Levenshtein distance as a measure of accuracy and precision in forensic PCR-MPS methods

Young, Brian; Faris, Tom; Armogida, Luigi

doi:10.1016/j.fsigen.2021.102594

Cited by 5 publications

(3 citation statements)

References 15 publications

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“…The amino acid sequences of CDR3 localized on TRB and TRA were in a perfect match with the TCR-antigen database developed by Immuquad @ biotech, respectively. The screening method was carried out based on the algorithm of Levenshtein distance 52 ≤ 3, along with V and J genes exactly matched with the ones in the database.…”

Section: Methodsmentioning

confidence: 99%

Neutrophil activation and clonal CAR-T re-expansion underpinning cytokine release syndrome during ciltacabtagene autoleucel therapy in multiple myeloma

Yang,

Xu,

Dai

et al. 2024

Nat Commun

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Cytokine release syndrome (CRS) is the most common complication of chimeric antigen receptor redirected T cells (CAR-T) therapy. CAR-T toxicity management has been greatly improved, but CRS remains a prime safety concern. Here we follow serum cytokine levels and circulating immune cell transcriptomes longitudinally in 26 relapsed/refractory multiple myeloma patients receiving the CAR-T product, ciltacabtagene autoleucel, to understand the immunological kinetics of CRS. We find that although T lymphocytes and monocytes/macrophages are the major overall cytokine source in manifest CRS, neutrophil activation peaks earlier, before the onset of severe symptoms. Intracellularly, signaling activation dominated by JAK/STAT pathway occurred prior to cytokine cascade and displayed regular kinetic changes. CRS severity is accurately described and potentially predicted by temporal cytokine secretion signatures. Notably, CAR-T re-expansion is found in three patients, including a fatal case characterized by somatic TET2-mutation, clonal expanded cytotoxic CAR-T, broadened cytokine profiles and irreversible hepatic toxicity. Together, our findings show that a latent phase with distinct immunological changes precedes manifest CRS, providing an optimal window and potential targets for CRS therapeutic intervention and that CAR-T re-expansion warrants close clinical attention and laboratory investigation to mitigate the lethal risk.

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Section: Methodsmentioning

confidence: 99%

Neutrophil activation and clonal CAR-T re-expansion underpinning cytokine release syndrome during ciltacabtagene autoleucel therapy in multiple myeloma

Yang,

Xu,

Dai

et al. 2024

Nat Commun

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“…To compare two character strings, we used the Levenshtein distance divided by the length of the longest character string to get a score between 0 and 1. The Levenshtein distance, sometimes also called the edit distance, is the number of single character edits (insertions, deletions, substitutions) that are needed to go from one character string to another; it is frequently used to identify similar character strings [ 28 , 29 ].…”

Section: Methodsmentioning

confidence: 99%

Optimizing the Retrieval of the Vital Status of Cancer Patients for Health Data Warehouses by Using Open Government Data in France

Lauzanne

Frenel

Baziz

et al. 2022

IJERPH

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Electronic Medical Records (EMR) and Electronic Health Records (EHR) are often missing critical information about the death of a patient, although it is an essential metric for medical research in oncology to assess survival outcomes, particularly for evaluating the efficacy of new therapeutic approaches. We used open government data in France from 1970 to September 2021 to identify deceased patients and match them with patient data collected from the Institut de Cancérologie de l’Ouest (ICO) data warehouse (Integrated Center of Oncology—the third largest cancer center in France) between January 2015 and November 2021. To meet our objective, we evaluated algorithms to perform a deterministic record linkage: an exact matching algorithm and a fuzzy matching algorithm. Because we lacked reference data, we needed to assess the algorithms by estimating the number of homonyms that could lead to false links, using the same open dataset of deceased persons in France. The exact matching algorithm allowed us to double the number of dates of death in the ICO data warehouse, and the fuzzy matching algorithm tripled it. Studying homonyms assured us that there was a low risk of misidentification, with precision values of 99.96% for the exact matching and 99.68% for the fuzzy matching. However, estimating the number of false negatives proved more difficult than anticipated. Nevertheless, using open government data can be a highly interesting way to improve the completeness of the date of death variable for oncology patients in data warehouses

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“…A procedure has been described to address calculation of match probabilities when results are generated using MPS kits with different trim sites than those present in the relevant population frequency database [ 364 ]. Performance of different MPS kits, markers, or methods can be compared for accuracy and precision using the Levenshtein distance metric [ 365 ].…”

Section: Emerging Technologies Research Studies and Other Topicsmentioning

confidence: 99%

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

Butler

2023

Forensic Science International: Synergy

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Levenshtein distance as a measure of accuracy and precision in forensic PCR-MPS methods

Cited by 5 publications

References 15 publications

Neutrophil activation and clonal CAR-T re-expansion underpinning cytokine release syndrome during ciltacabtagene autoleucel therapy in multiple myeloma

Neutrophil activation and clonal CAR-T re-expansion underpinning cytokine release syndrome during ciltacabtagene autoleucel therapy in multiple myeloma

Optimizing the Retrieval of the Vital Status of Cancer Patients for Health Data Warehouses by Using Open Government Data in France

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019–2022

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