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Miller AM, Bale TA. Leveraging archival cerebrospinal fluid samples for genetic insights from cell-free DNA. Cancer Cytopathol 2024; 132:212-213. [PMID: 38427323 DOI: 10.1002/cncy.22794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Cerebrospinal fluid (CSF) samples are often a rich source of tumor‐derived cell‐free DNA (cfDNA), a high degree of success in detecting tumor mutations can even be achieved with archival CSF samples.
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Affiliation(s)
- Alexandra M Miller
- Department of Neurology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tejus A Bale
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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2
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Clausen FB. Antenatal RHD screening to guide antenatal anti-D immunoprophylaxis in non-immunized D- pregnant women. Immunohematology 2024; 40:15-27. [PMID: 38739027 DOI: 10.2478/immunohematology-2024-004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
In pregnancy, D- pregnant women may be at risk of becoming immunized against D when carrying a D+ fetus, which may eventually lead to hemolytic disease of the fetus and newborn. Administrating antenatal and postnatal anti-D immunoglobulin prophylaxis decreases the risk of immunization substantially. Noninvasive fetal RHD genotyping, based on testing cell-free DNA extracted from maternal plasma, offers a reliable tool to predict the fetal RhD phenotype during pregnancy. Used as a screening program, antenatal RHD screening can guide the administration of antenatal prophylaxis in non-immunized D- pregnant women so that unnecessary prophylaxis is avoided in those women who carry a D- fetus. In Europe, antenatal RHD screening programs have been running since 2009, demonstrating high test accuracies and program feasibility. In this review, an overview is provided of current state-of-the-art antenatal RHD screening, which includes discussions on the rationale for its implementation, methodology, detection strategies, and test performance. The performance of antenatal RHD screening in a routine setting is characterized by high accuracy, with a high diagnostic sensitivity of ≥99.9 percent. The result of using antenatal RHD screening is that 97-99 percent of the women who carry a D- fetus avoid unnecessary prophylaxis. As such, this activity contributes to avoiding unnecessary treatment and saves valuable anti-D immunoglobulin, which has a shortage worldwide. The main challenges for a reliable noninvasive fetal RHD genotyping assay are low cell-free DNA levels, the genetics of the Rh blood group system, and choosing an appropriate detection strategy for an admixed population. In many parts of the world, however, the main challenge is to improve the basic care for D- pregnant women.
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Affiliation(s)
- Frederik B Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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3
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Cepeda J, Racca ME, Rossetti MF, Cardozo MA, Gaydou L, Luque EH, Muñoz-de-Toro M, Milesi MM, Varayoud J, Ramos JG. A Reliable Method for Quantifying Plasma Cell-Free DNA Using an Internal Standard Strategy: Evaluation in a Cohort of Non-Pregnant and Pregnant Women. Reprod Sci 2024; 31:987-996. [PMID: 38030813 DOI: 10.1007/s43032-023-01403-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023]
Abstract
The use of plasma cell-free DNA (cfDNA) as a useful biomarker in obstetric clinical practice has been delayed due to the lack of reliable quantification protocols. We developed a protocol to quantify plasma cfDNA using an internal standard strategy to overcome difficulties posed by low levels and high fragmentation of cfDNA. cfDNA was isolated from plasma samples of non-pregnant (NP, n = 26) and pregnant (P, n = 26) women using a commercial kit and several elution volumes were evaluated. qPCR parameters were optimized for cfDNA quantification, and several quantities of a recombinant standard were evaluated as internal standard. Absolute quantification was performed using a standard curve and the quality of the complete method was evaluated. cfDNA was eluted in a 50-μl volume, actin-β (ACTB) was selected as the target gene, and qPCR parameters were optimized. The ACTB standard was constructed and 1000 copies were selected as internal standard. The standard curve showed R2 = 0.993 and E = 109.7%, and the linear dynamic range was defined between 102 and 106 ACTB copies/tube. Repeatability and reproducibility in terms of CV were 19% and up to 49.5% for ACTB copies per milliliter of plasma, respectively. The range of cfDNA levels was 428-18,851 copies/mL in NP women and 4031-2,019,363 copies/mL in P women, showing significant differences between the groups. We recommend the application of internal standard strategy for a reliable plasma cfDNA quantification. This methodology holds great potential for a future application in the obstetric field.
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Affiliation(s)
- Julieta Cepeda
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
| | - M Emilia Racca
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - M Florencia Rossetti
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
| | - M Alejandra Cardozo
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
- Laboratorios BLUT, Santa Fe, Argentina
| | - Luisa Gaydou
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Enrique H Luque
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Cátedra de Fisiología Humana, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Mónica Muñoz-de-Toro
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Cátedra de Patología Humana, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - M Mercedes Milesi
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Cátedra de Fisiología Humana, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Jorgelina Varayoud
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina
- Facultad de Bioquímica y Ciencias Biológicas, Cátedra de Fisiología Humana, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina
| | - Jorge G Ramos
- Facultad de Bioquímica y Ciencias Biológicas, Instituto de Salud y Ambiente del Litoral (ISAL), Universidad Nacional del Litoral (UNL)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Santa Fe, Argentina.
- Departamento de Bioquímica Clínica y Cuantitativa, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral (UNL), Santa Fe, Argentina.
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4
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Cendejas-Gomez JJ, Inman BA. Liquid Biopsies Will Drive Treatment Decisions in the Future. Eur Urol Oncol 2024; 7:177-178. [PMID: 37980252 DOI: 10.1016/j.euo.2023.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 10/27/2023] [Indexed: 11/20/2023]
Affiliation(s)
| | - Brant A Inman
- Division of Urology, Western University, London, Canada; Department of Oncology, Western University, London, Canada; Lawson Health Research Institute, Western University, London, Canada.
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Kwon HJ, Yun S, Joo J, Park D, Do WJ, Lee S, Lee MS. Improving the accuracy of noninvasive prenatal testing through size-selection between fetal and maternal cfDNA. Prenat Diagn 2023; 43:1581-1592. [PMID: 37975672 DOI: 10.1002/pd.6464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 09/30/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023]
Abstract
OBJECTIVES In general, fetal cfDNA is shorter than maternal cfDNA, and accuracy of noninvasive prenatal testing (NIPT) results can be improved by selecting shorter cfDNA fragments to enrich fetal-derived cfDNA. This study investigated potential improvements in the accuracy of NIPT by performing classification and analysis based on differences in cfDNA size. METHODS We performed paired-end sequencing to identify size ranges of fetal and maternal cfDNA from 62,374 pregnant women. We then developed a size-selection method to isolate and analyze both fetal and maternal cfDNA, defining fetal-derived cfDNA as less than 150 bp and maternal-derived cfDNA as greater than 180 bp. RESULTS By implementing size-selection method, the accuracy of NIPT was improved, resulting in an increase in the overall positive predictive value for all aneuploidies from 89.57% to 97.1%. This was achieved by enriching both fetal and maternal-derived cfDNA, which increased fetal DNA fraction while the number of false positives for all aneuploidies was reduced by more than 70%. CONCLUSIONS We identified the differences in read length between fetal and maternal-derived cfDNA, and selectively enriched both shorter and longer cfDNA fragments for subsequent analysis. Our approach can increase the detection accuracy of NIPT for detecting fetal aneuploidies and reduce the number of false positives caused by maternal chromosomal abnormalities.
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Affiliation(s)
- Hyuk-Jung Kwon
- R&D Department, Eone-Diagnomics Genome Center, Incheon, Republic of Korea
| | - Seonyoung Yun
- R&D Department, Eone-Diagnomics Genome Center, Incheon, Republic of Korea
| | - Joungsu Joo
- R&D Department, Eone-Diagnomics Genome Center, Incheon, Republic of Korea
| | - Dabin Park
- R&D Department, Eone-Diagnomics Genome Center, Incheon, Republic of Korea
| | - Woo-Jung Do
- R&D Department, Eone-Diagnomics Genome Center, Incheon, Republic of Korea
| | - Sunghoon Lee
- R&D Department, Eone-Diagnomics Genome Center, Incheon, Republic of Korea
| | - Min-Seob Lee
- R&D Department, Eone-Diagnomics Genome Center, Incheon, Republic of Korea
- Diagnomics, San Diego, California, USA
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Liu DD, Muliaditan D, Viswanathan R, Cui X, Cheow LF. Melt-Encoded-Tags for Expanded Optical Readout in Digital PCR (METEOR-dPCR) Enables Highly Multiplexed Quantitative Gene Panel Profiling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301630. [PMID: 37485651 PMCID: PMC10520687 DOI: 10.1002/advs.202301630] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/27/2023] [Indexed: 07/25/2023]
Abstract
Digital PCR (dPCR) is an important tool for precise nucleic acid quantification in clinical setting, but the limited multiplexing capability restricts its applications for quantitative gene panel profiling. Here, this work describes melt-encoded-tags for expanded optical readout in digital PCR (METEOR-dPCR), a simple two-step assay that enables simultaneous quantification of a large panel of arbitrary genes in a dPCR platform. Target genes are quantitatively converted into DNA tags with unique melting temperatures through a ligation approach. These tags are then counted and distinguished by their melt-curve profiles on a dPCR platform. A multiplexing capacity of M^N, where M is the number of resolvable melting temperature and N is the number of fluorescence channel, can be achieved. This work validates METEOR-dPCR with simultaneous DNA copy number profiling of 60 targets using dPCR in cancer cells, and demonstrates its sensitivity for estimating tumor fraction in mixed tumor and normal DNA samples. The rapid, quantitative, and highly multiplexed METEOR-dPCR assay will have wide appeal for many clinical applications.
