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Madritsch S, Arnold V, Haider M, Bosenge J, Pfeifer M, Weil B, Zechmeister M, Hengstschläger M, Neesen J, Laccone F. Aneuploidy detection in pooled polar bodies using rapid nanopore sequencing. J Assist Reprod Genet 2024; 41:1261-1271. [PMID: 38642269 PMCID: PMC11143085 DOI: 10.1007/s10815-024-03108-7] [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: 11/23/2023] [Accepted: 03/25/2024] [Indexed: 04/22/2024] Open
Abstract
PURPOSE Various screening techniques have been developed for preimplantation genetic testing for aneuploidy (PGT-A) to reduce implantation failure and miscarriages in women undergoing in vitro fertilisation (IVF) treatment. Among these methods, the Oxford nanopore technology (ONT) has already been tested in several tissues. However, no studies have applied ONT to polar bodies, a cellular material that is less restrictively regulated for PGT-A in some countries. METHODS We performed rapid short nanopore sequencing on pooled first and second polar bodies of 102 oocytes from women undergoing IVF treatment to screen for aneuploidy. An automated analysis pipeline was developed with the expectation of three chromatids per chromosome. The results were compared to those obtained by array-based comparative genomic hybridisation (aCGH). RESULTS ONT and aCGH were consistent for 96% (98/102) of sample ploidy classification. Of those samples, 36 were classified as euploid, while 62 were classified as aneuploid. The four discordant samples were assessed as euploid using aCGH but classified as aneuploid using ONT. The concordance of the ploidy classification (euploid, gain, or loss) per chromosome was 92.5% (2169 of 2346 of analysed chromosomes) using aCGH and ONT and increased to 97.7% (2113/2162) without the eight samples assessed as highly complex aneuploid using ONT. CONCLUSION The automated detection of the ploidy classification per chromosome and shorter duplications or deletions depending on the sequencing depth demonstrates an advantage of the ONT method over standard, commercial aCGH methods, which do not consider the presence of three chromatids in pooled polar bodies.
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Affiliation(s)
- Silvia Madritsch
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria.
| | - Vivienne Arnold
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Martha Haider
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Julia Bosenge
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Mateja Pfeifer
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
| | - Beatrix Weil
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | | | - Markus Hengstschläger
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Jürgen Neesen
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
| | - Franco Laccone
- Institute of Medical Genetics, Medical University of Vienna, Währinger Straße 10, 1090, Vienna, Austria
- HLN-Genetik GmbH, Ortliebgasse 25/1, 1170, Vienna, Austria
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2
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Perez-Rodriguez D, Kalyva M, Santucci C, Proukakis C. Somatic CNV Detection by Single-Cell Whole-Genome Sequencing in Postmortem Human Brain. Methods Mol Biol 2023; 2561:205-230. [PMID: 36399272 DOI: 10.1007/978-1-0716-2655-9_11] [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: 06/16/2023]
Abstract
The evidence for a role of somatic mutations, including copy-number variants (CNVs), in neurodegeneration has increased in the last decade. However, the understanding of the types and origins of these mutations, and their exact contributions to disease onset and progression, is still in its infancy. The use of single-cell (or nuclear) whole-genome sequencing (scWGS) has emerged as a powerful tool to answer these questions. In the present chapter, we provide laboratory and bioinformatic protocols used successfully in our lab to detect megabase-scale CNVs in single cells from multiple system atrophy (MSA) human postmortem brains, using immunolabeling prior to selection of nuclei for whole-genome amplification (WGA). We also present an unpublished comparison of scWGS generated from the same control substantia nigra (SN) sample, using the latest versions of popular WGA chemistries, MDA and PicoPLEX. We have used this protocol to focus on brain cell types most relevant to synucleinopathies (dopaminergic [DA] neurons in Parkinson's disease [PD] and oligodendrocytes in MSA), but it can be applied to any tissue and/or cell type with appropriate markers.
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Affiliation(s)
- Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
| | - Maria Kalyva
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
| | - Catherine Santucci
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London, London, UK.
