Displaying publications 61 - 75 of 75 in total

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  1. Rehman ZU, Ahmad Fauzi MF, Wan Ahmad WSHM, Abas FS, Cheah PL, Chiew SF, et al.
    PeerJ Comput Sci, 2024;10:e2373.
    PMID: 39650490 DOI: 10.7717/peerj-cs.2373
    The human epidermal growth factor receptor 2 (HER2) gene is a critical biomarker for determining amplification status and targeting clinical therapies in breast cancer treatment. This study introduces a computer-aided method that automatically measures and scores HER2 gene status from invasive tissue regions of breast cancer using whole slide images (WSI) through silver in situ hybridization (SISH) staining. Image processing and deep learning techniques are employed to isolate untruncated and non-overlapping single nuclei from cancer regions. The Stardist deep learning model is fine-tuned on our HER2-SISH data to identify nuclei regions, followed by post-processing based on identified HER2 and CEP17 signals. Conventional thresholding techniques are used to segment HER2 and CEP17 signals. HER2 amplification status is determined by calculating the HER2-to-CEP17 signal ratio, in accordance with ASCO/CAP 2018 standards. The proposed method significantly reduces the effort and time required for quantification. Experimental results demonstrate a 0.91% correlation coefficient between pathologists manual enumeration and the proposed automatic SISH quantification approach. A one-sided paired t-test confirmed that the differences between the outcomes of the proposed method and the reference standard are statistically insignificant, with p-values exceeding 0.05. This study illustrates how deep learning can effectively automate HER2 status determination, demonstrating improvements over current manual methods and offering a robust, reproducible alternative for clinical practice.
  2. Rajadurai P, Yap NY, Chiew SF, Md Zin RR, Md Pauzi SH, Jaafar ASB, et al.
    J Breast Cancer, 2024 Dec;27(6):362-371.
    PMID: 39622509 DOI: 10.4048/jbc.2024.0040
    PURPOSE: Triple-negative breast cancer (TNBC) is a subtype of breast cancer known for its poor prognosis and the absence of viable targets for standard receptor-based therapies. Several studies have suggested that targeting programmed death-ligand 1 (PD-L1) in tumors that express this biomarker, either on tumor cells and/or in the tumor inflammatory infiltrate, may be beneficial in some patients. This study aimed to assess the overall prevalence of PD-L1 positivity using the SP142 antibody clone in patients with advanced TNBC in Malaysia.

    METHODS: This was a multicenter, cross-sectional prevalence study on PD-L1 positivity among patients with advanced-stage TNBC in Malaysia. Patients were identified using medical records and were enrolled in the study if they met the inclusion criteria. PD-L1 evaluation was performed using archived formalin-fixed paraffin-embedded tissue specimens. Demographic and clinical data were also obtained and summarized using descriptive statistics. The association of these parameters with PD-L1 positivity was assessed using chi-square and logistic regression analysis.

    RESULTS: Three medical centers provided 138 complete cases for analysis. Of these 138 cases, 52 (37.7%; 95% confidence interval, 29.6%-46.3%) showed positive PD-L1 expression, defined as immune cell PD-L1 expression ≥ 1%. In a univariate analysis, stage III of the disease and tumor samples from resected specimens were significantly associated with a positive PD-L1 status. However, further assessment using a multivariate model revealed that only resected tumor samples remained significantly associated with PD-L1 positivity after controlling for disease staging.

    CONCLUSION: The prevalence of PD-L1 positivity among patients with stage III or IV TNBC was 37.7%. A significant association was noted between PD-L1 positivity and the tumor tissue obtained from resected specimens. Although the mechanism and clinical significance of this association remain unclear, this finding indicates a possible disparity in the PD-L1 status of samples obtained using surgical resection or biopsy.

