Evaluation of variant calling tools for detection of SNVs in BRCA1 and BRCA2 genes in patients from the Institute of Oncology and Radiology of Serbia
Аутори
Pantović, IsidoraŽivić, Katarina
Boljević, Ivana
Nedeljković, Milica
Janković, Radmila
Tanić, Miljana
Остала ауторства
Morić, IvanaĐorđević, Valentina
Конференцијски прилог (Објављена верзија)
,
© 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade
Метаподаци
Приказ свих података о документуАпстракт
Serbia has one of the world’s highest incidences and mortality rates of ovarian cancer.
Germline or somatic mutations in BRCA1 and BRCA2 genes, such as single nucleotide
variants (SNVs), indels, insertions, deletions, commonly lead to development of breast
and ovary cancer. Targeted therapy with PARP inhibitors is the current standard of care for
serous epithelial BRCA-mutated ovarian cancer and depends on the accurate detection of
mutations in these genes.
In this study, a subset of patient specimens from Institute of Oncology and Radiology
were sequenced on MiSeq Illumina sequencer, raw data were analysed bioinformatically,
which included checking quality control of raw FASTQ sequences, trimming, mapping
them on reference genome(hg19), target coverage quality control and variant calling. We
tested various variant calling tools including Mutect2, GATK HaplotypeCaller, FreeBayes,
VarDict and MuSe callers. We evaluated the relative performance- concordance rate, false
positi...ve and false negative rates between the callers for SNV/indel detection in BRCA1
and BRCA2 genes.
Кључне речи:
genomics / variant calling / BRCA1 gene / BRCA2 gene / cancer / sequencingИзвор:
4th Belgrade Bioinformatics Conference, 2023, 4, 101-101Издавач:
- Belgrade : Institute of molecular genetics and genetic engineering
Финансирање / пројекти:
- Министарство науке, технолошког развоја и иновација Републике Србије, институционално финансирање - 200043 (Институт за онкологију и радиологију Србије, Београд) (RS-MESTD-inst-2020-200043)
Напомена:
- Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023
Колекције
Институција/група
Institut za molekularnu genetiku i genetičko inženjerstvoTY - CONF AU - Pantović, Isidora AU - Živić, Katarina AU - Boljević, Ivana AU - Nedeljković, Milica AU - Janković, Radmila AU - Tanić, Miljana PY - 2023 UR - https://belbi.bg.ac.rs/ UR - https://imagine.imgge.bg.ac.rs/handle/123456789/2046 AB - Serbia has one of the world’s highest incidences and mortality rates of ovarian cancer. Germline or somatic mutations in BRCA1 and BRCA2 genes, such as single nucleotide variants (SNVs), indels, insertions, deletions, commonly lead to development of breast and ovary cancer. Targeted therapy with PARP inhibitors is the current standard of care for serous epithelial BRCA-mutated ovarian cancer and depends on the accurate detection of mutations in these genes. In this study, a subset of patient specimens from Institute of Oncology and Radiology were sequenced on MiSeq Illumina sequencer, raw data were analysed bioinformatically, which included checking quality control of raw FASTQ sequences, trimming, mapping them on reference genome(hg19), target coverage quality control and variant calling. We tested various variant calling tools including Mutect2, GATK HaplotypeCaller, FreeBayes, VarDict and MuSe callers. We evaluated the relative performance- concordance rate, false positive and false negative rates between the callers for SNV/indel detection in BRCA1 and BRCA2 genes. PB - Belgrade : Institute of molecular genetics and genetic engineering C3 - 4th Belgrade Bioinformatics Conference T1 - Evaluation of variant calling tools for detection of SNVs in BRCA1 and BRCA2 genes in patients from the Institute of Oncology and Radiology of Serbia EP - 101 SP - 101 VL - 4 UR - https://hdl.handle.net/21.15107/rcub_imagine_2046 ER -
@conference{ author = "Pantović, Isidora and Živić, Katarina and Boljević, Ivana and Nedeljković, Milica and Janković, Radmila and Tanić, Miljana", year = "2023", abstract = "Serbia has one of the world’s highest incidences and mortality rates of ovarian cancer. Germline or somatic mutations in BRCA1 and BRCA2 genes, such as single nucleotide variants (SNVs), indels, insertions, deletions, commonly lead to development of breast and ovary cancer. Targeted therapy with PARP inhibitors is the current standard of care for serous epithelial BRCA-mutated ovarian cancer and depends on the accurate detection of mutations in these genes. In this study, a subset of patient specimens from Institute of Oncology and Radiology were sequenced on MiSeq Illumina sequencer, raw data were analysed bioinformatically, which included checking quality control of raw FASTQ sequences, trimming, mapping them on reference genome(hg19), target coverage quality control and variant calling. We tested various variant calling tools including Mutect2, GATK HaplotypeCaller, FreeBayes, VarDict and MuSe callers. We evaluated the relative performance- concordance rate, false positive and false negative rates between the callers for SNV/indel detection in BRCA1 and BRCA2 genes.", publisher = "Belgrade : Institute of molecular genetics and genetic engineering", journal = "4th Belgrade Bioinformatics Conference", title = "Evaluation of variant calling tools for detection of SNVs in BRCA1 and BRCA2 genes in patients from the Institute of Oncology and Radiology of Serbia", pages = "101-101", volume = "4", url = "https://hdl.handle.net/21.15107/rcub_imagine_2046" }
Pantović, I., Živić, K., Boljević, I., Nedeljković, M., Janković, R.,& Tanić, M.. (2023). Evaluation of variant calling tools for detection of SNVs in BRCA1 and BRCA2 genes in patients from the Institute of Oncology and Radiology of Serbia. in 4th Belgrade Bioinformatics Conference Belgrade : Institute of molecular genetics and genetic engineering., 4, 101-101. https://hdl.handle.net/21.15107/rcub_imagine_2046
Pantović I, Živić K, Boljević I, Nedeljković M, Janković R, Tanić M. Evaluation of variant calling tools for detection of SNVs in BRCA1 and BRCA2 genes in patients from the Institute of Oncology and Radiology of Serbia. in 4th Belgrade Bioinformatics Conference. 2023;4:101-101. https://hdl.handle.net/21.15107/rcub_imagine_2046 .
Pantović, Isidora, Živić, Katarina, Boljević, Ivana, Nedeljković, Milica, Janković, Radmila, Tanić, Miljana, "Evaluation of variant calling tools for detection of SNVs in BRCA1 and BRCA2 genes in patients from the Institute of Oncology and Radiology of Serbia" in 4th Belgrade Bioinformatics Conference, 4 (2023):101-101, https://hdl.handle.net/21.15107/rcub_imagine_2046 .