Culture Failure Research Articles

Culture failure and suboptimal analysis in cytogenetics: A data review as a quality improvement metric from a resource-limited country

Abstract Introduction/Objective Conventional cytogenetic failures can affect hematological cancer diagnosis and prognosis. Resource-constrained regions without contemporary genetic testing facilities may experience this impact more. The effectiveness of this technique is contingent on cultural success, availability of metaphases, and morphological adequacy. The results can be influenced by the underlying diagnosis, inherent biological features of the leukemic clone, sample conditions, and transit time. Culture failure (CF) and suboptimal analysis (SOA) data can identify problems and set standards. Thus, we designed a cohort to find areas of improvement and reduce negative contributing factors, making this cytogenetic technique more accessible and cost-effective. Methods/Case Report A retrospective study was conducted at Cytogenetics laboratory at Indus hospital, Karachi. From January 2021 to March 2023, 1234 blood and bone marrow samples were processed. CF was defined as no growth, whereas suboptimal cases showed a low mitotic index or poor morphology. Data analysis included collection and processing time, sample volume, cell count, specimen type, in-house or out-reach sample, and diagnosis. Armonk, NY-based IBM SPSS 24.0 used to analyze the data. Chi-square used to find association of various factors with karyotyping. A p-value < 0.05 indicated significance. Results (if a Case Study enter NA) Of 1234 samples, 1110 (90%) were bone marrow and 124 (10%) were peripheral blood. There were 32/1234 (2.6%) CF cases. Each CF case was found in bone marrow samples, making the true incidence 32/1110 (2.9%). Constitutional blood tests found no CF in 124 samples. Additionally, chromosomal analysis quality was assessed. SOA occurred in 105/1234 (8.5%) instances, with 58% having poor morphology and 31% having a low mitotic index. Among 137 CF and SOA patients, 134/1110 (12%) were found in marrow and 3/124 (2.4%) in blood. Conclusion Lower CF rates suggest that appropriate standards and quality management may reduce cytogenetic failure rates despite resource constraints and newly established services.

Evaluation of the cytogenetic profile in patients with acute leukaemia.

Acute leukaemia (AL) is aheterogeneous neoplastic disease that occurs by thegrowth ofabnormal lymphoid and myeloid cells in thebone marrow and blood leading to acute myeloid leukaemia (AML) and acute lymphocytic leukaemia (ALL). Conventional cytogenetics is acharacteristic technique to hunch chromosomal abnormalities, it helps in thediagnosis and therapeutic approach ofthedisease by themolecular cytogenetics technique offluorescence in situ hybridization (FISH). Chromosomal abnormalities in AL are performed by karyotyping to confirm specific chromosomal abnormalities using FISH. Thedescriptive study included 42 clinically diagnosed AL patients. Karyotyping analysis was performed using thestandard Giemsa banding procedure. To confirm specific chromosomal abnormalities and all culture failure (CF) cases, FISH was done. Among 42 cases, 29 (69.4%) males and 13 (30.9%) females, AML comprised 22 (52.38%) cases, ALL 14 (33.33%) cases, and AL 6 (14.2%) cases. Normal karyotype was found in 18 (42.85%), abnormal karyotype in 16 (39.09%), and 8 (19.09%) were CF. Specific abnormalities oft(15;17), hyperdiploidy; t(3;3) with monosomy 7 in; del(9q22); del(2p); del(17p); del(Xq); 1~2 dmin; der(3); +11, +13 and composite karyotype. Hypodiploidy was strongly associated with AL, which signifies theloss ofchromosomes causing potential risk. Composite karyotype, rare t(3;3) double minutes, +11,+13, del(9q), and del(Xq) were thenovel findings reported in theSouth Canara region ofKarnataka. Despite other molecular techniques, conventional cytogenetics remains thebaseline in thediagnosis ofmalignancies.

Correlation of preferentially expressed antigen of melanoma (PRAME) gene expression with clinical characteristics in acute leukemia patients

BackgroundPreferentially expressed antigen of melanoma (PRAME) gene is regularly overexpressed in acute leukemia (AL) and other malignant diseases which are recognized by human leucocyte antigen (HLA-24) located in the human chromosome of 22q11 coded by 509 amino acids. To rule out the PRAME gene expression in AL patients and its correlation with clinical characteristics in the Indian population set up by RT-qPCR. ResultsA total of 42 samples collected, 29 (69.4%) were males, and 13 (30.95%) were females, with a mean and standard deviation for age were 39.07 ± 22.22 years. Of which AML were of 22 (52.38%) cases, ALL were of 14 (33.33%) cases, and 6 (14.2%) cases which included other forms of leukemia. PRAME gene expression was highly expressed in thirty-three 27 (64.28%) AL patients compared to the least expression in healthy individuals. No significant difference between the different forms of AL (p=0.3203) was observed. Cytogenetic analysis of normal karyotype (NK), abnormal karyotype (Ab. K), and culture failure (CF) displayed statistical non-significance (p=0.5801). Among cytogenetic abnormalities obtained, no significant differences between the groups were observed (p=0.8507). Chloride, potassium, and absolute lymphocyte count (ALC) was found to be statistically significant with p=0.0038**, p=0.0358*, and p=0.0216*, respectively, between all other clinical characteristics. There was no correlation between the PRAME gene expression and clinical parameters. ConclusionPRAME gene expression in AL patients was highly expressed, comparable to studies reported globally with significant cytogenetic results. PRAME gene could be used as a potential diagnostic marker for monitoring the malignancies and minimal residual disease in AL.

