Objective: Management of thyroid nodules relies on the Thyroid Imaging Recording and Data System (TIRADS) for sonographic findings and the Bethesda System for Reporting Thyroid Cytopathology (TBSRTC). The proponents aimed to determine the concordance between sonographic TIRADS findings and cytological diagnosis by TBSRTC in the evaluation of malignancy of patients with thyroid nodules. Methodology: Sonographic and cytology results collected from 2018 to 2022 were obtained to determine whether there is an agreement between TIRADS and TBSRTC findings. Results: Two hundred sixty-two (262) samples were obtained. Overall accuracy of predicting TIRADS category was highest for echogenic foci. Thyroid nodule distribution was highest for TIRADS 3 and 4 sonographically and TBSRTC II cytologically. There is low agreement between TBSRTC and TIRADS in the categorization of nodules as benign, implying that nodules may show sonographic features suspicious of malignancy despite being categorized as TBSRTC I or II by cytology. However, nodules categorized as TBSRTC III to VI show sonographic features suspicious for malignancy at the very least. Conclusion The correctness of TIRADS prediction is highest for echogenic foci although not significantly higher than other parameters. The overall predicting power of TIRADS for the absence of malignancy is high for TIRADS 1 and 2, whereas TIRADS 5 predicts a 31.11% risk of malignancy making it a strong indication for FNAC. However, prediction of malignancy in TIRADS 3 and 4 nodules must be in association with other factors since a significant percentage may turn out to be TBSRTC II.
Thyroid Nodule

Objectives: The aim of this study is to evaluate the breast panel biomarker changes and tumor intrinsic subtype after neoadjuvant chemotherapy among patients with residual invasive breast carcinoma whose breast specimens were processed at St. Luke’s Medical Center - Quezon City SLMC-QC) from 1 January 2017 to 30 June 2023. Methodology: Cases of residual invasive breast carcinoma status post neoadjuvant systemic therapy were identified by retrospective review of cases. The baseline characteristics, type of biopsy and resection procedures, pre – and post–neoadjuvant ER, PR and HER2 status and pre – and post–neoadjuvant tumor intrinsic subtype were analyzed using frequency and percentage. The comparison of the changes in pre- and post-neoadjuvant breast panel biomarkers were analyzed by using McNemar test while the changes in the intrinsic tumor subtype was done using Wilcoxon signed-rank test. Results: This study encompassed a total of 43 cases of residual invasive breast carcinoma following neoadjuvant systemic therapy. The data disclosed shifts in the breast molecular profile and intrinsic subtype post-administration of neoadjuvant systemic therapy. The alterations in hormone receptor status, ER and PR, were observed in 11.6% of cases, while HER-2 status exhibited changes in 2.3%. A 14% change in the tumor intrinsic subtype is observed. Among the initial 18 Luminal A cases, 1 transitioned to Luminal B, and among the 6 Luminal B cases, 2 become HER2 enriched subtypes. Furthermore, among the initial 12 HER2 enriched cases, three shifted to Luminal B, while all triple-negative cases remained unchanged after chemotherapy. Conclusion Based on our findings, alterations in the molecular profile of breast tumors, including shifts in intrinsic subtype after neoadjuvant chemotherapy (NAC), could impact patient prognosis. While the data generated from this study may not exhibit statistical significance, its clinical relevance is noteworthy. In summary, retesting of breast biomarkers in the resection specimen is recommended to accurately ascertain the appropriate use of targeted therapy.
Neoadjuvant Therapy

Background: The Panbio™ COVID-19 Ag Rapid Test is a Food and Drug Administration (FDA)-approved point-of-care test (POCT) used for SARS-CoV-2 detection which has met minimum sensitivity and specificity requirements by the World Health Organization (WHO). Objective: The study aimed to compare the clinical performance of a commercial lateral flow assay (LFA) to reverse transcriptase polymerase reaction (RT-PCR) in SARS-CoV-2 infection diagnosis Methodology: Clinical data and simultaneous LFA and RT-PCR samples collected from June 2021 to June 2022 were obtained to analyze the diagnostic accuracy of LFA compared to RT-PCR. Results: A total of 265 samples was obtained. 34.45% of RT-PCR positive samples were reliably detected by LFA. COVID-19 was reliably ruled out by LFA in 99.32% RT-PCR negative samples. LFA sensitivity among symptomatic patients with ≤7 days of illness was 51.61%, slightly higher than those with >7 days of illness (18.92%), and significantly higher than asymptomatic patients (16.67%). Asymptomatic subjects have a varied range of Ct-values, indicating different stages of infection or viral loads. Individuals with symptoms for more than 7 days have higher Ct-values, suggesting they are in later stages of infection or have lower viral loads. The probability of a positive LFA result decreases significantly when the Ct-value is beyond 28-30. Conclusion The LFA evaluated in this study did not show significant sensitivity and specificity during the early disease course wherein viral loads are suggestively high. However, its utility to accurately rule out COVID-19 is quite reliable in subjects with symptoms that are >7 days since Ct-values are suggestively beyond 28-30 which implies a significantly decreased probability of a positive LFA result.
COVID-19 ; SARS-CoV-2

