scholarly journals Co-Inference of Data Mislabelings Reveals Improved Models in Genomics and Breast Cancer Diagnostics

2022 ◽  
Vol 4 ◽  
Author(s):  
Susanne Gerber ◽  
Lukas Pospisil ◽  
Stanislav Sys ◽  
Charlotte Hewel ◽  
Ali Torkamani ◽  
...  
Keyword(s):  
Breast Cancer ◽  
False Positive ◽  
Late Onset ◽  
Empirical Studies ◽  
False Negative ◽  
Cancer Diagnostics ◽  
Healthy Ageing ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Case Control Studies

Mislabeling of cases as well as controls in case–control studies is a frequent source of strong bias in prognostic and diagnostic tests and algorithms. Common data processing methods available to the researchers in the biomedical community do not allow for consistent and robust treatment of labeled data in the situations where both, the case and the control groups, contain a non-negligible proportion of mislabeled data instances. This is an especially prominent issue in studies regarding late-onset conditions, where individuals who may convert to cases may populate the control group, and for screening studies that often have high false-positive/-negative rates. To address this problem, we propose a method for a simultaneous robust inference of Lasso reduced discriminative models and of latent group-specific mislabeling risks, not requiring any exactly labeled data. We apply it to a standard breast cancer imaging dataset and infer the mislabeling probabilities (being rates of false-negative and false-positive core-needle biopsies) together with a small set of simple diagnostic rules, outperforming the state-of-the-art BI-RADS diagnostics on these data. The inferred mislabeling rates for breast cancer biopsies agree with the published purely empirical studies. Applying the method to human genomic data from a healthy-ageing cohort reveals a previously unreported compact combination of single-nucleotide polymorphisms that are strongly associated with a healthy-ageing phenotype for Caucasians. It determines that 7.5% of Caucasians in the 1000 Genomes dataset (selected as a control group) carry a pattern characteristic of healthy ageing.

Association of the CD14 C159T and the Toll-like receptor 4 Asp299Gly polymorphisms with various phenotypes of asthma in adults from Crimea

2020 ◽  
Vol 41 (2) ◽  
pp. 134-140
Author(s):  
Yuriy Bisyuk ◽  
Andrew Dubovyi ◽  
Ilona DuBuske ◽  
Viktor Litus ◽  
Lawrence M. DuBuske
Keyword(s):  
Late Onset ◽  
Adult Population ◽  
Additive Models ◽  
Atopic Asthma ◽  
Control Group ◽  
Nucleotide Polymorphisms ◽  
Toll Like Receptor ◽  
Toll Like Receptor 4 ◽  
Single Nucleotide ◽  
Gender And Age

Background: This study assessed gene polymorphisms of the CD14 receptor (C-159T) and Toll-like receptor 4 (Asp299Gly) in a patient population in Crimea, Ukraine, stratified by clinical (early versus late onset; frequent versus occasional relapses; fixed versus reversible obstruction) and immunologic (atopic versus nonatopic; eosinophilic; neutrophilic or paucigranulocytic inflammation) subtype. Methods: Two polymorphisms, CD14 C-159T and TLR4 Asp299Gly, were assessed in 331 patients with asthma. The control group included 285 volunteers who were nonatopic. The single nucleotide polymorphisms were studied by using polymerase chain reaction with electrophoretic detection. Results: There were increased odds of asthma development in patients with the Asp299Gly TLR4 mutation compared with the general population underdominant odds ratio (OR) 1.52 [95% confidence interval (CI), 1.00‐2.32] and overdominant (OR 1.55 [95% CI, 1.01‐2.38]) models after adjustment for gender and age. In addition, mutations in this gene decreased the odds of nonatopic asthma in underdominant (OR 0.26 [95% CI, 0.07‐0.93]; p = 0.027), overdominant (OR 0.27 [95% CI, 0.07‐0.96]; p = 0.033), and log-additive models (OR 0.26 [95% CI, 0.07‐0.93]; p = 0.026) compared with the atopic subgroup after adjustment for gender, age, number of exacerbations, and type of airway inflammation. Allele frequencies for CD14 and TLR4 polymorphisms did not show statistical differences between the patients with asthma and the control subjects. Conclusion: CD14 C-159T polymorphisms were not associated with asthma in the adult population in Crimea. TLR4 Asp299Gly polymorphisms were associated with asthma and with decreased odds of nonatopic asthma compared with atopic asthma in the adult population in Crimea.

