Connecting the Indian Ocean World

Seshan, Radhika; Shimada, Ryuto

doi:10.4324/9781003362487

Cited by 2 publications

(2 citation statements)

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“…All statistical analyses will be conducted using R 4.2 software [24]. Sample size calculations were done using the clinfun package of the R 4.2 software [25].…”

Section: Plos Onementioning

confidence: 99%

Improving access to breast cancer screening and treatment in Nigeria: The triple mobile assessment and patient navigation model (NCT05321823): A study protocol

et al. 2023

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Background In Nigeria, breast cancer incidence is rising, late presentation is common, and outcomes are poor. Patient-related factors such as lack of awareness and misperceptions in addition to health system deficiencies such as lack of a clearly defined framework for breast cancer screening and referral are some of the major drivers of this poor outlook. Guidelines for breast cancer screening in high-income countries have limited applicability in low-middle-income countries, hence the need for innovative, resource-compatible strategies to combat the negative trend. This manuscript presents our study protocol which aims to evaluate the impact of a novel breast cancer early detection program developed to address delayed presentation and lack of access to diagnostic and treatment facilities in South-West Nigeria. This entails the use of mobile technology (innovative handheld iBreast Exam [iBE] device, mobile breast ultrasound, and mobile mammography) and patient navigation as interventions at the community level. Methods The study (ClinicalTrials.gov identifier: NCT05321823) will adopt a randomized two group clinical trial design with one local government area (LGA) serving as an intervention arm and another serving as the control. Both LGAs will receive breast cancer awareness education but only one will receive the interventions. In the intervention arm, asymptomatic (40–70 years) and symptomatic (30–70 years) women will be invited for breast evaluation which will be performed by trained Community Health Nurses using Clinical Breast Exam (CBE), and iBE. Those with positive findings will proceed to imaging using mobile mammography and ultrasound brought to the LGA every month. Symptomatic women with negative findings on CBE and iBE will be scheduled for repeat clinical evaluation on a short-term basis (one month). The Radiologist will obtain core needle biopsies as indicated and transfer them for prompt pathological assessment. Women presenting to the Primary Healthcare Centers in the control LGA will be referred directly to Obafemi Awolowo University Teaching Hospitals Complex as per the current standard of care. Records of all breast cancer cases seen in the two LGAs during the study period will be obtained. The program metrics will include screening participation rate, cancer detection rate, stage at diagnosis, and timeline from detection to initiation of treatment. The stage at diagnosis and timeline from detection to treatment compared between the two LGAs will be used to assess the impact of the intervention. The study is proposed for 2 years; however, a descriptive analysis will be carried out at 1.5 years to evaluate the retention of the study participants. Study significance It is anticipated that this study will provide vital data to support wider breast cancer screening efforts in Nigeria.

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“…All statistical analyses will be conducted using R 4.2 software [24]. Sample size calculations were done using the clinfun package of the R 4.2 software [25].…”

Section: Plos Onementioning

confidence: 99%

Improving access to breast cancer screening and treatment in Nigeria: The triple mobile assessment and patient navigation model (NCT05321823): A study protocol

et al. 2023

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“…Copy number (CN) analysis was performed using its CNVpartition v3.2.0 plugin. Copy number logR-ratio, B-allele frequencies (BAF) and genotype calls were exported and further analyzed in R. Copy number data was segmented using R package DNAcopy (48) and significantly amplified and deleted regions across samples were identified using GISTIC analysis (49). Marcotte et al 2016 (Neel Lab) (12) Illumina Omni Quad CN and SNP dataset was reprocessed using above pipeline and merged with ICLE CN and SNP dataset to generate integrated breast cancer cell line CN and SNP dataset.…”

Section: Multi-omic Profiling Of Ilc and Ilc-like Cell Linesmentioning

confidence: 99%

Multi-omic characterization of ILC and ILC-like cell lines as part of ILC cell line encyclopedia (ICLE) defines new models to study potential biomarkers and explore therapeutic opportunities

Shah,

Chen,

Wedn

et al. 2023

Preprint

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Invasive lobular carcinoma (ILC), the most common histological “special type” of breast cancer, accounts for ∼10-15% of all breast cancer diagnoses and is characterized by unique clinical features and metastatic spread. Despite the unique pathobiology of ILC, studies of how its molecular alterations can be linked to new treatments have been hindered by the scarcity of well-characterized cell line models. To address this, we generated the ILC Cell Line Encyclopedia (ICLE), a comprehensive multi-omic characterization of cell lines derived from ILC or cell lines referred to as ILC-like derived from unannotated tumors with features of ILC such as loss of E-cadherin. Using consensus multi-omic subtyping, we confirmed the luminal status of previously established ILC cell lines and uncovered additional ILC/ILC-like cell lines with luminal features and RNA/DNA copy number similarity to ILC tumors. ICLE cell lines retained molecular alterations in key ILC genes at a similar frequency to both primary and metastatic ILC tumors. Importantly, ICLE cell lines recapitulated theCDH1alteration landscape of ILC tumors including enrichment of truncating mutations and biallelic inactivation ofCDH1. Optical genome mapping uncovered novel genomic rearrangements including structural variations inCDH1and other functional gene fusions and revealed breast cancer specific patterns of chromothripsis in chromosomes 8, 11 and 17. Aberrant DNAm events and integrative analysis with RNA expression revealed epigenetic activation ofTFAP2B, an emerging biomarker preferentially expressed in lobular disease. Finally, towards the goal of identifying novel druggable vulnerabilities in ILC, publicly available RNAi loss of function breast cancer cell line datasets revealed numerous putative vulnerabilities cytoskeletal components, focal adhesion and PI3K/AKT pathway in ICLE vs NST cell lines. We addressed the lack of suitable models to study E-cadherin deficient breast cancers by comprehensively characterizing multi-omic features of both established and putative ILC models and showed their similarity to tumors and highlighting novel druggable vulnerabilities.

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Connecting the Indian Ocean World

Cited by 2 publications

References 0 publications

Improving access to breast cancer screening and treatment in Nigeria: The triple mobile assessment and patient navigation model (NCT05321823): A study protocol

Improving access to breast cancer screening and treatment in Nigeria: The triple mobile assessment and patient navigation model (NCT05321823): A study protocol

Multi-omic characterization of ILC and ILC-like cell lines as part of ILC cell line encyclopedia (ICLE) defines new models to study potential biomarkers and explore therapeutic opportunities

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