1
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Yang Y, Song T, Liu S, Liu Z, Wang X, Li Y, Liu D. Circle-map profiling of extrachromosomal circular DNA as diagnostic biomarkers for lung cancer. PRECISION CLINICAL MEDICINE 2024; 7:pbae006. [PMID: 38616889 PMCID: PMC11015151 DOI: 10.1093/pcmedi/pbae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/11/2024] [Indexed: 04/16/2024] Open
Affiliation(s)
- Yongfeng Yang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tingting Song
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Sha Liu
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiqiang Liu
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuehui Wang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yi Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Dan Liu
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
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2
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Nishio K, Sakai K, Nishio M, Seto T, Visseren-Grul C, Carlsen M, Matsui T, Enatsu S, Nakagawa K. Impact of ramucirumab plus erlotinib on circulating cell-free DNA from patients with untreated metastatic non-small cell lung cancer with EGFR-activating mutations (RELAY phase 3 randomized study). Transl Lung Cancer Res 2023; 12:1702-1716. [PMID: 37691865 PMCID: PMC10483085 DOI: 10.21037/tlcr-22-736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 07/20/2023] [Indexed: 09/12/2023]
Abstract
Background An exploratory, proof-of-concept, liquid biopsy addendum to examine biomarkers within cell-free DNA (cfDNA) in the RELAY phase 3, randomized, double-blind, placebo-controlled study was conducted. RELAY showed improved progression-free survival (PFS) with ramucirumab (RAM), a human immunoglobulin G1 vascular endothelial growth factor receptor 2 antagonist, plus erlotinib (ERL), a tyrosine kinase inhibitor, compared with placebo (PL) plus ERL. Methods Treatment-naïve patients with endothelial growth factor receptor (EGFR)-mutated metastatic non-small cell lung cancer were randomized (1:1) to RAM + ERL or PL + ERL. Plasma samples were collected at baseline, on treatment, and at 30-day post-study treatment discontinuation follow-up. Baseline and treatment-emergent gene alterations and EGFR-activating mutation allele counts were investigated by next-generation sequencing (NGS) and droplet digital polymerase chain reaction (ddPCR), respectively. cfDNA concentration and fragment size were evaluated by real-time polymerase chain reaction and the BioAnalyzer. Patients with a valid baseline plasma sample were included (70 RAM + ERL, 61 PL + ERL). Results TP53 mutation was the most frequently co-occurring baseline gene alteration (43%). Post-study treatment discontinuation EGFR T790M mutation rates were 54.5% (6/11) and 41.2% (7/17) by ddPCR, and 22.2% (2/9) and 29.4% (5/17) by NGS, in the RAM + ERL and PL + ERL arms, respectively. EGFR-activating mutation allele count decreased at Cycle 4 in both treatment arms and was sustained at follow-up with RAM + ERL. PFS improved for patients with no detectable EGFR-activating mutation at Cycle 4 vs. those with detectable EGFR-activating mutation. Total cfDNA concentration increased from baseline at Cycle 4 and through to follow-up with RAM + ERL. cfDNA fragment size was similar between treatment arms at baseline [mean (standard deviation) base pairs: RAM + ERL, 173.4 (2.6); PL + ERL, 172.9 (3.2)] and was shorter at Cycle 4 with RAM + ERL vs. PL + ERL [169.5 (2.8) vs. 174.1 (3.3), respectively; P<0.0001]. Baseline vs. Cycle 4 paired analysis showed a decrease in cfDNA fragment size for 84% (48/57) and 23% (11/47) of patient samples in the RAM + ERL and PL + ERL arms, respectively. Conclusions EGFR-activating mutation allele count was suppressed, total cfDNA concentration increased, and short fragment-sized cfDNA increased with RAM + ERL, suggesting the additional anti-tumor effect of RAM may contribute to the PFS benefit observed in RELAY with RAM + ERL vs. PL + ERL. Trial Registration ClinicalTrials.gov; identifier: NCT02411448.
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Affiliation(s)
- Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takashi Seto
- National Hospital Organization Kyushu Cancer Center, Fukuoka, Japan
| | | | | | | | | | - Kazuhiko Nakagawa
- Department of Medical Oncology, Kindai University Faculty of Medicine, Osaka, Japan
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3
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D'Ippolito S, Longo G, Orteschi D, Busnelli A, Di Simone N, Pulcinelli E, Schettini G, Scambia G, Zollino M. Investigating the "Fetal Side" in Recurrent Pregnancy Loss: Reliability of Cell-Free DNA Testing in Detecting Chromosomal Abnormalities of Miscarriage Tissue. J Clin Med 2023; 12:3898. [PMID: 37373593 DOI: 10.3390/jcm12123898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/27/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
(1) Background: The aim of our study is to evaluate whether cell-free DNA testing can overlap the genetic testing of miscarriage tissue in women with early pregnancy loss (EPL) and length of recurrent pregnancy loss (RPL); (2) Methods: We conducted a prospective cohort study at the Pregnancy Loss Unit of the Fondazione Policlinico Universitario A. Gemelli (IRCCS), Rome, Italy between May 2021 and March 2022. We included women with EPL and length of RPL. Gestational age was >9 weeks + 2 days and <12 weeks + 0 days of gestation corresponding to a crown rump length measurement of >25 and <54 mm. Women underwent both dilation and curettage for the collection of miscarriage tissue and for blood sample collection. Chromosomal microarray analysis (CMA) on miscarriage tissues was performed by oligo-nucleotide- and single nucleotide polymorphisms (SNP)-based comparative genomic hybridization (CGH+SNP). Maternal blood samples were analyzed by Illumina VeriSeq non-invasive prenatal testing (NIPT) to evaluate the cell-free fetal DNA (cfDNA) and the corresponding fetal fraction and the presence of genetic abnormalities; (3) Results: CMA on miscarriage tissues revealed chromosome aneuploidies in 6/10 cases (60%), consisting of trisomy 21 (5 cases) and monosomy X (one case). cfDNA analysis was able to identify all cases of trisomy 21. It failed to detect monosomy X. A large 7p14.1p12.2 deletion concomitant to trisomy 21 was, in one case, detected by cfDNA analysis but it was not confirmed by CMA on miscarriage tissue. (4) Conclusions: cfDNA largely reproduces the chromosomal abnormalities underlying spontaneous miscarriages. However, diagnostic sensitivity of cfDNA analysis is lower with respect to the CMA of miscarriage tissues. In considering the limitations when obtaining biological samples from aborted fetuses suitable for CMA or standard chromosome analysis, cfDNA analysis is a useful, although not exhaustive, tool for the chromosome diagnosis of both early and recurrent pregnancy loss.
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Affiliation(s)
- Silvia D'Ippolito
- Dipartimento della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
| | - Giuliana Longo
- BioRep Srl, Centro di Risorse Biologiche, Sapio Group, 20900 Milan, Italy
| | - Daniela Orteschi
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Andrea Busnelli
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | - Nicoletta Di Simone
- Department of Biomedical Sciences, Humanitas University, 20072 Milan, Italy
- IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy
| | | | | | - Giovanni Scambia
- Dipartimento della Salute della Donna, del Bambino e di Sanità Pubblica, Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Marcella Zollino
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
- Genetica Medica, Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy
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4
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Becking EC, Linthorst J, Patton S, Gutowska-Ding W, Goodall R, Khawaja F, Morgan F, Deans Z, Chitty LS, Bekker MN, Scheffer PG, Sistermans EA. Variability in Fetal Fraction Estimation: Comparing Fetal Fractions Reported by Noninvasive Prenatal Testing Providers Globally. Clin Chem 2023; 69:160-167. [PMID: 36576352 DOI: 10.1093/clinchem/hvac207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/07/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Fetal fraction (FF) measurement is considered important for reliable noninvasive prenatal testing (NIPT). Using minimal FF threshold as a quality parameter is under debate. We evaluated the variability in reported FFs of individual samples between providers and laboratories and within a single laboratory. METHODS Genomic quality assessment and European Molecular Genetics Quality Network provide joint proficiency testing for NIPT. We compared reported FFs across all laboratories and stratified according to test methodologies. A single sample was sequenced repeatedly and FF estimated by 2 bioinformatics methods: Veriseq2 and SeqFF. Finally, we compared FFs by Veriseq and SeqFF in 87 351 NIPT samples. RESULTS For each proficiency test sample we observed a large variability in reported FF, SDs and CVs ranging from 1.7 to 3.6 and 17.0 to 35.8, respectively. FF measurements reported by single nucleotide polymorphism-based methods had smaller SDs (0.5 to 2.4) compared to whole genome sequencing-based methods (1.8 to 2.9). In the internal quality assessment, SDs were similar between SeqFF (SD 1.0) and Veriseq v2 (SD 0.9), but mean FF by Veriseq v2 was higher compared to SeqFF (9.0 vs 6.4, P 0.001). In patient samples, reported FFs were on average 1.12-points higher in Veriseq than in SeqFF (P 0.001). CONCLUSIONS Current methods do not allow for a reliable and consistent FF estimation. Our data show estimated FF should be regarded as a laboratory-specific range, rather than a precise number. Applying strict universal minimum thresholds might result in unnecessary test failures and should be used with caution.
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Affiliation(s)
- Ellis C Becking
- Department of Obstetrics, Division of Women and Baby, Wilhelmina Childrens Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jasper Linthorst
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development, Amsterdam, The Netherlands
| | - Simon Patton
- Manchester Science Park, EMQN CIC, Manchester, UK
| | | | | | - Farrah Khawaja
- Genomics Quality Assessment, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Fiona Morgan
- Genomics Quality Assessment, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Zandra Deans
- Genomics Quality Assessment, NHS Lothian, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust and Genetics and Genomics, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Mireille N Bekker
- Department of Obstetrics, Division of Women and Baby, Wilhelmina Childrens Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter G Scheffer
- Department of Obstetrics, Division of Women and Baby, Wilhelmina Childrens Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Erik A Sistermans
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Amsterdam Reproduction and Development, Amsterdam, The Netherlands
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5
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Qi T, Pan M, Shi H, Wang L, Bai Y, Ge Q. Cell-Free DNA Fragmentomics: The Novel Promising Biomarker. Int J Mol Sci 2023; 24:1503. [PMID: 36675018 PMCID: PMC9866579 DOI: 10.3390/ijms24021503] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Cell-free DNA molecules are released into the plasma via apoptotic or necrotic events and active release mechanisms, which carry the genetic and epigenetic information of its origin tissues. However, cfDNA is the mixture of various cell fragments, and the efficient enrichment of cfDNA fragments with diagnostic value remains a great challenge for application in the clinical setting. Evidence from recent years shows that cfDNA fragmentomics' characteristics differ in normal and diseased individuals without the need to distinguish the source of the cfDNA fragments, which makes it a promising novel biomarker. Moreover, cfDNA fragmentomics can identify tissue origins by inferring epigenetic information. Thus, further insights into the fragmentomics of plasma cfDNA shed light on the origin and fragmentation mechanisms of cfDNA during physiological and pathological processes in diseases and enhance our ability to take the advantage of plasma cfDNA as a molecular diagnostic tool. In this review, we focus on the cfDNA fragment characteristics and its potential application, such as fragment length, end motifs, jagged ends, preferred end coordinates, as well as nucleosome footprints, open chromatin region, and gene expression inferred by the cfDNA fragmentation pattern across the genome. Furthermore, we summarize the methods for deducing the tissue of origin by cfDNA fragmentomics.