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Affiliation(s)
- Dong Dong Liu
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
| | - Daniel Muliaditan
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
- Genome institute of SingaporeAgency for ScienceTechnology and ResearchSingapore138672Singapore
| | - Ramya Viswanathan
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
| | - Xu Cui
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
| | - Lih Feng Cheow
- Institute for Health Innovation and TechnologyNational University of SingaporeSingapore117599Singapore
- Department of Biomedical EngineeringFaculty of EngineeringNational University of SingaporeSingapore117583Singapore
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Diaz IM, Nocon A, Held SAE, Kobilay M, Skowasch D, Bronkhorst AJ, Ungerer V, Fredebohm J, Diehl F, Holdenrieder S, Holtrup F. Pre-Analytical Evaluation of Streck Cell-Free DNA Blood Collection Tubes for Liquid Profiling in Oncology. Diagnostics (Basel) 2023; 13:diagnostics13071288. [PMID: 37046506 PMCID: PMC10093569 DOI: 10.3390/diagnostics13071288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Excellent pre-analytical stability is an essential precondition for reliable molecular profiling of circulating tumor DNA (ctDNA) in oncological diagnostics. Therefore, in vitro degradation of ctDNA and the additional release of contaminating genomic DNA from lysed blood cells must be prevented. Streck Cell-Free DNA blood collection tubes (cfDNA BCTs) have proposed advantages over standard K2EDTA tubes, but mainly have been tested in healthy individuals. Blood was collected from cancer patients (n = 53) suffering from colorectal (n = 21), pancreatic (n = 11), and non-small-cell lung cancer (n = 21) using cfDNA BCT tubes and K2EDTA tubes that were processed immediately or after 3 days (BCTs) or 6 hours (K2EDTA) at room temperature. The cfDNA isolated from these samples was characterized in terms of yield using LINE-1 qPCR; the level of gDNA contamination; and the mutation status of KRAS, NRAS, and EGFR genes using BEAMing ddPCR. CfDNA yield and gDNA levels were comparable in both tube types and were not affected by prolonged storage of blood samples for at least 3 days in cfDNA BCTs or 6 hours in K2EDTA tubes. In addition, biospecimens collected in K2EDTA tubes and cfDNA BCTs stored for up to 3 days demonstrated highly comparable levels of mutational load across all respective cancer patient cohorts and a wide range of concentrations. Our data support the applicability of clinical oncology specimens collected and stored in cfDNA BCTs for up to 3 days for reliable cfDNA and mutation analyses.
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8
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Koval AP, Khromova AS, Blagodatskikh KA, Zhitnyuk YV, Shtykova YA, Alferov AA, Kushlinskii NE, Shcherbo DS. Application of PCR-based approaches for evaluation of cell-free DNA fragmentation in colorectal cancer. Front Mol Biosci 2023; 10:1101179. [PMID: 37051326 PMCID: PMC10083340 DOI: 10.3389/fmolb.2023.1101179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/14/2023] [Indexed: 03/29/2023] Open
Abstract
Cell-free DNA (cfDNA) testing is the core of most liquid biopsy assays. In particular, cfDNA fragmentation features could facilitate non-invasive cancer detection due to their interconnection with tumor-specific epigenetic alterations. However, the final cfDNA fragmentation profile in a purified sample is the result of a complex interplay between informative biological and artificial technical factors. In this work, we use ddPCR to study cfDNA lengths in colorectal cancer patients and observe shorter and more variable cfDNA fragments in accessible chromatin loci compared to the densely packed pericentromeric region. We also report a convenient qPCR system suitable for screening cfDNA samples for artificial high molecular weight DNA contamination.
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Affiliation(s)
- Anastasia P. Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexandra S. Khromova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A. Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Center of Genetics and Reproductive Medicine “Genetico”, Moscow, Russia
| | - Yulia V. Zhitnyuk
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Aleksandr A. Alferov
- Laboratory of Clinical Biochemistry, N. N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Nikolay E. Kushlinskii
- Laboratory of Clinical Biochemistry, N. N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S. Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- *Correspondence: Dmitry S. Shcherbo,
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Shaw J, Scotchman E, Paternoster B, Ramos M, Nesbitt S, Sheppard S, Snowsill T, Chitty LS, Chandler N. Non-invasive fetal genotyping for maternal alleles with droplet digital PCR: A comparative study of analytical approaches. Prenat Diagn 2023; 43:477-488. [PMID: 36760169 DOI: 10.1002/pd.6333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
OBJECTIVES To develop a flexible droplet digital PCR (ddPCR) workflow to perform non-invasive prenatal diagnosis via relative mutation dosage (RMD) for maternal pathogenic variants with a range of inheritance patterns, and to compare the accuracy of multiple analytical approaches. METHODS Cell free DNA (cfDNA) was tested from 124 archived maternal plasma samples: 88 cases for sickle cell disease and 36 for rare Mendelian conditions. Three analytical methods were compared: sequential probability ratio testing (SPRT), Bayesian and z-score analyses. RESULTS The SPRT, Bayesian and z-score analyses performed similarly well with correct prediction rates of 96%, 97% and 98%, respectively. However, there were high rates of inconclusive results for each cohort, particularly for z-score analysis which was 31% overall. Two samples were incorrectly classified by all three analytical methods; a false negative result predicted for a fetus affected with sickle cell disease and a false positive result predicting the presence of an X-linked IDS variant in an unaffected fetus. CONCLUSIONS ddPCR can be applied to RMD for diverse conditions and inheritance patterns, but all methods carry a small risk of erroneous results. Further evaluation is required both to reduce the rate of inconclusive results and explore discordant results in more detail.
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Affiliation(s)
- Joe Shaw
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Ben Paternoster
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Maureen Ramos
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sarah Nesbitt
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Sophie Sheppard
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | | | - Lyn S Chitty
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK.,Genetic and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
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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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Daryabari SS, Giroux S, Caron A, Chau B, Langlois S, Rousseau F. Improving Fetal Fraction of Noninvasive Prenatal Screening Samples Collected in EDTA-Gel Tubes Using Gel Size Selection: A Head-To-Head Comparison of Methods. J Mol Diagn 2022; 24:955-962. [PMID: 35820622 DOI: 10.1016/j.jmoldx.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/03/2022] [Accepted: 06/14/2022] [Indexed: 11/28/2022] Open
Abstract
The objective of this study was to compare the use of EDTA-gel blood collection tubes with and without size selection to cell-stabilizing collection tubes for remote blood sampling for noninvasive prenatal screening (NIPS). We recruited 61 pregnant women at 10 to 14 weeks' gestation undergoing NIPS. Participants were phlebotomized with Streck and EDTA-gel tubes. EDTA-gel tubes were centrifuged before shipping. Libraries prepared from cell-free DNA (cfDNA) extracted from both types of tubes were sequenced on Illumina NextSeq 500, and fetal fraction was estimated using SeqFF. EDTA-gel tube libraries were size selected on agarose gel to eliminate cfDNA fragments >160 bp and resequenced. The main outcome measure was fetal fraction expressed as percentage of total cfDNA sequenced, calculated from sequence read counts (SeqFF). Streck tube samples showed an average 1% higher fetal fraction than centrifuged EDTA-gel tubes without size selection. This difference increased with temperature. When EDTA-gel samples' libraries were size selected, the mean fetal fraction increased from 7% to 13%, with no sample having fetal fraction <4%. Using EDTA-gel tubes reduces NIPS sampling cost and tube processing time in the laboratory. Also, using EDTA-gel tubes does not lead to cfDNA degradation. Size selection increases fetal fraction, reduces the number of test failures, increases NIPS clinical performance, and may be helpful in situations asking for a higher fetal fraction, such as twin pregnancies or screening for sub-chromosomal imbalances.
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Affiliation(s)
- Seyedeh S Daryabari
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Sylvie Giroux
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada.
| | - André Caron
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Briana Chau
- UBC Department of Medical Genetics, BC Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - Sylvie Langlois
- UBC Department of Medical Genetics, BC Women's Hospital and Health Centre, Vancouver, British Columbia, Canada
| | - François Rousseau
- Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
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12
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Liu Y, Cheng L, Wang G, Lv J, He Y, Shao PL, Hu R, Xiao H, Tang J, Niu D, Yang J, Tang Z, Xu Z, Liu Y, Li Y, Song K, Wu B, Zhang B. A nano-magnetic size selective cfDNA extraction platform for liquid biopsy with enhanced precision. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1199:123236. [DOI: 10.1016/j.jchromb.2022.123236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
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13
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Voss T, Ullius A, Schönborn M, Oelmüller U. Sensitivity assessment of workflows detecting rare circulating cell-free DNA targets: A study design proposal. PLoS One 2021; 16:e0253401. [PMID: 34228726 PMCID: PMC8260181 DOI: 10.1371/journal.pone.0253401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/03/2021] [Indexed: 11/18/2022] Open
Abstract
The field of liquid biopsy has seen extensive growth in recent decades, making it one of the most promising areas in molecular diagnostics. Circulating cell-free DNA (ccfDNA) especially is used as an analyte in a growing number of diagnostic assays. These assays require specified preanalytical workflows delivering ccfDNA in qualities and quantities that facilitate correct and reliable results. As each step and component used in the preanalytical process has the potential to influence the assay sensitivity and other performance characteristics, it is key to find an unbiased experimental setup to test these factors in diagnostic or research laboratories. We defined one such setup by using blood from healthy subjects and commercially available products for blood collection, spike-in material, ccfDNA isolation, and qPCR assays. As the primary read-out, we calculated the probit model-based LOD95 (limit of detection of the 95th percentile) from the qPCR assay results. In a proof of principle study we tested two different but widely used blood ccfDNA profile stabilization technologies in blood collection tubes, the Cell-Free DNA BCT and the PAXgene Blood ccfDNA Tube. We tested assays for three different EGFR gene mutations and one BRAF gene mutation. The study design revealed differences in performance between the two tested technologies for all four mutations. In conclusion, we successfully established a blueprint for a test procedure capable of verifying and validating a liquid biopsy workflow from blood collection to the analytical result.
