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Ye Y, Li W, Wang G, Zhan L, Lin J, Li T, Zhang J. Identification of a novel COL10A1: c.1952 G>T variant in a family with Schmid metaphyseal chondrodysplasia and development of a noninvasive prenatal testing method. Mol Genet Genomic Med 2021; 9:e1758. [PMID: 34423584 PMCID: PMC8580095 DOI: 10.1002/mgg3.1758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/12/2021] [Accepted: 07/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background The collagen alpha‐1(X) chain gene (COL10A1) is a known causative gene for Schmid metaphyseal chondrodysplasia (SMCD). This study clinically examined a Chinese family (n = 42) for SMCD and inheritance pattern. Fifteen individuals were diagnosed with SMCD based on characteristic skeletal phenotypes with autosomal dominant inheritance mode. Methods Four clinically diagnosed patients and three healthy relatives were selected for subsequent genetic tests. Trio‐whole exome sequencing (Trio‐WES) followed by Sanger sequencing and familial co‐segregation analysis were performed to identify SMCD‐associated variants. Results COL10A1 (NM_000493.4):c.1952 G>T(p.Trp651Leu) variant was detected only in the four patients and not in the three healthy relatives. The variant was evaluated as “likely pathogenic” according to the American College of Medical Genetics and Genomics variation classification guidelines with evidence of PM2, PM5, PP1, and PP3. To test the presence of the target variant in proband's fetal offspring, we developed a noninvasive prenatal testing method by extracting cell‐free fetal DNA in maternal plasma followed by high‐depth sequencing. The variant was also detected in the fetus and later confirmed by amniocentesis. Conclusion We identified a new disease‐causing variant in COL10A1. Cell‐free fetal DNA in maternal peripheral blood can be used as the rapid and noninvasive prenatal diagnostic method to detect the pathogenic/or likely pathogenic variant.
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Affiliation(s)
- Yanchou Ye
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital Sun Yat-sen University, Shenzhen, China
| | - Weihao Li
- Reproductive Medicine Center, The Seventh Affiliated Hospital Sun Yat-sen University, Shenzhen, China
| | - Guan Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Longsheng Zhan
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Junwei Lin
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Tian Li
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital Sun Yat-sen University, Shenzhen, China
| | - Jun Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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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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Löwy I. Non-invasive prenatal testing: A diagnostic innovation shaped by commercial interests and the regulation conundrum. Soc Sci Med 2020; 304:113064. [PMID: 32534823 DOI: 10.1016/j.socscimed.2020.113064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/01/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022]
Abstract
Non-invasive prenatal testing (NIPT) is grounded in the analysis of free circulating fetal DNA (cfDNA) in pregnant women's blood. The rolling out of this screening method was in large part driven by commercial firms, which hoped to reach a huge potential market by offering a test that was expected to be risk-free, reliable, inexpensive, and able to detect a wide range of genetic traits of the future child. To date, most predictions about the scope and uses of NIPT have not materialized: in 2020 NIPT detects only a limited number of genetic anomalies, while results have to be confirmed by amniocentesis. NIPT has become a commercial success. Nevertheless the implementation of NIPT has tended to diverge across different national settings. In countries that already have state-sponsored screening for Down risk, NIPT has been offered by the state health insurance to women defined as "high risk", using a variant of the test that detects only three autosomal aneuploidies: trisomy 21, 13 and 18. These countries effectively regulate the supply of NIPT on grounds of cost-effectiveness and reliability. In countries without state-sponsored screening for Down risk, in contrast, multiple versions of NIPT covering a wider range of birth defects are commonly available on the free market, and purchased by women at low as well as high risk of having an affected child. Market-based healthcare systems tend to present women who can afford to pay for NIPT with a largely unregulated choice of technologies - though reimbursement rules imposed by private insurance providers may serve in effect to regulate use by those consumers who cannot afford to pay for tests from their own pockets. This regulatory divergence is shaped by the presence or absence of prior state-sponsored screening programs for Down risk.