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Affiliation(s)
- Ting Qi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing 210097, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liangying Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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6
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Zhang M, Li K, Qu S, Guo Z, Wang Y, Yang X, Zhou J, Ouyang G, Weng R, Li F, Wu Y, Yang X. Integrative analyses of maternal plasma cell-free DNA nucleosome footprint differences reveal chromosomal aneuploidy fetuses gene expression profile. J Transl Med 2022; 20:536. [PMID: 36401256 PMCID: PMC9673457 DOI: 10.1186/s12967-022-03735-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 10/30/2022] [Indexed: 11/19/2022] Open
Abstract
Background Chromosomal aneuploidy is the most common birth defect. However, the developmental mechanism and gene expression profile of fetuses with chromosomal aneuploidy are relatively unknown, and the maternal immune changes induced by fetal aneuploidy remain unclear. The inability to obtain the placenta multiple times in real-time is a bottleneck in research on aneuploid pregnancies. Plasma cell-free DNA (cfDNA) carries the gene expression profile information of its source cells and may be used to evaluate the development of fetuses with aneuploidy and the immune changes induced in the mother owing to fetal aneuploidy. Methods Here, we carried out whole-genome sequencing of the plasma cfDNA of 101 pregnant women carrying a fetus with trisomy (trisomy 21, n = 42; trisomy 18, n = 28; trisomy 13, n = 31) based on non-invasive prenatal testing (NIPT) screening and 140 normal pregnant women to identify differential genes according to the cfDNA nucleosome profile in the region around the transcription start sites (TSSs). Results The plasma cfDNA promoter profiles were found to differ between aneuploid and euploid pregnancies. A total of 158 genes with significant differences were identified, of which 43 genes were upregulated and 98 genes were downregulated. Functional enrichment and signaling pathway analysis were performed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases found that these signal pathways were mainly related to the coordination of developmental signals during embryonic development, the control of cell growth and development, regulation of neuronal survival, and immune regulation, such as the MAPK, Hippo, TGF-β, and Rap1 signaling pathways, which play important roles in the development of embryonic tissues and organs. Furthermore, based on the results of differential gene analysis, a total of 14 immune-related genes with significant differences from the ImmPort database were collected and analyzed. These significantly different immune genes were mainly associated with the maintenance of embryonic homeostasis and normal development. Conclusions These results suggest that the distribution characteristics of cfDNA nucleosomes in maternal plasma can be used to reflect the status of fetal development and changes of the immune responses in trisomic pregnancies. Overall, our findings may provide research ideas for non-invasive detection of the physiological and pathological states of other diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-022-03735-7.
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7
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Shekhawat DS, Sharma C, Singh K, Singh P, Bhardwaj A, Patwa P. Critical appraisal of droplet digital polymerase chain reaction application for noninvasive prenatal testing. Congenit Anom (Kyoto) 2022; 62:188-197. [PMID: 35662261 DOI: 10.1111/cga.12481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/29/2022]
Abstract
Maternal-fetal medicine (FM) is currently a highly demanding branch and is gaining importance as increasing number of genetic disorders rise in incidence. Prenatal testing helps to detect such abnormalities that could affect the health status of the developing fetus like birth defects or genetic disorders. Considering the rising trend of genetic disorders, there is a need for a highly sensitive way of noninvasive prenatal testing (NIPT) that may reduce the incidence of unnecessary invasive procedures and iatrogenic fetal loss. The concept of NIPT for screening of genetic disorders is continuously evolving over the last two decades and multiple techniques have come up to utilize this in the field of FM. The crucial factor which decides the accuracy of NIPS is cell free fetal DNA (cffDNA) that is present in extremely low fraction (10%-15%) in the maternal plasma. Among the available methods, the next generation sequencing (NGS) is considered as the gold standard. However, the higher cost diminishes its utility in low-resource settings. Droplet digital Polymerase chain reaction (ddPCR), a type of digital PCR is a novel technique that is frugal, equally sensitive, less labor intensive, less time-consuming and plain algorithm dependent method for detecting cffDNA fraction. Considering these impressive attributes of ddPCR, we decided to critically review the existing literature on ddPCR for NIPT whilst highlighting the clinical utility, challenges and its advantages over NGS.
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Affiliation(s)
| | - Charu Sharma
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
| | | | - Pratibha Singh
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
| | - Abhishek Bhardwaj
- Department of Dermatology, Venereology and Leprology, AIIMS, Jodhpur, India
| | - Payal Patwa
- Department of Obstetrics & Gynecology, AIIMS, Jodhpur, India
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8
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Vanderstichele A, Busschaert P, Landolfo C, Olbrecht S, Coosemans A, Froyman W, Loverix L, Concin N, Braicu EI, Wimberger P, Van Nieuwenhuysen E, Han SN, Van Gorp T, Venken T, Heremans R, Neven P, Bourne T, Van Calster B, Timmerman D, Lambrechts D, Vergote I. Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer. NPJ Genom Med 2022; 7:30. [PMID: 35484288 PMCID: PMC9050708 DOI: 10.1038/s41525-022-00300-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 03/04/2022] [Indexed: 11/09/2022] Open
Abstract
Fragmentation patterns of plasma cell-free DNA (cfDNA) are known to reflect nucleosome positions of cell types contributing to cfDNA. Based on cfDNA fragmentation patterns, the deviation in nucleosome footprints was quantified between diagnosed ovarian cancer patients and healthy individuals. Multinomial modeling was subsequently applied to capture these deviations in a per sample nucleosome footprint score. Validation was performed in 271 cfDNAs pre-surgically collected from women with an adnexal mass. We confirmed that nucleosome scores were elevated in invasive carcinoma patients, but not in patients with benign or borderline disease. Combining nucleosome scores with chromosomal instability scores assessed in the same cfDNA improved prediction of malignancy. Nucleosome scores were, however, more reliable to predict non-high-grade serous ovarian tumors, which are characterized by low chromosomal instability. These data highlight that compared to chromosomal instability, nucleosome footprinting provides a complementary and more generic read-out for pre-surgical diagnosis of invasive disease in women with adnexal masses.
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Affiliation(s)
- Adriaan Vanderstichele
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Pieter Busschaert
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chiara Landolfo
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Queen Charlotte's and Chelsea Hospital, Imperial College, London, UK
| | - Siel Olbrecht
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - An Coosemans
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, Laboratory of Tumor Immunology and Immunotherapy, Immunovar Research Group, KU Leuven, Leuven, Belgium
| | - Wouter Froyman
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Liselore Loverix
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.,VIB Center for Cancer Biology, Leuven, Belgium
| | - Nicole Concin
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Obstetrics and Gynecology, Innsbruck Medical University, Innsbruck, Austria
| | - Elena Ioana Braicu
- Department of Gynecology, Campus Virchow, Charité, Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Pauline Wimberger
- National Center for Tumor Diseases (NCT), Dresden, Germany.,German Cancer Consortium (DKTK), Dresden, Germany.,Department of Gynecology and Obstetrics, University Hospital Carl Gustav Carus Dresden, TU Dresden, Dresden, Germany
| | - Els Van Nieuwenhuysen
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Sileny N Han
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Toon Van Gorp
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Tom Venken
- VIB Center for Cancer Biology, Leuven, Belgium.,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ruben Heremans
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Patrick Neven
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
| | - Tom Bourne
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ben Van Calster
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Dirk Timmerman
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium.,Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium. .,Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Ignace Vergote
- Department of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven Cancer Institute, Leuven, Belgium.,Department of Oncology, KU Leuven, Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
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9
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Zhou J, Ouyang G, Wu L, Zhang M, Weng R, Lin S, Wang Y, Li K, Yang X, Wu Y, Liang Z, Li F, Qu S, Yang X. Simulated confined placental mosaicism proportion (SCPMP) based on cell-free fetal DNA fraction enrichment can reduce false-positive results in non-invasive prenatal testing. Prenat Diagn 2022; 42:1008-1014. [PMID: 35441712 DOI: 10.1002/pd.6150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/25/2022] [Accepted: 04/14/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To decrease the false-positive rate of NIPT using cell-free fetal DNA (cffDNA) fraction enrichment and the simulated confined placental mosaicism proportion (SCPMP) threshold application via cffDNA quantification. METHOD Using a cffDNA enrichment method, 303 plasma samples with positive NIPT results (Z-score > 3.0; 200 true-positive and 103 false-positive cases) were re-sequenced. A method to calculate the SCPMP based on the quantified cffDNA fraction was developed; the SCPMP threshold between true- and false-positive NIPT results was determined and used for re-analyses. RESULTS With enrichment, the fetal fraction of the 303 samples was 26.9 ± 8.4%, compared to 11.0 ± 3.2% without enrichment. The optimized threshold method with double determination using the Z-value-defined SCPMP can reduce the false-positive rates for trisomies 21, 18, and 13 by 87%, 80%, and 88.9%, respectively. CONCLUSION Our optimized method can decrease the false-positive rate of NIPT results. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Junhua Zhou
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Guojun Ouyang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Long Wu
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Min Zhang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Rongtao Weng
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Shuman Lin
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Yuanli Wang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Kun Li
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Xu Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Yingsong Wu
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Zhikun Liang
- Guangzhou Darui Biotechnology Co. Ltd., Guangzhou, Guangdong, 510665, P.R. China
| | - Fenxia Li
- Department of obstetrics and Gynecology, Nanfang Hospital, Southern Medical university, Guangzhou, Guangdong, China
| | - Shoufang Qu
- National Institutes for Food and Drug Control, Beijing, 100050
| | - Xuexi Yang
- Institute of Antibody Engineering, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
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10
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Cell-Free DNA Fragmentomics in Liquid Biopsy. Diagnostics (Basel) 2022; 12:diagnostics12040978. [PMID: 35454026 PMCID: PMC9027801 DOI: 10.3390/diagnostics12040978] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Cell-free DNA (cfDNA) in bodily fluids has rapidly transformed the development of noninvasive prenatal testing, cancer liquid biopsy, and transplantation monitoring. Plasma cfDNA consists of a mixture of molecules originating from various bodily tissues. The study of the fragmentation patterns of cfDNA, also referred to as ‘fragmentomics’, is now an actively pursued area of biomarker research. Clues that cfDNA fragmentation patterns might carry information concerning the tissue of origin of cfDNA molecules have come from works demonstrating that circulating fetal, tumor-derived, and transplanted liver-derived cfDNA molecules have a shorter size distribution than the background mainly of hematopoietic origin. More recently, an improved understanding of cfDNA fragmentation has provided many emerging fragmentomic markers, including fragment sizes, preferred ends, end motifs, single-stranded jagged ends, and nucleosomal footprints. The intrinsic biological link between activities of various DNA nucleases and characteristic fragmentations has been demonstrated. In this review, we focus on the biological properties of cell-free DNA unveiled recently and their potential clinical applications.
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11
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Persson F, Cuckle HS. Consequences of imprecision in fetal fraction estimation on performance of cell‐free DNA screening for Down syndrome. Prenat Diagn 2022; 42:512-517. [PMID: 35220579 PMCID: PMC9311738 DOI: 10.1002/pd.6126] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 11/08/2022]
Abstract
Background There is a significant variability in reported fetal fraction (FF), a common cause for no‐calls in cell‐free (cf)DNA based non‐invasive prenatal screening. We examine the effect of imprecision in FF measurement on the performance of cfDNA screening for Down syndrome, when low FF samples are classified as no‐calls. Methods A model for the reported FF was constructed from the FF measurement precision and the underlying true FF. The model was used to predict singleton Down syndrome detection rates (DRs) for various FF cut‐offs and underlying discriminatory powers of the test. Results Increasing the FF cut‐off led to slightly increased apparent DR, when no‐calls are excluded, and an associated larger decrease in effective DR, when no‐calls are included. These effects were smaller for tests with higher discriminatory power and larger as maternal weight increased. Conclusions Most no‐calls due to a low reported FF have a true FF above the cut‐off. The discriminatory power of a test limits its effective DR and FF precision determines the tradeoff between apparent and effective DR when low FF is used to discard samples. Tests with high discriminatory power do not benefit from current FF measurements.
What is already known about this topic?
Fetal fraction (FF) is often considered to be a crucial quality control parameter for interpretation of cell free DNA based non‐invasive prenatal testing (NIPT) There is a large variability in the measurement of FF for single samples A large fraction of test non‐reportable results (no‐calls) are due to a too low reported FF
What does this study add?
