1
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Hailu S, Kinde S, Cross M, Tsegaye A, Kelemu T, Seifu D, Alemayehu D, Tarekegn A, Jabessa G, Abeje D, Abebe M, Sherif A, Tadesse F, Platzbecker U, Howe R, Gebremedhin A. Estimating prognostic relevant cutoff values for a multiplex PCR detecting BCR::ABL1 in chronic myeloid leukemia patients on tyrosine kinase inhibitor therapy in resource-limited settings. Ann Hematol 2023:10.1007/s00277-023-05254-x. [PMID: 37212909 DOI: 10.1007/s00277-023-05254-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/23/2023] [Indexed: 05/23/2023]
Abstract
The prognosis of chronic myeloid leukemia (CML) on tyrosine kinase inhibitor (TKI) treatment is based on the quantification of BCR::ABL1 fusion gene transcript copy number, harmonized by an international scale (IS) based on TaqMan-based real-time quantitative PCR (qRT-PCR). In Ethiopia, as in most low- and middle-income countries (LMICs), access to standard diagnostic, follow-up, and prognostic tools is very limited, and it has been challenging to strictly follow international guidelines. This seriously compromises clinical outcome, despite the availability of TKIs through the Glivec International Patient Assistance Program (GIPAP). Multiplex PCR (mpx-PCR), conventionally regarded as a "screening tool," offers a potential solution to this problem. A total of 219 samples from confirmed CML patients were assayed. In reference to qRT-PCR, the AUC of ROC curve for mpx-PCR was 0.983 (95% CI: 0.957 to 0.997). At the optimum cut-off value, equivalent to BCR::ABL1 (IS) transcript copy number of 0.6%, the specificity and sensitivity were 93% and 95%, respectively, with 94% accuracy. Albeit the sensitivity and accuracy of mpx-PCR decrease below the optimum cutoff of 0.6% (IS), the specificity at 0.1% (IS) was 100%, making it an attractive means to rule-out relapse and drug non-adherence at later stages of treatment, which is particularly an issue in a low income setting. We conclude that the relative simplicity and low cost of mpx-PCR and prognostic relevant cutoff values (0.1-0.6% IS) should allow its use in peripheral clinics and thus maximize the positive impact of TKIs made available through GIPAP in most LMICs.
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Affiliation(s)
- Saifu Hailu
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Madda Walabu University, Bale Robe, Ethiopia
| | - Samuel Kinde
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
- Leipzig University Hospital, Leipzig, Germany.
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia.
| | | | - Aster Tsegaye
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Daniel Seifu
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Azeb Tarekegn
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Gutema Jabessa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Desalegn Abeje
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Abdulaziz Sherif
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | | | - Rawleigh Howe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Amha Gebremedhin
- College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
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2
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Hanbazazh M, Morlote D, Mackinnon AC, Harada S. Utility of Single-Gene Testing in Cancer Specimens. Clin Lab Med 2022; 42:385-394. [DOI: 10.1016/j.cll.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Radich JP, Briercheck E, Chiu DT, Menon MP, Sala Torra O, Yeung CCS, Warren EH. Precision Medicine in Low- and Middle-Income Countries. ANNUAL REVIEW OF PATHOLOGY 2022; 17:387-402. [PMID: 35073168 PMCID: PMC9275191 DOI: 10.1146/annurev-pathol-042320-034052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Most cancer cases occur in low- and middle-income countries (LMICs). The sophisticated technical and human infrastructure needed for optimal diagnosis, treatment, and monitoring of cancers is difficult enough in affluent countries; it is especially challenging in LMICs. In Western, educated, industrial, rich, democratic countries, there is a growing emphasis on and success with precision medicine, whereby targeted therapy is directed at cancers based on the specific genetic lesions in the cancer. Can such precision approaches be delivered in LMICs? We offer some examples of novel partnerships and creative solutions that suggest that precision medicine may be possible in LMICs given heavy doses of will, creativity, and persistence and a little luck.
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Affiliation(s)
- Jerald P Radich
- Global Oncology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Edward Briercheck
- Global Oncology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Daniel T Chiu
- Departments of Chemistry and Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Manoj P Menon
- Global Oncology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- School of Medicine, University of Washington, Seattle, WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Olga Sala Torra
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Cecilia C S Yeung
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Edus H Warren
- Global Oncology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- School of Medicine, University of Washington, Seattle, WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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4
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McDermott JH, Burn J, Donnai D, Newman WG. The rise of point-of-care genetics: how the SARS-CoV-2 pandemic will accelerate adoption of genetic testing in the acute setting. Eur J Hum Genet 2021; 29:891-893. [PMID: 33589764 PMCID: PMC7883875 DOI: 10.1038/s41431-021-00816-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 01/24/2023] Open
Affiliation(s)
- John H McDermott
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK. .,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.