  3. Bhoo-Pathy N, Yip CH, Hartman M, Saxena N, Taib NA, Ho GF, et al.
    Eur J Cancer, 2012 May;48(7):982-9.
    PMID: 22366561 DOI: 10.1016/j.ejca.2012.01.034
    Adjuvant! Online is a free web-based tool which predicts 10-year breast cancer outcomes and the efficacy of adjuvant therapy in patients with breast cancer. As its prognostic performance has only been validated in high income Caucasian populations, we validated the model in a middle income Asian setting.
  4. Saxena N, Hartman M, Yip CH, Bhoo-Pathy N, Khin LW, Taib NA, et al.
    PLoS One, 2012;7(9):e45809.
    PMID: 23029254 DOI: 10.1371/journal.pone.0045809
    Lymph node ratio (LNR, i.e. the ratio of the number of positive nodes to the total number of nodes excised) is reported to be superior to the absolute number of nodes involved (pN stage) in classifying patients at high versus low risk of death following breast cancer. The added prognostic value of LNR over pN in addition to other prognostic factors has never been assessed.
  5. Lee DS, Yoon SY, Looi LM, Kang P, Kang IN, Sivanandan K, et al.
    Breast Cancer Res, 2012;14(2):R66.
    PMID: 22507745
    Germline TP53 mutations cause an increased risk to early-onset breast cancer in Li-Fraumeni syndrome (LFS) families and the majority of carriers identified through breast cancer cohorts have LFS or Li-Fraumeni-like (LFL) features. However, in Asia and in many low resource settings, it is challenging to obtain accurate family history and we, therefore, sought to determine whether the presence of early-onset breast cancer is an appropriate selection criteria for germline TP53 testing.
  6. Fleming KA, Naidoo M, Wilson M, Flanigan J, Horton S, Kuti M, et al.
    Am J Clin Pathol, 2017 01 01;147(1):15-32.
    PMID: 28158414 DOI: 10.1093/ajcp/aqw143
    Objectives: We review the current status of pathology services in low- and middle-income countries and propose an “essential pathology package” along with estimated costs. The purpose is to provide guidance to policy makers as countries move toward universal health care systems.

    Methods: Five key themes were reviewed using existing literature (role of leadership; education, training, and continuing professional development; technology; accreditation, management, and quality standards; and reimbursement systems). A tiered system is described, building on existing proposals. The economic analysis draws on the very limited published studies, combined with expert opinion.

    Results: Countries have underinvested in pathology services, with detrimental effects on health care. The equipment needs for a tier 1 laboratory in a primary health facility are modest ($2-$5,000), compared with $150,000 to $200,000 in a district hospital, and higher in a referral hospital (depending on tests undertaken). Access to a national (or regional) specialized laboratory undertaking disease surveillance and registry is important. Recurrent costs of appropriate laboratories in district and referral hospitals are around 6% of the hospital budget in midsized hospitals and likely decline in the largest hospitals. Primary health facilities rely largely on single-use tests.

    Conclusions: Pathology is an essential component of good universal health care.

  7. Dean SJ, Perks CM, Holly JM, Bhoo-Pathy N, Looi LM, Mohammed NA, et al.
    Am J Clin Pathol, 2014 Mar;141(3):323-33.
    PMID: 24515759 DOI: 10.1309/AJCPR11DEAYPTUSL
    OBJECTIVES: To investigate the association between PTEN loss and IGFBP2 expression in a series of triple-negative breast cancers and to relate this expression to basal cytokeratin expression and clinicopathologic features.

    METHODS: One hundred and one formalin-fixed and paraffin-processed triple-negative breast cancer cases from the University of Malaya Medical Centre were tested immunohistochemically for cytokeratins 5/6 and 14, PTEN, and IGFBP2. The resulting slides were scored for proportion and intensity of staining.

    RESULTS: Loss of tumor nuclear and cytoplasmic staining for PTEN occurred in 48.3% of cases and was significantly associated with younger age at diagnosis (47 years compared with 57 years in those without PTEN loss; P = .005). Independent predictors of PTEN loss were late stage at presentation (P = .026), cytokeratin 5/6 positivity (P = .028), and IGFBP2 expression (P = .042). High levels of IGFBP2 expression were seen in 32% of cases; an independent predictor of high levels was cytokeratin 14 negativity (P = .005). PTEN loss and high levels of IGFBP2 expression were associated with poorer survival, but neither of these trends was significant.

    CONCLUSIONS: PTEN loss is a frequent event in triple-negative breast cancers and is significantly associated with younger age at onset of breast cancer, late stage, and IGFBP2 expression.