This article presents the consequences of the high variability in FF measurements in the context of screening NIPT test performance For tests with a high discriminatory power, discarding samples based on too low reported FF leads to a slight apparent increase in NIPT performance metrics but at a relatively large expense of unnecessary anxiety, clinical and financial burden of additional counseling and follow‐up procedures
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12
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Paul LT, Ergoren MC. Comparison of Bioinformatics Approaches for Fetal Microdeletions and Monogenic Variations Estimation in Non-invasive Prenatal Testing. Glob Med Genet 2022; 9:72-75. [PMID: 35707785 PMCID: PMC9192181 DOI: 10.1055/s-0042-1743573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/29/2021] [Indexed: 11/25/2022] Open
Abstract
Prenatal testing provides crucial information about the health status of fetuses as well as recommending better treatment. For the past decades, prenatal testing using chorionic villus sampling and amniocentesis were the two majorly used forms of invasive prenatal diagnostic approaches. However, to facilitate prenatal testing without causing any danger to the fetus, the noninvasive prenatal diagnostic method, which uses circulating cell-free deoxyribonucleic acid (DNA), has become a suitable method of prenatal diagnosis. This review discusses the recent bioinformatics approaches used for analyzing fetal DNA concentration.
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Affiliation(s)
- Lizzy Teleboshe Paul
- Department of Medical Biology, Faculty of Medicine, Near East University, Nicosia, Cyprus
| | - Mahmut Cerkez Ergoren
- Department of Medical Genetics, Faculty of Medicine, Near East University, Nicosia, Cyprus
- DESAM Research Institute, Near East University, Nicosia, Cyprus
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13
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High-resolution analysis for urinary DNA jagged ends. NPJ Genom Med 2022; 7:14. [PMID: 35197474 PMCID: PMC8866458 DOI: 10.1038/s41525-022-00285-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/22/2021] [Indexed: 12/05/2022] Open
Abstract
Single-stranded ends of double-stranded DNA (jagged ends) are more abundant in urinary DNA than in plasma DNA. However, the lengths of jagged ends in urinary DNA remained undetermined, as a previous method used for urinary DNA jagged end sequencing analysis (Jag-seq) relied on unmethylation at CpG sites, limiting the resolution. Here, we performed high-resolution Jag-seq analysis using methylation at non-CpG cytosine sites, allowing determination of exact length of jagged ends. The urinary DNA bore longer jagged ends (~26-nt) than plasma DNA (~17-nt). The jagged end length distribution displayed 10-nt periodicities in urinary DNA, which were much less observable in plasma DNA. Amplitude of the 10-nt periodicities increased in patients with renal cell carcinoma. Heparin treatment of urine diminished the 10-nt periodicities. The urinary DNA jagged ends often extended into nucleosomal cores, suggesting potential interactions with histones. This study has thus advanced our knowledge of jagged ends in urine DNA.
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14
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Deng C, Liu S. Factors Affecting the Fetal Fraction in Noninvasive Prenatal Screening: A Review. Front Pediatr 2022; 10:812781. [PMID: 35155308 PMCID: PMC8829468 DOI: 10.3389/fped.2022.812781] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/03/2022] [Indexed: 12/03/2022] Open
Abstract
A paradigm shift in noninvasive prenatal screening has been made with the discovery of cell-free fetal DNA in maternal plasma. Noninvasive prenatal screening is primarily used to screen for fetal aneuploidies, and has been used globally. Fetal fraction, an important parameter in the analysis of noninvasive prenatal screening results, is the proportion of fetal cell-free DNA present in the total maternal plasma cell-free DNA. It combines biological factors and bioinformatics algorithms to interpret noninvasive prenatal screening results and is an integral part of quality control. Maternal and fetal factors may influence fetal fraction. To date, there is no broad consensus on the factors that affect fetal fraction. There are many different approaches to evaluate this parameter, each with its advantages and disadvantages. Different fetal fraction calculation methods may be used in different testing platforms or laboratories. This review includes numerous publications that focused on the understanding of the significance, influencing factors, and interpretation of fetal fraction to provide a deeper understanding of this parameter.
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Affiliation(s)
- Cechuan Deng
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Shanling Liu
- Prenatal Diagnostic Center, Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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15
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Mokveld T, Al-Ars Z, Sistermans EA, Reinders M. WisecondorFF: Improved Fetal Aneuploidy Detection from Shallow WGS through Fragment Length Analysis. Diagnostics (Basel) 2021; 12:59. [PMID: 35054227 PMCID: PMC8774687 DOI: 10.3390/diagnostics12010059] [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: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/18/2022] Open
Abstract
In prenatal diagnostics, NIPT screening utilizing read coverage-based profiles obtained from shallow WGS data is routinely used to detect fetal CNVs. From this same data, fragment size distributions of fetal and maternal DNA fragments can be derived, which are known to be different, and often used to infer fetal fractions. We argue that the fragment size has the potential to aid in the detection of CNVs. By integrating, in parallel, fragment size and read coverage in a within-sample normalization approach, it is possible to construct a reference set encompassing both data types. This reference then allows the detection of CNVs within queried samples, utilizing both data sources. We present a new methodology, WisecondorFF, which improves sensitivity, while maintaining specificity, relative to existing approaches. WisecondorFF increases robustness of detected CNVs, and can reliably detect even at lower fetal fractions (<2%).
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Affiliation(s)
- Tom Mokveld
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
| | - Zaid Al-Ars
- Computer Engineering, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands;
| | - Erik A. Sistermans
- Department of Human Genetics and Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands;
| | - Marcel Reinders
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, 2628 XE Delft, The Netherlands;
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16
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Single-molecule sequencing reveals a large population of long cell-free DNA molecules in maternal plasma. Proc Natl Acad Sci U S A 2021; 118:2114937118. [PMID: 34873045 PMCID: PMC8685924 DOI: 10.1073/pnas.2114937118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2021] [Indexed: 11/18/2022] Open
Abstract
In the field of circulating cell-free DNA, most of the studies have focused on short DNA molecules (e.g., <500 bp). The existence of long cell-free DNA molecules has been poorly explored. In this study, we demonstrated that single-molecule real-time sequencing allowed us to detect and analyze a substantial proportion of long DNA molecules from both fetal and maternal sources in maternal plasma. Such molecules were beyond the size detection limits of short-read sequencing technologies. The proportions of long cell-free DNA molecules in maternal plasma over 500 bp were 15.5%, 19.8%, and 32.3% for the first, second, and third trimesters, respectively. The longest fetal-derived plasma DNA molecule observed was 23,635 bp. Long plasma DNA molecules demonstrated predominance of A or G 5' fragment ends. Pregnancies with preeclampsia demonstrated a reduction in long maternal plasma DNA molecules, reduced frequencies for selected 5' 4-mer end motifs ending with G or A, and increased frequencies for selected motifs ending with T or C. Finally, we have developed an approach that employs the analysis of methylation patterns of the series of CpG sites on a long DNA molecule for determining its tissue origin. This approach achieved an area under the curve of 0.88 in differentiating between fetal and maternal plasma DNA molecules, enabling the determination of maternal inheritance and recombination events in the fetal genome. This work opens up potential clinical utilities of long cell-free DNA analysis in maternal plasma including noninvasive prenatal testing of monogenic diseases and detection/monitoring of pregnancy-associated disorders such as preeclampsia.
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17
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Ju J, Li J, Liu S, Zhang H, Xu J, Lin Y, Gao Y, Zhou Y, Jin X. Estimation of cell-free fetal DNA fraction from maternal plasma based on linkage disequilibrium information. NPJ Genom Med 2021; 6:85. [PMID: 34642337 PMCID: PMC8511193 DOI: 10.1038/s41525-021-00247-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 09/23/2021] [Indexed: 11/21/2022] Open
Abstract
Cell-free fetal DNA fraction (FF) in maternal plasma is a key parameter affecting the performance of noninvasive prenatal testing (NIPT). Accurate quantitation of FF plays a pivotal role in these tests. However, there are few methods that could determine FF with high accuracy using shallow-depth whole-genome sequencing data. In this study, we hypothesized that the actual FF in maternal plasma should be proportional to the discrepancy rate between the observed genotypes and inferred genotypes based on the linkage disequilibrium rule in certain polymorphism sites. Based on this hypothesis, we developed a method named Linkage Disequilibrium information-based cell-free Fetal DNA Fraction (LDFF) to accurately quantify FF in maternal plasma. This method achieves a high performance and outperforms existing methods in the fetal DNA fraction estimation. As LDFF is a gender-independent method and developed on shallow-depth samples, it can be easily incorporated into routine NIPT test and may enhance the current NIPT performance.
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Affiliation(s)
- Jia Ju
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Jia Li
- BGI-genomics, BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Siyang Liu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | | | - Jinjin Xu
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Yu Lin
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Ya Gao
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China
| | - Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, 361102, Xiamen, Fujian, China.
| | - Xin Jin
- BGI-Shenzhen, 518083, Shenzhen, Guangdong, China.
- School of Medicine, South China University of Technology, 510006, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, BGI-Shenzhen, 518083, Shenzhen, China.
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18
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Duboc V, Pratella D, Milanesio M, Boudjarane J, Descombes S, Paquis-Flucklinger V, Bottini S. NiPTUNE: an automated pipeline for noninvasive prenatal testing in an accurate, integrative and flexible framework. Brief Bioinform 2021; 23:6370845. [PMID: 34529041 DOI: 10.1093/bib/bbab380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/14/2022] Open
Abstract
Noninvasive prenatal testing (NIPT) consists of determining fetal aneuploidies by quantifying copy number alteration from the sequencing of cell-free DNA (cfDNA) from maternal blood. Due to the presence of cfDNA of fetal origin in maternal blood, in silico approaches have been developed to accurately predict fetal aneuploidies. Although NIPT is becoming a new standard in prenatal screening of chromosomal abnormalities, there are no integrated pipelines available to allow rapid, accurate and standardized data analysis in any clinical setting. Several tools have been developed, however often optimized only for research purposes or requiring enormous amount of retrospective data, making hard their implementation in a clinical context. Furthermore, no guidelines have been provided on how to accomplish each step of the data analysis to achieve reliable results. Finally, there is no integrated pipeline to perform all steps of NIPT analysis. To address these needs, we tested several tools for performing NIPT data analysis. We provide extensive benchmark of tools performances but also guidelines for running them. We selected the best performing tools that we benchmarked and gathered them in a computational pipeline. NiPTUNE is an open source python package that includes methods for fetal fraction estimation, a novel method for accurate gender prediction, a principal component analysis based strategy for quality control and fetal aneuploidies prediction. NiPTUNE is constituted by seven modules allowing the user to run the entire pipeline or each module independently. Using two cohorts composed by 1439 samples with 31 confirmed aneuploidies, we demonstrated that NiPTUNE is a valuable resource for NIPT analysis.
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Affiliation(s)
- Véronique Duboc
- Department of Medical Genetics of Nice Universitary Hospital, in charge of NIPT, France
| | - David Pratella
- Center of Modeling, Simulation and Interaction at the Université Cote d'Azur in Nice, France
| | - Marco Milanesio
- Center of Modeling, Simulation and Interaction at the Université Cote d'Azur in Nice, France
| | - John Boudjarane
- Centre Hospitalier Universitaire la Timone in Marseille, France
| | - Stéphane Descombes
- Center of Modeling, Simulation and Interaction at the Université Cote d'Azur in Nice, France
| | | | - Silvia Bottini
- Medical Data Laboratory belonging to the Center of Modeling, Simulation and Interaction at the Université Cote d'Azur in Nice, France
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19
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Udomruk S, Orrapin S, Pruksakorn D, Chaiyawat P. Size distribution of cell-free DNA in oncology. Crit Rev Oncol Hematol 2021; 166:103455. [PMID: 34464717 DOI: 10.1016/j.critrevonc.2021.103455] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA (cfDNA) in liquid biopsy test is a novel promising biomarker in the advancement of cancer management, including early diagnosis, screening, prognosis, identification of actionable targets, and serial tumor monitoring. The specific size pattern of DNA fragments derived from cancer cells is observed to differ from that of cfDNA fragments shed by non-cancer cells. Research into the physiological and biological properties of cfDNA reveals the molecular signature carried by each cfDNA fragments, which can reflect their tissue origins, as well as the mutational profiles with significant genetic alterations. Understanding the fragmentation and size distribution of cfDNA might be a valuable hotspot in liquid biopsy research, with the potential to drive innovation in oncology.
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Affiliation(s)
- Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Santhasiri Orrapin
- Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Orthopedics, Faculty of Medicine, Chiang Mai University, 110 Intawaroros, Sriphoom, Muang, Chiang Mai 50200, Thailand.