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Affiliation(s)
- Thorsten Voss
- R&D Department, QIAGEN GmbH, Hilden, Germany
- * E-mail:
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14
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Kadivar A, Rashidzadeh H, Davoodian N, Nazari H, Dehghani Tafti R, Heidari Khoei H, Seidi Samani H, Modaresi J, Ahmadi E. Evaluation of the efficiency of TaqMan duplex real-time PCR assay for non-invasive pre-natal assessment of foetal sex in equine. Reprod Domest Anim 2020; 56:287-291. [PMID: 32978850 DOI: 10.1111/rda.13831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/07/2020] [Accepted: 09/19/2020] [Indexed: 11/30/2022]
Abstract
Accurate diagnosis of foetal sex in pregnant mare is helpful for many breeders, both for private or commercial purposes. In this study, in order to pre-natal foetal sexing in equine, we used TaqMan duplex real-time PCR to detect the specific regions of SRY and TSPY genes on extracted cell-free foetal DNA from maternal blood. Peripheral blood samples from 50 pregnant Arabian mares with singleton foetuses were collected. Cell-free foetal DNA was extracted from maternal plasma, and duplex real-time PCR assays were performed with TaqMan probes and primers. Amplification of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene was used as control of DNA extraction procedure. From the 50 sampled mares, 28 cases had female and 22 mares had male foetuses. The final results for 46 samples were conclusive, and from them, 43 cases were predicted correctly. Sensitivity, specificity and accuracy of the test were 90.48%, 96% and 93.48%, respectively. In conclusion, a TaqMan duplex real-time PCR was set up to pre-natal detection of foetal sex in equine. The method was fast and decreased the false-positive and false-negative results. The technique can be used as a routine procedure in farms by collecting only a blood sample.
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Affiliation(s)
- Ali Kadivar
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran.,Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Habiballah Rashidzadeh
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Najmeh Davoodian
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Hasan Nazari
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
| | - Rohallah Dehghani Tafti
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Heidar Heidari Khoei
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Hasan Seidi Samani
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Jahangir Modaresi
- Department of Clinical Science, Faculty of Veterinary Medicine, Shahrekord University, Shahrekord, Iran
| | - Ebrahim Ahmadi
- Research Institute of Animal Embryo Technology, Shahrekord University, Shahrekord, Iran
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15
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Giroux S, Badeau M, Jeuken J, Caron A, Girouard J, Rousseau F. Validation of a New Protocol to Collect and Isolate Plasma from Pregnant Women for Noninvasive Prenatal Testing (NIPT). J Appl Lab Med 2020; 6:743-749. [PMID: 33215208 DOI: 10.1093/jalm/jfaa155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/17/2020] [Indexed: 11/14/2022]
Abstract
BACKGROUND Most laboratories use specialized tubes (e.g., Streck) to recover circulating cell-free DNA (ccfDNA) for noninvasive prenatal testing (NIPT). We validated a low cost, simple procedure for collecting NIPT samples in remote laboratories that avoids highspeed centrifugation. EDTA gel blood sampling tube allows simple separation of plasma from blood cells. Decanted plasma is filtered to remove cell debris. The procedure can be performed within a few minutes after the blood centrifugation step, and ccfDNA-grade plasma can be frozen for transportation. METHODS We recruited 51 pregnant women and collected blood in one EDTA-gel Greiner tube and two Streck tubes. All tubes were centrifuged at 1600 g x 10 min within 6 h of sample collection. Plasma from EDTA tubes was poured into a syringe cylinder and filtered through a 0.45 µm Millipore filter. Plasma from Streck tubes was recovered with a pipette and one was filtered as above while the second was centrifuged at 16 000 g. The ccfDNA was isolated and NGS sequencing libraries were prepared and sequenced on an Illumina system. Fetal fractions were estimated using SeqFF. This study had a power of 79% to detect a decrease of 1% in fetal fractions with the new method. RESULTS We did not observe any significant difference between the three procedures for the fetal fraction nor for the quality or quantity of libraries produced. CONCLUSION EDTA-gel tubes with filtration provide high quality plasma for ccfDNA analysis and can be sent frozen to the NIPT laboratory. This is economical and it frees the laboratory of time-consuming steps.
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Affiliation(s)
- Sylvie Giroux
- CRCHU de Québec, Université Laval, Quebec City, Quebec, Canada
| | | | | | - Andre Caron
- CRCHU de Québec, Université Laval, Quebec City, Quebec, Canada
| | - Joël Girouard
- CHUL du CHU de Québec, Université Laval, Quebec City, Québec, Canada
| | - François Rousseau
- CRCHU de Québec, Université Laval, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada.,Department of Medical Biology, Service of Medical Biochemistry, CHU de Québec, Quebec City, Quebec, Canada
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16
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Mirzaei Gisomi N, Javadi G, Zare Karizi S, Miryounesi M, Keshavarz P. Evaluation of beta-thalassemia in the fetus through cffDNA with multiple polymorphisms as a haplotype in the beta-globin gene. Transfus Clin Biol 2020; 27:243-252. [PMID: 32798758 DOI: 10.1016/j.tracli.2020.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Invasive biopsy during the pregnancy is associated with an abortion risk of approximately 1% for the fetus. Free fetal DNA in maternal plasma is an excellent source of genetic material for prenatal molecular diagnoses. This study was conducted to investigate beta-thalassemia mutation in the fetus through maternal blood with multiple polymorphisms as haplotypes in the beta-globin gene. METHODS In this study, a total of 33 beta-thalassemia carrier (minor) couples were genotyped by ARMS-PCR for IVSII-IG>A mutation. During pregnancy, 10mL of blood was collected from pregnant women, and DNA was extracted by the magnetic bead-based extraction, and fetal DNA was enriched with AMPure XP kit. Five polymorphisms in 4 haplotype groups were evaluated by the Sanger Sequencing method. Finally, results were compared with those of the invasion method. RESULTS Participants in study were 33 couples, mean age of the men was 26±5 years, and mean age of women was 23±4 years, and mean MCV, MCH, HbA2 blood parameters were 62.4±5.3, 19.6±3.1, 4.2±2.1 respectively. A total of 33 fetuses were genotyped for IVSII-IG>A mutation. Nine fetuses were affected, 10 fetuses were normal and 14 fetuses were carrier of beta-thalassemia. Sensitivity and specificity of Sanger Sequencing were equal to 88.8% and 91.6% respectively. Positive and negative predictive values were obtained as 80% and 95.6%, respectively. CONCLUSION Mutational status of the fetus can be assessed by determining inheritance of paternally-derived alleles based on detection of haplotype-associated SNP in maternal plasma. Magnetic-based DNA extraction and fetal DNA enrichment are very simple and easy to perform and have satisfactory accuracy.
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Affiliation(s)
- Nadia Mirzaei Gisomi
- Department of biology, science and research branch, Islamic Azad university, Tehran, Iran
| | - Gholamreza Javadi
- Department of biology, science and research branch, Islamic Azad university, Tehran, Iran
| | - Shohre Zare Karizi
- Department of biology, faculty of biological sciences, Islamic Azad university, Varamin-Pishva Branch, Varamin, Iran
| | - Mohammad Miryounesi
- Department of medical genetics, Shahid Beheshti university of medical sciences, Tehran, Iran
| | - Parvaneh Keshavarz
- Cellular and molecular research center, faculty of medicine, Guilan university of medical sciences, Rasht, Iran; Medical genetics laboratory, Rasht, Iran.
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17
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Two Reliable Methodical Approaches for Non-Invasive RHD Genotyping of a Fetus from Maternal Plasma. Diagnostics (Basel) 2020; 10:diagnostics10080564. [PMID: 32764529 PMCID: PMC7460148 DOI: 10.3390/diagnostics10080564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/30/2020] [Accepted: 07/30/2020] [Indexed: 12/27/2022] Open
Abstract
Noninvasive fetal RHD genotyping is an important tool for predicting RhD incompatibility between a pregnant woman and a fetus. This study aimed to assess a methodological approach other than the commonly used one for noninvasive fetal RHD genotyping on a representative set of RhD-negative pregnant women. The methodology must be accurate, reliable, and broadly available for implementation into routine clinical practice. A total of 337 RhD-negative pregnant women from the Czech Republic region were tested in this study. The fetal RHD genotype was assessed using two methods: real-time PCR and endpoint quantitative fluorescent (QF) PCR. We used exon-7-specific primers from the RHD gene, along with internal controls. Plasma samples were analyzed and measured in four/two parallel reactions to determine the accuracy of the RHD genotyping. The RHD genotype was verified using DNA analysis from a newborn buccal swab. Both methods showed an excellent ability to predict the RHD genotype. Real-time PCR achieved its greatest accuracy of 98.6% (97.1% sensitivity and 100% specificity (95% CI)) if all four PCRs were positive/negative. The QF PCR method also achieved its greatest accuracy of 99.4% (100% sensitivity and 98.6% specificity (95% CI)) if all the measurements were positive/negative. Both real-time PCR and QF PCR were reliable methods for precisely assessing the fetal RHD allele from the plasma of RhD-negative pregnant women.