Detection of cytogenomic abnormalities by OncoScan microarray assay for products of conception from formalin-fixed paraffin-embedded and fresh fetal tissues

BackgroundThe OncoScan microarray assay (OMA) using highly multiplexed molecular inversion probes for single nucleotide polymorphism (SNP) loci enabled the detection of cytogenomic abnormalities of chromosomal imbalances and pathogenic copy number variants (pCNV). The small size of molecular inversion probes is optimal for SNP genotyping of fragmented DNA from fixed tissues. This retrospective study evaluated the clinical utility of OMA as a uniform platform to detect cytogenomic abnormalities for pregnancy loss from fresh and fixed tissues of products of conception (POC).ResultsFresh specimens of POC were routinely subjected to cell culture and then analyzed by karyotyping. POC specimens with a normal karyotype (NK) or culture failure (CF) and from formalin-fixed paraffin-embedded (FFPE) tissues were subjected to DNA extraction for OMA. The abnormality detection rate (ADR) by OMA on 94 cases of POC-NK, 38 cases of POC-CF, and 35 cases of POC-FFPE tissues were 2% (2/94), 26% (10/38), and 57% (20/35), respectively. The detected cytogenomic abnormalities of aneuploidies, triploidies and pCNV accounted for 50%, 40% and 10% in POC-CF and 85%, 10% and 5% in POC-FFPE, respectively. False negative result from cultured maternal cells and maternal cell contamination were each detected in one case. OMA on two cases with unbalanced structural chromosome abnormalities further defined genomic imbalances and breakpoints.ConclusionOMA on POC-CF and POC-FFPE showed a high diagnostic yield of cytogenomic abnormalities. This approach circumvented the obstacles of CF from fresh specimens and fragmented DNA from fixed tissues and provided a reliable and effective platform for detecting cytogenomic abnormalities and monitoring true fetal result from maternal cell contamination.

The Wounded Counselor: Battle for the Soul at an Elite Private School

A Jungian analyst describes her experiences as a counselor in an independent school. Inspired to work in a nontherapeutic setting by James Hillman's call for “a depth psychology of extraversion,” she initially finds the school tolerant of human vulnerability and shadow and receptive to her efforts to engage with psyche on the individual and group levels. However, under new leadership the school goes through a radical change and certain forces ascendant in the larger collective—technology, globalization, rationalism, and stepped-up demand for measurable outcomes—come to dominate the school's values and culture. The author explores the impact of these changes on her own role as well as on the social, emotional, and psychological lives of the students. Although tempted to despair over the marginalization of psyche in an increasingly dehumanized world, she also finds cause for optimism in the upcoming generation of young people, which she sees as possessing remarkable psychological and relational intelligence. She ventures some observations about the unique struggles and gifts of the millennial generation, coming of age in the hyperconnected era of the Internet and largely outside the purview of the adults in their lives. Given the culture's failure to provide the psychological eldering these young people crave, she suggests that Jungians are uniquely qualified to fill this role and urges depth psychologists to consider the possibilities that exist in schools for fostering individuation, initiation, and other forms of soul-making. Finally, she explores some ideas for “emotional intelligence” programs grounded not in the standard cognitive-behavioral approaches but in imaginal, archetypal, and psychodynamic perspectives.

Relative Impact of NOTCH1/SF3B1 Mutations, Complex Karyotype and TP53 Disruption in the Prognosis of Chronic Lymphocytic Leukemia Patients.