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Affiliation(s)
- Ilana Löwy
- Cermes3 : INSERM, U 988, CNRS, UMR 8211, EHESS and Paris Descartes University, France.
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Extracellular RNA in a single droplet of human serum reflects physiologic and disease states. Proc Natl Acad Sci U S A 2019; 116:19200-19208. [PMID: 31481608 PMCID: PMC6754586 DOI: 10.1073/pnas.1908252116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Extracellular RNAs (exRNAs) are present in human serum. It remains unclear to what extent these circulating exRNAs may reflect human physiologic and disease states. Here, we developed SILVER-seq (Small Input Liquid Volume Extracellular RNA Sequencing) to efficiently sequence both integral and fragmented exRNAs from a small droplet (5 μL to 7 μL) of liquid biopsy. We calibrated SILVER-seq in reference to other RNA sequencing methods based on milliliters of input serum and quantified droplet-to-droplet and donor-to-donor variations. We carried out SILVER-seq on more than 150 serum droplets from male and female donors ranging from 18 y to 48 y of age. SILVER-seq detected exRNAs from more than a quarter of the human genes, including small RNAs and fragments of mRNAs and long noncoding RNAs (lncRNAs). The detected exRNAs included those derived from genes with tissue (e.g., brain)-specific expression. The exRNA expression levels separated the male and female samples and were correlated with chronological age. Noncancer and breast cancer donors exhibited pronounced differences, whereas donors with or without cancer recurrence exhibited moderate differences in exRNA expression patterns. Even without using differentially expressed exRNAs as features, nearly all cancer and noncancer samples and a large portion of the recurrence and nonrecurrence samples could be correctly classified by exRNA expression values. These data suggest the potential of using exRNAs in a single droplet of serum for liquid biopsy-based diagnostics.
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Cree IA, Uttley L, Buckley Woods H, Kikuchi H, Reiman A, Harnan S, Whiteman BL, Philips ST, Messenger M, Cox A, Teare D, Sheils O, Shaw J. The evidence base for circulating tumour DNA blood-based biomarkers for the early detection of cancer: a systematic mapping review. BMC Cancer 2017; 17:697. [PMID: 29061138 PMCID: PMC5654013 DOI: 10.1186/s12885-017-3693-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 10/18/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The presence of circulating cell-free DNA from tumours in blood (ctDNA) is of major importance to those interested in early cancer detection, as well as to those wishing to monitor tumour progression or diagnose the presence of activating mutations to guide treatment. In 2014, the UK Early Cancer Detection Consortium undertook a systematic mapping review of the literature to identify blood-based biomarkers with potential for the development of a non-invasive blood test for cancer screening, and which identified this as a major area of interest. This review builds on the mapping review to expand the ctDNA dataset to examine the best options for the detection of multiple cancer types. METHODS The original mapping review was based on comprehensive searches of the electronic databases Medline, Embase, CINAHL, the Cochrane library, and Biosis to obtain relevant literature on blood-based biomarkers for cancer detection in humans (PROSPERO no. CRD42014010827). The abstracts for each paper were reviewed to determine whether validation data were reported, and then examined in full. Publications concentrating on monitoring of disease burden or mutations were excluded. RESULTS The search identified 94 ctDNA studies meeting the criteria for review. All but 5 studies examined one cancer type, with breast, colorectal and lung cancers representing 60% of studies. The size and design of the studies varied widely. Controls were included in 77% of publications. The largest study included 640 patients, but the median study size was 65 cases and 35 controls, and the bulk of studies (71%) included less than 100 patients. Studies either estimated cfDNA levels non-specifically or tested for cancer-specific mutations or methylation changes (the majority using PCR-based methods). CONCLUSION We have systematically reviewed ctDNA blood biomarkers for the early detection of cancer. Pre-analytical, analytical, and post-analytical considerations were identified which need to be addressed before such biomarkers enter clinical practice. The value of small studies with no comparison between methods, or even the inclusion of controls is highly questionable, and larger validation studies will be required before such methods can be considered for early cancer detection.