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18
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Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
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Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
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19
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Ungerer V, Bronkhorst AJ, Holdenrieder S. Preanalytical variables that affect the outcome of cell-free DNA measurements. Crit Rev Clin Lab Sci 2020; 57:484-507. [DOI: 10.1080/10408363.2020.1750558] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Vida Ungerer
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Abel J. Bronkhorst
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Stefan Holdenrieder
- Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
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20
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Clausen FB, Barrett AN, Advani HV, Choolani M, Dziegiel MH. Impact of long-term storage of plasma and cell-free DNA on measured DNA quantity and fetal fraction. Vox Sang 2020; 115:586-594. [PMID: 32342989 DOI: 10.1111/vox.12923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Optimal sample storage conditions are essential for non-invasive prenatal testing of cell-free fetal and total DNA. We investigated the effect of long-term storage of plasma samples and extracted cfDNA using qPCR. MATERIALS AND METHODS Fetal and total cfDNA yield and fetal fraction were calculated before and after storage of plasma for 0-6 years at -25°C. Dilution experiments were performed to investigate PCR inhibition. Extraction with or without proteinase K was used to examine protein dissociation. Storage of extracted cfDNA was investigated by testing aliquots immediately, and after 18 months and 3 years of storage at -25°C. RESULTS We observed a marked increase in the levels of amplifiable fetal and total DNA in plasma stored for 2-3 years, and fetal fraction was slightly decreased after 3 years of storage. cfDNA detection was independent of proteinase K during DNA extraction in plasma samples stored >2 years, indicating a loss of proteins from DNA over time, which was likely to account for the observed increase in DNA yields. Measured fetal and total DNA quantities, as well as fetal fraction, increased in stored, extracted cfDNA. CONCLUSION Fetal and total cell-free DNA is readily detectable in plasma after long-term storage at -25°C. However, substantial variation in measured DNA quantities and fetal fraction means caution may be required when using stored plasma and extracted cfDNA for test development or validation purposes.
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Affiliation(s)
- Frederik Banch Clausen
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Henna V Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Morten Hanefeld Dziegiel
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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21
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Greytak SR, Engel KB, Parpart-Li S, Murtaza M, Bronkhorst AJ, Pertile MD, Moore HM. Harmonizing Cell-Free DNA Collection and Processing Practices through Evidence-Based Guidance. Clin Cancer Res 2020; 26:3104-3109. [PMID: 32122922 DOI: 10.1158/1078-0432.ccr-19-3015] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/25/2019] [Accepted: 02/25/2020] [Indexed: 12/18/2022]
Abstract
Circulating cell-free DNA (cfDNA) is rapidly transitioning from discovery research to an important tool in clinical decision making. However, the lack of harmonization of preanalytic practices across institutions may compromise the reproducibility of cfDNA-derived data and hamper advancements in cfDNA testing in the clinic. Differences in cellular genomic contamination, cfDNA yield, integrity, and fragment length have been attributed to different collection tube types and anticoagulants, processing delays and temperatures, tube agitation, centrifugation protocols and speeds, plasma storage duration and temperature, the number of freeze-thaw events, and cfDNA extraction and quantification methods, all of which can also ultimately impact subsequent downstream analysis. Thus, there is a pressing need for widely applicable standards tailored for cfDNA analysis that include all preanalytic steps from blood draw to analysis. The NCI's Biorepositories and Biospecimen Research Branch has developed cfDNA-specific guidelines that are based upon published evidence and have been vetted by a panel of internationally recognized experts in the field. The guidelines include optimal procedures as well as acceptable alternatives to facilitate the generation of evidence-based protocols by individual laboratories and institutions. The aim of the document, which is entitled "Biospecimen Evidence-based Best Practices for Cell-free DNA: Biospecimen Collection and Processing," is to improve the accuracy of cfDNA analysis in both basic research and the clinic by improving and harmonizing practices across institutions.
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Affiliation(s)
| | | | | | - Muhammed Murtaza
- Center for Noninvasive Diagnostics, Translational Genomics Research Institute, Phoenix, Arizona
| | | | - Mark D Pertile
- Victorian Clinical Genetics Services (VCGS), Parkville, Australia
| | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, NCI, Bethesda, Maryland.
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22
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Wienzek-Lischka S, Bachmann S, Froehner V, Bein G. Potential of Next-Generation Sequencing in Noninvasive Fetal Molecular Blood Group Genotyping. Transfus Med Hemother 2020; 47:14-22. [PMID: 32110190 DOI: 10.1159/000505161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/28/2019] [Indexed: 12/23/2022] Open
Abstract
Hemolytic disease of the fetus and newborn and fetal and neonatal alloimmune thrombocytopenia are caused by maternal antibodies against fetal alloantigens on red blood cells or platelets that are inherited from the father. After transplacental transport to the fetal circulation, antibodies of the IgG class may cause severe fetal anemia or bleeding complications. The indication for noninvasive fetal blood group genotyping is given if a clinically relevant antibody is detected in a pregnant woman and if the father is heterozygous (or unknown) for the implicated blood group allele. This mini-review will focus on the advantages and current limitations of next-generation sequencing (NGS) for noninvasive diagnosis of fetal blood groups which is, in contrast to fetal aneuploidy screening, proposed only by some research groups. Targeted massively parallel sequencing of short DNA fragments from maternal cell-free plasma samples enables counting of fetal alleles for many single nucleotide polymorphisms in parallel. This information can be utilized for estimation of the fetal fraction of cell-free DNA (cfDNA) as well as detection of the paternal blood group allele in question. Adherence to a cut-off of ≥4% fetal fraction for reporting conclusive results is recommended to avoid false-negative results due to low fetal fraction. For screening purposes of fetal RHD in RhD-negative pregnant women, real-time PCR methods are very well established. However, for diagnostic purposes, the targeted amplicon-based NGS approach has the inherent capability to estimate the fetal fraction of cfDNA. In the future, improving the accuracy of NGS by consensus sequencing of single cfDNA molecules may enable reliable fetal blood group genotyping already in the first trimester of pregnancy.
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Affiliation(s)
- Sandra Wienzek-Lischka
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| | - Sandy Bachmann
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| | - Vanessa Froehner
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
| | - Gregor Bein
- Institute for Clinical Immunology and Transfusion Medicine, Justus-Liebig University, Giessen, Germany
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23
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Chandler NJ, Ahlfors H, Drury S, Mellis R, Hill M, McKay FJ, Collinson C, Hayward J, Jenkins L, Chitty LS. Noninvasive Prenatal Diagnosis for Cystic Fibrosis: Implementation, Uptake, Outcome, and Implications. Clin Chem 2019; 66:207-216. [DOI: 10.1373/clinchem.2019.305011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/09/2019] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Noninvasive prenatal diagnosis (NIPD) for monogenic disorders has a high uptake by families. Since 2013, our accredited public health service laboratory has offered NIPD for monogenic disorders, predominantly for de novo or paternally dominantly inherited mutations. Here we describe the extension of this service to include definitive NIPD for a recessive condition, cystic fibrosis (CF).
METHODS
Definitive NIPD for CF was developed using next-generation sequencing. Validation was performed on 13 cases from 10 families before implementation. All cases referred for CF NIPD were reviewed to determine turnaround times, genotyping results, and pregnancy outcomes.
RESULTS
Of 38 referrals, 36 received a result with a mean turnaround of 5.75 days (range, 3–11 days). Nine cases were initially inconclusive, with 3 reported unaffected because the low-risk paternal allele was inherited and 4 cases in which the high-risk paternal allele was inherited, receiving conclusive results following repeat testing. One case was inconclusive owing to a paternal recombination around the mutation site, and one case was uninformative because of no heterozygosity. Before 2016, 3 invasive referrals for CF were received annually compared with 38 for NIPD in the 24 months since offering a definitive NIPD service.
CONCLUSIONS
Timely and accurate NIPD for definitive prenatal diagnosis of CF is possible in a public health service laboratory. The method detects recombinations, and the service is well-received as evidenced by the significant increase in referrals. The bioinformatic approach is gene agnostic and will be used to expand the range of conditions tested for.
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Affiliation(s)
- Natalie J Chandler
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Helena Ahlfors
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Suzanne Drury
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Rhiannon Mellis
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Melissa Hill
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Fiona J McKay
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Claire Collinson
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Jane Hayward
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Lucy Jenkins
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
| | - Lyn S Chitty
- NE Thames Regional Genetics Laboratories, Great Ormond Street Hospital, London, UK
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
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24
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Dauber EM, Kollmann D, Kozakowski N, Rasoul-Rockenschaub S, Soliman T, Berlakovich GA, Mayr WR. Quantitative PCR of INDELs to measure donor-derived cell-free DNA-a potential method to detect acute rejection in kidney transplantation: a pilot study. Transpl Int 2019; 33:298-309. [PMID: 31710731 PMCID: PMC7065216 DOI: 10.1111/tri.13554] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/24/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
The quantification of donor‐derived cell‐free DNA (ddcfDNA) in recipient's plasma is a novel, but technically challenging noninvasive method to assist the diagnosis of acute rejection (AR). A quantitative real‐time PCR (qPCR) approach targeting insertion/deletion polymorphisms (INDEL) was adapted to measure ddcfNA in plasma samples from 29 kidney transplant recipients obtained at time of clinically indicated biopsies (eight patients with a histologically verified AR, nine with borderline rejection and 12 without evidence of rejection). Measured ddcfDNA levels of smaller INDEL amplicon targets differed significantly (P = 0.016, Kruskal–Wallis H test) between recipients with biopsy‐proven AR (median 5.24%; range 1.00–9.03), patients without (1.50%; 0.41–6.50) and patients with borderline AR (1.91%; 0.58–5.38). Similarly, pairwise testing by Mann–Whitney U‐tests revealed significant differences between recipients with AR and without AR (P = 0.012) as well as patients with AR and borderline histology (P = 0.015). Receiver operating characteristic (ROC) analysis revealed an area under the ROC curve for discriminating AR and non‐AR biopsies of 0.84 (95% CI: 0.66–1.00). The determined cutoff value of 2.7% ddcfDNA showed a sensitivity of 0.88 (95% CI: 0.63–1.00) and specificity of 0.81 (95% CI: 0.64–0.98). INDEL qPCR represents a novel method to quantify ddcfDNA on standard qPCR instruments within 6–8 h with high sensitivity and specificity to detect AR.