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3
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Whole-Genome Amplification—Surveying Yield, Reproducibility, and Heterozygous Balance, Reported by STR-Targeting MIPs. Int J Mol Sci 2022; 23:ijms23116161. [PMID: 35682839 PMCID: PMC9181316 DOI: 10.3390/ijms23116161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/27/2022] [Accepted: 05/27/2022] [Indexed: 02/01/2023] Open
Abstract
Whole-genome amplification is a crucial first step in nearly all single-cell genomic analyses, with the following steps focused on its products. Bias and variance caused by the whole-genome amplification process add numerous challenges to the world of single-cell genomics. Short tandem repeats are sensitive genomic markers used widely in population genetics, forensics, and retrospective lineage tracing. A previous evaluation of common whole-genome amplification targeting ~1000 non-autosomal short tandem repeat loci is extended here to ~12,000 loci across the entire genome via duplex molecular inversion probes. Other than its improved scale and reduced noise, this system detects an abundance of heterogeneous short tandem repeat loci, allowing the allelic balance to be reported. We show here that while the best overall yield is obtained using RepliG-SC, the maximum uniformity between alleles and reproducibility across cells are maximized by Ampli1, rendering it the best candidate for the comparative heterozygous analysis of single-cell genomes.
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4
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Comparison of seven single cell whole genome amplification commercial kits using targeted sequencing. Sci Rep 2021; 11:17171. [PMID: 34433869 PMCID: PMC8387353 DOI: 10.1038/s41598-021-96045-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 07/26/2021] [Indexed: 11/08/2022] Open
Abstract
Advances in whole genome amplification (WGA) techniques enable understanding of the genomic sequence at a single cell level. Demand for single cell dedicated WGA kits (scWGA) has led to the development of several commercial kit. To this point, no robust comparison of all available kits was performed. Here, we benchmark an economical assay, comparing all commercially available scWGA kits. Our comparison is based on targeted sequencing of thousands of genomic loci, including highly mutable regions, from a large cohort of human single cells. Using this approach we have demonstrated the superiority of Ampli1 in genome coverage and of RepliG in reduced error rate. In summary, we show that no single kit is optimal across all categories, highlighting the need for a dedicated kit selection in accordance with experimental requirements.
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5
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Ito N, Tsukamoto K, Taniguchi K, Takahashi K, Okamoto A, Aoki H, Otera‐Takahashi Y, Kitagawa M, Ogata‐Kawata H, Morita H, Hata K, Nakabayashi K. Isolation and characterization of fetal nucleated red blood cells from maternal blood as a target for single cell sequencing-based non-invasive genetic testing. Reprod Med Biol 2021; 20:352-360. [PMID: 34262404 PMCID: PMC8254165 DOI: 10.1002/rmb2.12392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 05/20/2021] [Indexed: 01/04/2023] Open
Abstract
PURPOSE Although non-invasive prenatal testing (NIPT) based on cell-free DNA (cfDNA) in maternal plasma has been prevailing worldwide, low levels of fetal DNA fraction may lead to false-negative results. Since fetal cells in maternal blood provide a pure source of fetal genomic DNA, we aimed to establish a workflow to isolate and sequence fetal nucleated red blood cells (fNRBCs) individually as a target for NIPT. METHODS Using male-bearing pregnancy cases, we isolated fNRBCs individually from maternal blood by FACS, and obtained their genomic sequence data through PCR screening with a Y-chromosome marker and whole-genome amplification (WGA)-based whole-genome sequencing. RESULTS The PCR and WGA efficiencies of fNRBC candidates were consistently lower than those of control cells. Sequencing data analyses revealed that although the majority of the fNRBC candidates were confirmed to be of fetal origin, many of the WGA-based genomic libraries from fNRBCs were considered to have been amplified from a portion of genomic DNA. CONCLUSIONS We established a workflow to isolate and sequence fNRBCs individually. However, our results demonstrated that, to make cell-based NIPT targeting fNRBCs feasible, cell isolation procedures need to be further refined such that the nuclei of fNRBCs are kept intact.
