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A Comparison between the Online Prognostic Tool PREDICT and myBeST for Women with Breast Cancer in Malaysia

Nik Ab Kadir MN, Mohd Hairon S, Ab Hadi IS, Yusof SN, Muhamat SM, Yaacob NM

Cancers (Basel), 2023 Mar 30;15(7).
PMID: 37046725 DOI: 10.3390/cancers15072064

The PREDICT breast cancer is a well-known online calculator to estimate survival probability. We developed a new prognostic model, myBeST, due to the PREDICT tool's limitations when applied to our patients. This study aims to compare the performance of the two models for women with breast cancer in Malaysia. A total of 532 stage I to III patient records who underwent surgical treatment were analysed. They were diagnosed between 2012 and 2016 in seven centres. We obtained baseline predictors and survival outcomes by reviewing patients' medical records. We compare PREDICT and myBeST tools' discriminant performance using receiver-operating characteristic (ROC) analysis. The five-year observed survival was 80.3% (95% CI: 77.0, 83.7). For this cohort, the median five-year survival probabilities estimated by PREDICT and myBeST were 85.8% and 82.6%, respectively. The area under the ROC curve for five-year survival by myBeST was 0.78 (95% CI: 0.73, 0.82) and for PREDICT was 0.75 (95% CI: 0.70, 0.80). Both tools show good performance, with myBeST marginally outperforms PREDICT discriminant performance. Thus, the new prognostic model is perhaps more suitable for women with breast cancer in Malaysia.
Data on genome resequencing of the rice cultivar MR219 and its abiotic stress tolerant mutant lines, NMR152 and NMR151

Ahmad F, Hasan N, Hisham SN, Yusof SN, Hassan AA, Hussein S, et al.

Data Brief, 2023 Feb;46:108815.
PMID: 36582993 DOI: 10.1016/j.dib.2022.108815

The genomics and genetic information of Malaysian rice (Oryza sativa L.) and their mutant lines are very limited. Therefore, the genome resequencing of two drought and submergence tolerant mutant rice lines, NMR152 and NMR151 and their parental line, MR219 was performed using Illumina Hi Seq 4000 platform with 20x sequencing coverage to facilitate the identification of causal mutations and the discovery of candidate variants of single nucleotide polymorphisms (SNPs) from their genome. The identification of SNPs would be useful in developing functional SNP markers related to drought and submergences resistance traits. Genome sequence data (FASTQ format) of the mutants and their parental line have been deposited into the National Center for Biotechnology Information (NCBI) database under sequence read archive (SRA) data with accessions SRR20824202 (NMR152), SRR20995190 (NMR151) and SRR21043964 (MR219), respectively.
Fulltext A failure in decryption process for bivariate polynomial reconstruction problem cryptosystem

Yusof SN, Kamel Ariffin MR, Yip SC, Lau TSC, Mahad Z, Chin JJ, et al.

Heliyon, 2024 Feb 29;10(4):e25470.
PMID: 38370193 DOI: 10.1016/j.heliyon.2024.e25470

In 1999, the Polynomial Reconstruction Problem (PRP) was put forward as a new hard mathematics problem. A univariate PRP scheme by Augot and Finiasz was introduced at Eurocrypt in 2003, and this cryptosystem was fully cryptanalyzed in 2004. In 2013, a bivariate PRP cryptosystem was developed, which is a modified version of Augot and Finiasz's original work. This study describes a decryption failure that can occur in both cryptosystems. We demonstrate that when the error has a weight greater than the number of monomials in a secret polynomial, p, decryption failure can occur. The result of this study also determines the upper bound that should be applied to avoid decryption failure.
Fulltext myBeST-A Web-Based Survival Prognostic Tool for Women with Breast Cancer in Malaysia: Development Process and Preliminary Validation Study

Nik Ab Kadir MN, Mohd Hairon S, Yaacob NM, Yusof SN, Musa KI, Yahya MM, et al.

Int J Environ Res Public Health, 2023 Feb 08;20(4).
PMID: 36833678 DOI: 10.3390/ijerph20042985

Women with breast cancer are keen to know their predicted survival. We developed a new prognostic model for women with breast cancer in Malaysia. Using the model, this study aimed to design the user interface and develop the contents of a web-based prognostic tool for the care provider to convey survival estimates. We employed an iterative website development process which includes: (1) an initial development stage informed by reviewing existing tools and deliberation among breast surgeons and epidemiologists, (2) content validation and feedback by medical specialists, and (3) face validation and end-user feedback among medical officers. Several iterative prototypes were produced and improved based on the feedback. The experts (n = 8) highly agreed on the website content and predictors for survival with content validity indices ≥ 0.88. Users (n = 20) scored face validity indices of more than 0.90. They expressed favourable responses. The tool, named Malaysian Breast cancer Survival prognostic Tool (myBeST), is accessible online. The tool estimates an individualised five-year survival prediction probability. Accompanying contents were included to explain the tool's aim, target user, and development process. The tool could act as an additional tool to provide evidence-based and personalised breast cancer outcomes.
Fulltext Development of Predictive Models for Survival among Women with Breast Cancer in Malaysia

Nik Ab Kadir MN, Yaacob NM, Yusof SN, Ab Hadi IS, Musa KI, Mohd Isa SA, et al.