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Affiliation(s)
- Eva-Maria Dauber
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Wien, Austria
| | - Dagmar Kollmann
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | | | | | - Thomas Soliman
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | - Gabriela A Berlakovich
- Division of Transplantation, Department of Surgery, Medical University of Vienna, Wien, Austria
| | - Wolfgang R Mayr
- Department of Blood Group Serology and Transfusion Medicine, Medical University of Vienna, Wien, Austria
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Genotyping of STR and DIP-STR Markers in Plasma Cell-Free DNA for Simple and Rapid Noninvasive Prenatal Diagnosis of Zygosity of Twin Pregnancies. Twin Res Hum Genet 2019; 22:321-329. [PMID: 31619303 DOI: 10.1017/thg.2019.89] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Due to the high rate of complications, special medical care must be provided especially for monozygotic twin pregnancies, which are characterized as having 2.5 times higher mortality of fetuses. In recent years, examination of cell-free DNA (cfDNA) circulating in maternal plasma has become a useful noninvasive method of prenatal diagnosis. However, fetal DNA constitutes only 3-20% of plasma cfDNA during pregnancy. Short tandem repeats (STRs) are routinely used in forensic examination of DNA mixtures and are able to identify 5% minority components. Haplotypes of deletion/insertion polymorphisms and STRs (DIP-STRs) are able to detect even 0.1% minority components of DNA mixtures. Thus, STRs and DIP-STRs seem to be a perfect tool for detection of fetal alleles in DNA isolated from maternal plasma. Here, we present a novel noninvasive prenatal diagnosis technique of determination of pregnancy zygosity based on examination of feto-maternal microchimerism of plasma cfDNA with the use of STRs and DIP-STRs. Our preliminary results based on 22 STR loci showed 67% sensitivity, 100% specificity and 82% accuracy for prenatal detection of twin dizygosity. The corresponding values for seven DIP-STRs were 13%, 100% and 54%, respectively. Owing to assay performance, low DNA input requirements, low costs (below 10 USD per patient) and simplicity of analysis, genotyping of STR/DIP-STR markers in maternal plasma cfDNA may become a useful supplementary test for noninvasive prenatal diagnosis of twin zygosity in cases when chorionicity and zygosity cannot be reliably determined by ultrasound examination and prognostic value may be provided by a DNA test determining pregnancy zygosity.
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Goggs R. Effect of sample type on plasma concentrations of cell-free DNA and nucleosomes in dogs. Vet Rec Open 2019; 6:e000357. [PMID: 31673376 PMCID: PMC6802997 DOI: 10.1136/vetreco-2019-000357] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/20/2019] [Accepted: 09/18/2019] [Indexed: 12/27/2022] Open
Abstract
Cell-free DNA (cfDNA) and nucleosomes are two biomarkers of cell death and neutrophil extracellular trap formation that are increased in dogs with sepsis, immune-mediated haemolytic anaemia, cancer and following trauma and have diagnostic and prognostic values. cfDNA and nucleosomes are typically measured in plasma samples using DNA-specific fluorophores and ELISA assays, respectively, but their concentrations may be affected by pre-analytical variables such as sample type. The present study aimed to investigate the influence of sample type on the plasma cfDNA and nucleosome concentrations of a heterogeneous group of dogs presenting to an emergency room. Triplicate samples were collected into K2-ethylenediamine tetraacetic acid, 3.2% citrate and a specialised DNA stabilisation tube (Streck BCT), processed rapidly and frozen for batch analysis. Biomarker concentrations were compared between sample types by calculation of Spearman’s correlation coefficients, and with Deming regression, Bland-Altman plots and the Friedman test. Overall, biomarker concentrations were highly correlated between the three sample types. The most concordant results were obtained using citrate samples and the DNA stabilisation tube. Matched cfDNA concentrations between the different sample types were significantly different but there was no significant difference between the nucleosome concentrations in any of the sample types. The present study suggests that cfDNA and nucleosomes can be successfully measured in various sample types, but distinct sample types do not produce interchangeable results. This argues for use of a consistent sample type within studies and suggests standardisation may be useful for the field.
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Affiliation(s)
- Robert Goggs
- Department of Clinical Sciences, Cornell University College of Veterinary Medicine, Ithaca, New York, USA
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Enko D, Halwachs-Baumann G, Kriegshäuser G. Plasma free DNA: Evaluation of temperature-associated storage effects observed for Roche Cell-Free DNA collection tubes. Biochem Med (Zagreb) 2019; 29:010904. [PMID: 30799979 PMCID: PMC6366949 DOI: 10.11613/bm.2019.010904] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/31/2018] [Indexed: 12/13/2022] Open
Abstract
Introduction Standardized pre-analytical blood sample procedures for the analysis of circulating cell-free DNA (ccfDNA) are still not available. Therefore, the present study aimed at evaluating the impact of storage conditions related to different times (24 and 48 h) and temperatures (room temperature (RT) and 4 - 8 °C) on the plasma ccfDNA concentration of blood samples drawn into Cell-Free DNA collection tubes (Roche Diagnostics GmbH, Mannheim, Germany). Materials and methods Venous blood from 30 healthy individuals was collected into five 8.5 mL Cell-Free DNA Collection Tubes (Roche Diagnostics GmbH) each. Plasma samples were processed at time point of blood collection (tube 1), and after storage under the following conditions: 24 h at RT (tube 2) or 4-8 °C (tube 3), and 48 h at RT (tube 4) or 4 - 8 °C (tube 5). Circulating cell-free DNA concentrations were determined by EvaGreen chemistry-based droplet digital PCR (ddPCR). Results No statistically significant differences between median (interquartile range) plasma ccfDNA concentrations (ng/mL) at time point of blood collection (3.17 (2.13 – 3.76)) and after storage for 24 h (RT: 3.02 (2.41 – 3.68); 4-8 °C: 3.21 (2.19 – 3.46)) and 48 h (RT: 3.13 (2.10 – 3.76); 4-8 °C: 3.09 (2.19 – 3.50)) were observed (P values from 0.102 – 0.975). Conclusions No unwanted release of genomic DNA from white blood cells could be detected in plasma samples after tube storage for 24 and 48 h regardless of storage temperature.
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Affiliation(s)
- Dietmar Enko
- Institute of Clinical Chemistry and Laboratory Medicine, General Hospital Steyr, Steyr, Austria.,Clinical Institute of Medical and Laboratory Diagnostics, Medical University Graz, Graz, Austria
| | | | - Gernot Kriegshäuser
- Institute of Clinical Chemistry and Laboratory Medicine, General Hospital Steyr, Steyr, Austria.,Clinical Institute of Medical and Laboratory Diagnostics, Medical University Graz, Graz, Austria
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29
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Muluhngwi P, Valdes Jr R, Fernandez-Botran R, Burton E, Williams B, Linder MW. Cell-free DNA diagnostics: current and emerging applications in oncology. Pharmacogenomics 2019; 20:357-380. [DOI: 10.2217/pgs-2018-0174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Liquid biopsy is a noninvasive dynamic approach for monitoring disease over time. It offers advantages including limited risks of blood sampling, opportunity for more frequent sampling, lower costs and theoretically non-biased sampling compared with tissue biopsy. There is a high degree of concordance between circulating tumor DNA mutations versus primary tumor mutations. Remote sampling of circulating tumor DNA can serve as viable option in clinical diagnostics. Here, we discuss the progress toward broad adoption of liquid biopsy as a diagnostic tool and discuss knowledge gaps that remain to be addressed.
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Affiliation(s)
- Penn Muluhngwi
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Roland Valdes Jr
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Rafael Fernandez-Botran
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Eric Burton
- Department of Neurology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Brian Williams
- Department of Neurosurgery, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mark W Linder
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
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Jensen MPS, Damkjaer MB, Clausen FB, Ali HA, Hare KJ, Dziegiel MH, Jørgensen FS. Targeted Rhesus immunoglobulin for RhD-negative women undergoing an induced abortion: A clinical pilot study. Acta Obstet Gynecol Scand 2019; 98:1164-1171. [PMID: 30860294 DOI: 10.1111/aogs.13606] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 03/07/2019] [Indexed: 11/27/2022]
Abstract
INTRODUCTION The aim of this clinical pilot study was to examine the accuracy of noninvasive fetal RHD genotyping in early pregnancy (8+0 to 11+6 weeks) and to clarify whether targeted administration of Rhesus immunoglobulin (RhIg) is possible for women undergoing an induced abortion such that unnecessary injections can be avoided. The study examines the correlation between gestational age and the amount of cell-free fetal DNA in maternal plasma, the fetal fraction of DNA and whether transportation time or body mass index affects these parameters. MATERIAL AND METHODS Fifty-two RhD-negative women undergoing a surgically induced abortion were included. A maternal blood sample was collected prior to the abortion and a tissue sample was collected from the placental part of the abortion material after the intervention. Fetal RhD type was determined by PCR analysis of cell-free fetal DNA extracted from maternal plasma and on DNA from the tissue sample, with the latter providing a reference standard. Copies of RHD/mL were determined on RHD-positive samples and the fetal fraction of DNA was calculated. RESULTS We demonstrated complete concordance between results from plasma and tissue, with 31 RhD-positive and 21 RhD-negative samples, corresponding to 40% being RhD-negative, specificity 100% [95% confidence interval (CI) 88.8-100] and sensitivity 100% (95% CI 83.9-100). We found no significant correlation between gestational age and the amount or the fraction of cell-free fetal DNA in maternal plasma, nor did we find that transportation time or BMI significantly affected these factors in this setup. CONCLUSIONS Fetal RHD genotyping can be accurately performed from the 8th week of gestation and unnecessary injections of RhIg can be avoided for women undergoing an induced abortion. A larger study is needed to determine a more accurate sensitivity for the analysis early in pregnancy.