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Affiliation(s)
- Noriko Ito
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
- Department of Pharmacotherapeutics, Course of Medical and Dental SciencesNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kazuhiro Tsukamoto
- Department of Pharmacotherapeutics, Course of Medical and Dental SciencesNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kosuke Taniguchi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Ken Takahashi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
- Department of Obstetrics and GynecologyThe Jikei University School of MedicineTokyoJapan
| | - Aikou Okamoto
- Department of Obstetrics and GynecologyThe Jikei University School of MedicineTokyoJapan
| | | | | | | | - Hiroko Ogata‐Kawata
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Hideaki Morita
- Department of Allergy and Clinical ImmunologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Kenichiro Hata
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Kazuhiko Nakabayashi
- Department of Maternal‐Fetal BiologyNational Center for Child Health and DevelopmentTokyoJapan
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6
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Vossaert L, Chakchouk I, Zemet R, Van den Veyver IB. Overview and recent developments in cell-based noninvasive prenatal testing. Prenat Diagn 2021; 41:1202-1214. [PMID: 33974713 DOI: 10.1002/pd.5957] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022]
Abstract
Investigators have long been interested in the natural phenomenon of fetal and placental cell trafficking into the maternal circulation. The scarcity of these circulating cells makes their detection and isolation technically challenging. However, as a DNA source of fetal origin not mixed with maternal DNA, they have the potential of considerable benefit over circulating cell-free DNA-based noninvasive prenatal genetic testing (NIPT). Endocervical trophoblasts, which are less rare but more challenging to recover are also being investigated as an approach for cell-based NIPT. We review published studies from around the world describing both forms of cell-based NIPT and highlight the different approaches' advantages and drawbacks. We also offer guidance for developing a sound cell-based NIPT protocol.
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Affiliation(s)
- Liesbeth Vossaert
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Imen Chakchouk
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Roni Zemet
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ignatia B Van den Veyver
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA.,Pavillion for Women, Texas Children's Hospital, Houston, TX, USA
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7
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Nakamura IT, Ikegami M, Hasegawa N, Hayashi T, Ueno T, Kawazu M, Yagishita S, Goto Y, Shinno Y, Kojima Y, Takamochi K, Takahashi F, Takahashi K, Mano H, Kohsaka S. Development of an optimal protocol for molecular profiling of tumor cells in pleural effusions at single-cell level. Cancer Sci 2021; 112:2006-2019. [PMID: 33484069 PMCID: PMC8088920 DOI: 10.1111/cas.14821] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 12/11/2022] Open
Abstract
Liquid biopsy analyzes the current status of primary tumors and their metastatic regions. We aimed to develop an optimized protocol for single-cell sequencing of floating tumor cells (FTCs) in pleural effusion as a laboratory test. FTCs were enriched using a negative selection of white blood cells by a magnetic-activated cell sorting system, and CD45-negative and cytokeratin-positive selection using a microfluidic cell separation system with a dielectrophoretic array. The enriched tumor cells were subjected to whole-genome amplification (WGA) followed by genome sequencing. The FTC analysis detected an EGFR exon 19 deletion in Case 1 (12/19 cells, 63.2%), and EML4-ALK fusion (17/20 cells, 85%) with an alectinib-resistant mutation of ALK (p.G1202R) in Case 2. To eliminate WGA-associated errors and increase the uniformity of the WGA product, the protocol was revised to sequence multiple single FTCs individually. An analytical pipeline, accurate single-cell mutation detector (ASMD), was developed to identify somatic mutations of FTCs. The large numbers of WGA-associated errors were cleaned up, and the somatic mutations detected in FTCs by ASMD were concordant with those found in tissue specimens. This protocol is applicable to circulating tumor cells analysis of peripheral blood and expands the possibility of utilizing molecular profiling of cancers.
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Affiliation(s)
- Ikuko Takeda Nakamura
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Masachika Ikegami
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Orthopedic Surgery, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nobuhiko Hasegawa
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan.,Department of Orthopedic Surgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takuo Hayashi
- Department of Human Pathology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Shigehiro Yagishita
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Goto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Shinno
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Kojima
- Department of Breast and Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Kazuya Takamochi
- Department of General Thoracic Surgery, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Fumiyuki Takahashi
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
| | - Shinji Kohsaka
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo, Japan
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8
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Weymaere J, Vander Plaetsen AS, Tilleman L, Tytgat O, Rubben K, Geeraert S, Deforce D, Van Nieuwerburgh F. Kinship analysis on single cells after whole genome amplification. Sci Rep 2020; 10:14647. [PMID: 32887915 PMCID: PMC7474072 DOI: 10.1038/s41598-020-71562-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/18/2020] [Indexed: 11/18/2022] Open
Abstract
Short Tandem Repeat (STR-) and Single Nucleotide Polymorphism (SNP-) genotyping have been extensively studied within forensic kinship analysis. Nevertheless, no results have been reported on kinship analysis after whole genome amplification (WGA) of single cells. This WGA step is a necessary procedure in several applications, such as cell-based non-invasive prenatal testing (cbNIPT) and pre-implantation genetic diagnosis (PGD). In cbNIPT, all putative fetal cells must be discriminated from maternal cells after enrichment from whole blood. This study investigates the efficacy and evidential value of STR- and SNP-genotyping methods for the discrimination of 24 single cells after WGA, within three families. Formaldehyde-fixed and unfixed cells are assessed in offspring-parent duos and offspring-mother-father trios. Results demonstrate that both genotyping methods can be used in all tested conditions and scenarios with 100% sensitivity and 100% specificity, with a similar evidential value for fixed and unfixed cells. Moreover, sequence-based SNP-genotyping results in a higher evidential value than length-based STR-genotyping after WGA, which is not observed using high-quality offspring bulk DNA samples. Finally, it is also demonstrated that the availability of the DNA genotypes of both parents strongly increases the evidential value of the results.