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Affiliation(s)
- Ian A. Cree
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
| | - Lesley Uttley
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Helen Buckley Woods
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Hugh Kikuchi
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
| | - Anne Reiman
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
| | - Susan Harnan
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Becky L. Whiteman
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
| | | | - Michael Messenger
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
| | - Angela Cox
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
| | - Dawn Teare
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
| | - Orla Sheils
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
| | - Jacqui Shaw
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
| | - For the UK Early Cancer Detection Consortium
- WHO Classification of Tumours Group, International Agency for Research on Cancer (IARC), World Health Organization, 150 Cours Albert Thomas, 69372 Lyon, CEDEX 08 France
- Faculty of Health and Life Sciences, Coventry University, Priory Street, Coventry, CV1 5FB UK
- Institute of Ophthalmology, University College London, EC1V 9EL, London, UK
- The School of Health and Related Research, The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA UK
- Department of Pathology, University Hospitals Coventry and Warwickshire, Coventry, CV2 2DX UK
- London North West Healthcare NHS Trust, Northwick Park Hospital, Watford Road, Harrow, HA1 3UJ UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL UK
- Leeds Centre for Personalised Medicine and Health, University of Leeds and NIHR Diagnostic Evidence Co-Operative Leeds, Leeds Teaching Hospitals NHS Trust, Leeds, LS9 7TF UK
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield, S10 2RX UK
- Sir Patrick Dun Research Laboratory, Central Pathology Laboratory, St James’s Hospital & Trinity College Dublin, Dublin 8, Ireland
- University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX UK
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Oepkes D, Page-Christiaens GCL, Bax CJ, Bekker MN, Bilardo CM, Boon EMJ, Schuring-Blom GH, Coumans ABC, Faas BH, Galjaard RJH, Go AT, Henneman L, Macville MVE, Pajkrt E, Suijkerbuijk RF, Huijsdens-van Amsterdam K, Van Opstal D, Verweij EJJ, Weiss MM, Sistermans EA. Trial by Dutch laboratories for evaluation of non-invasive prenatal testing. Part I-clinical impact. Prenat Diagn 2016; 36:1083-1090. [PMID: 27750376 PMCID: PMC5214231 DOI: 10.1002/pd.4945] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 12/15/2022]
Abstract
Objective To evaluate the clinical impact of nationwide implementation of genome‐wide non‐invasive prenatal testing (NIPT) in pregnancies at increased risk for fetal trisomies 21, 18 and 13 (TRIDENT study). Method Women with elevated risk based on first trimester combined testing (FCT ≥ 1:200) or medical history, not advanced maternal age alone, were offered NIPT as contingent screening test, performed by Dutch University Medical laboratories. We analyzed uptake, test performance, redraw/failure rate, turn‐around time and pregnancy outcome. Results Between 1 April and 1 September 2014, 1413/23 232 (6%) women received a high‐risk FCT result. Of these, 1211 (85.7%) chose NIPT. One hundred seventy‐nine women had NIPT based on medical history. In total, 1386/1390 (99.7%) women received a result, 6 (0.4%) after redraw. Mean turn‐around time was 14 days. Follow‐up was available in 1376 (99.0%) pregnancies. NIPT correctly predicted 37/38 (97.4%) trisomies 21, 18 or 13 (29/30, 4/4 and 4/4 respectively); 5/1376 (0.4%) cases proved to be false positives: trisomies 21 (n = 2), 18 (n = 1) and 13 (n = 2). Estimated reduction in invasive testing was 62%. Conclusion Introduction of NIPT in the Dutch National healthcare‐funded Prenatal Screening Program resulted in high uptake and a vast reduction of invasive testing. Our study supports offering NIPT to pregnant women at increased risk for fetal trisomy. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. © 2016 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic?Non‐invasive prenatal testing (NIPT) for trisomies 21, 18 and 13 is mainly offered in a commercial setting. Offering NIPT to pregnant women at increased risk for fetal trisomy leads to a reduction in invasive testing.
