially available WGA kits for downstream human identification STR profiling on a B-lymphoblastoid cell line. The performance was assessed using an input of one or three micromanipulated cells. REPLI-g showed a very low dropout rate, as it was the only WGA method in this study that could provide a complete STR profile in some of its samples. Although Ampli1, DOPlify and PicoPLEX did not detect all selected STR markers, they seem suitable for genetic identification in single-cell applications.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Ann-Sophie Vander Plaetsen
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Jana Weymaere
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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Prenatal Genetic Testing and Screening. CHIMERISM 2018. [DOI: 10.1007/978-3-319-89866-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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