| | - John Burn
- Institute of Translational and Clinical Research, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.,QuantuMDx Group Ltd, Lugano Building, 57 Melbourne St, Newcastle upon Tyne, NE1 2JQ, UK.,The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE7 7DN, UK
| | - Dian Donnai
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - William G Newman
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
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5
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Nikolova D, Damyanova V, Radinov A, Toncheva D. Molecular response in long-term monitoring of patients with chronic myelogenic leukemia (CML) on nilotinib therapy. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1912639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Dragomira Nikolova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
- Genetic Laboratory, University Hospital “St.Ivan Rilski”, Sofia, Bulgaria
| | - Vera Damyanova
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
- Genetic Laboratory, University Hospital “St.Ivan Rilski”, Sofia, Bulgaria
| | - Atanas Radinov
- Clinic of Hematology, University Hospital “St.Ivan Rilski”, Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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6
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Folta A, Jurcek T, Kubesova B, Zackova D, Semerad L, Mayer J, Jeziskova I. Evaluation of two CE-IVD tests for BCR-ABL1 transcript monitoring of chronic myeloid leukemia patients. Leuk Lymphoma 2020; 62:1239-1242. [PMID: 33356699 DOI: 10.1080/10428194.2020.1861274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Adam Folta
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Tomas Jurcek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Blanka Kubesova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
| | - Daniela Zackova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lukas Semerad
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Ivana Jeziskova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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7
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Kockerols CC, Valk PJ, Levin MD, Pallisgaard N, Cornelissen JJ, Westerweel PE. Digital PCR for BCR-ABL1 Quantification in CML: Current Applications in Clinical Practice. Hemasphere 2020; 4:e496. [PMID: 33283168 PMCID: PMC7710259 DOI: 10.1097/hs9.0000000000000496] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/29/2020] [Indexed: 02/06/2023] Open
Abstract
Molecular monitoring of the BCR-ABL1 transcript for patients with chronic phase chronic myeloid leukemia (CML) has become increasingly demanding. Real-time quantitative PCR (qPCR) is the routinely used method, but has limitations in quantification accuracy due to its inherent technical variation. Treatment recommendations rely on specific BCR-ABL1 values set at timed response milestones, making precise measurement of BCR-ABL1 a requisite. Furthermore, the sensitivity of qPCR may be insufficient to reliably quantify low levels of residual BCR-ABL1 in patients in deep molecular response (DMR) who could qualify for an attempt to discontinue Tyrosine Kinase Inhibitor (TKI) therapy. We reviewed the current use of digital PCR (dPCR) as a promising alternative for response monitoring in CML. dPCR offers an absolute BCR-ABL1 quantification at various disease levels with remarkable precision and a clinical sensitivity reaching down to at least MR5.0. Moreover, dPCR has been validated in multiple studies as prognostic marker for successful TKI treatment discontinuation, while this could not be achieved using classical qPCR. dPCR may thus prospectively be the preferred method to reliably identify patients achieving treatment milestones after initiation of TKI therapy as well as for the selection and timing for TKI discontinuation.
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Affiliation(s)
| | - Peter J.M. Valk
- Department of Molecular Biology and Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mark-David Levin
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
| | | | - Jan J. Cornelissen
- Department of Molecular Biology and Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter E. Westerweel
- Department of Internal Medicine, Albert Schweitzer Hospital, Dordrecht, The Netherlands
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8
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O'Leary TJ. The Journal of Molecular Diagnostics: 20 Years of Clinical Innovation. J Mol Diagn 2019; 21:935-937. [PMID: 31635796 DOI: 10.1016/j.jmoldx.2019.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 02/03/2023] Open
Abstract
This guest editorial highlights 20 years of clinical innovation in JMD.
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Affiliation(s)
- Timothy J O'Leary
- Office of Research and Development, Veterans Health Administration, Washington District of Columbia; Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland.
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9
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Krumbholz M, Goerlitz K, Albert C, Lawlor J, Suttorp M, Metzler M. Large amplicon droplet digital PCR for DNA-based monitoring of pediatric chronic myeloid leukaemia. J Cell Mol Med 2019; 23:4955-4961. [PMID: 31199062 PMCID: PMC6653534 DOI: 10.1111/jcmm.14321] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/27/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Quantification of tumour‐specific molecular markers at the RNA and DNA level for treatment response monitoring is crucial for risk‐adapted stratification and guidance of individualized therapy in leukaemia and other malignancies. Most pediatric leukaemias and solid tumours of mesenchymal origin are characterized by a relatively low mutation burden at the single nucleotide level and the presence of recurrent chromosomal translocations. The genomic fusion sites resulting from translocations are stable molecular tumour markers; however, repeat‐rich DNA sequences flanking intronic breakpoints limit the design of high sensitivity PCR assays for minimal residual disease (MRD) monitoring. Here, we quantitatively evaluated the impact of repeat elements on assay selection and the feasibility of using extended amplicons (≤1330 bp) amplified by droplet digital PCR to monitor pediatric chronic myeloid leukaemia (CML). Molecular characterization of 178 genomic BCR‐ABL1 fusion sites showed that 64% were located within sequence repeat elements, impeding optimal primer/probe design. Comparative quantification of DNA and RNA BCR‐ABL1 copy numbers in 687 specimens from 55 pediatric patients revealed that their levels were highly correlated. The combination of droplet digital PCR, double quenched probes and extended amplicons represents a valuable tool for sensitive MRD assessment in CML and may be adapted to other translocation‐positive tumours.