AbstractAbstract 2879 Introduction:Whole genome and exome sequencing studies recently revealed that CLL genome harbors frequent recurrent mutations as NOTCH1, TP53 and SF3B1 genes. Mutational status of these three genes strongly impacted on treatment-free survival (TFS) and overall survival (OS) in pioneer reports. In this retrospective series, we evaluated the relative role of these mutations along with the karyotype in untreated CLL patients, and after immunochemotherapy given first-line. Patients and methods:164 patients were included (all naïve from chemotherapy), including 108 who further necessitated therapy according to NCI2008 guidelines. Mutational studies (IgVH sequence, NOTCH1, SF3B1, and TP53 genes) were available in 164/164, FISH (del17p and 11q) in 156/164, and conventional karyotype in 140/164. TFS and OS were calculated from diagnosis and first-line treatment or death respectively, progression-free survival (PFS) was calculated in 108 patients who received rituximab-based immunochemotherapy frontline (94 FCR, 14 R-alkylators), from end of therapy to relapse (according to NCI2008 definition). In 60/94 patients, minimal residual disease (MRD) was assessed three months after completion of FCR by 4-color flow cytometry, according to published guidelines for MRD monitoring. Results:Thirty-seven patients (22.6%) have at least one somatic mutation (TP53, SF3B1 or NOTCH1 genes), 22 NOTCH1 mutations (13.4%), 10 SF3B1 mutations (6.1%) and 8 TP53 mutations (4.5%). SF3B1 mutations are located mainly on the exon 14. TP53 mutations are located mainly on the exon 8 (4/9) and double mutation of TP53 was not detected. Three patients had a mutation of NOTCH1 or SF3B1 combined to a TP53 mutation. Conventional karyotype was obtained in 135/140 CLL (96.4%, 5 culture failures) and 116/135 (85.9%) were associated with chromosomal aberrations. Complex karyotype (CK) and balanced translocations involving IgH locus were shown in 23.9% and 8.1% of patients, respectively. NOTCH1 mutations were found significantly associated with unmutated IgVH and trisomy 12, SF3B1 mutations with male gender and advanced Binet stage, both somatic mutations being mutually exclusive. As expected, TP53 mutations associated with del17p.After a median follow-up of 5 years, 108/164 patients had received frontline immunochemotherapy, for a median treatment-free survival (TFS) of 41.6 months from diagnosis of CLL. Only 8/164 had died, for a median overall survival (OS) not reached, but a 10y probability of survival of 92%. On univariate analysis, shorter TFS was correlated with age<65y, del11q, mutation of SF3B1, CK, IgVH unmutated, and Binet stage (B versus A), only the two latter remaining significant on multivariate analysis. Shorter OS was correlated to male sex, mutation of SF3B1, CK, and dysfunctional TP53 pathway (by mutation and/or deletion), only the three latter remaining significant on multivariate analysis.A total of 108 patients received immunochemotherapy first-line (FCR in 94 patients, and rituximab-alkylating agent in 14 patients (R-CHOP, R-CVP, R-CD, R-bendamustine). Frequencies of NOTCH1 and SF3B1 mutations, and of CK were 17.7%, 8% and 32.2% respectively. On multivariate analysis, variables associated with PFS (older age, TP53 disruption, and MRD level 3 months after completion of FCR), time-to-next-treatment and OS (CK and TP53 disruption) further demonstrated that TP53 deletion/mutation and conventional karyotyping should be prospectively assessed before initiation of FCR. Of note, our data also suggested that FCR could have overcome the previously reported prognostic impact of NOTCH1 and SF3B1 mutations. Conclusions:Despite similar frequencies and distributions among defined prognostic groups (Binet, IgVH, FISH), NOTCH1 mutations were not associated with reduced TFS or OS in CLL patients naive from treatment, whereas SF3B1 mutations correlated with OS. In the 108 patients receiving immunochemotherapy, TP53 disruption and complex karyotype were independently and significantly linked to OS. This study is the first to suggest that FCR therapy may overcome the reported adverse prognosis endowed with NOTCH1 mutations. Disclosures:No relevant conflicts of interest to declare.

The curriculum is dead! Long live the curriculum! Designing an undergraduate medicine and surgery curriculum for the future

Where changing social circumstances demand reform of medicine, this in turn provokes new thinking in medical education. Curriculum changes, however, are often ill conceived, consisting of syllabus (content) modification, rather than careful consideration of fundamental principles and theory shaping a curriculum process initiative. The undergraduate medicine and surgery curriculum of the future must address some basic fault lines in current provision, such as medical culture's failure to democratise work practices ensuring patient safety. While acquiring a reputation as innovative and progressive, and after a decade of success with current provision, Peninsula Medical School (UK) has recognised the need to develop its curriculum for the future. Such a curriculum will be guided by best evidence from medical education to inform pedagogical practices and by sophisticated curriculum theory. Drawing on social learning pedagogies and curriculum reconceptualisation models for guidance, and incorporating evaluation of its current provision and published evaluations of other curricula (particularly Longitudinal Integrated models), fundamental principles were conceived to guide curriculum reform.

The Drama of Possibility: Experience as Philosophy of Culture

This book traces the trajectory of John J. McDermott's philosophical career through a selection of his essays. Many were originally occasional pieces and address specific issues in American thought and culture. Together they constitute a mosaic of McDermott's philosophy, showing its roots in an American conception of experience. Though he draws heavily on the thought of William James and the pragmatists, McDermott has his own unique perspective on philosophy and American life. He presents this to the reader in exquisitely crafted prose. Drawing inspiration from American history, from existentialist themes, and from personal experiences, he offers a dramatic consideration of our culture's failures and successes. McDermott crosses disciplinary boundaries to draw on whatever works to help make sense of the issues with which he is dealing-issues rooted in medical practice, political events, pedagogical habits, and the worlds of the arts. His work thus resists simple categorization. It is precisely this that makes his vibrant prose appealing to so many both inside and outside the world of American philosophy.