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Koh WLC, Poh SE, Lee CK, Chan THM, Yan G, Kong KW, Lau L, Lee WYT, Cheng C, Hoon S, Seow Y. Towards a Rapid-Turnaround Low-Depth Unbiased Metagenomics Sequencing Workflow on the Illumina Platforms. Bioengineering (Basel) 2023; 10:bioengineering10050520. [PMID: 37237590 DOI: 10.3390/bioengineering10050520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Unbiased metagenomic sequencing is conceptually well-suited for first-line diagnosis as all known and unknown infectious entities can be detected, but costs, turnaround time and human background reads in complex biofluids, such as plasma, hinder widespread deployment. Separate preparations of DNA and RNA also increases costs. In this study, we developed a rapid unbiased metagenomics next-generation sequencing (mNGS) workflow with a human background depletion method (HostEL) and a combined DNA/RNA library preparation kit (AmpRE) to address this issue. We enriched and detected bacterial and fungal standards spiked in plasma at physiological levels with low-depth sequencing (<1 million reads) for analytical validation. Clinical validation also showed 93% of plasma samples agreed with the clinical diagnostic test results when the diagnostic qPCR had a Ct < 33. The effect of different sequencing times was evaluated with the 19 h iSeq 100 paired end run, a more clinically palatable simulated iSeq 100 truncated run and the rapid 7 h MiniSeq platform. Our results demonstrate the ability to detect both DNA and RNA pathogens with low-depth sequencing and that iSeq 100 and MiniSeq platforms are compatible with unbiased low-depth metagenomics identification with the HostEL and AmpRE workflow.
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Affiliation(s)
- Winston Lian Chye Koh
- Bioinformatic Institute, A*STAR (Agency for Science, Technology and Research), Singapore 138632, Singapore
| | - Si En Poh
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Chun Kiat Lee
- Department of Laboratory Medicine, National University Hospital, Singapore 119228, Singapore
| | - Tim Hon Man Chan
- Department of Laboratory Medicine, National University Hospital, Singapore 119228, Singapore
| | - Gabriel Yan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Division of Microbiology, Department of Laboratory Medicine, National University Health System, Singapore 119228, Singapore
| | - Kiat Whye Kong
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Lalita Lau
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | | | - Clark Cheng
- Paths Diagnostics Pte Limited, Singapore 349317, Singapore
| | - Shawn Hoon
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Yiqi Seow
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
- Genome Institute of Singapore, A*STAR (Agency for Science, Technology and Research), Singapore 138672, Singapore
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2
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Kant S, Brennan DC. Donor Derived Cell Free DNA in Kidney Transplantation: The Circa 2020–2021 Update. Transpl Int 2022; 35:10448. [PMID: 35721467 PMCID: PMC9198901 DOI: 10.3389/ti.2022.10448] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/29/2022] [Indexed: 12/11/2022]
Abstract
The routine surveillance of kidney transplant allografts has relied on imperfect non-invasive biomarkers such as creatinine and urinary indices, while the gold standard allograft biopsy is associated with risk of bleeding, organ injury and sampling errors. Donor derived cell free DNA (dd-cfDNA) is being employed as a biomarker that addresses limitations of these surveillance methods, albeit has inherent drawbacks. This review provides an update on the enhanced understanding of dd-cfDNA and its expanded use beyond the conventional indication of detecting allograft rejection.
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Affiliation(s)
- Sam Kant
- Division of Nephrology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Comprehensive Transplant Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: Sam Kant,
| | - Daniel C. Brennan
- Division of Nephrology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Comprehensive Transplant Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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3
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Abuhelaiqa E, Snopkowski C, Li C, Salvatore S, Lee JR, Muthukumar T, Lee JB, Hartono C, Ding R, Seshan SV, Suthanthiran M, Dadhania DM. Validation of a noninvasive prognostic signature for allograft failure following BK virus associated nephropathy. Clin Transplant 2021; 35:e14200. [PMID: 33349997 DOI: 10.1111/ctr.14200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/18/2020] [Indexed: 12/13/2022]
Abstract
Identifying kidney transplant recipients at risk for graft failure following BK virus nephropathy (BKVN) may allow personalization of therapy. We have reported that a noninvasive composite signature of urinary cell level of plasminogen activator inhibitor-1(PAI-1) mRNA and serum creatinine level, measured at the time of BKVN diagnosis, is prognostic of graft failure. In this investigation, we determined whether the composite signature is prognostic of graft failure in an independent cohort of 25 patients with BKVN. Of the 25 patients, 8 developed graft failure and 17 did not. We measured urinary cell levels of PAI-1 mRNA, 18S rRNA, and BKV VP1 mRNA at the time of BKVN diagnosis and evaluated clinical parameters including Banff pathology scores, acute rejection, and graft function. The area under the receiver operating characteristic curve for the noninvasive composite signature was 0.95 (P < .001) for prognosticating graft failure. The previously reported threshold of -0.858 predicted graft failure with a sensitivity of 75% and a specificity of 94%. Our current study validates the use of composite signature and the threshold of -0.858 to identify those at risk for graft failure following BKVN diagnosis, and supports future studies utilizing the composite signature score to personalize treatment of BKVN.