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Affiliation(s)
- Mia P S Jensen
- Fetal Medicine Unit, Department of Obstetrics and Gynecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Merete B Damkjaer
- Fetal Medicine Unit, Department of Obstetrics and Gynecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Frederik B Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Rigshospitalet, Copenhagen, Denmark
| | - Haivin A Ali
- Fetal Medicine Unit, Department of Obstetrics and Gynecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Kristine J Hare
- Section of Gynecology, Department of Obstetrics and Gynecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Morten H Dziegiel
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, Rigshospitalet, Copenhagen, Denmark
| | - Finn S Jørgensen
- Fetal Medicine Unit, Department of Obstetrics and Gynecology, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
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Deans ZC, Allen S, Jenkins L, Khawaja F, Gutowska-Ding W, Patton SJ, Chitty LS, Hastings RJ. Ensuring high standards for the delivery of NIPT world-wide: Development of an international external quality assessment scheme. Prenat Diagn 2019; 39:379-387. [PMID: 30767256 PMCID: PMC6619285 DOI: 10.1002/pd.5438] [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: 08/29/2018] [Revised: 02/04/2019] [Accepted: 02/11/2019] [Indexed: 02/05/2023]
Abstract
Objective To ensure accurate and appropriate reporting of non‐invasive prenatal testing (NIPT) results, the standard of testing should be measured and monitored by participation in external quality assessment (EQA) schemes. The findings from international pilot EQAs for NIPT for the common trisomies are presented. Methods In the first pilot, three EQA providers used artificially manufactured reference materials to deliver an EQA for NIPT. The second pilot used clinically collected maternal plasma samples. The testing and reporting for aneuploidy status was performed by participating laboratories using routine procedures. Reports were assessed against peer ratified criteria and EQA scores were returned to participants. Results Forty laboratories participated in the first. Genotyping accuracy was high; four laboratories reported a critical genotyping error (10%) and two reported partial results. Eighty seven laboratories participated in the second pilot using maternal plasma, two reporting a critical genotyping error (2.3%). For both rounds, report content was variable with key information frequently omitted or difficult to identify within the report. Conclusions We have successfully delivered an international pilot EQA for NIPT. When compared with currently available manufactured materials, EQA for NIPT was best performed using clinically collected maternal plasma. Work is required to define and improve the standard of reporting. What is already known about this topic?
To ensure laboratories deliver accurate, appropriate, and effective reporting of tests performed in their laboratories participation in external quality assessment (EQA) schemes is required by accrediting bodies. There is no international EQA scheme available for NIPT for aneuploidy.
What does this study add?
EQA for the common trisomies can be successfully delivered across multiple laboratories worldwide. The EQA is best delivered using clinically collected maternal plasma samples which can be transported at room temperature. Reporting standards are very variable with key information often omitted. Further work is required to develop internationally acceptable EQA for NIPT aneuploidy including reporting standards. The high level of participation in these pilots suggests the need for continued delivery of EQA.
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Affiliation(s)
- Zandra C Deans
- UK NEQAS for Molecular Genetics/GenQA, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Lucy Jenkins
- Great Ormond Street Hospital, North East Thames Regional Genetics Laboratory, London, UK
| | - Farrah Khawaja
- UK NEQAS for Molecular Genetics/GenQA, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Weronika Gutowska-Ding
- EMQN, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Simon J Patton
- EMQN, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Lyn S Chitty
- UCL Great Ormond Street Institute of Child Health and Great Ormond Street NHS Foundation Trust, London, UK
| | - Ros J Hastings
- CEQAS/GenQA, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Abstract
Noninvasive prenatal genetic tests analyzing the cell-free fetal DNA in the circulation of expectant mothers are now performed routinely in clinical diagnostic laboratories. Leveraging the power of next generation sequencing (NGS), these tests can detect variation in chromosomal copy number or microdeletions early in gestation. All methods begin with blood collection followed by transport to the diagnostic lab, plasma separation, and purification of ccfDNA from the plasma to prepare it for molecular analysis. Preservation of ccfDNA in blood samples and highly efficient purification from plasma are paramount since the quality and quantity of target nucleic acids determine the sensitivity and therefore success of these assays. Maximizing quality and quantity and minimizing variation in extraction yield pose significant challenges for diagnostic labs, many of which use manual isolation methods for plasma volumes greater than 5 mL. One way to reduce variability is to automate the extraction processes and, to the extent possible, minimize hand-on operations. This chapter details two procedures for isolating ccfDNA from 10 mL plasma by manual and automated means using the QIAamp Circulating Nucleic Acid Kit and the QIAsymphony Circulating DNA Kit. The ccfDNA recovered is suitable for downstream processing in noninvasive prenatal tests for aneuploidy detection.
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Sosiawan A, Raharjo D, Nuraini I, Kartikasari N, Nugraha AP, Ari MDA. Detection of short tandem repeats at 5 loci and amelogenin with cell-free fetal DNA as a specimen in the development of prenatal paternity diagnostic tests. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0047-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Characteristics, properties, and potential applications of circulating cell-free dna in clinical diagnostics: a focus on transplantation. J Immunol Methods 2018; 463:27-38. [DOI: 10.1016/j.jim.2018.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022]
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Risberg B, Tsui DWY, Biggs H, Ruiz-Valdepenas Martin de Almagro A, Dawson SJ, Hodgkin C, Jones L, Parkinson C, Piskorz A, Marass F, Chandrananda D, Moore E, Morris J, Plagnol V, Rosenfeld N, Caldas C, Brenton JD, Gale D. Effects of Collection and Processing Procedures on Plasma Circulating Cell-Free DNA from Cancer Patients. J Mol Diagn 2018; 20:883-892. [PMID: 30165204 PMCID: PMC6197164 DOI: 10.1016/j.jmoldx.2018.07.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 07/06/2018] [Accepted: 07/26/2018] [Indexed: 01/26/2023] Open
Abstract
Circulating tumor DNA (ctDNA) offers new opportunities for noninvasive cancer management. Detecting ctDNA in plasma is challenging because it constitutes only a minor fraction of the total cell-free DNA (cfDNA). Pre-analytical factors affect cfDNA levels contributed from leukocyte lysis, hence the ability to detect low-frequency mutant alleles. This study investigates the effects of the delay in processing, storage temperatures, different blood collection tubes, centrifugation protocols, and sample shipment on cfDNA levels. Peripheral blood (n = 231) from cancer patients (n = 62) were collected into K3EDTA or Cell-free DNA BCT tubes and analyzed by digital PCR, targeted amplicon, or shallow whole-genome sequencing. To assess pre-analytic effects, plasma was processed under different conditions after 0, 6, 24, 48, 96 hours, and 1 week at room temperature or 4°C, or using different centrifugation protocols. Digital PCR showed that cfDNA levels increased gradually with time in K3EDTA tubes, but were stable in BCT tubes. K3EDTA samples stored at 4°C showed less variation than room temperature storage, but levels were elevated compared with BCT. A second centrifugation at 3000 × g gave similar cfDNA yields compared with higher-speed centrifugation. Next-generation sequencing showed negligible differences in background error or copy number changes between K3EDTA and BCT, or following shipment in BCT. This study provides insights into the effects of sample processing on ctDNA analysis.
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Affiliation(s)
- Bente Risberg
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Norway; Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Dana W Y Tsui
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom.
| | - Heather Biggs
- Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Andrea Ruiz-Valdepenas Martin de Almagro
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Sarah-Jane Dawson
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Charlotte Hodgkin
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Linda Jones
- Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Christine Parkinson
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Francesco Marass
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Dineika Chandrananda
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Elizabeth Moore
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - James Morris
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Vincent Plagnol
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom; Cambridge Breast Unit, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - James D Brenton
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Davina Gale
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, University of Cambridge, Cambridge, United Kingdom; Cancer Research UK Major Centre, Cambridge, United Kingdom.
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Grölz D, Hauch S, Schlumpberger M, Guenther K, Voss T, Sprenger-Haussels M, Oelmüller U. Liquid Biopsy Preservation Solutions for Standardized Pre-Analytical Workflows-Venous Whole Blood and Plasma. CURRENT PATHOBIOLOGY REPORTS 2018; 6:275-286. [PMID: 30595972 PMCID: PMC6290703 DOI: 10.1007/s40139-018-0180-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsy analyses based on circulating cell-free nucleic acids, circulating tumor cells or other diseased cells from organs, and exosomes or other microvesicles in blood offer new means for non-invasive diagnostic applications. The main goal of this review is to explain the importance of preserving whole blood specimens after blood draw for use as liquid biopsies, and to summarize preservation solutions that are currently available. RECENT FINDINGS Despite the great potential of liquid biopsies for diagnostics and disease management, besides non-invasive prenatal testing (NIPT), only a few liquid biopsy applications are fully implemented for routine in vitro diagnostic testing. One major barrier is the lack of standardized pre-analytical workflows, including the collection of consistent quality blood specimens and the generation of good-quality plasma samples therefrom. Broader use of liquid biopsies in clinical routine applications therefore requires improved pre-analytical procedures to enable high-quality specimens to obtain unbiased analyte profiles (DNA, RNA, proteins, etc.) as they are in the patient's body. SUMMARY A growing number of stabilizing reagents and dedicated blood collection tubes are available for the post-collection preservation of circulating cell-free DNA (ccfDNA) profiles in whole blood. In contrast, solutions for the preservation of circulating tumor cells (CTC) that enable both, enumeration and molecular analyses are rare. Solutions for extracellular vesicle (EV) populations, including exosomes, do not yet exist.