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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20
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Calculation of Fetal Fraction for Non-Invasive Prenatal Testing. BIOTECH 2021; 10:biotech10030017. [PMID: 35822771 PMCID: PMC9245487 DOI: 10.3390/biotech10030017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/05/2022] Open
Abstract
Estimating the fetal fraction of DNA in a pregnant mother’s blood is a risk-free, non-invasive way of predicting fetal aneuploidy. It is a rapidly developing field of study, offering researchers a plethora of different complementary methods. Such methods include examining the differences in methylation profiles between the fetus and the mother. Others include calculating the average allele frequency based on the difference in genotype of a number of single-nucleotide polymorphisms. Differences in the length distribution of DNA fragments between the mother and the fetus as well as measuring the proportion of DNA reads mapping to the Y chromosome also constitute fetal fraction estimation methods. The advantages and disadvantages of each of these main method types are discussed. Moreover, several well-known fetal fraction estimation methods, such as SeqFF, are described and compared with other methods. These methods are amenable to not only the estimation of fetal fraction but also paternity, cancer, and transplantation monitoring studies. NIPT is safe, and should aneuploidy be detected, this information can help parents prepare mentally and emotionally for the birth of a special needs child.
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21
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Lo YMD, Han DSC, Jiang P, Chiu RWK. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science 2021; 372:372/6538/eaaw3616. [PMID: 33833097 DOI: 10.1126/science.aaw3616] [Citation(s) in RCA: 270] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze cell-free DNA in blood plasma are used for noninvasive prenatal testing, oncology, and monitoring of organ transplant recipients. DNA molecules are released into the plasma from various bodily tissues. Physical and molecular features of cell-free DNA fragments and their distribution over the genome bear information about their tissues of origin. Moreover, patterns of DNA methylation of these molecules reflect those of their tissue sources. The nucleosomal organization and nuclease content of the tissue of origin affect the fragmentation profile of plasma DNA molecules, such as fragment size and end motifs. Besides double-stranded linear fragments, other topological forms of cell-free DNA also exist-namely circular and single-stranded molecules. Enhanced by these features, liquid biopsies hold promise for the noninvasive detection of tissue-specific pathologies with a range of clinical applications.
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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, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory in Translational Oncology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Diana S C Han
- 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, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- 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, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- 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, Shatin, New Territories, Hong Kong SAR, China
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22
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Chiu RWK, Lo YMD. Cell-free fetal DNA coming in all sizes and shapes. Prenat Diagn 2021; 41:1193-1201. [PMID: 33882153 PMCID: PMC8518878 DOI: 10.1002/pd.5952] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 03/29/2021] [Accepted: 04/16/2021] [Indexed: 02/01/2023]
Abstract
Cell‐free fetal DNA analysis has an established role in prenatal assessments. It serves as a source of fetal genetic material that is accessible non‐invasively from maternal blood. Through the years, evidence has accumulated to show that cell‐free fetal DNA molecules are derived from placental tissues, are mainly of short DNA fragments and have rapid post‐delivery clearance profiles. But questions regarding how they come to being short molecules from placental cells and in which physical forms do they exist remained largely unanswered until recently. We now know that the distributions of ending sites of cell‐free DNA molecules are non‐random across the genome and bear correlations with the chromatin structures of cells from which they have originated. Such an insight offers ways to deduce the tissue‐of‐origin of these molecules. Besides, the physical nature and sequence characteristics of the ends of each cell‐free DNA molecule provide tell‐tale signs of how the DNA fragmentation processes are orchestrated by nuclease enzymes. These realizations offered opportunities to develop methods for enriching cell‐free fetal DNA to facilitate non‐invasive prenatal diagnostics. Here we aimed to collate what is known about the biological and physical characteristics of cell‐free fetal DNA into one article and explain the implications of these observations.
What’s already known about this topic?
Cell‐free fetal DNA originates from placental tissues and circulates in maternal plasma as a minor population in the form of short fragments which disappears from maternal circulation rapidly after delivery.
What does this study add?
Cell‐free DNA studies at the per molecule per nucleotide level documented the detailed genomic distributions, fragment end characteristics and physical forms of cell‐free DNA unveiling the fine feature differences between maternal and fetal DNA as well as their intricate relationships with the chromatin structure of the cells‐of‐origin. These studies have substantially bridged the knowledge gaps in the biology of cell‐free fetal DNA and may provide insights on how to enhance prenatal tests based on their analyses.
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Affiliation(s)
- Rossa W K Chiu
- Centre for Novostics, Hong Kong Science Park, New Territories, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences and Department of Chemical Pathology, The Chinese University of Hong Kong, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, New Territories, Hong Kong SAR, China.,Li Ka Shing Institute of Health Sciences and Department of Chemical Pathology, The Chinese University of Hong Kong, New Territories, Hong Kong SAR, China
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23
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Persson F, Prensky L. Variability of "Reported Fetal Fraction" in Noninvasive Prenatal Screening (NIPS). Clin Chem 2021; 67:863-866. [PMID: 33734324 DOI: 10.1093/clinchem/hvab014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/08/2021] [Indexed: 02/01/2023]
Abstract
BACKGROUND Fetal fraction is often used to designate no-calls in noninvasive prenatal screening (NIPS). We wished to compare the variability in determining fetal fraction to gold standard methods. METHODS We identified 6 publications with datasets consisting of methods capable of measuring fetal fraction for all samples that also had comparison data from gold standard methods. Examples of gold standard methods included relative Y-chromosome quantification in cases of male fetus pregnancies or relative quantification of the relevant chromosome for pregnancies affected by one of the 3 major trisomies. RESULTS The studies showed that the differences of the various fetal fraction measurement assays as compared to a gold standard measurement displayed a standard deviation (SD) in the range of 1.3-3.4% fetal fraction (FF). The 4 studies that measured FF from fragment size and genomic coordinates or single nucleotide polymorphisms had a lower variability, with a median SD of about 1.6%, whereas 2 other studies using different methods displayed significantly higher variability. CONCLUSION When deciding whether to use the reported FF as a reason to discard samples as no-calls or not, we recommend taking the variability of the FF measurement into consideration.
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24
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Miceikaitė I, Brasch-Andersen C, Fagerberg C, Larsen MJ. Total number of reads affects the accuracy of fetal fraction estimates in NIPT. Mol Genet Genomic Med 2021; 9:e1653. [PMID: 33687149 PMCID: PMC8123752 DOI: 10.1002/mgg3.1653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/20/2020] [Accepted: 02/19/2021] [Indexed: 11/25/2022] Open
Abstract
Background Sufficient fetal fraction (FF) is crucial for quality control of NIPT (Non‐Invasive Prenatal Test) results. Different factors influencing bioinformatic estimation of FF should be considered when implementing NIPT. To what extent the total number of sequencing reads influences FF estimate has been unexplored. In this study, to test the robustness of SeqFF FF estimation and provide additional recommendations for NIPT analysis quality control, we compared the SeqFF FF estimates with two other methods and investigated how the number of sequencing reads and FF level affects the accuracy and precision of FF estimates. Methods WGS data of 516 NIPT samples from a prenatal screening program was obtained. Sample data were randomly downsampled by the read count, and FF was calculated by SeqFF software. Then, the outcome was compared with FF estimates from SNP‐ and chrY‐based methods. FF estimated with different read counts and FF levels were compared with FF at 30 M reads as a reference. Results SeqFF FF highly correlates with SNP‐ and chrY‐based FF estimates. Raising read count from 2 M to 10 M drastically increased the accuracy of FF estimates. After adding more reads, we saw a further improvement in FF accuracy, reaching a plateau at 20 M reads. Precision of SeqFF FF estimate is independent of FF level in the sample. Conclusion SeqFF is a robust method for FF estimation for both genders and for any FF level in range 2–13%. Accuracy of FF estimates highly depends on the read count. We recommend using no less than 10 M reads to achieve accurate FF estimates for NIPT analysis in clinical settings.
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Affiliation(s)
- Ieva Miceikaitė
- Clinical Genome Center & Human Genetics, Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Charlotte Brasch-Andersen
- Clinical Genome Center & Human Genetics, Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Martin Jakob Larsen
- Clinical Genome Center & Human Genetics, Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
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25
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Han BW, Yang F, Guo ZW, Ouyang GJ, Liang ZK, Weng RT, Yang X, Huang LP, Wang K, Li FX, Huang J, Yang XX, Wu YS. Noninvasive inferring expressed genes and in vivo monitoring of the physiology and pathology of pregnancy using cell-free DNA. Am J Obstet Gynecol 2021; 224:300.e1-300.e9. [PMID: 32871130 DOI: 10.1016/j.ajog.2020.08.104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/21/2020] [Accepted: 08/26/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Noninvasive monitoring of fetal development and the early detection of pregnancy-associated complications is challenging, largely because of the lack of information about the molecular spectrum during pregnancy. Recently, cell-free DNA in plasma was found to reflect the global nucleosome footprint and status of gene expression and showed potential for noninvasive health monitoring during pregnancy. OBJECTIVE We aimed to test the relationships between plasma cell-free DNA profiles and pregnancy biology and evaluate the use of a cell-free DNA profile as a noninvasive method for physiological and pathologic status monitoring during pregnancy. STUDY DESIGN We used genome cell-free DNA sequencing data generated from noninvasive prenatal testing in a total of 2937 pregnant women. For each physiological and pathologic condition, features of the cell-free DNA profile were identified using the discovery cohort, and support vector machine classifiers were built and evaluated using independent training and validation cohorts. RESULTS We established nucleosome occupancy profiles at transcription start sites in different gestational trimesters, demonstrated the relationships between gene expression and cell-free DNA coverage at transcription start sites, and showed that the cell-free DNA profiles at transcription start sites represented the biological processes of pregnancy. In addition, using cell-free DNA data, nucleosome profiles of transcription factor binding sites were identified to reflect the transcription factor footprint, which may help to reveal the molecular mechanisms underlying pregnancy. Finally, by using machine-learning models on low-coverage noninvasive prenatal testing data, we evaluated the use of cell-free DNA nucleosome profiles for distinguishing gestational trimesters, fetal sex, and fetal trisomy 21 and highlighted its potential utility for predicting physiological and pathologic fetal conditions by using low-coverage noninvasive prenatal testing data. CONCLUSION Our analyses profiled nucleosome footprints and regulatory networks during pregnancy and established a noninvasive proof-of-principle methodology for health monitoring during pregnancy.
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26
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Zhou Z, Cheng SH, Ding SC, Heung MMS, Xie T, Cheng THT, Lam WKJ, Peng W, Teoh JYC, Chiu PKF, Ng CF, Jiang P, Chan KCA, Chiu RWK, Lo YMD. Jagged Ends of Urinary Cell-Free DNA: Characterization and Feasibility Assessment in Bladder Cancer Detection. Clin Chem 2021; 67:621-630. [PMID: 33604652 DOI: 10.1093/clinchem/hvaa325] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/23/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Double-stranded DNA in plasma is known to carry single-stranded ends, called jagged ends. Plasma DNA jagged ends are biomarkers for pathophysiologic states such as pregnancy and cancer. It remains unknown whether urinary cell-free DNA (cfDNA) molecules have jagged ends. METHODS Jagged ends of cfDNA were detected by incorporating unmethylated cytosines during a DNA end-repair process, followed by bisulfite sequencing. Incorporation of unmethylated cytosines during the repair of the jagged ends lowered the apparent methylation levels measured by bisulfite sequencing and were used to calculate a jagged end index. This approach is called jagged end analysis by sequencing. RESULTS The jagged end index of urinary cfDNA was higher than that of plasma DNA. The jagged end index profile of plasma DNA displayed several strongly oscillating major peaks at intervals of approximately 165 bp (i.e., nucleosome size) and weakly oscillating minor peaks with periodicities of approximately 10 bp. In contrast, the urinary DNA jagged end index profile showed weakly oscillating major peaks but strongly oscillating minor peaks. The jagged end index was generally higher in nucleosomal linker DNA regions. Patients with bladder cancer (n = 46) had lower jagged end indexed of urinary DNA than participants without bladder cancer (n = 39). The area under the curve for differentiating between patients with and without bladder cancer was 0.83. CONCLUSIONS Jagged ends represent a property of urinary cfDNA. The generation of jagged ends might be related to nucleosomal structures, with enrichment in linker DNA regions. Jagged ends of urinary DNA could potentially serve as a new biomarker for bladder cancer detection.