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Affiliation(s)
- Essa Abuhelaiqa
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Catherine Snopkowski
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Carol Li
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Steve Salvatore
- Department of Pathology, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - John R Lee
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Thangamani Muthukumar
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Jun B Lee
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Choli Hartono
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Ruchuang Ding
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Surya V Seshan
- Department of Pathology, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Manikkam Suthanthiran
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
| | - Darshana M Dadhania
- Division of Nephrology and Hypertension, Department of Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA.,Department of Transplantation Medicine, New York Presbyterian Hospital-Weill Cornell Medical College, New York, NY, USA
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4
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Donor-derived Cell-free DNA and the Prediction of BK Virus-associated Nephropathy. Transplant Direct 2020; 6:e622. [PMID: 33134498 PMCID: PMC7587413 DOI: 10.1097/txd.0000000000001061] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/03/2020] [Accepted: 08/05/2020] [Indexed: 12/23/2022] Open
Abstract
Approximately 15% of kidney transplant recipients (KTRs) develop BK viremia (BKV), with 1%-10% developing BK virus-associated nephropathy (BKVAN), which histologically resembles rejection. The Diagnosing Acute Rejection in Kidney Transplant Recipients (DART) study showed that donor-derived cell-free DNA (dd-cfDNA) levels <1% have a negative predictive value of 85% for active allograft rejection. Using data from this study, we evaluated the association of dd-cfDNA with plasma BK viral loads and biopsy findings to determine if dd-cfDNA can distinguish asymptomatic BKV from BKVAN. Methods Data on dd-cfDNA, plasma BK viral loads, and biopsy findings from patients from the DART study were retrospectively examined. BKV was defined as 500-10 000 copies/mL. Presumptive BKVAN was defined as BK >10 000 copies/mL. Results Of 102 participants with biopsies, 10 patients with BKV and BKVAN had paired dd-cfDNA, and viral loads available for analysis. Patients diagnosed with BKV and BKVAN had a median dd-cfDNA of 0.58% (IQR 0.43-1.15) and 3.38% (IQR 2.3-4.56, P = 0.001), respectively. dd-cfDNA titers correlated with BK PCR viral loads (R = 0.874, P = 0.01) and the presence of histologic evidence of BKVAN (100% sensitivity, 50% specificity). Five of 7 patients with BKVAN, but only 2 of 7 with BKV, had biopsies meeting Banff criteria for T-cell-mediated rejection. Median dd-cfDNA in nonrejection patients was 0.43% versus 2.84% in rejection patients (P = 0.001). Conclusion Higher dd-cfDNA titers were associated with higher BK viral loads, biopsy-diagnosed BVAN, as well histologic changes meeting Banff criteria for as T-cell-mediated rejection. dd-cfDNA may be a useful noninvasive test to assess for progression of BKV to BKVAN.
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Raupp FVV, Meinerz G, da Silva CK, Bianco PCD, Goldani JC, Pegas KL, Stolfo JB, Garcia VD, Keitel E. BK Polyomavirus-associated nephropathy managed by screening policy in a real-life setting. Transpl Infect Dis 2019; 22:e13213. [PMID: 31724282 DOI: 10.1111/tid.13213] [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: 07/25/2019] [Revised: 10/13/2019] [Accepted: 11/04/2019] [Indexed: 11/28/2022]
Abstract
BACKGROUND BK polyomavirus-associated nephropathy (PyVAN) is an important complication after kidney transplantation. Prevalence ranges from 1% to 10%, and graft loss occurs in approximately 50% of the cases. There is no effective treatment, so early viral detection with immunosuppression tapering is the current strategy to prevent PyVAN. AIMS To verify the frequency of PyVAN in a single center and evaluate the response to immunosuppressive adjustments through graft survival analysis. METHODS Retrospective evaluation of a cohort of kidney transplant recipients with biopsy-proven PyVAN, compared with no-PyVAN patients regarding clinical aspects, immunosuppression, and graft survival over at least 2 years. RESULTS There were 1404 kidney transplants analyzed in the study period, 58 with biopsy-proven PyVAN. Cumulative incidence was 4.1%. Median time from transplantation to PyVAN diagnosis was 6 (1-41) months. PyVAN was associated with recipient male gender (P = .041) and deceased donation (P = .005). Graft survival was inferior for PyVAN compared to no-PyVAN patients, 81.8% vs 75.2%, P = .019. Thirteen (22.4%) PyVAN patients lost their grafts, nine (15.5%) losses attributed to BKPyV infection. Three patients with BKPyV-associated graft losses were submitted to a successful second kidney transplant, with no evidence of viral replication during follow-up. CONCLUSION PyVAN still is an important cause of kidney graft failure. Even though implementing active vigilance and immunosuppressive adjustment, this real-life single-center study demonstrated inferior graft survival in PyVAN patients compared to non-PyVAN.
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Affiliation(s)
| | - Gisele Meinerz
- Post Graduation Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.,Department of Nephrology and Kidney Transplantation, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, Brazil
| | - Cynthia Keitel da Silva
- Post Graduation Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.,Department of Nephrology and Kidney Transplantation, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, Brazil
| | | | - João Carlos Goldani
- Department of Nephrology and Kidney Transplantation, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, Brazil
| | - Karla Lais Pegas
- Post Graduation Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.,Department of Pathology, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, Brazil
| | - Josiane Borges Stolfo
- Department of Pathology, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, Brazil
| | - Valter Duro Garcia
- Department of Nephrology and Kidney Transplantation, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, Brazil
| | - Elizete Keitel
- Post Graduation Program in Pathology, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.,Department of Nephrology and Kidney Transplantation, Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, Brazil
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