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Affiliation(s)
- Jana Weymaere
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Ann-Sophie Vander Plaetsen
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Olivier Tytgat
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium.,Department of Life Science Technologies, Imec, 3001, Leuven, Belgium
| | - Kaat Rubben
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Sofie Geeraert
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Gent, Belgium.
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9
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Shafei N, Hakhamaneshi MS, Houshmand M, Gerayeshnejad S, Fathi F, Sharifzadeh S. Diagnostic Value of Non-Invasive Prenatal Screening of β-thalassemia by Cell Free Fetal DNA and Fetal NRBC. Curr Mol Med 2020; 19:105-111. [PMID: 30813874 DOI: 10.2174/1566524019666190226124135] [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: 07/22/2018] [Revised: 01/08/2019] [Accepted: 02/18/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Beta thalassemia is a common disorder with autosomal recessive inheritance. The most prenatal diagnostic methods are the invasive techniques that have the risk of miscarriage. Now the non-invasive methods will be gradually alternative for these invasive techniques. OBJECTIVE The aim of this study is to evaluate and compare the diagnostic value of two non-invasive diagnostic methods for fetal thalassemia using cell free fetal DNA (cff-DNA) and nucleated RBC (NRBC) in one sampling community. METHODS 10 ml of blood was taken in two k3EDTA tube from 32 pregnant women (mean of gestational age = 11 weeks), who themselves and their husbands had minor thalassemia. One tube was used to enrich NRBC and other was used for cff-DNA extraction. NRBCs were isolated by MACS method and immunohistochemistry; the genome of stained cells was amplified by multiple displacement amplification (MDA) procedure. These products were used as template in b-globin segments PCR. cff-DNA was extracted by THP method and 300 bp areas were recovered from the agarose gel as fetus DNA. These DNA were used as template in touch down PCR to amplify b-globin gen. The amplified b-globin segments were sequenced and the results compared with CVS resul. RESULTS The data showed that sensitivity and specificity of thalassemia diagnosis by NRBC were 100% and 92% respectively and sensitivity and specificity of thalassemia diagnosis by cff-DNA were 100% and 84% respectively. CONCLUSION These methods with high sensitivity can be used as screening test but due to their lower specificity than CVS, they cannot be used as diagnostic test.
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Affiliation(s)
- Nadia Shafei
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | | | - Massoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Siavash Gerayeshnejad
- Department of Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fardin Fathi
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Sardar Sharifzadeh
- PhD student, Department of Clinical Biochemistry, School of Medicine, Tarbiat Modares University, Tehran, Iran
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10
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Negishi R, Iwata R, Tanaka T, Kisailus D, Maeda Y, Matsunaga T, Yoshino T. Gel-based cell manipulation method for isolation and genotyping of single-adherent cells. Analyst 2019; 144:990-996. [DOI: 10.1039/c8an01456f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The simple and rapid method for isolation of single-adherent cells from a culture dish was developed and applied to genetic analysis of single-cells.