  8. Sayed S, Cherniak W, Lawler M, Tan SY, El Sadr W, Wolf N, et al.
    Lancet, 2018 05 12;391(10133):1939-1952.
    PMID: 29550027 DOI: 10.1016/S0140-6736(18)30459-8
    Insufficient awareness of the centrality of pathology and laboratory medicine (PALM) to a functioning health-care system at policy and governmental level, with the resultant inadequate investment, has meant that efforts to enhance PALM in low-income and middle-income countries have been local, fragmented, and mostly unsustainable. Responding to the four major barriers in PALM service delivery that were identified in the first paper of this Series (workforce, infrastructure, education and training, and quality assurance), this second paper identifies potential solutions that can be applied in low-income and middle-income countries (LMICs). Increasing and retaining a quality PALM workforce requires access to mentorship and continuing professional development, task sharing, and the development of short-term visitor programmes. Opportunities to enhance the training of pathologists and allied PALM personnel by increasing and improving education provision must be explored and implemented. PALM infrastructure must be strengthened by addressing supply chain barriers, and ensuring laboratory information systems are in place. New technologies, including telepathology and point-of-care testing, can have a substantial role in PALM service delivery, if used appropriately. We emphasise the crucial importance of maintaining PALM quality and posit that all laboratories in LMICs should participate in quality assurance and accreditation programmes. A potential role for public-private partnerships in filling PALM services gaps should also be investigated. Finally, to deliver these solutions and ensure equitable access to essential services in LMICs, we propose a PALM package focused on these countries, integrated within a nationally tiered laboratory system, as part of an overarching national laboratory strategic plan.
  9. Kong YC, Bhoo-Pathy N, O'Rorke M, Subramaniam S, Bhoo-Pathy NT, See MH, et al.
    Medicine (Baltimore), 2020 Feb;99(6):e19093.
    PMID: 32028433 DOI: 10.1097/MD.0000000000019093
    Percutaneous biopsy in breast cancer has been associated with an increased risk of malignant cell seeding. However, the importance of these observations remains obscure due to lack of corroborating evidence from clinical studies. We determined whether method of biopsy is associated with breast cancer survival. This hospital registry-based cohort study included 3416 non-metastatic breast cancer patients diagnosed from 1993 to 2011 in a tertiary setting. Factors associated with biopsy methods were assessed. Multivariable Cox regression analysis was used to determine the independent prognostic impact of method of biopsy. Overall, 990 patients were diagnosed by core needle biopsy (CNB), 1364 by fine needle aspiration cytology (FNAC), and 1062 by excision biopsy. Excision biopsy was significantly associated with more favorable tumor characteristics. Radiotherapy modified the prognostic impact of biopsy method (Pinteraction 
  10. Soo CI, Leong WL, Ong DB, Looi LM, Sia LC, Munusamy V, et al.
    Respirol Case Rep, 2024 Dec;12(12):e70082.
    PMID: 39654987 DOI: 10.1002/rcr2.70082
    Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is an established technique for lung cancer staging and the diagnosis of mediastinal diseases. Recently, the paradigm of EBUS guided mediastinal sampling with conventional cytology has shifted over to histology specimens through the use of cryobiopsy. This case series explores the novel technique, key enablers, and potential advantages of endoscopic ultrasound with bronchoscope-guided transesophageal cryobiopsy (EUS-B-TEC). The findings of this case series suggest that EUS-B-TEC is a safe and valuable addition to the bronchoscopic procedural armamentarium. Further studies are warranted to validate the potential of EUS-B-TEC.
  11. Fleming KA, Horton S, Wilson ML, Atun R, DeStigter K, Flanigan J, et al.
    Lancet, 2021 Nov 27;398(10315):1997-2050.
    PMID: 34626542 DOI: 10.1016/S0140-6736(21)00673-5
  12. Pan JW, Tan ZC, Ng PS, Zabidi MMA, Nur Fatin P, Teo JY, et al.
    NPJ Breast Cancer, 2024 Jul 19;10(1):60.
    PMID: 39030225 DOI: 10.1038/s41523-024-00671-1