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Affiliation(s)
- Manuela Krumbholz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Katharina Goerlitz
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Christian Albert
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
| | - Jennifer Lawlor
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany.,Department of Biology, Division of Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Meinolf Suttorp
- Medical Faculty, Pediatric Hemato-Oncology, Technical University, Dresden, Germany
| | - Markus Metzler
- Department of Pediatrics, University Hospital Erlangen, Erlangen, Germany
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10
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Robetorye RS, Maguire A, Rosenthal AC, Rimsza LM. Profiling of lymphoma from formalin-fixed paraffin-embedded tissue. Semin Hematol 2018; 56:46-51. [PMID: 30573044 DOI: 10.1053/j.seminhematol.2018.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/07/2018] [Indexed: 12/21/2022]
Abstract
Molecular profiling of lymphoma samples has contributed enormously to our understanding of disease biology leading to detailed descriptions of diagnostic categories. These studies have also helped the field to recognize different subtypes of disease, different diseases that share similar cellular pathway perturbations, different immune responses, and different prognostic groups. While nearly all of these discoveries were made using unfixed, snap-frozen materials, with few exceptions, clinical biopsy materials are comprised of formalin-fixed and paraffin-embedded (FFPE) tissues. Here, we describe the impact of molecular profiling on the field of lymphoma, the challenges associated with using FFPE tissues for downstream molecular diagnostic testing, the various molecular profiling techniques, and also provide an example of the clinical application of a molecular profiling test of lymphoma using FFPE tissues.
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Affiliation(s)
- Ryan S Robetorye
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix, AZ.
| | - Alanna Maguire
- Department of Research, Mayo Clinic Arizona, Phoenix, AZ
| | - Alison C Rosenthal
- Department of Medicine, Division of Hematology-Oncology, Mayo Clinic Arizona, Phoenix, AZ
| | - Lisa M Rimsza
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix, AZ
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11
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Al-Khallaf H, Alali H, Alkhatti A. Precursor B cell lymphoid blast crisis of chronic myeloid leukemia with novel chromosomal abnormalities: A case report. Oncol Lett 2018; 16:6691-6696. [PMID: 30405810 DOI: 10.3892/ol.2018.9497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/19/2018] [Indexed: 11/06/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a clonal hematopoietic stem cell disorder. It is characterized by the presence of the Philadelphia (Ph) chromosome, t(9;22)(q34.1;q11.2), which carries the BCR-ABL1 fusion gene. Tyrosine kinase inhibitors (TKIs) have markedly changed the treatment approach of CML and have become the first-line agents for almost all CML patients. However, certain patients experience resistance to these medications, which occurs through several mechanisms, including the accumulation of TKI-resistant chromosomal abnormalities. The present study reports a case of a 27-year-old Saudi male with CML receiving TKI treatment, who presented with precursor B-cell lymphoblastic crisis demonstrating the presence of the novel combined chromosomal abnormalities; non-Ph der(22), i(9) and der(20), carrying the BCR-ABL1 fusion gene. This case report adds to the literature on novel TKI-resistance-conferring chromosomal abnormalities and links them to precursor B-cell lymphoblastic crisis.
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Affiliation(s)
- Hamoud Al-Khallaf
- Department of Pathology and Laboratory Medicine, King Fahad Specialist Hospital, Dammam 32253, Saudi Arabia
| | - Hani Alali
- Department of Pathology and Laboratory Medicine, King Fahad Specialist Hospital, Dammam 32253, Saudi Arabia
| | - Adil Alkhatti
- Cancer Institute, Johns Hopkins Aramco Healthcare, Dhahran 34465, Saudi Arabia
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12
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Debeljak M, Noë M, Riel SL, Haley LM, Norris AL, Anderson DA, Adams EM, Suenaga M, Beierl KF, Lin MT, Goggins MG, Gocke CD, Eshleman JR. Validation Strategy for Ultrasensitive Mutation Detection. Mol Diagn Ther 2018; 22:603-611. [PMID: 29974360 DOI: 10.1007/s40291-018-0350-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Ultrasensitive detection of low-abundance DNA point mutations is a challenging molecular biology problem, because nearly identical mutant and wild-type molecules exhibit crosstalk. Reliable ultrasensitive point mutation detection will facilitate early detection of cancer and therapeutic monitoring of cancer patients. OBJECTIVE The objective of this study was to develop a method to correct errors in low-level cell line mixes. MATERIALS AND METHODS We tested sample mixes with digital-droplet PCR (ddPCR) and next-generation sequencing. RESULTS We introduced two corrections: baseline variant allele frequency (VAF) in the parental cell line was used to correct for copy number variation; and haplotype counting was used to correct errors in cell counting and pipetting. We found ddPCR to have better correlation for detecting low-level mutations without applying any correction (R2 = 0.80) and be more linear after introducing both corrections (R2 = 0.99). CONCLUSIONS The VAF correction was found to be more significant than haplotype correction. It is imperative that various technologies be evaluated against each other and laboratories be provided with defined quality control samples for proficiency testing.
