Sequencing technology status of BRCA1/2 testing in Latin American Countries

Solano, Ángela R.; Palmero, Edenir Inêz; Delgado, Lucı́a; Carraro, Dirce Maria; Ortı́z-López, Rocio; Carranza, Claudia; Santamaría, Carlos; Cifuentes, Laura; Sosa, Lilian E Jara; Toland, Amanda E.

doi:10.1038/s41525-020-0126-3

Cited by 2 publications

(2 citation statements)

References 17 publications

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“…When compared to Sanger sequencing, NGS can offer doctors comparable genetic information at a cheaper cost and shorter time to results [ 2 , 34 ], yet the NGS limitations are the small read size and the difficulty in analyzing large alterations as structural variants. Many studies employed the NGS as a technology in the detection of BRCA1/2 gene variants in various ethnic groups to implement the detection of gene variants using NGS in the routine line of diagnostics and may allow doctors to make more prompt and informed decisions about surgery or neo-adjuvant chemotherapy in breast cancer patients [ 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 ].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer

Helal¹,

Saad²,

Saad³

et al. 2022

Genes

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The goal of biomarker testing, in the field of personalized medicine, is to guide treatments to achieve the best possible results for each patient. The accurate and reliable identification of everyone’s genome variants is essential for the success of clinical genomics, employing third-generation sequencing. Different variant calling techniques have been used and recommended by both Oxford Nanopore Technologies (ONT) and Nanopore communities. A thorough examination of the variant callers might give critical guidance for third-generation sequencing-based clinical genomics. In this study, two reference genome sample datasets (NA12878) and (NA24385) and the set of high-confidence variant calls provided by the Genome in a Bottle (GIAB) were used to allow the evaluation of the performance of six variant calling tools, including Human-SNP-wf, Clair3, Clair, NanoCaller, Longshot, and Medaka, as an integral step in the in-house variant detection workflow. Out of the six variant callers understudy, Clair3 and Human-SNP-wf that has Clair3 incorporated into it achieved the highest performance rates in comparison to the other variant callers. Evaluation of the results for the tool was expressed in terms of Precision, Recall, and F1-score using Hap.py tools for the comparison. In conclusion, our findings give important insights for identifying accurate variants from third-generation sequencing of personal genomes using different variant detection tools available for long-read sequencing.

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Section: Discussionmentioning

confidence: 99%

Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer

Helal¹,

Saad²,

Saad³

et al. 2022

Genes

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show abstract

“…For BRCA1/2 testing, LAC laboratories use state-of-the-art platforms with similar quality control metrics and variant classification protocols as laboratories in Europe and other areas of the world [ 51 ]. Quality standards for pathology tests (e.g., immunohistochemistry) are still a matter of concern in LAC, and access to genetic testing is far from ideal because of its high cost and lack of insurance coverage for supportive healthcare policies [ 40 , 44 , 52 ].…”

Section: Methodsmentioning

confidence: 99%

Real-world data on triple-negative breast cancer in Latin America and the Caribbean

Tiscoski,

Giacomazzi,

Soares Rocha

et al. 2023

ecancer Journal

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Breast cancer (BC) is the most prevalent cancer in women in Latin America and the Caribbean. We compiled real-world data (RWD) on the epidemiology, diagnosis, treatment, and patient outcomes of triple-negative breast cancer (TNBC), addressing the main barriers to optimal care in Latin America. The prevalence of TNBC varies between 11% and 38.5% of all BC cases diagnosed in the region, and TNBC primarily affects young patients. Delays in BC diagnosis, with consequent advanced disease stages and barriers to access efficient therapies, particularly due to high costs, negatively impact patient outcomes. Cancer clinical trials are an opportunity to access standard and novel therapies for patients with this aggressive BC subtype and thus must be prioritised. Finally, generating RWD and cost-effectiveness studies in a region with limited resources is critical for decision-makers to define the incorporation of new technologies for the treatment of BC.

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Sequencing technology status of BRCA1/2 testing in Latin American Countries

Cited by 2 publications

References 17 publications

Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer

Evaluation of the Available Variant Calling Tools for Oxford Nanopore Sequencing in Breast Cancer

Real-world data on triple-negative breast cancer in Latin America and the Caribbean

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