    Triple-negative breast cancers (TNBCs) are a subset of breast cancers that have remained difficult to treat. A proportion of TNBCs arising in non-carriers of BRCA pathogenic variants have genomic features that are similar to BRCA carriers and may also benefit from PARP inhibitor treatment. Using genomic data from 129 TNBC samples from the Malaysian Breast Cancer (MyBrCa) cohort, we developed a gene expression-based machine learning classifier for homologous recombination deficiency (HRD) in TNBCs. The classifier identified samples with HRD mutational signature at an AUROC of 0.93 in MyBrCa validation datasets and 0.84 in TCGA TNBCs. Additionally, the classifier strongly segregated HRD-associated genomic features in TNBCs from TCGA, METABRIC, and ICGC. Thus, our gene expression classifier may identify triple-negative breast cancer patients with homologous recombination deficiency, suggesting an alternative method to identify individuals who may benefit from treatment with PARP inhibitors or platinum chemotherapy.
  13. Li A, Geyer FC, Blecua P, Lee JY, Selenica P, Brown DN, et al.
    NPJ Breast Cancer, 2019 11 19;5:44.
    PMID: 31754629 DOI: 10.1038/s41523-019-0140-8
    [This corrects the article DOI: 10.1038/s41523-019-0115-9.].
  14. Li A, Geyer FC, Blecua P, Lee JY, Selenica P, Brown DN, et al.
    NPJ Breast Cancer, 2019;5:23.
    PMID: 31428676 DOI: 10.1038/s41523-019-0115-9
    Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD.
  15. Jamison DT, Alwan A, Mock CN, Nugent R, Watkins D, Adeyi O, et al.
    Lancet, 2018 03 17;391(10125):1108-1120.
    PMID: 29179954 DOI: 10.1016/S0140-6736(17)32906-9
    The World Bank is publishing nine volumes of Disease Control Priorities, 3rd edition (DCP3) between 2015 and 2018. Volume 9, Improving Health and Reducing Poverty, summarises the main messages from all the volumes and contains cross-cutting analyses. This Review draws on all nine volumes to convey conclusions. The analysis in DCP3 is built around 21 essential packages that were developed in the nine volumes. Each essential package addresses the concerns of a major professional community (eg, child health or surgery) and contains a mix of intersectoral policies and health-sector interventions. 71 intersectoral prevention policies were identified in total, 29 of which are priorities for early introduction. Interventions within the health sector were grouped onto five platforms (population based, community level, health centre, first-level hospital, and referral hospital). DCP3 defines a model concept of essential universal health coverage (EUHC) with 218 interventions that provides a starting point for country-specific analysis of priorities. Assuming steady-state implementation by 2030, EUHC in lower-middle-income countries would reduce premature deaths by an estimated 4·2 million per year. Estimated total costs prove substantial: about 9·1% of (current) gross national income (GNI) in low-income countries and 5·2% of GNI in lower-middle-income countries. Financing provision of continuing intervention against chronic conditions accounts for about half of estimated incremental costs. For lower-middle-income countries, the mortality reduction from implementing the EUHC can only reach about half the mortality reduction in non-communicable diseases called for by the Sustainable Development Goals. Full achievement will require increased investment or sustained intersectoral action, and actions by finance ministries to tax smoking and polluting emissions and to reduce or eliminate (often large) subsidies on fossil fuels appear of central importance. DCP3 is intended to be a model starting point for analyses at the country level, but country-specific cost structures, epidemiological needs, and national priorities will generally lead to definitions of EUHC that differ from country to country and from the model in this Review. DCP3 is particularly relevant as achievement of EUHC relies increasingly on greater domestic finance, with global developmental assistance in health focusing more on global public goods. In addition to assessing effects on mortality, DCP3 looked at outcomes of EUHC not encompassed by the disability-adjusted life-year metric and related cost-effectiveness analyses. The other objectives included financial protection (potentially better provided upstream by keeping people out of the hospital rather than downstream by paying their hospital bills for them), stillbirths averted, palliative care, contraception, and child physical and intellectual growth. The first 1000 days after conception are highly important for child development, but the next 7000 days are likewise important and often neglected.
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