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Affiliation(s)
- Marija Debeljak
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Michael Noë
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Stacy L Riel
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Lisa M Haley
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Alexis L Norris
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Derek A Anderson
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Emily M Adams
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Masaya Suenaga
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Katie F Beierl
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Michael G Goggins
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA.,The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, CRB II, Room 344, 1550 Orleans Street, Baltimore, MD, 21231, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - James R Eshleman
- Department of Pathology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA. .,Department of Oncology, Johns Hopkins University, Johns Hopkins Medical Institutions, Baltimore, MD, USA. .,The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, CRB II, Room 344, 1550 Orleans Street, Baltimore, MD, 21231, USA.
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13
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Blombery P, Jones K, Doig K, Ryland G, McBean M, Thompson E, Yannakou CK, Westerman D. Sensitive NPM1 Mutation Quantitation in Acute Myeloid Leukemia Using Ultradeep Next-Generation Sequencing in the Diagnostic Laboratory. Arch Pathol Lab Med 2018; 142:606-612. [PMID: 29425073 DOI: 10.5858/arpa.2017-0229-oa] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Context Detection of measurable residual disease after therapy is an important predictor of outcome in acute myeloid leukemia. Objective To investigate the feasibility of using next-generation sequencing (NGS) in the diagnostic laboratory to perform quantitative NPM1 mutation assessment using ultradeep (approximately 300 000×-500 000×) sequencing (NGS-q NPM1) as a method of assessing residual disease burden in patients with acute myeloid leukemia. Design A flexible NGS-based assay for the detection and quantitation of NPM1 mutations was developed by polymerase chain reaction amplification of target DNA sequences, sequencing on an Illumina (San Diego, California) MiSeq, and analyzing data with an in-house-designed bioinformatic pipeline. NGS-q NPM1 was compared with current NPM1 quantitation methods (real-time quantitative-polymerase chain reaction and multiparameter flow cytometry). Results The NGS-q NPM1 assay had a sensitivity of between 10-4 and 10-5 and showed high concordance and correlation with reference methodologies. Moreover, the NGS-q NPM1 assay was able to be integrated into the laboratory's existing, targeted amplicon-based sequencing workflow. Conclusions An NGS-based, quantitative NPM1-mutation assessment can be used to monitor patients with acute myeloid leukemia, and it has some practical advantages over existing modalities.
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Affiliation(s)
| | | | | | | | | | | | | | - David Westerman
- From the Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Australia (Drs Blombery, Jones, Ryland, Thompson, Yannakou, and Westerman; Mr Doig; and Ms McBean); and the Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia (Drs Blombery, Thompson, Yannakou, and Westerman). Drs Blombery and Jones contributed equally to this work
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14
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Sreenivasan Tantuan S, du Plessis H, Stemmet M, Viljoen CD. Quantification of BCR - ABL1 on the GeneXpert: From diagnostics to research. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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15
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Marum JE, Branford S. Current developments in molecular monitoring in chronic myeloid leukemia. Ther Adv Hematol 2016; 7:237-251. [PMID: 27695615 PMCID: PMC5026293 DOI: 10.1177/2040620716657994] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular monitoring plays an essential role in the clinical management of chronic myeloid leukemia (CML) patients, and now guides clinical decision making. Quantitative reverse-transcriptase-polymerase-chain-reaction (qRT-PCR) assessment of BCR-ABL1 transcript levels has become the standard of care protocol in CML. However, further developments are required to assess leukemic burden more efficiently, monitor minimal residual disease (MRD), detect mutations that drive resistance to tyrosine kinase inhibitor (TKI) therapy and identify predictors of response to TKI therapy. Cartridge-based BCR-ABL1 quantitation, digital PCR and next generation sequencing are examples of technologies which are currently being explored, evaluated and translated into the clinic. Here we review the emerging molecular methods/technologies currently being developed to advance molecular monitoring in CML.