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Affiliation(s)
- Ze Zhou
- 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
| | - Suk Hang Cheng
- 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
| | - Spencer C Ding
- 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
| | - Macy M S Heung
- 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
| | - Tingting Xie
- 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
| | - Timothy H T Cheng
- 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
| | - W K Jacky Lam
- 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
| | - Wenlei Peng
- 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
| | - Jeremy Y C Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peter K F Chiu
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Chi-Fai Ng
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- 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
| | - K C Allen Chan
- 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
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- 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
| | - 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
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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27
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Zednikova I, Pazourkova E, Lassakova S, Vesela B, Korabecna M. Detection of cell-free foetal DNA fraction in female-foetus bearing pregnancies using X-chromosomal insertion/deletion polymorphisms examined by digital droplet PCR. Sci Rep 2020; 10:20036. [PMID: 33208834 PMCID: PMC7676229 DOI: 10.1038/s41598-020-77084-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 10/23/2020] [Indexed: 12/03/2022] Open
Abstract
In families with X-linked recessive diseases, foetal sex is determined prenatally by detection of Y-chromosomal sequences in cell-free foetal DNA (cffDNA) in maternal plasma. The same procedure is used to confirm the cffDNA presence during non-invasive prenatal RhD incompatibility testing but there are no generally accepted markers for the detection of cffDNA fraction in female-foetus bearing pregnancies. We present a methodology allowing the detection of paternal X-chromosomal alleles on maternal background and the confirmation of female sex of the foetus by positive amplification signals. Using digital droplet PCR (ddPCR) we examined X-chromosomal INDEL (insertion/deletion) polymorphisms: rs2307932, rs16397, rs16637, rs3048996, rs16680 in buccal swabs of 50 females to obtain the population data. For all INDELs, we determined the limits of detection for each ddPCR assay. We examined the cffDNA from 63 pregnant women bearing Y-chromosome negative foetuses. The analysis with this set of INDELs led to informative results in 66.67% of examined female-foetus bearing pregnancies. Although the population data predicted higher informativity (74%) we provided the proof of principle of this methodology. We successfully applied this methodology in prenatal diagnostics in a family with Wiscott-Aldrich syndrome and in pregnancies tested for the risk of RhD incompatibility.
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Affiliation(s)
- Iveta Zednikova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
| | - Eva Pazourkova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic
- Department of Nephrology, First Faculty of Medicine, Charles University and General University Hospital in Prague, U nemocnice 2, 128 08, Prague, Czech Republic
| | - Sona Lassakova
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Barbora Vesela
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Marie Korabecna
- Department of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00, Prague, Czech Republic.
- Department of Biology and Medical Genetics, General University Hospital in Prague, Albertov 4, 128 00, Prague, Czech Republic.
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28
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Pös Z, Pös O, Styk J, Mocova A, Strieskova L, Budis J, Kadasi L, Radvanszky J, Szemes T. Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes. Int J Mol Sci 2020; 21:ijms21228634. [PMID: 33207777 PMCID: PMC7697251 DOI: 10.3390/ijms21228634] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Analyzes of cell-free nucleic acids (cfNAs) have shown huge potential in many biomedical applications, gradually entering several fields of research and everyday clinical care. Many biological properties of cfNAs can be informative to gain deeper insights into the function of the organism, such as their different types (DNA, RNAs) and subtypes (gDNA, mtDNA, bacterial DNA, miRNAs, etc.), forms (naked or vesicle bound NAs), fragmentation profiles, sequence composition, epigenetic modifications, and many others. On the other hand, the workflows of their analyzes comprise many important steps, from sample collection, storage and transportation, through extraction and laboratory analysis, up to bioinformatic analyzes and statistical evaluations, where each of these steps has the potential to affect the outcome and informational value of the performed analyzes. There are, however, no universal or standard protocols on how to exactly proceed when analyzing different cfNAs for different applications, at least according to our best knowledge. We decided therefore to prepare an overview of the available literature and products commercialized for cfNAs processing, in an attempt to summarize the benefits and limitations of the currently available approaches, devices, consumables, and protocols, together with various factors influencing the workflow, its processes, and outcomes.
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Affiliation(s)
- Zuzana Pös
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
| | - Ondrej Pös
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jakub Styk
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Faculty of Medicine, Institute of Medical Biology, Genetics and Clinical Genetics, 811 08 Bratislava, Slovakia
| | - Angelika Mocova
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | | | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Slovak Center of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Ludevit Kadasi
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
| | - Jan Radvanszky
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia; (Z.P.); (A.M.); (L.K.)
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
| | - Tomas Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia;
- Geneton Ltd., 841 04 Bratislava, Slovakia; (L.S.); (J.B.)
- Comenius University Science Park, Comenius University, 841 04 Bratislava, Slovakia;
- Correspondence: (J.R.); (T.S.); Tel.: +421-2-60296637 (J.R.); +421-2-9026-8807 (T.S.)
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29
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Ma MJL, Yakovenko S, Zhang H, Cheng SH, Apryshko V, Zhavoronkov A, Jiang P, Chan KCA, Chiu RWK, Lo YMD. Fetal mitochondrial DNA in maternal plasma in surrogate pregnancies: Detection and topology. Prenat Diagn 2020; 41:368-375. [PMID: 33140416 PMCID: PMC7984455 DOI: 10.1002/pd.5860] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/30/2023]
Abstract
Objectives Due to the maternally‐inherited nature of mitochondrial DNA (mtDNA), there is a lack of information regarding fetal mtDNA in the plasma of pregnant women. We aim to explore the presence and topologic forms of circulating fetal and maternal mtDNA molecules in surrogate pregnancies. Methods Genotypic differences between fetal and surrogate maternal mtDNA were used to identify the fetal and maternal mtDNA molecules in plasma. Plasma samples were obtained from the surrogate pregnant mothers. Using cleavage‐end signatures of BfaI restriction enzyme, linear and circular mtDNA molecules in maternal plasma could be differentiated. Results Fetal‐derived mtDNA molecules were mainly linear (median: 88%; range: 80%–96%), whereas approximately half of the maternal‐derived mtDNA molecules were circular (median: 51%; range: 42%–60%). The fetal DNA fraction of linear mtDNA was lower (median absolute difference: 9.8%; range: 1.1%–27%) than that of nuclear DNA (median: 20%; range: 9.7%–35%). The fetal‐derived linear mtDNA molecules were shorter than the maternal‐derived ones. Conclusion Fetal mtDNA is present in maternal plasma, and consists mainly of linear molecules. Surrogate pregnancies represent a valuable clinical scenario for exploring the biology and potential clinical applications of circulating mtDNA, for example, for pregnancies conceived following mitochondrial replacement therapy.
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Affiliation(s)
- Mary-Jane L Ma
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Sergey Yakovenko
- Altravita IVF-clinic, ECO Center, Moscow, Russia.,Biophysics Department, Faculty of Physics, Moscow State University, Moscow, Russia
| | - Haiqiang Zhang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Suk Hang Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | | | - Alex Zhavoronkov
- Insilico Medicine Ltd, Hong Kong Science and Technology Park, Hong Kong, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Hong Kong, China
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30
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Pan M, Chen P, Lu J, Liu Z, Jia E, Ge Q. The fragmentation patterns of maternal plasma cell-free DNA and its applications in non-invasive prenatal testing. Prenat Diagn 2020; 40:911-917. [PMID: 32147843 DOI: 10.1002/pd.5680] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Revised: 02/10/2020] [Accepted: 02/29/2020] [Indexed: 12/11/2022]
Abstract
The discovery of cell-free DNA (cfDNA) in maternal plasma has opened up new promises for the development of non-invasive prenatal testing (NIPT). Application of cfDNA in NIPT of fetus diseases and abnormalities is restricted by the low amount of fetal DNA molecules in maternal plasma. Fetus-derived cfDNA in maternal plasma are shorter than maternal DNA, thus leveraging the maternal and fetus-derived cfDNA molecules size difference has become a novel and more accurate method for NIPT. However, multiple biological properties such as size distribution of plasma DNA, proportion of fetal-derived DNA and methylation levels in maternal plasma across different gestational ages still remain largely unknown. Further insights into the size distribution and fragmentation pattern of circulating plasma cfDNA will shed light on the origin and fragmentation mechanisms of cfDNA during physiological and pathological processes in prenatal diseases and enhance our ability to take the advantage of plasma cfDNA as a molecular diagnostic tool. In the review, we start by summarizing the research techniques for the determination of the fragmentation profiles of cfDNA in maternal plasma. We then summarize the main progress and findings in size profiles of maternal plasma cfDNA and cffDNA. Finally, we discuss the potential diagnostic applications of plasma cfDNA size profiling.
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Affiliation(s)
- Min Pan
- Department of Pathology and Pathophysiology, Medical School, Southeast University, Nanjing, China
| | - Pingsheng Chen
- Department of Pathology and Pathophysiology, Medical School, Southeast University, Nanjing, China
| | - Jiafeng Lu
- Center of Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, China
| | - Zhiyu Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Erteng Jia
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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31
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Yuan Y, Chai X, Liu N, Gu B, Li S, Gao Y, Zhou L, Liu Q, Yang F, Liu J, Qiu J, Zhang J, Hou Y, Cen M, Tian Z, Tang W, Zhang H, Chen F, Yin Y, Wang W. FF-QuantSC: accurate quantification of fetal fraction by a neural network model. Mol Genet Genomic Med 2020; 8:e1232. [PMID: 32281746 PMCID: PMC7284026 DOI: 10.1002/mgg3.1232] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Noninvasive prenatal testing (NIPT) is one of the most commonly employed clinical measures for screening of fetal aneuploidy. Fetal Fraction (ff) has been demonstrated to be one of the key factors affecting the performance of NIPT. Accurate quantification of ff plays vital role in NIPT. METHODS In this study, we present a new approach, the accurate Quantification of Fetal Fraction with Shallow-Coverage sequencing of maternal plasma DNA (FF-QuantSC), for the estimation of ff in NIPT. The method employs neural network model and utilizes differential genomic patterns between fetal and maternal genomes to quantify ff. RESULTS Our results show that the predicted ff by FF-QuantSC exhibit high correlation with the Y chromosome-based method on male pregnancies, and achieves the highest accuracy compared with other ff estimation approaches. We also demonstrate that the model generates statistically similar results on both male and female pregnancies. CONCLUSION FF-QuantSC achieves high accuracy in ff quantification. The method is suitable for application in both male and female pregnancies. Since the method does not require additional information upon NIPT routines, it can be easily incorporated into current NIPT settings without causing extra costs. We believe that FF-QuantSC shall provide valuable additions to NIPT.