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Affiliation(s)
- Ryo Negishi
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - Reito Iwata
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - Tsuyoshi Tanaka
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - David Kisailus
- Department of Chemical and Environmental Engineering
- University of California
- Riverside
- Riverside
- USA
| | - Yoshiaki Maeda
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - Tadashi Matsunaga
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
| | - Tomoko Yoshino
- Division of Biotechnology and Life Science
- Institute of Engineering
- Tokyo University of Agriculture and Technology
- Tokyo
- Japan
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11
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Tyler AD, Mataseje L, Urfano CJ, Schmidt L, Antonation KS, Mulvey MR, Corbett CR. Evaluation of Oxford Nanopore's MinION Sequencing Device for Microbial Whole Genome Sequencing Applications. Sci Rep 2018; 8:10931. [PMID: 30026559 PMCID: PMC6053456 DOI: 10.1038/s41598-018-29334-5] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/03/2018] [Indexed: 01/15/2023] Open
Abstract
The MinION sequencer (Oxford Nanopore Technologies) is a paradigm shifting device allowing rapid, real time long read sequencing of nucleic acids. Yet external benchmarking of this technologies' capabilities has not been extensively reported, nor has thorough evaluation of its utility for field-based analysis with sub-optimal sample types been described. The aim of this study was to evaluate the capability of the MinION sequencer for bacterial genomic and metagenomic applications, with specific emphasis placed on the quality, yield, and accuracy of generated sequence data. Two independent laboratories at the National Microbiology Laboratory (Public Health Agency of Canada), sequenced a set of microbes in replicate, using the currently available flowcells, sequencing chemistries, and software available at the time of the experiment. Overall sequencing yield and quality improved through the course of this set of experiments. Sequencing alignment accuracy was high reaching 97% for all 2D experiments, though was slightly lower for 1D sequencing (94%). 1D sequencing provided much longer sequences than 2D. Both sequencing chemistries performed equally well in constructing genomic assemblies. There was evidence of barcode cross-over using both the native and PCR barcoding methods. Despite the sub-optimal nature of samples sequenced in the field, sequences attributable to B. anthracis the target organism used in this scenario, could none-the-less be detected. Together, this report showcases the rapid advancement in this technology and its utility in the context of genomic sequencing of microbial isolates of importance to public health.
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Affiliation(s)
- Andrea D Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada.
| | - Laura Mataseje
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Chantel J Urfano
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Lisa Schmidt
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Kym S Antonation
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Michael R Mulvey
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
| | - Cindi R Corbett
- National Microbiology Laboratory, Public Health Agency of Canada, 1015 Arlington Street, Winnipeg, Manitoba, R3E 3R2, Canada
- University of Manitoba, Department of Medical Microbiology and Infectious Diseases, Winnipeg, Manitoba, R3E 0J9, Canada
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12
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Deleye L, Gansemans Y, De Coninck D, Van Nieuwerburgh F, Deforce D. Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods. PLoS One 2018; 13:e0196334. [PMID: 29698522 PMCID: PMC5919401 DOI: 10.1371/journal.pone.0196334] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 04/11/2018] [Indexed: 12/28/2022] Open
Abstract
Single Gene Disorders (SGD) are still routinely diagnosed using PCR-based assays that need to be developed and validated for each individual disease-specific gene fragment. The TruSight One sequencing panel currently covers 12 Mb of genomic content, including 4813 genes associated with a clinical phenotype. When only a limited number of cells are available, whole genome amplification (WGA) is required prior to DNA target capture techniques such as the TruSight One panel. In this study, we compared 4 different WGA methods in combination with the TruSight One sequencing panel to perform single nucleotide polymorphism (SNP) genotyping starting from 3 micro-manipulated cells. This setting simulates clinical settings such as day-5 blastocyst biopsy for Preimplantation Genetic Testing (PGT), liquid biopsy of circulating tumor cells (CTCs) and cancer-cell profiling. Bulk cell samples were processed alongside these WGA samples to serve as a performance reference. Target coverage, coverage uniformity and SNP calling accuracy obtained using any of the WGA, is inferior to the results obtained on bulk cell samples. However, results after REPLI-g come close. Compared to the other WGA methods, the method using REPLI-g WGA results in a better coverage of the targeted genomic regions with a more uniform read depth. Consequently, this method also results in a more accurate SNP calling and could be considered for clinical genotyping of a limited number of cells.