This is a case of a 54-year-old, perimenopausal, Asian, woman, who presented with an enlarging left breast mass associated with whitish to bloody nipple discharge. A core needle biopsy, done in another institution, showed histologic findings of a mucinous carcinoma with triple negative “basal-like” biomarker status (ER, PR, HER2/neu). Six cycles of neoadjuvant chemotherapy were given after which the subsequent modified radical mastectomy revealed a centrally located, 10.0 cm, well-circumscribed, nodular, ovoid mass on gross examination. Microscopic findings showed tall columnar cells in stratification, tufts and papillary formations, with surrounding abundant extracellular mucin. The individual tumor cells exhibit enlarged, hyperchromatic, basally located nuclei with prominent nucleoli, abundant amphophilic and occasionally oncocytic cytoplasm which contains intracytoplasmic mucin. Based on the histologic features, “basal-like” biomarker expression, and additional immunohistochemical studies (positive CK7, negative CK20 and CDX2), this case demonstrates a pure mucinous cystadenocarcinoma of the breast. In addition to the rare histologic type, this case is exceptional since, despite multiple cycles of neoadjuvant chemotherapy, presence of extensive lymphovascular invasion and axillary lymph node involvement with extranodal extension remain evident.
Cystadenocarcinoma, Mucinous ; Breast Neoplasms

INTRODUCTION: Ovarian cancer is one of the leading causes of mortality in women. In 2020, 5,395 (6.2%) of diagnosed malignancies in females were ovarian in origin. It also ranked second among gynecologic malignancies after cervical cancer. The prevalence in Asian /Pacific women is 9.2 per 100,000 population. Increased mortality and poor prognosis in ovarian cancer are caused by asymptomatic growth and delayed or absent symptoms for which about 70% of women have an advanced stage (III/IV) by the time of diagnosis. The most associated gene mutations are Breast Cancer gene 1 (BRCA1) which is identified in chromosome 17q21 and Breast Cancer gene 2 (BRCA2) identified in chromosome 13. Both proteins function in the double-strand DNA break repair pathway especially in the large framework repair molecules. Olaparib is a first-line drug used in the management of ovarian cancer. It targets affected cells by inhibition of poly (ADP-ribose) polymerase (PARP) activity which induces synthetic lethality in mutated BRCA1/2 cancers by selectively targeting tumor cells that fail to repair DNA double-strand breaks (DSBs). OBJECTIVE: The study aims to determine the prevalence of pathogenic somatic mutations in BRCA1 and BRCA2 among patients diagnosed of having ovarian cancer, to characterize the identified variants into benign/ no pathogenic variant identified, variant of uncertain significance (VUS), and pathogenic, and to determine the relationship of specific mutations detected with histomorphologic findings and clinical attributes. METHODOLOGY: Ovarian cancer tissues available at the St. Luke’s Medical Center Human Cancer Biobank and formalin-fixed paraffin-embedded (FFPE) tissue blocks diagnosed as ovarian cancer from the year 2016 to 2020 were included. Determination of the prevalence of somatic BRCA1 and BRCA2 mutations using Next Generation Sequencing (NGS). RESULTS: A total of 60 samples were processed, and three samples were excluded from the analysis due to an inadequate number of cells. In the remaining 57 samples diagnosed ovarian tumors, pathogenic BRCA1/2 variants were identified in 10 (17.5%) samples. Among the BRCA1/2 positive samples, 3 (5.3%) BRCA1 and 7 (12.3%) BRCA2 somatic mutations were identified. CONCLUSION Identification of specific BRCA1/2 mutations in FFPE samples with NGS plays a big role in the management of ovarian cancer, particularly with the use of targeted therapies such as Olaparib. The use of this drug could provide a longer disease-free survival for these patients. Furthermore, we recommend that women diagnosed with ovarian cancer should be subjected to genetic testing regardless of the histologic subtypes or clinical features. Lastly, genetic testing should be done along with proper genetic counseling, especially for patients who are susceptible to these mutations.
ovarian cancer