scholarly journals Oral Contraceptive Use and Breast Cancer Risk Assessment: A Systematic Review and Meta-Analysis of Case-Control Studies, 2009–2020

Cancers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 5654
Author(s):  
Agnieszka Barańska ◽  
Agata Błaszczuk ◽  
Wiesław Kanadys ◽  
Maria Malm ◽  
Katarzyna Drop ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Oral Contraceptive ◽  
Cancer Risk ◽  
Meta Analysis ◽  
Case Control ◽  
Cochrane Library ◽  
Control Group ◽  
Case Control Studies ◽  
Increased Risk ◽  
Breast Cancer Risk Assessment

To perform a meta-analysis of case-control studies that addressed the association between oral contraceptive pills (OC) use and breast cancer (BrCa), PubMED (MEDLINE), Embase, and the Cochrane Library were searched to identify case-control studies of OC and BrCa published between 2009 and 2020. We used the DerSimonian–Laird method to compute pooled odds ratios (ORs) and confidence intervals (CIs), and the Mantel–Haenszel test to assess the association between OC use and cancer. Forty-two studies were identified that met the inclusion criteria and we included a total of 110,580 women (30,778 into the BrCa group and 79,802 into the control group, of which 15,722 and 38,334 were using OC, respectively). The conducted meta-analysis showed that the use of OC was associated with a significantly increased risk of BrCa in general, OR = 1.15, 95% CI: 1.01 to 1.31, p = 0.0358. Regarding other risk factors for BrCa, we found that increased risk was associated significantly with early menarche, nulliparous, non-breastfeeding, older age at first parity, postmenopause, obesity, smoking, and family history of BrCa. Despite our conclusion that birth control pills increase the cancer risk being supported by extensive previous studies and meta-analyzes, further confirmation is required.

False-Negative and False-Positive Results in FDG-PET and PET/CT in Breast Cancer

PET Clinics ◽  
2009 ◽  
Vol 4 (3) ◽  
pp. 289-298 ◽  
Author(s):  
Rakesh Kumar ◽  
Neerja Rani ◽  
Chetan Patel ◽  
Sandip Basu ◽  
Abass Alavi
Keyword(s):  
Breast Cancer ◽  
False Positive ◽  
Fdg Pet ◽  
False Negative ◽  
Pet Ct ◽  
Positive Results

scholarly journals Evaluation of inadequate, indeterminate, false-negative and false-positive cases in cytological examination for breast cancer according to histological type

2012 ◽  
Vol 7 (1) ◽  
Author(s):  
Rin Yamaguchi ◽  
Shin-ichi Tsuchiya ◽  
Takashi Koshikawa ◽  
Toshiro Yokoyama ◽  
Kuniko Mibuchi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
False Positive ◽  
False Negative ◽  
Histological Type ◽  
Cytological Examination

False-positive diagnosis of breast cancer by diffused optical tomography with ultrasound

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e22085-e22085
Author(s):  
X. Wang ◽  
Y. Li ◽  
X. Cao
Keyword(s):  
Breast Cancer ◽  
Early Diagnosis ◽  
Diagnostic Tool ◽  
False Positive ◽  
Breast Tumor ◽  
Optical Tomography ◽  
False Negative ◽  
False Negative Rate ◽  
Breast Disease ◽  
Study Results

e22085 Background: Breast cancer is one of the most common cancer in women. Early detection, early diagnosis and early treatment play key role in fighting against breast cancer. OPTIMUS system is a system of diffused optical tomography with ultrasound. It provides dual modality images for early diagnosis of breast cancer. The aim of this study was to evaluate the OPTIMUS system on diagnosis of breast disease. Methods: OPTIMUS system was applied to 160 breast tumor patients. All patients had received surgical treatment and had definite pathological diagnosis. OPTIMUS system was evaluated as diagnostic tool of breast tumor in this study. Results: There were 42 cases diagnosed as benign breast disease and 118 cases diagnosed as breast cancer by OPTIMUS system. Pathology confirmed 60 cases of benign disease and 100 cases of breast cancer. False positive rate of breast cancer was 30% (18/60). False negative rate of breast cancer was 0% (0/100). The pathology of false positive cases was mild and severe papillomatosis (6/18), non-typical hyperplasia (4/18), chronic inflammation (3/18), fibroadenoma (3/18) and fat necrosis (2/18). Papillomatosis and non-typical hyperplasia are precancerous lesions and often difficult for clinical diagnosis. In this study the false positive diagnostic rate of mammography and ultrasonography is 13% and 11.1% respectively. Conclusions: OPTIMUS system is a non- invasive and highly effective diagnostic tool for breast disease. Its sensitivity is reached to 100% and specificity is about 70% on the diagnosis of breast cancer. OPTIMUS system could be used as assistant diagnostic tool for breast tumor. No significant financial relationships to disclose.