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Affiliation(s)
- Yuying Yuan
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Xianghua Chai
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Na Liu
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Bida Gu
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | | | - Ya Gao
- BGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
| | - Lijun Zhou
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Qiang Liu
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Fan Yang
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Jingjuan Liu
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Jiao Qiu
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Jinjin Zhang
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Yumei Hou
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Miaolan Cen
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | - Zhongming Tian
- Tianjin Medical LaboratoryBGI‐TianjinBGI‐ShenzhenTianjinChina
| | - Weijiang Tang
- BGI‐Wuhan Clinical LaboratoriesBGI‐ShenzhenWuhanChina
| | - Hongyun Zhang
- Clinical laboratory of BGI HealthBGI‐ShenzhenShenzhenChina
| | | | - Ye Yin
- BGI GenomicsBGI‐ShenzhenShenzhenChina
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Chitty LS, Hui L, Ghidini A, Levy B, Deprest J, Van Mieghem T, Bianchi DW. In case you missed it: The Prenatal Diagnosis editors bring you the most significant advances of 2019. Prenat Diagn 2020; 40:287-293. [PMID: 31875323 DOI: 10.1002/pd.5632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 12/21/2022]
Affiliation(s)
- L S Chitty
- London North Genomic Laboratory, Great Ormond Street NHS Foundation Trust, and Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - L Hui
- Department of Obstetrics and Gynaecology, University of Melbourne, Melbourne, Victoria, Australia
| | - A Ghidini
- Antenatal Testing Centre, Inova Alexandria Hospital, Alexandria, VA
| | - B Levy
- Departments of Pathology and Cell Biology, Columbia University, New York, NY
| | - J Deprest
- Departments of Obstetrics and Gynaecology, University Hospitals Leuven, Leuven, Belgium
| | - T Van Mieghem
- Department of Obstetrics and Gynaecology, Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | - D W Bianchi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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Identification and characterization of extrachromosomal circular DNA in maternal plasma. Proc Natl Acad Sci U S A 2020; 117:1658-1665. [PMID: 31900366 PMCID: PMC6983429 DOI: 10.1073/pnas.1914949117] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We observed the presence of extrachromosomal circular DNA (eccDNA) in the plasma of pregnant women. We found that the plasma eccDNA molecules were longer than their linear counterparts. Among such eccDNA molecules, those of fetal origin were shorter than those of maternal origin. Characteristic dual-repeat patterns of eccDNA junctions might shed light on their possible generation mechanisms and provide them with distinctive signatures over linear cell-free DNA. Furthermore, the closed circular structure of eccDNA might allow resistance to exonucleases and thus higher stability of these molecules over their linear counterparts. These features of eccDNA provide opportunities for research and biomarker development. This work represents an example in the nascent field of plasma DNA topologics. We explored the presence of extrachromosomal circular DNA (eccDNA) in the plasma of pregnant women. Through sequencing following either restriction enzyme or Tn5 transposase treatment, we identified eccDNA molecules in the plasma of pregnant women. These eccDNA molecules showed bimodal size distributions peaking at ∼202 and ∼338 bp with distinct 10-bp periodicity observed throughout the size ranges within both peaks, suggestive of their nucleosomal origin. Also, the predominance of the 338-bp peak of eccDNA indicated that eccDNA had a larger size distribution than linear DNA in human plasma. Moreover, eccDNA of fetal origin were shorter than the maternal eccDNA. Genomic annotation of the overall population of eccDNA molecules revealed a preference of these molecules to be generated from 5′-untranslated regions (5′-UTRs), exonic regions, and CpG island regions. Two sets of trinucleotide repeat motifs flanking the junctional sites of eccDNA supported multiple possible models for eccDNA generation. This work highlights the topologic analysis of plasma DNA, which is an emerging direction for circulating nucleic acid research and applications.
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Shi J, Zhang R, Li J, Zhang R. Size profile of cell-free DNA: A beacon guiding the practice and innovation of clinical testing. Theranostics 2020; 10:4737-4748. [PMID: 32308746 PMCID: PMC7163439 DOI: 10.7150/thno.42565] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/06/2020] [Indexed: 12/25/2022] Open
Abstract
Cell-free DNA (cfDNA) has pioneered the development of noninvasive prenatal testing and liquid biopsy, its emerging applications include organ transplantation, autoimmune diseases, and many other disorders; size profile of cfDNA is a crucial biological property and is essential for its clinical applications. Therefore, a thorough mastery of the characteristic and potential applications of cfDNA size profile is needed. Methods: Based on the recent researches, we summarized the size profile of cfDNA in pregnant women, tumor patients, transplant recipients and systemic lupus erythematosus (SLE) patients to explore the common features. We also concluded the applications of size profile in pre-analytical phases, analytical phases for novel assays, and preparation of quality control materials (QCMs). Results: The size profile of cfDNA shared common features in different populations, and was distributed as a "ladder" pattern with a dominant peak at ~166 bp. However, cfDNA entailed slightly discrepant characteristics due to specific tissues of origin. The dominant peaks of fetal and maternal cfDNA fragments in pregnant women were at 143 bp and 166 bp, respectively. The plasma cfDNA in tumor patients, transplant recipients, and SLE patients had a peak of around 166 bp. In pre-analytical phases, size profile served as a vital indicator to judge the eligibility of specimens, thus ensuring the successful implementation of assays. More importantly, the size profile had the potential to enrich short fragments, calculate fetal fraction, detect fetal abnormalities, predict tumor progress in analytical phase and to guide the preparation of QCMs. Conclusions: Our finding summarized the characteristics and potential applications of cfDNA size profile, providing clinical researchers with novel assays by the extensive application of cfDNA.
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Affiliation(s)
- Jiping Shi
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Runling Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology; Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100730, People's Republic of China
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
- ✉ Corresponding author: Rui Zhang, Ph.D, Mailing address: National Center for Clinical Laboratories, Beijing Hospital, No.1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China. Tel: 86-10-58115053; Fax: 86-10-65212064; E-mail:
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Hui L, Bianchi DW. Fetal fraction and noninvasive prenatal testing: What clinicians need to know. Prenat Diagn 2019; 40:155-163. [PMID: 31821597 PMCID: PMC10040212 DOI: 10.1002/pd.5620] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/15/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022]
Abstract
The fetal fraction (FF) is a function of both biological factors and bioinformatics algorithms used to interpret DNA sequencing results. It is an essential quality control component of noninvasive prenatal testing (NIPT) results. Clinicians need to understand the biological influences on FF to be able to provide optimal post-test counseling and clinical management. There are many different technologies available for the measurement of FF. Clinicians do not need to know the details behind the bioinformatics algorithms of FF measurements, but they do need to appreciate the significant variations between the different sequencing technologies used by different laboratories. There is no universal FF threshold that is applicable across all platforms and there have not been any differences demonstrated in NIPT performance by sequencing platform or method of FF calculation. Importantly, while FF should be routinely measured, there is not yet a consensus as to whether it should be routinely reported to the clinician. The clinician should know what to expect from a standard test report and whether reasons for failed NIPT results are revealed. Emerging solutions to the challenges of samples with low FF should reduce rates of failed NIPT in the future. In the meantime, having a "plan B" prepared for those patients for whom NIPT is unsuccessful is essential in today's clinical practice.
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Affiliation(s)
- Lisa Hui
- Reproductive Epidemiology Group, Murdoch Children's Research Institute, Parkville, Victoria, Australia.,Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia.,Department of Perinatal Medicine, Mercy Hospital for Women, Heidelberg, Victoria, Australia.,Department of Obstetrics and Gynaecology, Northern Health, Epping, Victoria, Australia
| | - Diana W Bianchi
- Prenatal Genomics and Therapy Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland.,Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
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Ioannides M, Achilleos A, Kyriakou S, Kypri E, Loizides C, Tsangaras K, Constantinou L, Koumbaris G, Patsalis PC. Development of a new methylation-based fetal fraction estimation assay using multiplex ddPCR. Mol Genet Genomic Med 2019; 8:e1094. [PMID: 31821748 PMCID: PMC7005606 DOI: 10.1002/mgg3.1094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/17/2019] [Indexed: 01/12/2023] Open
Abstract
Background Non‐invasive prenatal testing (NIPT) for fetal aneuploidies has rapidly been incorporated into clinical practice. Current NGS‐based methods can reliably detect fetal aneuploidies non‐invasively with fetal fraction of at least 4%. Inaccurate fetal fraction assessment can compromise the accuracy of the test as affected samples with low fetal fraction have an increased risk for misdiagnosis. Using a novel set of fetal‐specific differentially methylated regions (DMRs) and methylation sensitive restriction digestion (MSRD), we developed a multiplex ddPCR assay for accurate detection of fetal fraction in maternal plasma. Methods We initially performed MSRD followed by methylation DNA immunoprecipitation (MeDIP) and NGS on fetal and non‐pregnant female tissues to identify fetal‐specific DMRs. DMRs with the highest methylation difference between the two tissues were selected for fetal fraction estimation employing MSRD and multiplex ddPCR. Chromosome Y multiplex ddPCR assay (YMM) was used as a reference standard, to develop our fetal fraction estimation model in male pregnancy samples. Additional 123 samples were tested to examine whether the model is sex dependent and/or ploidy dependent. Results In all, 93 DMRs were identified of which seven were selected for fetal fraction estimation. Statistical analysis resulted in the final model which included four DMRs (FFMM). High correlation with YMM‐based fetal fractions was observed using 85 male pregnancies (r = 0.86 95% CI: 0.80–0.91). The model was confirmed using an independent set of 53 male pregnancies. Conclusion By employing a set of well‐characterized DMRs, we developed a SNP‐, sex‐ and ploidy‐independent methylation‐based multiplex ddPCR assay for accurate fetal fraction estimation.
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de Wergifosse S, Bevilacqua E, Mezela I, El Haddad S, Gounongbe C, de Marchin J, Maggi V, Conotte S, Badr DA, Fils JF, Guizani M, Jani JC. Cell-free DNA analysis in maternal blood: comparing genome-wide versus targeted approach as a first-line screening test. J Matern Fetal Neonatal Med 2019; 34:3552-3561. [PMID: 31722585 DOI: 10.1080/14767058.2019.1686478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Objectives: To evaluate the failure rate and performance of cell-free DNA (cfDNA) testing as a first-line screening method for major trisomies, performed by two laboratories using different analytical methods: a targeted chromosome-selective method (Harmony® prenatal Test) versus a home-brew genome-wide (GW) massively parallel sequencing method (HB-cfDNA test), and to evaluate the clinical value of incidental findings for the latter method.Methods: CfDNA testing was performed in 3137 pregnancies with the Harmony® prenatal Test and in 3373 pregnancies with the HB-cfDNA test. Propensity score analysis was used to match women between both groups for maternal age, weight, gestational age at testing, in vitro fertilization, rate of twin pregnancies and that of aneuploidies. Detection rates for trisomy 21 were compared between the 2 laboratories. For the HB-cfDNA test, cases with rare incidental findings were reported, including their clinical follow-up.Results: The Harmony® prenatal Test failed at the first attempt in 90 (2.9%) of 3114 women and the HB-cfDNA test in 413 (12.2%) of 3373 women. Postmatched comparisons of the women's characteristics indicate a significantly lower failure rate in the Harmony® group (2.8%) than in the HB cfDNA group (12.4%; p < .001). Of the 90 women in whom the Harmony® prenatal Test failed, 61 had a repeat test, which still failed in 10, and of the 413 women in whom the HB-cfDNA test failed, 379 had a repeat test, which still failed in 110. The total failure rate after one or two attempts was therefore 1.3% (39/3114) for Harmony® and 4.3% (144/3373) for the HB cfDNA test. After the first or second Harmony® prenatal Test, a high-risk result was noted in 17 of the 17 cases with trisomy 21, in 5 of the seven cases with trisomy 18, and a no-call in two cases, and in the one case with trisomy 13. The respective numbers for the HB-cfDNA test are 17 of the 18 cases with trisomy 21, and a no-call in one case, 2 of the two cases with trisomy 18, and in 2 of the three cases with trisomy 13, and a no-call in one. Of the 3373 women with the HB-cfDNA test, a rare incidental finding was noted in 28 (0.8%) of the cases, of which only 2 were confirmed on amniocytes (one with microduplication 1q21.1q21.2 and one with a deletion Xp21.1), and in another case a deletion rather than a duplication of the long arm of chromosome 8 was found. In all 28 cases, there was normal clinical follow-up.Conclusions: Comparison of cfDNA testing between these two laboratories showed a four-fold lower failure rate with the Harmony® prenatal Test, with a similar detection rate for trisomy 21. We showed no clinical relevance of disclosing additional findings beyond common trisomies with the GW HB-cfDNA test.
