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Hose L, Schürmann M, Mennebröcker I, Kim R, Busche T, Goon P, Sudhoff H. Characterization of non-invasive oropharyngeal samples and nucleic acid isolation for molecular diagnostics. Sci Rep 2024; 14:4061. [PMID: 38374370 PMCID: PMC10876689 DOI: 10.1038/s41598-024-54179-6] [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: 10/18/2023] [Accepted: 02/09/2024] [Indexed: 02/21/2024] Open
Abstract
Molecular diagnostics is an increasingly important clinical tool, especially in routine sampling. We evaluated two non-invasive methods (oral swabs and mouthwashes) for sampling nucleic acids from the oral/pharyngeal area. We created a workflow from sample collection (n = 59) to RT-qPCR based analysis. The samples were further characterized in terms of their cellular composition as well as the purity, degradation and microbial content of the derived DNA/RNA. We determined the optimal housekeeping genes applicable for these types of samples. The cellular composition indicated that mouthwashes contained more immune cells and bacteria. Even though the protocol was not specifically optimized to extract bacterial RNA it was possible to derive microbial RNA, from both sampling methods. Optimizing the protocol allowed us to generate stable quantities of DNA/RNA. DNA/RNA purity parameters were not significantly different between the two sampling methods. Even though integrity analysis demonstrated a high level of degradation of RNA, corresponding parameters confirmed their sequencing potential. RT-qPCR analysis determined TATA-Box Binding Protein as the most favorable housekeeping gene. In summary, we have developed a robust method suitable for multiple downstream diagnostic techniques. This protocol can be used as a foundation for further research endeavors focusing on developing molecular diagnostics for the oropharyngeal cavity.
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Affiliation(s)
- Leonie Hose
- Department of Otolaryngology, Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Teutoburger Str. 50, 33604, Bielefeld, Germany.
| | - Matthias Schürmann
- Department of Otolaryngology, Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Teutoburger Str. 50, 33604, Bielefeld, Germany
| | - Inga Mennebröcker
- Department of Otolaryngology, Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Teutoburger Str. 50, 33604, Bielefeld, Germany
| | - Rayoung Kim
- Department of Otolaryngology, Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Teutoburger Str. 50, 33604, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), University Hospital OWL of Bielefeld University, Bielefeld, Germany
| | - Peter Goon
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore, Singapore
| | - Holger Sudhoff
- Department of Otolaryngology, Head and Neck Surgery, Campus Klinikum Bielefeld Mitte, University Hospital OWL of Bielefeld University, Teutoburger Str. 50, 33604, Bielefeld, Germany
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Andres O, König EM, Althaus K, Bakchoul T, Bugert P, Eber S, Knöfler R, Kunstmann E, Manukjan G, Meyer O, Strauß G, Streif W, Thiele T, Wiegering V, Klopocki E, Schulze H. Use of Targeted High-Throughput Sequencing for Genetic Classification of Patients with Bleeding Diathesis and Suspected Platelet Disorder. TH OPEN 2018; 2:e445-e454. [PMID: 31249973 PMCID: PMC6524924 DOI: 10.1055/s-0038-1676813] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
Inherited platelet disorders (IPD) form a rare and heterogeneous disease entity that is present in about 8% of patients with non-acquired bleeding diathesis. Identification of the defective cellular pathway is an important criterion for stratifying the patient's individual risk profile and for choosing personalized therapeutic options. While costs of high-throughput sequencing technologies have rapidly declined over the last decade, molecular genetic diagnosis of bleeding and platelet disorders is getting more and more suitable within the diagnostic algorithms. In this study, we developed, verified, and evaluated a targeted, panel-based next-generation sequencing approach comprising 59 genes associated with IPD for a cohort of 38 patients with a history of recurrent bleeding episodes and functionally suspected, but so far genetically undefined IPD. DNA samples from five patients with genetically defined IPD with disease-causing variants in
WAS
,
RBM8A
,
FERMT3
,
P2YR12
, and
MYH9
served as controls during the validation process. In 40% of 35 patients analyzed, we were able to finally detect 15 variants, eight of which were novel, in 11 genes,
ACTN1
,
AP3B1
,
GFI1B
,
HPS1
,
HPS4
,
HPS6
,
MPL
,
MYH9
,
TBXA2R
,
TPM4
, and
TUBB1
, and classified them according to current guidelines. Apart from seven variants of uncertain significance in 11% of patients, nine variants were classified as likely pathogenic or pathogenic providing a molecular diagnosis for 26% of patients. This report also emphasizes on potentials and pitfalls of this tool and prospectively proposes its rational implementation within the diagnostic algorithms of IPD.