INTRODUCTION: Complete blood count (CBC) and cell population data (CPD) are hematologic parameters used in several clinical scenarios including infection and neoplastic processes. In the setting of COVID-19 infection, there is relative paucity of data in their use as possible prognostic markers. OBJECTIVE: We aim to evaluate the utility of the baseline CBC and CPD as prognostic markers for in-hospital mortality among COVID-19 patients admitted in Philippine General Hospital from March 2020 to January 2022. METHODOLOGY: This is a case-control study. Expired patients served as cases, and recovered patients served as controls. Data from eligible patients including age, sex, admitting COVID diagnosis with severity, final disposition, baseline CBC and CPD results were collected from the hospital medical records and hematology section of the Department of Laboratories. Statistical analyses were done to determine the prognostic value of these parameters for in-hospital mortality. RESULTS: Among the different CBC and CPD parameters, the study shows total white blood cell (WBC) count, absolute neutrophil count (ANC), absolute eosinophil count (AEC), and neutrophil-lymphocyte ratio (NLR) were statistically significant predictors for in-hospital mortality. For total WBC count, at a cut off 9.9 x 10 9 /L, the sensitivity and specificity is 70.9% and 66.2%, respectively. For ANC, at a cut off of 7.3 x 10 9 /L, the specificity is 76.4% and the specificity is 68.2%. At a cut off of 7.62, the NLR shows a sensitivity of 76.4% and specificity of 70.1%. For AEC, at a cut off of 0.006 x 10 9 /L, the sensitivity is 53.3% and the specificity is 87.3%. AEC predicts towards the direction of survival rather than to the direction of in-hospital mortality. CONCLUSION The total WBC count, ANC, and NLR were statistically significant predictors for in-hospital mortality, while AEC predicts towards the direction of survival. The sensitivities and specificities of the cut off for these parameters were less than ideal. Correlation with clinical and other laboratory parameters is still recommended. For future studies, the authors recommend monitoring CBC and CPD parameters at different time points during the patients’ hospital course.
COVID-19 ; hematology ; blood cell count ; complete blood count ; prognosis

INTRODUCTION: Among patients with Acute Myeloid Leukemia (AML), the karyotype at diagnosis is an important prognostic indicator for predicting outcomes. Several studies have been done to identify the most common cytogenetic abnormalities seen in patients in other countries, however, limited studies have been done in our setting. OBJECTIVE: The study aims to determine the most common abnormalities present among patients with AML referred for Fluorescence in situ Hybridization (FISH) at the National Kidney and Transplant Institute. METHODOLOGY: The study included 131 adult patients with a mean age o 46. Fluorescence in situ Hybridization was used to identify the following cytogenetic abnormalities: t(8;21), 11q23 (MLL), 16q22 (CBFB-MYH11), t(15;17) (PML/RARA), t(9;22) (BCR/ABL), 7q31 deletion, and Monosomy 7. RESULTS: FISH was negative in 40% (n=53) of patients. 7q31 deletion is the most frequently identified cytogenetic abnormality among patients with a single abnormality (n=17, 13%) present and is the most frequently identified abnormality among patients with multiple abnormalities (n=26). 7q31 deletion is more frequently observed among patients between the ages 51 to 60 years old and among patients with AML with monocytic differentiation. 22% (n=29) of patients have multiple abnormalities, with the most common abnormalities to occur together are 7q31 deletion and t(8;21) (n=20, 15%). Patients with negative results and patients with multiple cytogenetic abnormalities are commonly seen within the 41 to 50 age group. CONCLUSION The current study provides a single-institution view of the cytogenetic abnormalities among adult Filipino patients with AML using FISH. Further investigation on the clinical history of these patients, with correlation with other methods, as well as epidemiologic studies are needed to better understand the similarities and differences seen from previously reported incidences.
acute myeloid leukemia ; fluorescence in situ hybridization ; cytogenetics ; profiling ; hematology ; Filipino

