X-Meeting presentations

WHOLE EXOME SEQUENCING OF BRAZILIAN LUMINAL SPORADIC BREAST CANCER

Published in 21/11/2024 - ISBN: 978-65-272-0843-3

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Paper Title
WHOLE EXOME SEQUENCING OF BRAZILIAN LUMINAL SPORADIC BREAST CANCER
Authors
  • Marco Antonio Campanário
  • Ana Carolina Rodrigues
  • Beatriz Rosa De Azevedo
  • Bruno Janke do Nascimento
  • Tiago Minuzzi Freire da Fontoura Gomes
  • Alysson Henrique Urbanski
  • Vinícius Da Silva Coutinho Parreira
  • Flávia Cristina de Paula Freitas
  • Michelle Orane Schemberger
  • Rubens Silveira de Lima
  • Flavia Kuroda
  • Jaqueline Yu Ting Wang
  • Victor Hugo Calegari De Toledo
  • Valter Antonio de Baura
  • Emanuel Maltempi de Souza
  • Daniela F. Gradia
  • Michel Satya Naslavsky
  • Mayana Zatz
  • Maria Rita Passos-Bueno
  • Hellen Geremias Dos Santos
  • Jaqueline Carvalho de Oliveira
  • Fabio Passetti
Modality
Poster
Subject area
DNA and Genomics
Publishing Date
21/11/2024
Country of Publishing
Brazil | Brasil
Language of Publishing
Inglês
Paper Page
https://www.even3.com.br/anais/xmeeting-2024/831997-whole-exome-sequencing-of-brazilian-luminal-sporadic-breast-cancer
ISBN
978-65-272-0843-3
Keywords
breast cancer; whole exome sequencing; luminal A; luminal B
Summary
Breast cancer (BC) is a complex genomic disease and a major public health issue in Brazil and worldwide. Global efforts are directed towards understanding cancer from a genomic perspective, but genomic research on BC is still scarce in the highly admixed Brazilian population. Considering constitutive whole exome sequencing (WES) and analysis of BC patients, the vast majority focuses on hereditary BC, which corresponds to just 5-10% of the cases. Besides, the few which generated high-throughput data of sporadic BC have not encompassed its major immunohistochemical subtypes, including luminal A and B. Therefore, this ongoing study aims to characterize constitutional genetic variation of Brazilian adult women who were diagnosed with the two most common immunohistochemical subtypes of sporadic BC: luminal A and luminal B. For this, we collected peripheral blood of 89 patients with age between 25 and 85 years (mean = 59.3 years) diagnosed with sporadic luminal BC in the state of Paraná, Brasil, between 2003 and 2020. The blood DNA was extracted, and the whole exome sequencing (WES) was performed in the Illumina NovaSeq 6000 platform. The data was processed under the version 4.2.1.0 of Genome Analysis Toolkit (GATK) protocol, which consists of the read quality control (fastQC v. 0.12.0), mapping to reference (bwa-mem v. 0.7.1), mapping quality control (samtools v. 1.19.2, picard v. 2.25.4, BQSR), variant calling (HaplotypeCaller), genotyping (GenotypeGVCF) and variant call quality control (VQSR). The sequencing coverage ranged from 45x to 134.6x (mean = 80.4x). Annotation was carried out using ANNOVAR and the filter was adapted using the CEGH Filter signaling algorithm, created by the Online Brazilian Archive of Mutations (ABraOM) project. In order to study subtype-specific luminal BC risk variants in the Brazilian population, it is intended to analyze the common and rare variants separately based on the minor frequency allele (MAF). For the common variants (MAF > 5%), we will use a simple logistic regression model, considering having the luminal A or B phenotype as the response of interest. As for the rare variants (MAF < 5%), the method is based on variant clustering methods on the corresponding genes. The structural and regulatory impacts of the genetic variants will be investigated through online tools such as SNiPA, HaploReg, RegulomeDB and the GTEx Portal database. Our results have the potential to advance the knowledge of the genetic factors underlying sporadic luminal breast cancer in Brazilian women and contribute to the development of more personalized and effective approaches for its detection and treatment.
Title of the Event
20º Congresso Brasileiro de Bioinformática: X-Meeting 2024
City of the Event
Salvador
Title of the Proceedings of the event
X-Meeting presentations
Name of the Publisher
Even3
Means of Dissemination
Meio Digital

How to cite

CAMPANÁRIO, Marco Antonio et al.. WHOLE EXOME SEQUENCING OF BRAZILIAN LUMINAL SPORADIC BREAST CANCER.. In: X-Meeting presentations. Anais...Salvador(BA) Hotel Deville Prime, 2024. Available in: https//www.even3.com.br/anais/xmeeting-2024/831997-WHOLE-EXOME-SEQUENCING-OF-BRAZILIAN-LUMINAL-SPORADIC-BREAST-CANCER. Access in: 05/07/2025

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