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Affiliation(s)
- Justine Ellen Marum
- Centre for Cancer Biology, SA Pathology, Adelaide, Australia
- Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Susan Branford
- Centre for Cancer Biology, SA Pathology, Adelaide, Australia
- School of Pharmacy and Medical Science, University of South Australia, Adelaide, SA, Australia
- School of Medicine, University of Adelaide, SA, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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16
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A longitudinal evaluation of performance of automated BCR-ABL1 quantitation using cartridge-based detection system. Pathology 2016; 47:570-4. [PMID: 26166664 PMCID: PMC4699369 DOI: 10.1097/pat.0000000000000293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
SummaryAn automated cartridge-based detection system (GeneXpert; Cepheid) is being widely adopted in low throughput laboratories for monitoring BCR-ABL1 transcript in chronic myelogenous leukaemia. This Australian study evaluated the longitudinal performance specific characteristics of the automated system. The automated cartridge-based system was compared prospectively with the manual qRT-PCR-based reference method at SA Pathology, Adelaide, over a period of 2.5 years. A conversion factor determination was followed by four re-validations. Peripheral blood samples (n = 129) with international scale (IS) values within detectable range were selected for assessment. The mean bias, proportion of results within specified fold difference (2-, 3- and 5-fold), the concordance rate of major molecular remission (MMR) and concordance across a range of IS values on paired samples were evaluated. The initial conversion factor for the automated system was determined as 0.43. Except for the second re-validation, where a negative bias of 1.9-fold was detected, all other biases fell within desirable limits. A cartridge-specific conversion factor and efficiency value was introduced and the conversion factor was confirmed to be stable in subsequent re-validation cycles. Concordance with the reference method/laboratory at >0.1–≤10 IS was 78.2% and at ≤0.001 was 80%, compared to 86.8% in the >0.01–≤0.1 IS range. The overall and MMR concordance were 85.7% and 94% respectively, for samples that fell within ± 5-fold of the reference laboratory value over the entire period of study. Conversion factor and performance specific characteristics for the automated system were longitudinally stable in the clinically relevant range, following introduction by the manufacturer of lot specific efficiency values.
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Li C, Wu D, Hu X, Xiang Y, Shu Y, Li G. One-Step Modification of Electrode Surface for Ultrasensitive and Highly Selective Detection of Nucleic Acids with Practical Applications. Anal Chem 2016; 88:7583-90. [DOI: 10.1021/acs.analchem.6b01250] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chao Li
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Dan Wu
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Xiaolu Hu
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Yang Xiang
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Genxi Li
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
- Laboratory of Biosensing Technology, School
of Life Sciences, Shanghai University, Shanghai, 200444, China
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Soverini S, De Benedittis C, Mancini M, Martinelli G. Present and future of molecular monitoring in chronic myeloid leukaemia. Br J Haematol 2016; 173:337-49. [PMID: 26947577 DOI: 10.1111/bjh.13966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Currently, physicians treating chronic myeloid leukaemia (CML) patients can rely on a wide spectrum of therapeutic options: the best use of such options is essential to achieve excellent clinical outcomes and, possibly, treatment-free remission (TFR). To accomplish this, proper integration of expert clinical and laboratory monitoring of CML patients is fundamental. Molecular response (MR) monitoring of patients at defined time points has emerged as an important success factor for optimal disease management and BCR-ABL1 kinase domain mutation screening is useful to guide therapeutic reassessment in patients who do not achieve optimal responses to tyrosine kinase inhibitor therapy. Deeper MRs might be associated with improved long-term survival outcomes. More importantly, they are considered a gateway to TFR. In molecular biology, novel procedures and technologies are continually being developed. More sophisticated molecular tools and automated analytical solutions are emerging as CML treatment endpoints and expectations become more and more ambitious. Here we provide a critical overview of current and novel methodologies, present their strengths and pitfalls and discuss what their present and future role might be.
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Affiliation(s)
- Simona Soverini
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Caterina De Benedittis
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Manuela Mancini
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Haematology/Oncology "L. e A. Seràgnoli", University of Bologna, Bologna, Italy
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Boeckx N, Laer CV, Roover JD, Wilmsen B, Bruyninckx K, Pauwels S. Comparison of molecular responses based on BCR-ABL1% (IS) results from an in-house TaqMan-based qPCR versus Xpert(®) assay in CML patients on tyrosine kinase inhibitor therapy. Acta Clin Belg 2015; 70:237-43. [PMID: 26166681 DOI: 10.1179/2295333715y.0000000009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
OBJECTIVES Tyrosine kinase inhibitors (TKIs) have drastically changed the prospects for chronic myeloid leukemia (CML) patients. The European LeukemiaNet (ELN) recommends molecular monitoring of BCR-ABL1 mRNA levels at distinct time points to define an optimal response, warning, or failure of treatment. METHODS Sixty-four follow-up peripheral blood samples from CML patients on TKI were tested by two methods. Molecular responses based on BCR-ABL1% (IS) from an Xpert(®) BCR-ABL1 Monitor assay were compared with TaqMan-based qPCR. RESULTS Seven samples showed 'molecularly undetectable leukaemia' by both methods (11%). In-house qPCR showed 57 BCR-ABL1+ samples; 45/57 samples (79%) were concordant for 'major molecular response' (MMR, n = 32) and 'no MMR' (n = 13) by both assays, whereas nine were BCR-ABL1 negative by Xpert(®). Identical molecular responses (i.e. 'optimal') were defined in 41 samples. Discordances seen in patients < 10 months on TKI (n = 2) had no impact on clinical management, whereas for patients >12 months on TKI, a different molecular response was defined ('warning' versus 'optimal'). Thirteen samples had 'no MMR' by both methods. 10/13 showed identical intervals (>10%(IS), 1-10%(IS) or 0·1-1%(IS)), corresponding to seven 'failures' and three 'warnings'. Discordant intervals were seen in 3/13 samples (all defined as 'failures'). Deep molecular responses (MR(4·0) or MR(5·0)) with detectable BCR-ABL1 showed some fluctuations between both methods, nevertheless, all had 'optimal' responses. 'Molecularly undetectable leukaemia' was observed more frequently by Xpert(®) (n = 16) as by our in-house assay (n = 7). DISCUSSION Based on current ELN recommendations, Xpert(®) BCR-ABL1 assay defines identical molecular responses as TaqMan-based qPCR BCR-ABL1% (IS) data in 98% (63/64) of samples.