What does this study adds?NIPT implemented as a contingent test under the umbrella of a national health authority‐supported fetal trisomy screening program facilitates optimal counseling with close to 100% follow‐up, results in 86% uptake and confirms a major reduction of invasive tests.
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Affiliation(s)
- Dick Oepkes
- Department of Obstetrics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Caroline J Bax
- Department of Obstetrics and Gynaecology, VU University Medical Center, Amsterdam, The Netherlands
| | - Mireille N Bekker
- Department of Obstetrics and Gynaecology, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Obstetrics and Gynaecology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Catia M Bilardo
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Elles M J Boon
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Audrey B C Coumans
- Department of Obstetrics and Gynaecology, Maastricht UMC+, Maastricht, The Netherlands
| | - Brigitte H Faas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Attie T Go
- Department of Obstetrics and Gynecology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lidewij Henneman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Merryn V E Macville
- Department of Clinical Genetics, Maastricht UMC+, Maastricht, The Netherlands
| | - Eva Pajkrt
- Department of Obstetrics and Gynaecology, Academic Medical Centre, Amsterdam, The Netherlands
| | - Ron F Suijkerbuijk
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Diane Van Opstal
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - E J Joanne Verweij
- Department of Obstetrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
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Sur Chowdhury C, Hahn S, Hasler P, Hoesli I, Lapaire O, Giaglis S. Elevated Levels of Total Cell-Free DNA in Maternal Serum Samples Arise from the Generation of Neutrophil Extracellular Traps. Fetal Diagn Ther 2016; 40:263-267. [PMID: 26998969 DOI: 10.1159/000444853] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/16/2016] [Indexed: 11/19/2022]
Abstract
INTRODUCTION The analysis of cell-free DNA from maternal blood samples has facilitated the noninvasive detection of fetal aneuploidies or hereditary Mendelian disorders. In this context, previous studies have indicated that the pool of cell-free DNA is greater in maternal serum than in plasma samples, necessitating optimized collection and storage protocols. As the source of this increased amount of cell-free DNA is not clear, we have now examined whether neutrophil extracellular traps (NETs) contribute to this material. MATERIAL AND METHODS Serum samples were collected in all three trimesters of normal healthy pregnant women, and at term from cases with manifest preeclampsia. The presence of NET-derived material was demonstrated by the detection of cell-free DNA fragments complexed to neutrophil granular proteins (i.e. myeloperoxidase). RESULTS Our data indicate that NET-derived cell-free DNA/myeloperoxidase complexes were greater in serum from normal pregnant women than in normal matching nonpregnant controls. This neutrophil chromosomal material increased incrementally throughout gestation and was most pronounced in cases with preeclampsia. DISCUSSION By detecting increased levels of cell-free DNA/myeloperoxidase complexes in maternal serum samples, our data indicate that a significant proportion of this material is derived from the generation of NETs.
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Hahn S, Lapaire O, Than NG. Biomarker development for presymptomatic molecular diagnosis of preeclampsia: feasible, useful or even unnecessary? Expert Rev Mol Diagn 2015; 15:617-29. [PMID: 25774007 PMCID: PMC4673513 DOI: 10.1586/14737159.2015.1025757] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The past decade saw the advent of a number of promising biomarkers to detect pregnancies at risk for preeclampsia (PE), the foremost being those associated with an imbalance of angiogenic factors. In late pregnancy, these are useful for the detection of imminent cases of PE, while earlier they were more predictive for early- than late-onset PE. This suggests that there may be fundamental differences between the underlying pathology of these two PE forms. Therefore, it is possible that such a biological premise may limit the development of biomarkers that will permit the efficacious detection of both early- and late-onset PE via an analysis of first-trimester maternal blood samples. Consequently, a significant increase in our understanding of the underlying pathology of PE, using a variety of approaches ranging from systems biology to animal models, will be necessary in order to overcome this obstacle.
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Affiliation(s)
- Sinuhe Hahn
- Laboratory for Prenatal Medicine, Department of Biomedicine, University Hospital Basel, Hebelstrasse 20, CH 4031 Basel, Switzerland
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