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Affiliation(s)
- Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter De Coninck
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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13
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Ferrarini A, Forcato C, Buson G, Tononi P, del Monaco V, Terracciano M, Bolognesi C, Fontana F, Medoro G, Neves R, Möhlendick B, Rihawi K, Ardizzoni A, Sumanasuriya S, Flohr P, Lambros M, de Bono J, Stoecklein NH, Manaresi N. A streamlined workflow for single-cells genome-wide copy-number profiling by low-pass sequencing of LM-PCR whole-genome amplification products. PLoS One 2018; 13:e0193689. [PMID: 29494651 PMCID: PMC5832318 DOI: 10.1371/journal.pone.0193689] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/19/2018] [Indexed: 11/23/2022] Open
Abstract
Chromosomal instability and associated chromosomal aberrations are hallmarks of cancer and play a critical role in disease progression and development of resistance to drugs. Single-cell genome analysis has gained interest in latest years as a source of biomarkers for targeted-therapy selection and drug resistance, and several methods have been developed to amplify the genomic DNA and to produce libraries suitable for Whole Genome Sequencing (WGS). However, most protocols require several enzymatic and cleanup steps, thus increasing the complexity and length of protocols, while robustness and speed are key factors for clinical applications. To tackle this issue, we developed a single-tube, single-step, streamlined protocol, exploiting ligation mediated PCR (LM-PCR) Whole Genome Amplification (WGA) method, for low-pass genome sequencing with the Ion Torrent™ platform and copy number alterations (CNAs) calling from single cells. The method was evaluated on single cells isolated from 6 aberrant cell lines of the NCI-H series. In addition, to demonstrate the feasibility of the workflow on clinical samples, we analyzed single circulating tumor cells (CTCs) and white blood cells (WBCs) isolated from the blood of patients affected by prostate cancer or lung adenocarcinoma. The results obtained show that the developed workflow generates data accurately representing whole genome absolute copy number profiles of single cell and allows alterations calling at resolutions down to 100 Kbp with as few as 200,000 reads. The presented data demonstrate the feasibility of the Ampli1™ WGA-based low-pass workflow for detection of CNAs in single tumor cells which would be of particular interest for genome-driven targeted therapy selection and for monitoring of disease progression.
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Affiliation(s)
| | | | - Genny Buson
- Menarini Silicon Biosystems spa, Bologna, Italy
| | | | | | | | | | | | | | - Rui Neves
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich- Heine-University Düsseldorf, Düsseldorf, Germany
| | - Birte Möhlendick
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich- Heine-University Düsseldorf, Düsseldorf, Germany
| | - Karim Rihawi
- Unità Operativa di Oncologia Medica, Policlinico Sant’Orsola – Malpighi, Bologna, Italy
| | - Andrea Ardizzoni
- Unità Operativa di Oncologia Medica, Policlinico Sant’Orsola – Malpighi, Bologna, Italy
| | - Semini Sumanasuriya
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Penny Flohr
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Maryou Lambros
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Johann de Bono
- The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Nikolas H. Stoecklein
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich- Heine-University Düsseldorf, Düsseldorf, Germany
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14
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Systematic assessment of the performance of whole-genome amplification for SNP/CNV detection and β-thalassemia genotyping. J Hum Genet 2018; 63:407-416. [PMID: 29440707 DOI: 10.1038/s10038-018-0411-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/04/2018] [Accepted: 01/04/2018] [Indexed: 11/08/2022]
Abstract
In this study, we aimed to assess the performance of two whole-genome amplification methods, multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycle (MALBAC), for β-thalassemia genotyping and single-nucleotide polymorphism (SNP)/copy-number variant (CNV) detection using two DNA sequencing assays. We collected peripheral blood, cell lines, and discarded embryos, and carried out MALBAC and MDA on single-cell and five-cell samples. We detected and statistically analyzed differences in the amplification efficiency, positive predictive value, sensitivity, allele dropout (ADO) rate, SNPs, and CV values between the two methods. Through Sanger sequencing at the single-cell and five-cell levels, we showed that both the amplification rate and ADO rate of MDA were better than those using MALBAC, and the sensitivity and positive predictive value obtained from MDA were higher than those from MALBAC for β-thalassemia genotyping. Using next-generation sequencing (NGS) at the single-cell level, we confirmed that MDA has better properties than MALBAC for SNP detection. However, MALBAC was more stable and homogeneous than MDA using low-depth NGS at the single-cell level for CNV detection. We conclude that MALBAC is the better option for CNV detection, while MDA is better suited for SNV detection.
