Evidence map›Paper›PMID 34936260›Full record

ArticleBiomedica : revista del Instituto Nacional de Salud2021

Correlation between the number of false positive variants and the quality of results using Ion Torrent PGM™ sequencing to screen BRCA genes.

Tiago César Gouvêa Moreira, Pricila Da Silva Spínola, Micheline Campos Rezende, Carla Simone Moreira de Freitas, Fábio Borges Mury, Cibele Rodrigues Bonvicino, Luciana De Andrade Agostinho

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Article in Biomedica : revista del Instituto Nacional de Salud, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

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4 · The record

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5 · Who and what money

Authors and funding

7 authors.

Tiago César Gouvêa MoreiraHospital do Câncer de Muriaé, Fundação Cristiano Varella, Muriaé, Brazil; Centro Universitário UNIFAMINAS, Muriaé, Brazil. biomedica@ins.gov.co.
Pricila Da Silva SpínolaDivisão de Genética, Instituto Nacional do Câncer, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. biomedica@ins.gov.co.
Micheline Campos RezendeHospital do Câncer de Muriaé, Fundação Cristiano Varella, Muriaé, Brazil; Instituto de Ensino e Pesquisa Santa Casa BH, Belo Horizonte, Brazil. biomedica@ins.gov.co.
Carla Simone Moreira de FreitasHospital do Câncer de Muriaé, Fundação Cristiano Varella, Muriaé, Brazil; Instituto de Ensino e Pesquisa Santa Casa BH, Belo Horizonte, Brazil. biomedica@ins.gov.co.
Fábio Borges MuryThermo Fisher Scientific, São Paulo, Brazil. biomedica@ins.gov.co.
Cibele Rodrigues BonvicinoDivisão de Genética, Instituto Nacional do Câncer, Rio de Janeiro, Brazil; Programa de Pós-Graduação em Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. biomedica@ins.gov.co.
Luciana De Andrade AgostinhoUNIFAMINASHospital do Câncer de Muriaé, Fundação Cristiano Varella, Muriaé, Brazil; Centro Universitário UNIFAMINAS, Muriaé, Brazil; Programa de Pós-Graduação em Neurologia, Universidade Federal do Estado do Rio de Janeiro Rio de Janeiro, Brazil. polucita@yahoo.com.br.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

introductionNext Generation Sequencing (NGS) is cost-effective and a faster method to study genes, but its protocol is challenging.

objectiveTo analyze different adjustments to the protocol for screening the BRCA genes using Ion Torrent PGM sequencing and correlate the results with the number of false positive (FP) variants. MATERIAL AND

methodsWe conducted a library preparation process and analyzed the number of FP InDels, the library concentration, the number of cycles in the target amplification step, the purity of the nucleic acid, the input, and the number of samples/Ion 314 chips in association with the results obtained by NGS.

resultsWe carried out 51 reactions and nine adjustments of protocols and observed eight FP InDels in homopolymer regions. No FP Single-Nucleotide Polymorphism variant was observed; 67.5% of protocol variables were jointly associated with the quality of the results obtained (p<0.05). The number of FP InDels decreased when the quality of results increased.

conclusionThe Ion AmpliSeq BRCA1/BRCA2 Community Panel had a better performance using four samples per Ion-314 chip instead of eight and the optimum number of cycles in the amplification step, even when using high-quality DNA, was 23. We observed better results with the manual equalization process and not using the Ion Library Equalizer kit. These adjustments provided a higher coverage of the variants and fewer artifacts (6.7-fold). Laboratories must perform internal validation because FP InDel variants can vary according to the quality of results while the NGS assay should be validated with Sanger.

Indexed as

Genes, BRCA1Genes, BRCA2High-Throughput Nucleotide SequencingPolymorphism, Single NucleotideFalse Positive ReactionsGenetic TestingHumansMutationSensitivity and SpecificitySequence Analysis, DNABRCA1BRCA2DNAgeneshigh-throughput nucleotide sequencingSequence analysis

Identifiers

PMID34936260
PMCPMC8768485

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.