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Affiliation(s)
- Sidonie de Wergifosse
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium.,Department of Obstetrics and Gynecology, University Hospital St Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - Elisa Bevilacqua
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Iris Mezela
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah El Haddad
- Department of Obstetrics and Gynecology, University Hospital St Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - Caroline Gounongbe
- Department of Obstetrics and Gynecology, University Hospital St Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Valeria Maggi
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | - Stéphanie Conotte
- Department of Blood Transfusion, University Hospital Brugmann, Brussels, Belgium
| | - Dominique A Badr
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Meriem Guizani
- Department of Obstetrics and Gynecology, University Hospital St Pierre, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques C Jani
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Brussels, Belgium
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van der Pol Y, Mouliere F. Toward the Early Detection of Cancer by Decoding the Epigenetic and Environmental Fingerprints of Cell-Free DNA. Cancer Cell 2019; 36:350-368. [PMID: 31614115 DOI: 10.1016/j.ccell.2019.09.003] [Citation(s) in RCA: 166] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/18/2019] [Accepted: 09/06/2019] [Indexed: 12/15/2022]
Abstract
Widespread adaptation of liquid biopsy for the early detection of cancer has yet to reach clinical utility. Circulating tumor DNA is commonly detected though the presence of genetic alterations, but only a minor fraction of tumor-derived cell-free DNA (cfDNA) fragments exhibit mutations. The cellular processes occurring in cancer development mark the chromatin. These epigenetic marks are reflected by modifications in the cfDNA methylation, fragment size, and structure. In this review, we describe how going beyond DNA sequence information alone, by analyzing cfDNA epigenetic and immune signatures, boosts the potential of liquid biopsy for the early detection of cancer.
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Affiliation(s)
- Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.
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Inferring fetal fractions from read heterozygosity empowers the noninvasive prenatal screening. Genet Med 2019; 22:301-308. [PMID: 31467446 PMCID: PMC7000331 DOI: 10.1038/s41436-019-0636-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/01/2019] [Indexed: 02/02/2023] Open
Abstract
Purpose Fetal fraction (FF) is the percent of cell-free DNA (cfDNA) in the
mother’s peripheral blood that is of fetal origin, which plays a pivotal role in
noninvasive prenatal screening (NIPS). We present a method that can reliably
estimate FFs by examining autosome single-nucleotide polymorphisms
(SNPs). Methods Even at a very low sequencing depth, there are plenty of SNPs
covered by more than one read. At those SNPs, we define read heterozygosity and
demonstrate that the percent of read heterozygosity is a function of FF, which
allows FF to be inferred. Results We first demonstrated the effectiveness of our method in inferring
FF. Then we used the inferred FF as an informative alternative prior to
computing Bayes factors to test for aneuploidy, and observed better power than
the Z-test. In analysis of clinical samples,
we were able to identify female–male twins thanks to the accurate FF
inference. Conclusion Knowing FF improves efficacy of NIPS. It brings a powerful Bayesian
method, allows “no call” for samples with small FFs, renders screening for XXY
syndrome simpler, and permits an adaptive design to sequence at a higher depth
for samples with small FFs.
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Gazdarica J, Hekel R, Budis J, Kucharik M, Duris F, Radvanszky J, Turna J, Szemes T. Combination of Fetal Fraction Estimators Based on Fragment Lengths and Fragment Counts in Non-Invasive Prenatal Testing. Int J Mol Sci 2019; 20:E3959. [PMID: 31416246 PMCID: PMC6719007 DOI: 10.3390/ijms20163959] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 11/17/2022] Open
Abstract
The reliability of non-invasive prenatal testing is highly dependent on accurate estimation of fetal fraction. Several methods have been proposed up to date, utilizing different attributes of analyzed genomic material, for example length and genomic location of sequenced DNA fragments. These two sources of information are relatively unrelated, but so far, there have been no published attempts to combine them to get an improved predictor. We collected 2454 single euploid male fetus samples from women undergoing NIPT testing. Fetal fractions were calculated using several proposed predictors and the state-of-the-art SeqFF method. Predictions were compared with the reference Y-based method. We demonstrate that prediction based on length of sequenced DNA fragments may achieve nearly the same precision as the state-of-the-art methods based on their genomic locations. We also show that combination of several sample attributes leads to a predictor that has superior prediction accuracy over any single approach. Finally, appropriate weighting of samples in the training process may achieve higher accuracy for samples with low fetal fraction and so allow more reliability for subsequent testing for genomic aberrations. We propose several improvements in fetal fraction estimation with a special focus on the samples most prone to wrong conclusion.
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Affiliation(s)
- Juraj Gazdarica
- Geneton Ltd., Bratislava 84104, Slovakia.
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 84104, Slovakia.
- Slovak Centre of Scientific and Technical Information, Bratislava 81104, Slovakia.
| | - Rastislav Hekel
- Geneton Ltd., Bratislava 84104, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 84104, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 81104, Slovakia
| | - Jaroslav Budis
- Geneton Ltd., Bratislava 84104, Slovakia
- Slovak Centre of Scientific and Technical Information, Bratislava 81104, Slovakia
- Comenius University Science Park, Bratislava 84104, Slovakia
| | | | - Frantisek Duris
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava 84248, Slovakia
| | - Jan Radvanszky
- Geneton Ltd., Bratislava 84104, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava 84505, Slovakia
| | - Jan Turna
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 84104, Slovakia
- Comenius University Science Park, Bratislava 84104, Slovakia
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava 84505, Slovakia
| | - Tomas Szemes
- Geneton Ltd., Bratislava 84104, Slovakia
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava 84104, Slovakia
- Comenius University Science Park, Bratislava 84104, Slovakia
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El Khattabi LA, Brun S, Gueguen P, Chatron N, Guichoux E, Schutz S, Nectoux J, Sorlin A, Quere M, Boudjarane J, Tsatsaris V, Mandelbrot L, Schluth-Bolard C, Dupont JM, Rooryck C. Performance of semiconductor sequencing platform for non-invasive prenatal genetic screening for fetal aneuploidy: results from a multicenter prospective cohort study in a clinical setting. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2019; 54:246-254. [PMID: 30191619 DOI: 10.1002/uog.20112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 08/03/2018] [Accepted: 08/15/2018] [Indexed: 06/08/2023]
Abstract
OBJECTIVE To validate and evaluate the performance metrics of the high-throughput semiconductor sequencing platform, Ion Proton®, in non-invasive prenatal genetic screening (NIPS) for common fetal aneuploidies in a clinical setting. METHODS This prospective cohort study included 2505 pregnant women from eight academic genetics laboratories (695 high risk for trisomy 21 (risk ≥ 1/250) pregnancies in a validation study, and 1810 such pregnancies, without ultrasound anomalies, in a real-life NIPS clinical setting). Outcome was available for all cases in the validation cohort and for 521 in the clinical cohort. Cell-free DNA from plasma samples was sequenced using the Ion Proton sequencer, and sequencing data were analyzed using the open-access software, WISECONDOR. Performance metrics for detection of trisomies 21, 18 and 13 were calculated based on either fetal karyotype result or clinical data collected at birth. We also evaluated the failure rate and compared three methods of fetal fraction quantification (RASSF1A assay, and DEFRAG and SANEFALCON software). RESULTS Results from both cohorts were consistent and their gestational age was not significantly different so their data were combined to increase the sample size for analysis. Sensitivities and specificities, respectively, were as follows: for trisomy 21, 98.3% (95% CI, 93.5-99.7%) and 99.9% (95% CI, 99.4-100%); for trisomy 18, 96.7% (95% CI, 80.9-99.8%) and 100% (95% CI, 99.6-100%); and for trisomy 13, 94.1% (95% CI, 69.2-99.7%) and 100% (95% CI, 99.6-100%). Our failure rate was 1.2% initially and as low as 0.6% after retesting some of the failed samples. Fetal fraction estimation by the RASSF1A assay was consistent with DEFRAG results, and both were adequate for routine diagnosis. CONCLUSIONS We describe one of the largest studies evaluating Ion Proton-based NIPS and the first clinical study reporting pregnancy outcome in a large series of patients. This platform is highly efficient in detecting the three most common trisomies. Our protocol is robust and can be implemented easily in any medical genetics laboratory. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- L Allach El Khattabi
- Service de Cytogénétique, Hôpital Cochin, Hôpitaux Universitaires Paris Centre, Assistance Publique Hôpitaux de Paris, INSERM U1016, Université Paris Descartes, Paris, France
| | - S Brun
- Maternité Centre Aliénor d'Aquitaine, CHU de Bordeaux, Bordeaux, France
| | - P Gueguen
- Laboratoire de Génétique Moléculaire, INSERM U1078, CHRU de Brest, Brest, France
| | - N Chatron
- Service de Génétique, HCL, UCBL1, Lyon, France
| | - E Guichoux
- BIOGECO, INRA, University de Bordeaux, Cestas, France
| | - S Schutz
- Laboratoire de Génétique Moléculaire, INSERM U1078, CHRU de Brest, Brest, France
| | - J Nectoux
- Service de Biochimie et Génétique Moléculaire, Hôpital Cochin, Assistance Publique Hôpitaux de Paris, Hôpitaux Universitaires Paris Centre, Paris, France
| | - A Sorlin
- Service de Génétique, CHRU Nancy, INSERM U1256, Université de Lorraine, Nancy, France
| | - M Quere
- Service de Génétique Médicale, Hôpital de l'Archet II, CHU de Nice, Nice, France
| | - J Boudjarane
- Département de Génétique Médicale, CHU la Timone, Marseille, France
| | - V Tsatsaris
- Maternité Port-Royal, Hôpital Cochin, Hôpitaux Universitaires Paris Centre, Assistance Publique Hôpitaux de Paris, Université Paris Descartes, Paris, France
| | - L Mandelbrot
- Département de Gynécologie Obstétrique, Hôpital Louis Mourier, Assistance Publique des Hôpitaux de Paris, Université Paris Diderot, Colombes, France
| | | | - J M Dupont
- Service de Cytogénétique, Hôpital Cochin, Hôpitaux Universitaires Paris Centre, Assistance Publique Hôpitaux de Paris, INSERM U1016, Université Paris Descartes, Paris, France
| | - C Rooryck
- Service de Génétique Médicale, CHU de Bordeaux, Université de Bordeaux, Bordeaux, France
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Raman L, Baetens M, De Smet M, Dheedene A, Van Dorpe J, Menten B. PREFACE: In silico pipeline for accurate cell-free fetal DNA fraction prediction. Prenat Diagn 2019; 39:925-933. [PMID: 31219182 PMCID: PMC6771918 DOI: 10.1002/pd.5508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/16/2019] [Accepted: 06/15/2019] [Indexed: 12/12/2022]
Abstract
Objective During routine noninvasive prenatal testing (NIPT), cell‐free fetal DNA fraction is ideally derived from shallow‐depth whole‐genome sequencing data, preventing the need for additional experimental assays. The fraction of aligned reads to chromosome Y enables proper quantification for male fetuses, unlike for females, where advanced predictive procedures are required. This study introduces PREdict FetAl ComponEnt (PREFACE), a novel bioinformatics pipeline to establish fetal fraction in a gender‐independent manner. Methods PREFACE combines the strengths of principal component analysis and neural networks to model copy number profiles. Results For sets of roughly 1100 male NIPT samples, a cross‐validated Pearson correlation of 0.9 between predictions and fetal fractions according to Y chromosomal read counts was noted. PREFACE enables training with both male and unlabeled female fetuses. Using our complete cohort (nfemale = 2468, nmale = 2723), the correlation metric reached 0.94. Conclusions Allowing individual institutions to generate optimized models sidelines between‐laboratory bias, as PREFACE enables user‐friendly training with a limited amount of retrospective data. In addition, our software provides the fetal fraction based on the copy number state of chromosome X. We show that these measures can predict mixed multiple pregnancies, sex chromosomal aneuploidies, and the source of observed aberrations. What's already known about this topic?
Cell‐free fetal DNA fraction is an important estimate during noninvasive prenatal testing (NIPT). Most techniques to establish fetal fraction require experimental procedures, which impede routine execution.
What does this study add?
PREFACE is a novel software to accurately predict fetal fraction based on solely shallow‐depth whole‐genome sequencing data, the fundamental base of a default NIPT assay. In contrast to previous efforts, PREFACE enables user‐friendly model training with a limited amount of retrospective data.
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Affiliation(s)
- Lennart Raman
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Machteld Baetens
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Matthias De Smet
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University, Ghent University Hospital, Ghent, Belgium
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Korostin DO, Plakhina DA, Belova VA. Noninvasive prenatal testing: the aspects of its introduction into clinical practice. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2019. [DOI: 10.24075/brsmu.2019.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The last couple of years have witnessed the rapid development of prenatal molecular-based screening for fetal aneuploidies that utilizes the analysis of cell-free DNA circulating in the bloodstream of a pregnant woman. The present review looks at the potential and limitations of such testing and the possible causes of false-positive and false-negative results. The review also describes the underlying principles of data acquisition and analysis the testing involves. In addition, we talk about the opinions held by the expert community and some aspects of legislation on the use of noninvasive prenatal testing (NIPT) in clinical practice in the countries where NIPT is much more widespread than in Russia.