OBJECTIVES: This study aims to evaluate the effectiveness of the Lean Six Sigma approach in improving procedure for (TAT) of reverse transcriptase polymerase chain reaction (RT-PCR) for SARS-CoV-2 testing at The Medical City. Specific objectives of the study are to determine the following: 1) baseline sigma and average TAT (in hours); 2) post-implementation sigma and average TAT (in hours) 3) compare if there is a significant improvement between baseline and post-implementation sigma and average TAT (in hours) 4) effect on workflow efficiency. METHODOLOGY: Lean Six Sigma method for quality improvement was applied using DMAIC: Define, Measure, Improve, and Control. The root causes identified were lack of manpower, equipment, space, and manual and complex processes. Then, process wastes were identified, and corresponding proposed solutions were sustained in the control phase, such as standardization and the use of automation. Measurement of turn-around time and six sigma of the process were performed for evaluation. RESULTS: Results showed a significant improvement in the TAT in RT-PCR results, with most results released within 24 hours. The pre-Lean Six Sigma data on TAT were as ollows: 24.88% released within 24 hours; 65.14% released within 24-48 hours; 3.56% released within 48-72 hours, and 6.42% released in more than 72 hours. The post Lean Six Sigma TAT were as ollows: 95.32% released within 24 hours; 4.29% released within 24 to 48 hours; 0.13% released within 48-72 hours, and 0.12% released more than 72 hours. The computed sigma post-implementation was increased from 3.56 to 4.82. The p-value was calculated using the chi-square test, and the computed chi-square statistic is 1894.1021. The p-value is <0.00001 and the result is significant at p<.05. Although there is a significant decrease in the volume of samples post implementation due to the changing COVID-19 situation, real time TAT was improved. It also resulted to increased workflow efficiency with the use of lesser manpower with more appropriate utilization. CONCLUSION Applying the Lean Six Sigma method to improve quality processes in the laboratory is shown to be practical, cost-effective, and straightforward.
Lean Six Sigma ; SARS-CoV-2

INTRODUCTION: The role of the laboratory during the COVID-19 pandemic is not limited to just diagnosis of the disease, but also in clinical decision-making, by providing information on relevant laboratory biomarkers. Clinicians also use Ct value to guide patient management. There are limited studies available locally regarding the significance of Ct value and pertinent laboratory biomarkers in COVID-19 patients. This study aimed to assess the aforementioned laboratory data, along with the clinicopathologic characteristics of affected patients, and determined if this information may be useful for robust clinical decision-makin METHODOLOGY: In this retrospective analytic study, we identified 325 out of 1,049 adult Filipino inpatients diagnosed with COVID-19 and analyzed their Ct values and pertinent laboratory biomarkers such as neutrophil and lymphocyte count, platelet count, LDH, ferritin, procalcitonin, CRP, AST/SGOT, ALT/SGPT, PT/ INR, and D-dimer, and correlated them with the severity of the disease. RESULTS: Two hundred twenty (67.7%) patients had non-severe disease, while 105 (32.3%) had severe disease. Lower Ct values of ORF1ab (median = 26.4) and N (median = 24.8) genes were seen in the severe group compared to the non-severe group and were found to be significant (p<0.001). Laboratory markers (neutrophil, platelet counts, LDH, ferritin, procalcitonin, CRP, AST, PT/INR, and D-dimer) were associated with severe COVID-19. On the other hand, ALT was not associated with severe disease. CONCLUSION The laboratory biomarkers together with Ct value and overall clinical picture may provide valuable information to physicians for more robust clinical decision-making.
COVID-19 ; laboratory biomarkers ; SARS-CoV-2 ; RT-PCR

RUNX1::RUNX1T1 is a core-binding factor driving fusion gene which arises from t(8;21)(q22;q22). It is one of the most common chromosomal rearrangements in both pediatric and adult Acute Myeloid Leukemia (AML) with a reported incidence o 15% in children and young adults. There are few case reports documenting RUNX1::RUNX1T1 translocation in pediatric AML. Although this is generally associated with a favorable prognosis, we report two (2) cases of de novo pediatric AML in the Philippines harboring a RUNX1::RUNX1T1 translocation, one eventually relapsed while the other attained remission but succumbed to sepsis.
Next Generation Sequencing ; RUNX1::RUNX1T1 fusion