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Affiliation(s)
- Daniel Grölz
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Siegfried Hauch
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Kalle Guenther
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | - Thorsten Voss
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
| | | | - Uwe Oelmüller
- QIAGEN GmbH, Research & Development, QIAGEN Strasse 1, 40724 Hilden, Germany
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Zhao Y, Li Y, Chen P, Li S, Luo J, Xia H. Performance comparison of blood collection tubes as liquid biopsy storage system for minimizing cfDNA contamination from genomic DNA. J Clin Lab Anal 2018; 33:e22670. [PMID: 30191594 DOI: 10.1002/jcla.22670] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/03/2018] [Accepted: 08/14/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The ratio of target cfDNA in total plasma is low. The abundant gDNA background resulting from blood cell lysis caused by improper operation has become a major obstacle to accurately measure cfDNA. In this study, we investigated the storage capacity of three blood cell collection tubes (BCTs) in the prevention of genomic DNA contamination caused by white blood cell rupture and evaluated their performance when they were utilized combining with highly sensitive mutation detection technology. METHODS Blood samples were drawn from six healthy blood donors and stored in three types of BCTs (BD K2 -EDTA tube, Roche tube, and Streck tube). Plasma samples were isolated at specific time points (day 0, day 3, day 7, and day 14) for content analysis. RESULTS Roche BCT was more capable for preventing cfDNA contamination caused by white blood cell disruption within 14 days, comparing with BD K2 -EDTA tube and Streck tube. Severe white blood cell lysis and gDNA contamination were found in the BD tube. The impacts of Roche and Streck tubes on the quantity and complexity of next-generation sequencing (NGS) libraries did not differ significantly within 3 days, satisfying most of our daily demands. In addition, the rupture of WBC was not synchronized with hemolysis in BCTs. CONCLUSION This study showed that capacities of blood collection tubes differed considerably in preservation of blood samples. Therefore, suitable blood collection devices should be selected to minimize gDNA contamination and to standardize blood samples processing for achieving more accurate and reliable clinical analysis of cfDNA.
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Affiliation(s)
- Yunlong Zhao
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Yingjie Li
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Ping Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Shaojun Li
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
| | - Jian Luo
- Burning Rock Biotech, Guangzhou, China
| | - Hui Xia
- Department of Cardiothoracic Surgery, First Affiliated Hospital of PLA General Hospital, Beijing, China
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Mellis R, Chandler N, Chitty LS. Next-generation sequencing and the impact on prenatal diagnosis. Expert Rev Mol Diagn 2018; 18:689-699. [PMID: 29962246 DOI: 10.1080/14737159.2018.1493924] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
INTRODUCTION The advent of affordable and rapid next-generation sequencing has been transformative for prenatal diagnosis. Sequencing of cell-free DNA in maternal plasma has enabled the development of not only a highly sensitive screening test for fetal aneuploidies, but now definitive noninvasive prenatal diagnosis for monogenic disorders at an early gestation. Sequencing of fetal exomes offers broad diagnostic capability for pregnancies with unexpected fetal anomalies, improving the yield and accuracy of diagnoses and allowing better counseling for parents. The challenge now is to translate these approaches into mainstream use in the clinic. Areas covered: Here, the authors review the current literature to describe the technologies available and how these have evolved. The opportunities and challenges at hand, including considerations for service delivery, counseling, and development of ethical guidelines, are discussed. Expert commentary: As technology continues to advance, future developments may be toward noninvasive fetal whole exome or whole genome sequencing and a universal method for noninvasive prenatal diagnosis without the need to sequence both parents or an affected proband. Expansion of cell-free fetal DNA analysis to include the transcriptome and the methylome is likely to yield clinical benefits for monitoring other pregnancy-related pathologies such as preeclampsia and intrauterine growth restriction.
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Affiliation(s)
- Rhiannon Mellis
- a Genetics and Genomic Medicine , Great Ormond Street NHS Foundation Trust , London , UK
| | - Natalie Chandler
- b North Thames NHS Regional Genetics Service , Great Ormond Street NHS Foundation Trust , London , UK
| | - Lyn S Chitty
- a Genetics and Genomic Medicine , Great Ormond Street NHS Foundation Trust , London , UK.,c Genetics and Genomic Medicine , UCL Great Ormond Street Institute of Child Health , London , UK
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Clausen FB. Lessons learned from the implementation of non-invasive fetalRHDscreening. Expert Rev Mol Diagn 2018; 18:423-431. [DOI: 10.1080/14737159.2018.1461562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Frederik Banch Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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Rodda AE, Parker BJ, Spencer A, Corrie SR. Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges. ACS Sens 2018; 3:540-560. [PMID: 29441780 DOI: 10.1021/acssensors.7b00953] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.
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Affiliation(s)
| | | | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne, Victoria 3004, Australia
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41
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Stewart CM, Kothari PD, Mouliere F, Mair R, Somnay S, Benayed R, Zehir A, Weigelt B, Dawson SJ, Arcila ME, Berger MF, Tsui DW. The value of cell-free DNA for molecular pathology. J Pathol 2018; 244:616-627. [PMID: 29380875 DOI: 10.1002/path.5048] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/23/2018] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
Over the past decade, advances in molecular biology and genomics techniques have revolutionized the diagnosis and treatment of cancer. The technological advances in tissue profiling have also been applied to the study of cell-free nucleic acids, an area of increasing interest for molecular pathology. Cell-free nucleic acids are released from tumour cells into the surrounding body fluids and can be assayed non-invasively. The repertoire of genomic alterations in circulating tumour DNA (ctDNA) is reflective of both primary tumours and distant metastatic sites, and ctDNA can be sampled multiple times, thereby overcoming the limitations of the analysis of single biopsies. Furthermore, ctDNA can be sampled regularly to monitor response to treatment, to define the evolution of the tumour genome, and to assess the acquisition of resistance and minimal residual disease. Recently, clinical ctDNA assays have been approved for guidance of therapy, which is an exciting first step in translating cell-free nucleic acid research tests into clinical use for oncology. In this review, we discuss the advantages of cell-free nucleic acids as analytes in different body fluids, including blood plasma, urine, and cerebrospinal fluid, and their clinical applications in solid tumours and haematological malignancies. We will also discuss practical considerations for clinical deployment, such as preanalytical factors and regulatory requirements. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Caitlin M Stewart
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Prachi D Kothari
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florent Mouliere
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Richard Mair
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.,Cancer Research UK Major Centre - Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK.,Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, UK
| | - Saira Somnay
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria, Australia.,Centre for Cancer Research, University of Melbourne, Victoria, Australia
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dana Wy Tsui
- Marie-José and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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42
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Jenkins LA, Deans ZC, Lewis C, Allen S. Delivering an accredited non-invasive prenatal diagnosis service for monogenic disorders and recommendations for best practice. Prenat Diagn 2018; 38:44-51. [PMID: 29266293 DOI: 10.1002/pd.5197] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 12/05/2017] [Accepted: 12/09/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Lucy A. Jenkins
- North East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
| | - Zandra C. Deans
- UK NEQAS for Molecular Genetics, Department of Laboratory Medicine; Royal Infirmary of Edinburgh; Edinburgh UK
| | - Celine Lewis
- North East Thames Regional Genetics Service; Great Ormond Street Hospital for Children NHS Foundation Trust; London UK
- Genetics and Genomic Medicine; UCL Great Ormond Street Institute of Child Health; London UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory; Birmingham Women's NHS Foundation Trust; Birmingham UK
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Nectoux J. Current, Emerging, and Future Applications of Digital PCR in Non-Invasive Prenatal Diagnosis. Mol Diagn Ther 2017; 22:139-148. [DOI: 10.1007/s40291-017-0312-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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44
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Barrett AN, Xiong L, Tan TZ, Advani HV, Hua R, Laureano-Asibal C, Soong R, Biswas A, Nagarajan N, Choolani M. Measurement of fetal fraction in cell-free DNA from maternal plasma using a panel of insertion/deletion polymorphisms. PLoS One 2017; 12:e0186771. [PMID: 29084245 PMCID: PMC5662091 DOI: 10.1371/journal.pone.0186771] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/07/2017] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE Cell-free DNA from maternal plasma can be used for non-invasive prenatal testing for aneuploidies and single gene disorders, and also has applications as a biomarker for monitoring high-risk pregnancies, such as those at risk of pre-eclampsia. On average, the fractional cell-free fetal DNA concentration in plasma is approximately 15%, but can vary from less than 4% to greater than 30%. Although quantification of cell-free fetal DNA is straightforward in the case of a male fetus, there is no universal fetal marker; in a female fetus measurement is more challenging. We have developed a panel of multiplexed insertion/deletion polymorphisms that can measure fetal fraction in all pregnancies in a simple, targeted sequencing reaction. METHODS A multiplex panel of primers was designed for 35 indels plus a ZFX/ZFY amplicon. cfDNA was extracted from plasma from 157 pregnant women, and maternal genomic DNA was extracted for 20 of these samples for panel validation. Sixty-one samples from pregnancies with a male fetus were subjected to whole genome sequencing on the Ion Proton sequencing platform, and fetal fraction derived from Y chromosome counts was compared to fetal fraction measured using the indel panel. A total of 157 cell-free DNA samples were sequenced using the indel panel, and informativity was assessed, along with the proportion of fetal DNA. RESULTS Using gDNA we optimised the indel panel, removing amplicons giving rise to PCR bias. Good correlation was found between fetal fraction using indels and using whole genome sequencing of the Y chromosome (Spearmans r = 0.69). A median of 12 indels were informative per sample. The indel panel was informative in 157/157 cases (mean fetal fraction 14.4% (±0.58%)). CONCLUSIONS Using our targeted next generation sequencing panel we can readily assess the fetal DNA percentage in male and female pregnancies.