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Affiliation(s)
- Oliver Andres
- University Children's Hospital, University of Würzburg, Würzburg, Germany
| | - Eva-Maria König
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Karina Althaus
- Centre for Clinical Transfusion Medicine, University Hospital of Tübingen, Tübingen, Germany.,Institute for Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Tamam Bakchoul
- Centre for Clinical Transfusion Medicine, University Hospital of Tübingen, Tübingen, Germany.,Institute for Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Peter Bugert
- DRK-Blutspendedienst Baden-Württemberg-Hessen, Institute for Transfusion Medicine and Immunology, Heidelberg University, Mannheim, Germany
| | - Stefan Eber
- University Children's Hospital, Technical University Munich, Munich, Germany
| | - Ralf Knöfler
- Department of Pediatrics, Carl Gustav Carus University Hospital, Dresden, Germany
| | - Erdmute Kunstmann
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Georgi Manukjan
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
| | - Oliver Meyer
- Institute for Transfusion Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriele Strauß
- Department for Pediatric Oncology and Hematology, HELIOS Klinikum Berlin-Buch, Berlin, Germany
| | - Werner Streif
- Department of Pediatrics, Medical University Innsbruck, Innsbruck, Austria
| | - Thomas Thiele
- Institute for Transfusion Medicine, University of Greifswald, Greifswald, Germany
| | - Verena Wiegering
- University Children's Hospital, University of Würzburg, Würzburg, Germany
| | - Eva Klopocki
- Institute of Human Genetics, University of Würzburg, Würzburg, Germany
| | - Harald Schulze
- Institute of Experimental Biomedicine, University Hospital Würzburg, Würzburg, Germany
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Sharma V, Chow HY, Siegel D, Wurmbach E. Qualitative and quantitative assessment of Illumina's forensic STR and SNP kits on MiSeq FGx™. PLoS One 2017; 12:e0187932. [PMID: 29121662 PMCID: PMC5679668 DOI: 10.1371/journal.pone.0187932] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/27/2017] [Indexed: 11/30/2022] Open
Abstract
Massively parallel sequencing (MPS) is a powerful tool transforming DNA analysis in multiple fields ranging from medicine, to environmental science, to evolutionary biology. In forensic applications, MPS offers the ability to significantly increase the discriminatory power of human identification as well as aid in mixture deconvolution. However, before the benefits of any new technology can be employed, a thorough evaluation of its quality, consistency, sensitivity, and specificity must be rigorously evaluated in order to gain a detailed understanding of the technique including sources of error, error rates, and other restrictions/limitations. This extensive study assessed the performance of Illumina’s MiSeq FGx MPS system and ForenSeq™ kit in nine experimental runs including 314 reaction samples. In-depth data analysis evaluated the consequences of different assay conditions on test results. Variables included: sample numbers per run, targets per run, DNA input per sample, and replications. Results are presented as heat maps revealing patterns for each locus. Data analysis focused on read numbers (allele coverage), drop-outs, drop-ins, and sequence analysis. The study revealed that loci with high read numbers performed better and resulted in fewer drop-outs and well balanced heterozygous alleles. Several loci were prone to drop-outs which led to falsely typed homozygotes and therefore to genotype errors. Sequence analysis of allele drop-in typically revealed a single nucleotide change (deletion, insertion, or substitution). Analyses of sequences, no template controls, and spurious alleles suggest no contamination during library preparation, pooling, and sequencing, but indicate that sequencing or PCR errors may have occurred due to DNA polymerase infidelities. Finally, we found utilizing Illumina’s FGx System at recommended conditions does not guarantee 100% outcomes for all samples tested, including the positive control, and required manual editing due to low read numbers and/or allele drop-in. These findings are important for progressing towards implementation of MPS in forensic DNA testing.
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Affiliation(s)
- Vishakha Sharma
- Department of Forensic Biology, Office of Chief Medical Examiner, New York, NY, United States of America
| | - Hoi Yan Chow
- Department of Forensic Biology, Office of Chief Medical Examiner, New York, NY, United States of America
| | - Donald Siegel
- Department of Forensic Biology, Office of Chief Medical Examiner, New York, NY, United States of America
| | - Elisa Wurmbach
- Department of Forensic Biology, Office of Chief Medical Examiner, New York, NY, United States of America
- * E-mail:
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