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20
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Marturano A, Bury L, Gresele P. Possible incorrect genotyping of heterozygous factor V Leiden and Prothrombin 20210 gene mutations by the GeneXpert assay. Clin Chim Acta 2014; 435:36-9. [PMID: 24785585 DOI: 10.1016/j.cca.2014.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 04/10/2014] [Accepted: 04/13/2014] [Indexed: 11/17/2022]
Abstract
BACKGROUND The GeneXpert analyzer is a hands-off system for the detection of Factor V Leiden and of Prothrombin G20210A (GPRO) gene thrombophilic mutations. Although the system is efficient and easy to use, we report the rare possibility of incorrect genotyping. METHODS 1648 samples were evaluated using the GeneXpert HemosIL Factor II and Factor V assay: 1319 were freshly analyzed while 329 were frozen, thawed and diluted with saline prior to analysis to avoid clogging of the instrument syringe. RESULTS Two samples, both heterozygous, one for the factor V Leiden and the other for the GPRO gene, were incorrectly genotyped as homozygous for the relative mutation. Inspection of the Ct values and amplification curves and genotyping with PCR revealed the correct genotype as heterozygous for factor V Leiden and GPRO mutation. DISCUSSION The GeneXpert HemosIL Factor II and Factor V assay is an automated, fast genotyping assay requiring almost no sample manipulation, advantageous characteristics if compared with other PCR-based methods. However, an inattentive use of it can generate incorrect diagnosis. A careful handling of the sample, in particular correct dilution of frozen/thawed samples before analysis, and the inspection of the amplification curves and Ct values are required to avoid artifacts.
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Affiliation(s)
- Alessandro Marturano
- Division of Internal and Cardiovascular Medicine, Department of Medicine, University of Perugia, Perugia, Italy
| | - Loredana Bury
- Division of Internal and Cardiovascular Medicine, Department of Medicine, University of Perugia, Perugia, Italy
| | - Paolo Gresele
- Division of Internal and Cardiovascular Medicine, Department of Medicine, University of Perugia, Perugia, Italy.
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O’Dwyer ME, Swords R, Nagler A, McMullin MF, le Coutre PD, Langabeer SE, Alvarez-Iglesias A, Fan H, Woodman RC, Giles FJ, Conneally E. Nilotinib 300 mg BID as frontline treatment of CML: Prospective analysis of the Xpert BCR-ABL Monitor system and significance of 3-month molecular response. Leuk Res 2014; 38:310-5. [DOI: 10.1016/j.leukres.2013.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 11/21/2013] [Indexed: 10/25/2022]
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22
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Clinical application of catalytically cleavable fluorescence probe technology for multiplexing quantification of BCR–ABL1 fusion transcripts. Clin Chim Acta 2014. [DOI: 10.1016/j.cca.2013.10.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Vigil CE, Griffiths EA, Wang ES, Wetzler M. Improving the Quality of Quantitative Real-Time Polymerase Chain Reaction Laboratory Reporting in Chronic Myeloid Leukemia. Lab Med 2012. [DOI: 10.1309/lmse7m60tabhdnev] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Jangam SR, Agarwal AK, Sur K, Kelso DM. A point-of-care PCR test for HIV-1 detection in resource-limited settings. Biosens Bioelectron 2012. [PMID: 23202333 DOI: 10.1016/j.bios.2012.10.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A low-cost, fully integrated sample-to-answer, quantitative PCR (qPCR) system that can be used for detection of HIV-1 proviral DNA in infants at the point-of-care in resource-limited settings has been developed and tested. The system is based on a novel DNA extraction method, which uses a glass fiber membrane, a disposable assay card that includes on-board reagent storage, provisions for thermal cycling and fluorescence detection, and a battery-operated portable analyzer. The system is capable of automated PCR mix assembly using a novel reagent delivery system and performing qPCR. HIV-1 and internal control targets are detected using two spectrally separated fluorophores, FAM and Quasar 670. In this report, a proof-of-concept of the platform is demonstrated. Initial results with whole blood demonstrate that the test is capable of detecting HIV-1 in blood samples containing greater than 5000 copies of HIV-1. In resource-limited settings, a point-of-care HIV-1 qPCR test would greatly increase the number of test results that reach the infants caregivers, allowing them to pursue anti-retroviral therapy.