Int J Environ Res Public Health, 2022 Nov 20;19(22).
PMID: 36430052 DOI: 10.3390/ijerph192215335

Prediction of survival probabilities based on models developed by other countries has shown inconsistent findings among Malaysian patients. This study aimed to develop predictive models for survival among women with breast cancer in Malaysia. A retrospective cohort study was conducted involving patients who were diagnosed between 2012 and 2016 in seven breast cancer centres, where their survival status was followed until 31 December 2021. A total of 13 predictors were selected to model five-year survival probabilities by applying Cox proportional hazards (PH), artificial neural networks (ANN), and decision tree (DT) classification analysis. The random-split dataset strategy was used to develop and measure the models' performance. Among 1006 patients, the majority were Malay, with ductal carcinoma, hormone-sensitive, HER2-negative, at T2-, N1-stage, without metastasis, received surgery and chemotherapy. The estimated five-year survival rate was 60.5% (95% CI: 57.6, 63.6). For Cox PH, the c-index was 0.82 for model derivation and 0.81 for validation. The model was well-calibrated. The Cox PH model outperformed the DT and ANN models in most performance indices, with the Cox PH model having the highest accuracy of 0.841. The accuracies of the DT and ANN models were 0.811 and 0.821, respectively. The Cox PH model is more useful for survival prediction in this study's setting.
Fulltext Whole genome resequencing data and grain quality traits of the rice cultivar Mahsuri and its blast disease resistant mutant line, Mahsuri Mutant

Kamarudin SAA, Ahmad F, Hasan N, Hisham SN, Yusof SN, Abu Hassan A, et al.

Data Brief, 2024 Feb;52:109974.
PMID: 38229927 DOI: 10.1016/j.dib.2023.109974

In Malaysia, rice mutant varieties that are genetically altered to confer resistance against blast disease have been substantially developed through mutational breeding program. However, due to the limited accessible information on the mutant lines, mutant gene variants corresponding to the disease resistance and other useful agronomic traits are yet to be exploited. Here, we conducted whole genome re-sequencing of blast resistance with kernel elongation traits in mutant line, Mahsuri Mutant (87,639,446 bp raw reads), and its parental line, Mahsuri (85,156,783 bp raw reads) using Illumina Novaseq 6000 sequencing platform with 30x sequencing coverage. The generated genome sequences are aimed to facilitate the discovery of causal mutation and single nucleotide polymorphisms (SNPs) related to the intended traits. The identified SNPs can be further employed to develop allele-specific SNP molecular markers to locate the mutant gene regions. The NGS data obtained (FASTQ format) of the parental and mutant lines have been deposited in the National Center for Biotechnology Information (NCBI) database under sequence read archive (SRA) xwith accession numbers SRR24388814 (Mahsuri) and SRR22952097 (Mahsuri Mutant) respectively.
Fulltext Achieving cervical cancer elimination: The simulated impacts of HPV vaccination and transitioning from liquid-based cytology to HPV-based screening test

Balqis-Ali NZ, Anis-Syakira J, Fun WH, Mohd Said Z, Abdul Samad S, Zainal Abidin N, et al.

PLoS One, 2024;19(7):e0307880.
PMID: 39052665 DOI: 10.1371/journal.pone.0307880

The Ministry of Health Malaysia aims to fully replace liquid-based cytology (LBC) with Human Papillomavirus (HPV) tests and increase the screening coverage from a baseline of 25% to 40% by 2023, followed by a 10% yearly increment until 70% coverage. This transition requires proper planning, including the number of tests needed and budget allocation. This study aims to simulate different transition strategies involving the shift from LBC to HPV testing with expanded screening coverage to predict their impact on cervical cancer elimination in Malaysia. A system dynamics model was developed to simulate the transition from LBC to HPV testing and HPV vaccination coverage in Malaysia. The dynamic model utilised local epidemiological data, published research, and expert opinion when data was unavailable. The simulation showed that a combination of high HPV vaccination coverage and transitioning fully to five-yearly HPV testing by 2030, coupled with a 70% screening uptake by 2040, would accelerate cancer elimination in Malaysia by 18 years with an estimated screening cost of MYR1.81 billion equivalent to USD 411 millions compared to the baseline of using LBC as the primary screening method (MYR1.39 billion, USD 315 millions). Sustained, it would lead to averting 6,000 new cancer cases by 2070. Alternatively, conducting HPV screenings twice before age 50 would advance cervical cancer elimination by 14 years and prevent approximately 1000 new cases by 2070, with an estimated cost of MYR1.13 billion equivalent to USD 257 millions. A delay in achieving the full transition prolonged the elimination more than a delay in increasing the screening coverage. In all scenarios, yearly vaccination of 90% of girls age 13 is crucial to achieving elimination. In the Malaysian context, where HPV vaccination coverage has reached considerable levels, the evidence advocates for a full transition from LBC to HPV testing, ideally by 2030. While expanding screening coverage remains a critical factor in this endeavour, the findings unequivocally endorse prioritising the transition process. Trial registration: Trial registration number: NMRR ID-22-00187-DJU.
Fulltext Feasibility of monitoring Global Breast Cancer Initiative Framework key performance indicators in 21 Asian National Cancer Centers Alliance member countries

Ong SK, Haruyama R, Yip CH, Ngan TT, Li J, Lai D, et al.