scholarly journals The Lifetime Economic Burden of Inaccurate HER2 Testing: Estimating the Costs of False-Positive and False-Negative HER2 Test Results in US Patients with Early-Stage Breast Cancer

2015 ◽  
Vol 18 (4) ◽  
pp. 541-546 ◽  
Author(s):  
Louis P. Garrison ◽  
Joseph B. Babigumira ◽  
Anthony Masaquel ◽  
Bruce C.M. Wang ◽  
Deepa Lalla ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Economic Burden ◽  
False Positive ◽  
Early Stage ◽  
False Negative ◽  
Early Stage Breast Cancer ◽  
Test Results ◽  
Her2 Testing

scholarly journals Is there a role of frozen section of sentinel lymph node in patients with early breast cancer for the management of axilla in India: a prospective study

2019 ◽  
Vol 6 (6) ◽  
pp. 2126
Author(s):  
Anshika Arora ◽  
Neena Chauhan ◽  
Sunil Saini ◽  
Nishish Vishwakarma ◽  
Tanvi Luthra
Keyword(s):  
Breast Cancer ◽  
Lymph Node ◽  
Sentinel Lymph Node ◽  
Early Breast Cancer ◽  
False Positive ◽  
Frozen Section ◽  
False Negative ◽  
Lymph Node Biopsy ◽  
True Negative ◽  
Node Negative

Background: Evaluation of axilla using sentinel lymph node biopsy (SLNB) is the standard of care in node negative early breast cancer. Intra operative assessment of SLNB with frozen section (FS) often guides the surgeon regarding decision for level of axillary dissection. The aim of this study was to evaluate accuracy of FS of SLNB in these patients with histopathology examination (HPE) as the gold standard.Methods: This study was performed between July 2017 and November 2018. After gross evaluation of SLNB, nodes were cut in half and frozen; the other half was preserved for HPE. For FS, nodes were sectioned to 4 mm width and examined.Results: A total of 61 patients underwent SLNB, 55 patients undergoing intra-operative FS. The mean age was 53 years (range 30-84, ± 15.09 SD), primary tumor was clinically T1 in 23.6%, T2 in 76.4% patients. A median of four sentinel nodes were identified, mean size 13.84 mm. On FS SLNB was positive for metastasis in 14 (25.5%), on HPE in 16 (29.1%) patients. There were 13 true positive, 38 true negative, 3 false negative and 1 false positive result for FS. The sensitivity, specificity, positive and negative predictive value, false negative and false positive rates were 81.25%, 97.44%, 92.86%, 92.73%, 18.75% and 2.56% respectively in this study. The overall accuracy of FS of SLNB in early carcinoma breast was found to be 92.73%.Conclusions: An intra-operative FS of the SLN in node negative early breast cancer is a highly sensitive tool in axilla management.

scholarly journals Breast Cancer and miR-SNPs: The Importance of miR Germ-Line Genetics

2019 ◽  
Vol 5 (1) ◽  
pp. 27 ◽  
Author(s):  
Poonam Malhotra ◽  
Graham Read ◽  
Joanne Weidhaas
Keyword(s):  
Breast Cancer ◽  
Cancer Risk ◽  
Binding Sites ◽  
Germ Line ◽  
Cancer Diagnostics ◽  
Mirna Biogenesis ◽  
Nucleotide Polymorphisms ◽  
Patient Factors ◽  
Single Nucleotide ◽  
Risk Prognosis

Recent studies in cancer diagnostics have identified microRNAs (miRNAs) as promising cancer biomarkers. Single nucleotide polymorphisms (SNPs) in miRNA binding sites, seed regions, and coding sequences can help predict breast cancer risk, aggressiveness, response to stimuli, and prognosis. This review also documents significant known miR-SNPs in miRNA biogenesis genes and their effects on gene regulation in breast cancer, taking into account the genetic background and ethnicity of the sampled populations. When applicable, miR-SNPs are evaluated in the context of other patient factors, including mutations, hormonal status, and demographics. Given the power of miR-SNPs to predict patient cancer risk, prognosis, and outcomes, further study of miR-SNPs is warranted to improve efforts towards personalized medicine.

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