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15
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Palmirotta R, Lovero D, Silvestris E, Felici C, Quaresmini D, Cafforio P, Silvestris F. Next-generation Sequencing (NGS) Analysis on Single Circulating Tumor Cells (CTCs) with No Need of Whole-genome Amplification (WGA). Cancer Genomics Proteomics 2018; 14:173-179. [PMID: 28446532 DOI: 10.21873/cgp.20029] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/04/2017] [Accepted: 04/05/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Isolation and genotyping of circulating tumor cells (CTCs) is gaining an increasing interest by clinical researchers in oncology not only for investigative purposes, but also for concrete application in clinical practice in terms of diagnosis, prognosis and decision treatment with targeted therapies. For the mutational analysis of single CTCs, the most advanced biotechnology methodology currently available includes the combination of whole genome amplification (WGA) followed by next-generation sequencing (NGS). However, the sequence of these molecular techniques is time-consuming and may also favor operator-dependent errors, related to the procedures themselves that, as in the case of the WGA technique, might affect downstream molecular analyses. MATERIALS AND METHODS A preliminary approach of molecular analysis by NGS on a model of CTCs without previous WGA procedural step was performed. We set-up an artificial sample obtained by spiking the SK-MEL-28 melanoma cell line in normal donor peripheral whole blood. Melanoma cells were first enriched using an AutoMACS® (Miltenyi) cell separator and then isolated as single and pooled CTCs by DEPArray™ System (Silicon Biosystems). NGS analysis, using the Ion AmpliSeq™ Cancer Hotspot Panel v2 (Life Technologies) with the Ion Torrent PGM™ system (Life Technologies), was performed on the SK-MEL-28 cell pellet, a single CTC previously processed with WGA and on 1, 2, 4 and 8 recovered CTCs without WGA pre-amplification. RESULTS NGS directly carried out on CTCs without WGA showed the same mutations identified in SK-MEL-28 cell line pellet, with a considerable efficiency and avoiding the errors induced by the WGA procedure. CONCLUSION We identified a cost-effective, time-saving and reliable methodological approach that could improve the analytical accuracy of the liquid biopsy and appears promising in studying CTCs from cancer patients for both research and clinical purposes.
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Affiliation(s)
- Raffaele Palmirotta
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Domenica Lovero
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Erica Silvestris
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Claudia Felici
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Davide Quaresmini
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Paola Cafforio
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
| | - Franco Silvestris
- Department of Biomedical Sciences and Human Oncology, University of Bari 'Aldo Moro', Bari, Italy
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16
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Vander Plaetsen AS, Deleye L, Cornelis S, Tilleman L, Van Nieuwerburgh F, Deforce D. STR profiling and Copy Number Variation analysis on single, preserved cells using current Whole Genome Amplification methods. Sci Rep 2017; 7:17189. [PMID: 29215049 PMCID: PMC5719346 DOI: 10.1038/s41598-017-17525-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023] Open
Abstract
The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation. The suitability of the DNA, amplified with Ampli1, DOPlify, PicoPLEX and REPLI-g, was assessed for both short tandem repeat (STR) profiling and copy number variant (CNV) analysis after shallow whole genome massively parallel sequencing (MPS). Results demonstrate that Ampli1, DOPlify and PicoPLEX perform well for both applications, with some differences between the methods. Samples amplified with REPLI-g did not result in suitable STR or CNV profiles, indicating that this WGA method is not able to generate high quality DNA after Streck Cell-Free DNA BCT stabilization of the cells.
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Affiliation(s)
- Ann-Sophie Vander Plaetsen
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Lieselot Deleye
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Senne Cornelis
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.,Department of Life Science Technologies, imec, 3001, Leuven, Belgium
| | - Laurentijn Tilleman
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
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17
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Fontana F, Rapone C, Bregola G, Aversa R, de Meo A, Signorini G, Sergio M, Ferrarini A, Lanzellotto R, Medoro G, Giorgini G, Manaresi N, Berti A. Isolation and genetic analysis of pure cells from forensic biological mixtures: The precision of a digital approach. Forensic Sci Int Genet 2017; 29:225-241. [PMID: 28511094 DOI: 10.1016/j.fsigen.2017.04.023] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/20/2017] [Accepted: 04/30/2017] [Indexed: 12/17/2022]
Abstract
Latest genotyping technologies allow to achieve a reliable genetic profile for the offender identification even from extremely minute biological evidence. The ultimate challenge occurs when genetic profiles need to be retrieved from a mixture, which is composed of biological material from two or more individuals. In this case, DNA profiling will often result in a complex genetic profile, which is then subject matter for statistical analysis. In principle, when more individuals contribute to a mixture with different biological fluids, their single genetic profiles can be obtained by separating the distinct cell types (e.g. epithelial cells, blood cells, sperm), prior to genotyping. Different approaches have been investigated for this purpose, such as fluorescent-activated cell sorting (FACS) or laser capture microdissection (LCM), but currently none of these methods can guarantee the complete separation of different type of cells present in a mixture. In other fields of application, such as oncology, DEPArray™ technology, an image-based, microfluidic digital sorter, has been widely proven to enable the separation of pure cells, with single-cell precision. This study investigates the applicability of DEPArray™ technology to forensic samples analysis, focusing on the resolution of the forensic mixture problem. For the first time, we report here the development of an application-specific DEPArray™ workflow enabling the detection and recovery of pure homogeneous cell pools from simulated blood/saliva and semen/saliva mixtures, providing full genetic match with genetic profiles of corresponding donors. In addition, we assess the performance of standard forensic methods for DNA quantitation and genotyping on low-count, DEPArray™-isolated cells, showing that pure, almost complete profiles can be obtained from as few as ten haploid cells. Finally, we explore the applicability in real casework samples, demonstrating that the described approach provides complete separation of cells with outstanding precision. In all examined cases, DEPArray™ technology proves to be a groundbreaking technology for the resolution of forensic biological mixtures, through the precise isolation of pure cells for an incontrovertible attribution of the obtained genetic profiles.
