ArticleThe Journal of molecular diagnostics : JMD2014
Detection of mutations in myeloid malignancies through paired-sample analysis of microdroplet-PCR deep sequencing data.
Article in The Journal of molecular diagnostics : JMD, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 28 citations in OpenAlex.
- Diagnostic challenges and proposed classification of myeloid neoplasms with overlapping features of thrombocytosis, ring sideroblasts and concurrent del(5q) andHaematologica · 2024Article
- Loss of plasmacytoid dendritic cell differentiation is highly predictive for post-induction measurable residual disease and inferior outcomes in acute myeloid leukemia.Haematologica · 2019Article
- Article
- Isoform Switching as a Mechanism of Acquired Resistance to Mutant Isocitrate Dehydrogenase Inhibition.Cancer discovery · 2018Article
- Hsp90 inhibition disrupts JAK-STAT signaling and leads to reductions in splenomegaly in patients with myeloproliferative neoplasms.Haematologica · 2018Article
- Allogeneic Hematopoietic Stem Cell Transplantation with Myeloablative Conditioning Is Associated with Favorable Outcomes in Mixed Phenotype Acute Leukemia.Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation · 2017Article
- The relative utilities of genome-wide, gene panel, and individual gene sequencing in clinical practice.Blood · 2017Review
- Multicolor Flow Cytometry and Multigene Next-Generation Sequencing Are Complementary and Highly Predictive for Relapse in Acute Myeloid Leukemia after Allogeneic Transplantation.Biology of blood and marrow transplantation : journal of the American Society for Blood and Marrow Transplantation · 2017Article
- Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification.International journal of molecular sciences · 2017Review
- Patient-derived xenotransplants can recapitulate the genetic driver landscape of acute leukemias.Leukemia · 2017Article
- Mutational correlates of response to hypomethylating agent therapy in acute myeloid leukemia.Haematologica · 2016Article
- The oncocytic subtype is genetically distinct from other pancreatic intraductal papillary mucinous neoplasm subtypes.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2016Article
- Integrating Genomics Into Clinical Pediatric Oncology Using the Molecular Tumor Board at the Memorial Sloan Kettering Cancer Center.Pediatric blood & cancer · 2016Article
- Validation and Implementation of a Custom Next-Generation Sequencing Clinical Assay for Hematologic Malignancies.The Journal of molecular diagnostics : JMD · 2016Article
- Molecular therapy for acute myeloid leukaemia.Nature reviews. Clinical oncology · 2016Review
- Bulk Genotyping of Biopsies Can Create Spurious Evidence for Hetereogeneity in Mutation Content.PLoS computational biology · 2016Article
- Review
- Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT): A Hybridization Capture-Based Next-Generation Sequencing Clinical Assay for Solid Tumor Molecular Oncology.The Journal of molecular diagnostics : JMD · 2015Article
- Genomic assays for Epstein-Barr virus-positive gastric adenocarcinoma.Experimental & molecular medicine · 2015Review
Corrections and comments
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Authors and funding
12 authors at 1 institution in 1 country.
Funding
Abstract
Amplicon-based methods for targeted resequencing of cancer genes have gained traction in the clinic as a strategy for molecular diagnostic testing. An 847-amplicon panel was designed with the RainDance DeepSeq system, covering most exons of 28 genes relevant to acute myeloid leukemia and myeloproliferative neoplasms. We developed a paired-sample analysis pipeline for variant calling and sought to assess its sensitivity and specificity relative to a set of samples with previously identified mutations. Thirty samples with known mutations in JAK2, NPM1, DNMT3A, MPL, IDH1, IDH2, CEBPA, and FLT3, were profiled and sequenced to high depth. Variant calling using an unmatched Hapmap DNA control removed a substantial number of artifactual calls regardless of algorithm used or variant class. The removed calls were nonunique, had lower variant frequencies, and tended to recur in multiple unrelated samples. Analysis of sample replicates revealed that reproducible calls had distinctly higher variant allele depths and frequencies compared to nonreproducible calls. On the basis of these differences, filters on variant frequency were chosen to select for reproducible calls. The analysis pipeline successfully retrieved the associated known variant in all tested samples and uncovered additional mutations in some samples corresponding to well-characterized hotspot mutations in acute myeloid leukemia. We have developed a paired-sample analysis pipeline capable of robust identification of mutations from microdroplet-PCR sequencing data with high sensitivity and specificity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.