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Affiliation(s)
- Sujit R Jangam
- Center for Innovation in Global Health Technologies, Biomedical Engineering, 2145 Sheridan Road E310, Northwestern University, Evanston, IL 60208-3107, USA.
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Comparative study of BCR-ABL1 quantification: Xpert assay, a feasible solution to standardization concerns. Ann Hematol 2012; 91:1245-50. [PMID: 22526369 DOI: 10.1007/s00277-012-1468-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 04/02/2012] [Indexed: 01/07/2023]
Abstract
The level of BCR-ABL1 reached after treatment with tyrosine kinase inhibitors is an effective marker of the therapeutic response and a good survival predictor in chronic myeloid leukemia (CML) patients. However, no agreement has yet been achieved about either the standardization of the technique to determine BCR-ABL1 or the interpretation of the results. The aim of this study was to compare the method currently recommended by the European Leukemia Net, which includes the application of a conversion factor to express the results in international scale, with an automated method (Xpert BCR-ABL™, Cepheid). BCR-ABL1 transcript quantification was performed in 117 samples from CML patients in two different laboratories by both methods, and the results were compared by statistical procedures. A high linear correlation was obtained in the results between the two methods. The concordance at logarithmic intervals reached 62 %. When the major molecular response (MMR) was analyzed, 85 % agreement was achieved. The automated method provides reproducible results and does not show significant differences compared with the traditional method. As a clinical tool, Xpert correctly classified the patients in MMR and can be considered a useful alternative for the molecular follow-up of CML patients.
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27
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Vasilyeva E, Lam B, Fang Z, Minden MD, Sargent EH, Kelley SO. Direct genetic analysis of ten cancer cells: tuning sensor structure and molecular probe design for efficient mRNA capture. Angew Chem Int Ed Engl 2011; 50:4137-41. [PMID: 21472916 DOI: 10.1002/anie.201006793] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 01/02/2011] [Indexed: 11/09/2022]
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28
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Vasilyeva E, Lam B, Fang Z, Minden MD, Sargent EH, Kelley SO. Direct Genetic Analysis of Ten Cancer Cells: Tuning Sensor Structure and Molecular Probe Design for Efficient mRNA Capture. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Cayuela JM, Macintyre E, Darlington M, Abdelali RB, Fund X, Villarese P, Tulliez M, Raffoux E, Sigaux F, Réa D, Seror V. Cartridge-based automated BCR-ABL1 mRNA quantification: solving the issues of standardization, at what cost? Haematologica 2011; 96:664-71. [PMID: 21330326 DOI: 10.3324/haematol.2010.034389] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Molecular monitoring of chronic myeloid leukemia patients treated with tyrosine kinase inhibitors is essential for therapeutic stratification. Inter-laboratory reproducibility is, therefore, a crucial issue which requires standardization and strict alignment of BCR-ABL1 values to the international scale. An automated cartridge-based assay (Xpert BCR-ABL Monitor(™), Cepheid) had been proposed as a robust alternative to non-automated assays. This study aimed to compare inter-laboratory reproducibility of automated and non-automated quantification, the possibility of converting automated results to the international scale, and the potential economic impact of automation. DESIGN AND METHODS One hundred and eighteen blood samples from chronic myeloid leukemia patients treated with tyrosine kinase inhibitors were prospectively analyzed in two laboratories using both automated and non-automated assays. The economic evaluation involved a micro-costing study and average costs were assessed as a function of sample throughput. RESULTS Automated assays achieved similar inter-laboratory reproducibility to highly standardized non-automated assays and a short delay (≤6 h) between sampling and blood lysis had a positive impact on inter-laboratory reproducibility. Reporting automated BCR-ABL1 ratios on the international scale was possible using a specific conversion factor which may vary with batches. Cost assessment showed that automated assays could be relevant for annual activity levels below 300 since average costs were lower than those of the non-automated assays. CONCLUSIONS The Xpert BCR-ABL Monitor(™) assay could be appropriately used in a near-patient setting for routine quantification of e13/e14-a2 transcripts, preferably in partnership with a regional reference laboratory. However, its prognostic impact relative to non-automated quantification remains to be tested prospectively within appropriate clinical trials.
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Affiliation(s)
- Jean-Michel Cayuela
- Laboratoire Central d'Hématologie, Hôpital Saint-Louis, 1 av. Claude Vellefaux, 75475 Paris cedex 10, France.