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Affiliation(s)
- D. O. Korostin
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
| | | | - V. A. Belova
- Pirogov Russian National Research Medical University, Moscow, Russia; Genotek Ltd., Moscow, Russia
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Abstract
Prenatal testing in recent years has been moving toward non-invasive methods to determine the fetal risk for genetic disorders without incurring the risk of miscarriage. Rapid progress of modern high-throughput molecular technologies along with the discovery of cell-free fetal DNA in maternal plasma led to novel screening methods for fetal chromosomal aneuploidies. Such tests are referred to as non-invasive prenatal tests (NIPTs), non-invasive prenatal screening, or prenatal cell-free DNA screening. Owing to many advantages, the adoption of NIPT in routine clinical practice was very rapid and global. As an example, NIPT has recently become a standard screening procedure for all pregnant women in the Netherlands. On the other hand, invasive sampling procedures remain important, especially for their diagnostic value in the confirmation of NIPT-positive findings and the detection of Mendelian disorders. In this review, we focus on current trends in the field of NIPT and discuss their benefits, drawbacks, and consequences in regard to routine diagnostics.
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Affiliation(s)
- Ondrej Pös
- Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia
| | - Jaroslav Budiš
- University Science Park, Comenius University, Bratislava, 84104, Slovakia
| | - Tomáš Szemes
- Faculty of Natural Sciences, Comenius University, Bratislava, 84215, Slovakia.,University Science Park, Comenius University, Bratislava, 84104, Slovakia
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45
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Sistermans EA. The Importance of Reliable Quality Control Materials for Noninvasive Prenatal Testing. Clin Chem 2019; 65:720-722. [PMID: 30996053 DOI: 10.1373/clinchem.2019.303701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Erik A Sistermans
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
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Vong JSL, Jiang P, Cheng SH, Lee WS, Tsang JCH, Leung TY, Chan KCA, Chiu RWK, Lo YMD. Enrichment of fetal and maternal long cell-free DNA fragments from maternal plasma following DNA repair. Prenat Diagn 2019; 39:88-99. [PMID: 30575063 PMCID: PMC6619283 DOI: 10.1002/pd.5406] [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: 07/11/2018] [Revised: 12/09/2018] [Accepted: 12/16/2018] [Indexed: 12/19/2022]
Abstract
Objective Cell‐free DNA (cfDNA) fragments in maternal plasma contain DNA damage and may negatively impact the sensitivity of noninvasive prenatal testing (NIPT). However, some of these DNA damages are potentially reparable. We aimed to recover these damaged cfDNA molecules using PreCR DNA repair mix. Methods cfDNA was extracted from 20 maternal plasma samples and was repaired and sequenced by the Illumina platform. Size profiles and fetal DNA fraction changes of repaired samples were characterized. Targeted sequencing of chromosome Y sequences was used to enrich fetal cfDNA molecules following repair. Single‐molecule real‐time (SMRT) sequencing platform was employed to characterize long (>250 bp) cfDNA molecules. NIPT of five trisomy 21 samples was performed. Results Size profiles of repaired libraries were altered, with significantly increased long (>250 bp) cfDNA molecules. Single nucleotide polymorphism (SNP)‐based analyses showed that both fetal‐ and maternal‐derived cfDNA molecules were enriched by the repair. Fetal DNA fractions in maternal plasma showed a small but consistent (4.8%) increase, which were contributed by a higher increment of long fetal cfDNA molecules. z‐score values were improved in NIPT of all trisomy 21 samples. Conclusion Plasma DNA repair recovers and enriches long cfDNA molecules of both fetal and maternal origins in maternal plasma. What is already known about this topic?
Most of the cell‐free DNA (cfDNA) fragments in maternal plasma have sizes less than 200 bp, with fetal molecules being shorter than maternal ones. DNA damages exist in cfDNA, particularly single‐strand nicks. Occasional no call for noninvasive prenatal testing (NIPT) can be caused by insufficient fetal DNA fraction.
What does this study add?
Repair of cfDNA by PreCR repair mix can recover a subset of long (>250 bp) cfDNA molecules. Both fetal and maternal long cfDNA are enriched by PreCR repair treatment. Mild but consistent increments in fetal DNA fractions after PreCR repair, which are contributed by higher enrichment of long fetal cfDNA molecules. PreCR repair treatment improves NIPT of trisomy 21 by elevating z scores resulting in better discrimination of aneuploid from euploid samples.
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Affiliation(s)
- Joaquim S L Vong
- Centre for Research Into Circulating Fetal Nucleic Acids, 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, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Research Into Circulating Fetal Nucleic Acids, 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, Shatin, New Territories, Hong Kong SAR, China
| | - Suk-Hang Cheng
- Centre for Research Into Circulating Fetal Nucleic Acids, 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, Shatin, New Territories, Hong Kong SAR, China
| | - Wing-Shan Lee
- Centre for Research Into Circulating Fetal Nucleic Acids, 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, Shatin, New Territories, Hong Kong SAR, China
| | - Jason C H Tsang
- Centre for Research Into Circulating Fetal Nucleic Acids, 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, Shatin, New Territories, Hong Kong SAR, China
| | - Tak-Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Centre for Research Into Circulating Fetal Nucleic Acids, 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, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Centre for Research Into Circulating Fetal Nucleic Acids, 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, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Research Into Circulating Fetal Nucleic Acids, 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, Shatin, New Territories, Hong Kong SAR, China
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Epigenetic Biomarkers in Cell-Free DNA and Applications in Liquid Biopsy. Genes (Basel) 2019; 10:genes10010032. [PMID: 30634483 PMCID: PMC6356936 DOI: 10.3390/genes10010032] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 12/20/2018] [Accepted: 01/02/2019] [Indexed: 12/21/2022] Open
Abstract
Cell-free circulating DNA (cfDNA) in plasma has gained global interest as a diagnostic material for noninvasive prenatal testing and cancer diagnosis, or the so-called “liquid biopsy”. Recent studies have discovered a great number of valuable genetic and epigenetic biomarkers for cfDNA-based liquid biopsy. Considering that the genetic biomarkers, e.g., somatic mutations, usually vary from case to case in most cancer patients, epigenetic biomarkers that are generalizable across various samples thus possess certain advantages. In this study, we reviewed the most recent studies and advances on utilizing epigenetic biomarkers for liquid biopsies. We first reviewed more traditional methods of using tissue/cancer-specific DNA methylation biomarkers and digital PCR or sequencing technologies for cancer diagnosis, as well as tumor origin determination. In the second part, we discussed the emerging novel approaches for exploring the biological basis and clinical applications of cfDNA fragmentation patterns. We further provided our comments and points of view on the future directions on epigenetic biomarker development for cfDNA-based liquid biopsies.
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Fetal fraction evaluation in non-invasive prenatal screening (NIPS). Eur J Hum Genet 2018; 27:198-202. [PMID: 30254213 DOI: 10.1038/s41431-018-0271-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/03/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022] Open
Abstract
An important factor in quality control of non-invasive prenatal screening (NIPS) or testing (NIPT) is a sufficient percentage of fetal DNA to avoid false-negative results. Here we evaluate 14,379 shallow whole-genome sequenced diagnostic NIPS samples, as well as negative controls, for both technical and biological factors that can influence fetal fraction and its assessment. Technically, bioinformatics analyses can have a profound impact on fetal fraction determination. We found best performance for fetal fraction determination with the Y chromosome based tool DEFRAG for male fetuses and the count based tool SeqFF for female fetuses. Biologically, gestational age of up to 21 weeks and maternal age had no influence on fetal fraction, while an increase in weight and BMI had a negative influence on fetal fraction. While a trend was observed, no statistically significant difference in fetal fraction was found between trisomy and normal samples. Overall, these results confirm the influence of biological factors and give insight into technical factors that can affect fetal fractions in NIPS.
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49
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Tian Y, Zhang L, Tian W, Gao J, Jia L, Cui S. Analysis of the accuracy of Z-scores of non-invasive prenatal testing for fetal Trisomies 13, 18, and 21 that employs the ion proton semiconductor sequencing platform. Mol Cytogenet 2018; 11:49. [PMID: 30159034 PMCID: PMC6109306 DOI: 10.1186/s13039-018-0397-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022] Open
Abstract
Background Non-invasive prenatal testing (NIPT) is frequently being used to screen for trisomies 13, 18 and 21 for prenatal diagnosis. However, NIPT performs poorly when compared with invasive testing and thus should not be used to diagnose trisomies. The result of NIPT for an individual woman in most genome-wide methods is calculated as a Z-score. The aim of this study was to assess the correlation between Z-scores of NIPT results and the accuracy of non-invasive prenatal testing. Results We evaluated 108 pregnant women with positive NIPT results, which were validated through karyotype analysis of amniotic fluid puncture by means of sequencing, bioinformatics analysis, and follow-up. Utilizing the ion proton semiconductor sequencing platform, we report a performance evaluation of NIPT-positive results at Third Affiliated Hospital of Zhengzhou University of Henan Province, China, by classifying Z-scores as 3 ≤ Z<5, 5 ≤ Z < 9 and Z ≥ 9. The findings indicate that positive NIPT results at Z ≥ 9 have a higher accuracy compared with positive NIPT results at 5 ≤ Z < 9 and 3 ≤ Z<5. Conclusions The findings show that Z-scores of NIPT results are closely related to the accuracy of non-invasive prenatal testing. However, false-positive NIPT results at 3 ≤ Z<5 may occur due to confined placental mosaicism (CPM).
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Affiliation(s)
- Yuan Tian
- 1Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052 China
| | - Linlin Zhang
- 1Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052 China
| | - Weifang Tian
- 1Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052 China
| | - Jinshuang Gao
- 1Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052 China
| | - Liting Jia
- 1Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052 China
| | - Shihong Cui
- 2Department of gynaecology and obstetrics, The Third Affiliated Hospital of Zhengzhou University, No. 7 Front Kangfu Street, Er'qi District, Zhengzhou, 450052 China
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50
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Isochromosome 21q is overrepresented among false-negative cell-free DNA prenatal screening results involving Down syndrome. Eur J Hum Genet 2018; 26:1490-1496. [PMID: 29899373 DOI: 10.1038/s41431-018-0188-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/17/2018] [Accepted: 05/15/2018] [Indexed: 11/09/2022] Open
Abstract
False-negative cell-free DNA (cfDNA) screening results involving Down syndrome are rare, but have high clinical impact on patients and their healthcare providers. Understanding the biology behind these results may allow for improved diagnostic follow-up and counseling. In 5 different centers offering cfDNA prenatal screening, 9 false-negative results were documented in 646 confirmed cases of trisomy 21; a false-negative rate of 1.4% (95% CI, 0.7-2.6). False-negative results included 4 cases of classical trisomy 21 and 5 cases with a de novo 21q;21q rearrangement. Two out of five rearrangements had molecular studies and were confirmed as isochromosomes. When combined with reports from the cfDNA screening literature, 8 out of 29 (28%) Down syndrome cases with a false-negative "non-invasive prenatal test" (NIPT) were associated with a 21q;21q rearrangement, compared with 2% reported in live born children with Down syndrome. In our laboratory series, evidence for placental or fetal mosaicism was present in 3 out of 3 true-positive cases involving a 21q;21q rearrangement and was confirmed in one false-negative case where placental material was available for study. Isochromosome 21q rearrangements are thus overrepresented among false-negative cfDNA screening results involving Down syndrome. Postzygotic isochromosome formation leading to placental mosaicism provides a biological cause for the increased prevalence of these rearrangements among false-negative cases. For clinical practice, a low trisomic fraction (z-score or equivalent measure) relative to the fetal fraction suggests placental mosaicism. Care should be taken as these cases may not reflect confined placental mosaicism, but rather full trisomy in the presence of a placenta containing normal cells.
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