EClinicalMedicine, 2024 Jan;67:102365.
PMID: 38125964 DOI: 10.1016/j.eclinm.2023.102365

BACKGROUND: The Global Breast Cancer Initiative (GBCI) Framework, launched by the World Health Organisation (WHO) in 2023, emphasises assessing, strengthening, and scaling up services for the early detection and management of breast cancer. This study aims to determine the feasibility of monitoring the status of breast cancer control in the 21 Asian National Cancer Centers Alliance (ANCCA) countries based on the three GBCI Framework key performance indicators (KPIs): stage at diagnosis, time to diagnosis, and treatment completion.
METHODS: We reviewed published literature on breast cancer control among 21 ANCCA countries from May to July 2023 to establish data availability and compiled the latest descriptive statistics and sources of the indicators using a standardised data collection form. We performed bivariate Pearson's correlation analysis to measure the strength of correlation between stage at diagnosis, mortality and survival rates, and universal health coverage.
FINDINGS: Only 12 (57%) ANCCA member countries published national cancer registry reports on breast cancer age-standardised incidence rate (ASIR) and age-standardised mortality rate (ASMR). Indonesia, Myanmar, and Nepal had provincial data and others relied on WHO's Global Cancer Observatory (GLOBOCAN) estimates. GLOBOCAN data differed from the reported national statistics by 5-10% in Bhutan, Indonesia, Iran, the Republic of Korea, Singapore, and Thailand and >10% in China, India, Malaysia, Mongolia, and Sri Lanka. The proportion of patients diagnosed in stages I and II strongly correlated with the five-year survival rate and with the universal health coverage (UHC) index. Three countries (14%) reported national data with >60% of invasive breast cancer patients diagnosed at stages I and II, and a five-year survival rate of >80%. Over 60% of the ANCCA countries had no published national data on breast cancer staging, the time interval from presentation to diagnosis, and diagnosis to treatment. Five (24%) countries reported data on treatment completion. The definition of delayed diagnosis and treatment completion varied across countries.
INTERPRETATION: GBCI's Pillar 1 KPI correlates strongly with five-year survival rate and with the UHC index. Most ANCCA countries lacked national data on cancer staging, timely diagnosis, and treatment completion KPIs. While institutional-level data were available in some countries, they may not represent the nationwide status. Strengthening cancer surveillance is crucial for effective breast cancer control. The GBCI Framework indicators warrant more detailed definitions for standardised data collection. Surrogate indicators which are measurable and manageable in country-specific settings, could be considered for monitoring GBCI indicators. Ensuring UHC and addressing health inequalities are essential to early diagnosis and treatment of breast cancer.
FUNDING: Funding for this research article's processing fee (APC) will be provided by the affiliated institution to support the open-access publication of this work. The funding body is not involved in the study design; collection, management, analysis and interpretation of data; or the decision to submit for publication. The funding body will be informed of any planned publications, and documentation provided.
Mapping recommendations towards an Asian Code Against Cancer (ACAC) as part of the World Code Against Cancer Framework: an Asian National Cancer Centers Alliance (ANCCA) initiative

Ong SK, Abe SK, Gek Phua GL, Jayasekara H, Togawa K, Gatellier L, et al.

Lancet Reg Health Southeast Asia, 2024 May;24:100316.
PMID: 38756166 DOI: 10.1016/j.lansea.2023.100316

This paper outlines the process undertaken by Asian National Cancer Centers Alliance (ANCCA) members in working towards an Asian Code Against Cancer (ACAC). The process involves: (i) identification of the criteria for selecting the existing set of national recommendations for ACAC (ii) compilation of existing national codes or recommendations on cancer prevention (iii) reviewing the scientific evidence on cancer risk factors in Asia and (iv) establishment of one or more ACAC under the World Code Against Cancer Framework. A matrix of national codes or key recommendations against cancer in ANCCA member countries is presented. These include taking actions to prevent or control tobacco consumption, obesity, unhealthy diet, physical inactivity, alcohol consumption, exposure to occupational and environmental toxins; and to promote breastfeeding, vaccination against infectious agents and cancer screening. ANCCA will continue to serve as a supportive platform for collaboration, development, and advocacy of an ACAC jointly with the International Agency for Research on Cancer/World Health Organization (IARC/WHO).