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Desirable performance characteristics for BCR-ABL measurement on an international reporting scale to allow consistent interpretation of individual patient response and comparison of response rates between clinical trials. Blood 2008; 112:3330-8. [DOI: 10.1182/blood-2008-04-150680] [Citation(s) in RCA: 312] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractAn international basis for comparison of BCR-ABL mRNA levels is required for the common interpretation of data derived from individual laboratories. This will aid clinical decisions for individual patients with chronic myeloid leukemia (CML) and assist interpretation of results from clinical studies. We aligned BCR-ABL values generated by 38 laboratories to an international scale (IS) where a major molecular response (MMR) is 0.1% or less. Alignment was achieved by application of laboratory-specific conversion factors calculated by comparisons performed with patient samples against a reference method. A validation procedure was completed for 19 methods. We determined performance characteristics (bias and precision) for consistent interpretation of MMR after IS conversion. When methods achieved an average BCR-ABL difference of plus or minus 1.2-fold from the reference method and 95% limits of agreement within plus or minus 5-fold, the MMR concordance was 91%. These criteria were met by 58% of methods. When not met, the MMR concordance was 74% or less. However, irrespective of precision, when the bias was plus or minus 1.2-fold as achieved by 89% of methods, there was good agreement between the overall MMR rates. This indicates that the IS can deliver accurate comparison of molecular response rates between clinical trials when measured by different laboratories.
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Winn-Deen ES, Helton B, Van Atta R, Wong W, Peralta J, Wang J, Tsongalis GJ, Belloni D, Chan D, Eshleman JR, Gocke CD, Jobbagy Z, Beppu L, Radich JP. Development of an integrated assay for detection of BCR-ABL RNA. Clin Chem 2007; 53:1593-600. [PMID: 17660274 DOI: 10.1373/clinchem.2007.085472] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Current practice guidelines for managing patients with chronic myelogenous leukemia (CML) call for monitoring BCR-ABL transcript concentrations with a quantitative reverse transcription-PCR (qRT-PCR) assay. Because the available laboratory-developed assays lack consensus on the appropriate design, reporting of results, and reference intervals, we developed and evaluated an integrated BCR-ABL assay that yields standardized results for any laboratory and can be performed by technicians with no specialized training. METHODS We used the Cepheid Xpert BCR-ABL Monitor assay to measure both BCR-ABL and ABL (endogenous control) transcripts in blood samples from CML patients and healthy individuals. The assay involves 8 manual pipetting steps, fully automated nucleic acid purification, a nested qRT-PCR step, and data analysis. RESULTS The BCR-ABL assay requires approximately 2 h 20 min and covers a 5-log concentration range with a lower detection limit for the BCR-ABL:ABL ratio of approximately 0.005%. Assay results were negative for 100% of the 56 known CML-negative samples (12 patients with other hematologic disorders and 44 healthy blood donors). Testing of CML-positive patients undergoing disease monitoring showed 85% agreement with negative results (17 of 20) and 100% agreement with positive results (26 of 26). An imprecision/portability study revealed no differences in performance between sites, days, instruments, and operators. CONCLUSIONS The Xpert BCR-ABL Monitor assay provides a robust and reproducible alternative to laboratory-developed assays. Its ease of use may allow more laboratories to offer BCR-ABL testing for patients, and the short assay time enables same-day results for treating physicians.
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Branford S. Chronic myeloid leukemia: molecular monitoring in clinical practice. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2007; 2007:376-383. [PMID: 18024654 DOI: 10.1182/asheducation-2007.1.376] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The role of molecular monitoring for patients with chronic myeloid leukemia (CML) is multifaceted. Milestone measurements up to 18 months of first-line imatinib therapy are prognostic and provide warning signals of suboptimal response. Serial measurements for patients with a complete cytogenetic response determine ongoing treatment efficacy or signal pending relapse. The pattern of molecular and cytogenetic response is generally comparable, but only cytogenetic analysis can monitor for the acquisition of clonal abnormalities and has an important role in case of loss of molecular response. For patients treated with imatinib, a rising level of BCR-ABL is a trigger for kinase domain mutation analysis. The characterization of BCR-ABL inhibitor-resistant mutations is important to direct therapeutic intervention because it is now apparent that each resistant mutation functions as a distinct protein with unique biological properties that may confer a gain or loss of function. The benefit to patients of regular molecular analysis is a reassurance of ongoing response using the most sensitive of techniques or a potential improvement in outcome for those where relapse is indicated early. However, despite the obvious benefits of molecular analysis, the measurement techniques may not be quite ready for acceptance into the routine clinical monitoring practices of all clinicians. The challenge now is to standardize and simplify the method so that it can be readily and reliably incorporated into routine laboratory testing procedures.
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MESH Headings
- Genes, abl
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/surgery
- Monitoring, Physiologic/methods
- Mutation
- Polymerase Chain Reaction
- Stem Cell Transplantation
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Affiliation(s)
- Susan Branford
- Inst. of Medical and Veterinary Science, Frome Rd., Adelaide, SA 5000, Australia.
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