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Affiliation(s)
- F Fontana
- Menarini Silicon Biosystems S.p.A., Bologna, Italy.
| | - C Rapone
- Reparto Investigazioni Scientifiche Carabinieri R.I.S., Roma, Italy
| | - G Bregola
- Menarini Silicon Biosystems S.p.A., Bologna, Italy
| | - R Aversa
- Menarini Silicon Biosystems S.p.A., Bologna, Italy
| | - A de Meo
- Reparto Investigazioni Scientifiche Carabinieri R.I.S., Roma, Italy
| | - G Signorini
- Menarini Silicon Biosystems S.p.A., Bologna, Italy
| | - M Sergio
- Menarini Silicon Biosystems S.p.A., Bologna, Italy
| | - A Ferrarini
- Menarini Silicon Biosystems S.p.A., Bologna, Italy
| | | | - G Medoro
- Menarini Silicon Biosystems S.p.A., Bologna, Italy
| | - G Giorgini
- Menarini Silicon Biosystems S.p.A., Bologna, Italy
| | - N Manaresi
- Menarini Silicon Biosystems S.p.A., Bologna, Italy
| | - A Berti
- Reparto Investigazioni Scientifiche Carabinieri R.I.S., Roma, Italy
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18
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Kølvraa S, Singh R, Normand EA, Qdaisat S, van den Veyver IB, Jackson L, Hatt L, Schelde P, Uldbjerg N, Vestergaard EM, Zhao L, Chen R, Shaw CA, Breman AM, Beaudet AL. Genome-wide copy number analysis on DNA from fetal cells isolated from the blood of pregnant women. Prenat Diagn 2016; 36:1127-1134. [PMID: 27761919 DOI: 10.1002/pd.4948] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 10/13/2016] [Accepted: 10/15/2016] [Indexed: 01/24/2023]
Abstract
OBJECTIVE Non-invasive prenatal testing (NIPT) based on fetal cells in maternal blood has the advantage over NIPT based on circulating cell-free fetal DNA in that there is no contamination with maternal DNA. This will most likely result in better detection of chromosomal aberrations including subchromosomal defects. The objective of this study was to test whether fetal cells enriched from maternal blood can be used for cell-based NIPT. METHODS We present a method for enriching fetal cells from maternal blood, subsequent amplification of the fetal genome and detection of chromosomal and subchromosomal variations in the genome. RESULTS An average of 12.8 fetal cells from 30 mL of maternal blood were recovered using our method. Subsequently, whole genome amplification on fetal cells resulted in amplified fetal DNA in amounts and quality high enough to generate array comparative genomic hybridization as well as next-generation sequencing profiles. From one to two fetal cells, we were able to demonstrate copy number differences of whole chromosomes (21, X-, and Y) as well as subchromosomal aberrations (ring X). CONCLUSION Intact fetal cells can be isolated from every maternal blood sample. Amplified DNA from isolated fetal cells enabled genetic analysis by array comparative genomic hybridization and next-generation sequencing. © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
| | | | - Elizabeth A Normand
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sadeem Qdaisat
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ignatia B van den Veyver
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, USA
| | - Laird Jackson
- Department of OB-Gyn, Drexel University College of Medicine, Philadelphia, PA, USA
| | | | | | - Niels Uldbjerg
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Aarhus N, Denmark
| | | | - Li Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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