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Affiliation(s)
- Angela N. Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail: (AB); (MC)
| | - Li Xiong
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Gynecology & Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Tuan Z. Tan
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Henna V. Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Rui Hua
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Gynecology & Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Cecille Laureano-Asibal
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Richie Soong
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Arijit Biswas
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | | | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- * E-mail: (AB); (MC)
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Lee JE, Kim YY. Impact of Preanalytical Variations in Blood-Derived Biospecimens on Omics Studies: Toward Precision Biobanking? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:499-508. [PMID: 28873014 DOI: 10.1089/omi.2017.0109] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Research data and outcomes do vary across populations and persons, but this is not always due to experimental or true biological variation. Preanalytical components of experiments, be they biospecimen acquisition, preparation, storage, or transportation to the laboratory, may all contribute to apparent variability in research data, outcomes, and interpretation. The present review article and biobanking innovation analysis offer new insights with a summary of such preanalytical variables, for example, the type of blood collection tube, centrifugation conditions, long-term sample storage temperature, and duration, on output of omics analyses of blood-derived biospecimens: whole blood, serum, plasma, buffy coat, and peripheral blood mononuclear cells. Furthermore, we draw parallels from the field of precision medicine in this study, with a view to the future of "precision biobanking" wherein such preanalytical variations are carefully taken into consideration so as to minimize their influence on outcomes of omics data, analyses, and sensemaking, particularly in clinical omics applications. We underscore the need for using broadly framed, critical, independent, social and political science, and humanities research so as to understand the multiple possible future trajectories of, and the motivations and values embedded in, precision biobanking that is increasingly relevant in the current age of Big Data.
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Affiliation(s)
- Jae-Eun Lee
- Division of Biobank for Health Sciences, Center for Genome Science, Korea National Institute of Health , Korea Centers for Disease Control and Prevention, Cheongju-si, Korea
| | - Young-Youl Kim
- Division of Biobank for Health Sciences, Center for Genome Science, Korea National Institute of Health , Korea Centers for Disease Control and Prevention, Cheongju-si, Korea
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Parks M, Court S, Bowns B, Cleary S, Clokie S, Hewitt J, Williams D, Cole T, MacDonald F, Griffiths M, Allen S. Non-invasive prenatal diagnosis of spinal muscular atrophy by relative haplotype dosage. Eur J Hum Genet 2017; 25:416-422. [PMID: 28120840 PMCID: PMC5386415 DOI: 10.1038/ejhg.2016.195] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 11/02/2016] [Accepted: 11/22/2016] [Indexed: 11/10/2022] Open
Abstract
Although technically possible, few clinical laboratories across the world have implemented non-invasive prenatal diagnosis (NIPD) for selected single-gene disorders, mostly owing to the elevated costs incurred. Having previously proven that NIPD for X-linked disorders can be feasibly implemented in clinical practice, we have now developed a test for the NIPD of an autosomal-recessive disorder, spinal muscular atrophy (SMA). Cell-free DNA was extracted from maternal blood and prepared for massively parallel sequencing on an Illumina MiSeq by targeted capture enrichment of single-nucleotide polymorphisms across a 6 Mb genomic window on chromosome 5 containing the SMN1 gene. Maternal, paternal and proband DNA samples were also tested for haplotyping purposes. Sequencing data was analysed by relative haplotype dosage (RHDO). Six pregnant SMA carriers and 10 healthy pregnant donors were recruited through the NIPSIGEN study. Inheritance of the maternally and paternally derived alleles of the affected SMN1 gene was determined in the foetus by RHDO analysis for autosomal-recessive disorders. DNA from the proband (for SMA carriers) or an invasively obtained foetal sample (for healthy pregnant donors) was used to identify the maternal and paternal reference haplotypes associated with the affected SMN1 gene. Results for all patients correlated with known outcomes and showed a testing specificity and sensitivity of 100%. On top of showing high accuracy and reliability throughout the stages of validation, our novel test for NIPD of SMA is also affordable and viable for implementation into clinical service.
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Affiliation(s)
- Michael Parks
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samantha Court
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Benjamin Bowns
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Siobhan Cleary
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Samuel Clokie
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Julie Hewitt
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Trevor Cole
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Fiona MacDonald
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Mike Griffiths
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | - Stephanie Allen
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham, UK
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47
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Silver RM, Myatt L, Hauth JC, Leveno KJ, Peaceman AM, Ramin SM, Samuels P, Saade G, Sorokin Y, Clifton RG, Reddy UM. Cell-Free Total and Fetal DNA in First Trimester Maternal Serum and Subsequent Development of Preeclampsia. Am J Perinatol 2017; 34:191-198. [PMID: 27398706 PMCID: PMC5358543 DOI: 10.1055/s-0035-1570383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Objective The objective of this study was to assess the relationship between first trimester cell-free total and fetal DNA in maternal plasma and the subsequent development of preeclampsia. Study Design Nested case-control study of patients enrolled in the Combined Antioxidant and Preeclampsia Prediction Studies prediction study of 175 women who did and 175 women who did not develop preeclampsia. The predictive values of cell-free total and fetal DNA and the subsequent development of preeclampsia were measured using receiver operating characteristic curves. Results Cell-free total DNA was higher in African American (median; 25-75%; 6.15; 0.14-28.73; p = 0.02) and Hispanic (4.95; 0.20-26.82; p = 0.037) compared with white women (2.33; 0.03-13.10). Levels of cell-free total DNA were also associated with maternal body mass index (BMI) (p = 0.02). Cell-free total DNA levels were similar between women who later developed preeclampsia (3.52; 0.11-25.3) and controls (3.74; 0.12-21.14, p = 0.96). Conclusion There is no significant difference in levels of cell-free total DNA in the first trimester in women who subsequently develop preeclampsia. Levels of cell-free total DNA in the first trimester are increased in African American and Hispanic compared with white women, and levels increase with increasing BMI.
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Affiliation(s)
- Robert M Silver
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Leslie Myatt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - John C Hauth
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Kenneth J Leveno
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Alan M Peaceman
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Susan M Ramin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Philip Samuels
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - George Saade
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Yoram Sorokin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Rebecca G Clifton
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Uma M Reddy
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
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The In Vitro Stability of Circulating Tumour DNA. PLoS One 2016; 11:e0168153. [PMID: 27959945 PMCID: PMC5154581 DOI: 10.1371/journal.pone.0168153] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/26/2016] [Indexed: 01/06/2023] Open
Abstract
Objective DNA from apoptotic cancer cells, present in the circulation, has the potential to facilitate genomic profiling and disease monitoring. However, only low fractions of total cell-free DNA originates from cancer cells, limiting the applicability of circulating tumour DNA (ctDNA). Optimal sample processing is consequently of uttermost importance. Therefore, we evaluated the in vitro stability of ctDNA. Experimental design Blood was collected in 10 ml EDTA or Streck tubes. Three conditions (EDTA and Streck tubes in room temperature, EDTA tubes at five degrees) and four time points (plasma harvested from blood aliquots of each 10 ml tube in a time series up to 24 h) were investigated. Each condition was evaluated in five metastatic prostate cancer patients. Subsequently, three additional patients were collected enabling investigation of the in vitro stability in EDTA tubes up to 48 h. Methods The in vitro stability of ctDNA was interrogated by low-pass whole genome sequencing which allows for the identification of somatic copy-number alterations (CNAs). In silico simulations demonstrated that non-parametric testing could detect a 1% contamination by white blood cell DNA. Mutational profiling was performed by targeted, in-solution based hybridization capture and subsequent sequencing. The allelic fraction of individual mutations was used as an estimate of the in vitro stability. Results Somatic CNAs were detected in all patients. Surprisingly, the ctDNA levels at zero hours were not significantly different to 24 or 48 hour in vitro incubation in any investigated condition. Subsequently, mutational profiling corroborated the conclusions from the CNA analysis. Conclusions The stability of ctDNA simplifies logistics without the requirement of immediate processing or applying fixatives to prevent white blood cell lysis.
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Lu JL, Liang ZY. Circulating free DNA in the era of precision oncology: Pre- and post-analytical concerns. Chronic Dis Transl Med 2016; 2:223-230. [PMID: 29063046 PMCID: PMC5643833 DOI: 10.1016/j.cdtm.2016.12.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Indexed: 02/06/2023] Open
Abstract
Cancer treatment has entered the era of precision medicine, where knowledge of a patient's genetic profile is used to facilitate early diagnosis, drug selection, prognosis, prediction of drug responsiveness, the onset of secondary resistance, and relapse. Circulating free DNA (cfDNA) has emerged as an ideal source of genetic information for cancer patients, and numerous studies have explored its validity in various clinical applications. However, clinical implementation of cfDNA-based tests has been slow. In this review, we addressed some of the pre- and post-analytical issues regarding cfDNA tests. First, we summarized the characteristics of cfDNA and reviewed the methods used to identify tumor-derived cfDNA from the pool of total cfDNA. Second, we described the procedures used to extract cfDNA, which have a great impact on representativeness and yield. Finally, we discussed our thoughts on the validation of cfDNA-based tests and the reporting of test results amid drastic limitations.
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Affiliation(s)
| | - Zhi-Yong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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50
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Comparative analysis of circulating tumor DNA stability In K3EDTA, Streck, and CellSave blood collection tubes. Clin Biochem 2016; 49:1354-1360. [DOI: 10.1016/j.clinbiochem.2016.03.012] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/09/2016] [Accepted: 03/07/2016] [Indexed: 12/24/2022]
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