Evidence map›Paper›PMID 37391719›Full record

ArticleBMC genomic data2023

Assessing whole-exome sequencing data from undiagnosed Brazilian patients to improve the diagnostic yield of inborn errors of immunity.

Cristina Santos Ferreira, Ronaldo da Silva Francisco Junior, Alexandra Lehmkuhl Gerber, Ana Paula de Campos Guimarães, Flávia Anisio Amendola, Fernanda Pinto-Mariz, Monica Soares de Souza, Patrícia Carvalho Batista Miranda, Zilton Farias Meira de Vasconcelos, Ekaterini Simões Goudouris and 1 more

Abstract read
In one paragraph

Article in BMC genomic data, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Cristina Santos Ferreira *Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651-075, Brazil.
Ronaldo da Silva Francisco Junior *Bioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651-075, Brazil.
Alexandra Lehmkuhl GerberBioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651-075, Brazil.
Ana Paula de Campos GuimarãesBioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651-075, Brazil.
Flávia Anisio AmendolaAllergy and Immunology Service of Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF) - Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.
Fernanda Pinto-MarizAllergy and Immunology Service of the Martagão Gesteira Institute for Childcare and Pediatrics (IPPMG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro-RJ, Brazil.
Monica Soares de SouzaFederal Hospital for State Employees (HFSE)-Health Ministry, Rio de Janeiro, RJ, Brazil.
Patrícia Carvalho Batista MirandaLagoon Federal Hospital (HFL)-Health Ministry, Rio de Janeiro, RJ, Brazil.
Zilton Farias Meira de VasconcelosLaboratory of High Complexity of the Institute of Women, Children and Adolescents' Health Fernandes Figueira (IFF) - Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.
Ekaterini Simões GoudourisAllergy and Immunology Service of the Martagão Gesteira Institute for Childcare and Pediatrics (IPPMG), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro-RJ, Brazil.
Ana Tereza Ribeiro VasconcelosBioinformatics Laboratory-LABINFO, National Laboratory of Scientific Computation LNCC/MCTIC, Av. Getúlio Vargas, 333, Quitandinha, Petrópolis, Rio de Janeiro, 25651-075, Brazil. atrv@lncc.br.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

objectivesInborn error of immunity (IEI) comprises a broad group of inherited immunological disorders that usually display an overlap in many clinical manifestations challenging their diagnosis. The identification of disease-causing variants from whole-exome sequencing (WES) data comprises the gold-standard approach to ascertain IEI diagnosis. The efforts to increase the availability of clinically relevant genomic data for these disorders constitute an important improvement in the study of rare genetic disorders. This work aims to make available WES data of Brazilian patients' suspicion of IEI without a genetic diagnosis. We foresee a broad use of this dataset by the scientific community in order to provide a more accurate diagnosis of IEI disorders. DATA DESCRIPTION: Twenty singleton unrelated patients treated at four different hospitals in the state of Rio de Janeiro, Brazil were enrolled in our study. Half of the patients were male with mean ages of 9 ± 3, while females were 12 ± 10 years old. The WES was performed in the Illumina NextSeq platform with at least 90% of sequenced bases with a minimum of 30 reads depth. Each sample had an average of 20,274 variants, comprising 116 classified as rare pathogenic or likely pathogenic according to American College of Medical Genetics and Genomics and the Association (ACMG) guidelines. The genotype-phenotype association was impaired by the lack of detailed clinical and laboratory information, besides the unavailability of molecular and functional studies which, comprise the limitations of this study. Overall, the access to clinical exome sequencing data is limited, challenging exploratory analyses and the understanding of genetic mechanisms underlying disorders. Therefore, by making these data available, we aim to increase the number of WES data from Brazilian samples despite contributing to the study of monogenic IEI-disorders.

Indexed as

AffectGenomicsBrazilExome SequencingFemaleHospitalsHumansMaleRare DiseasesInborn errors of immunityMonogenic disorderSingle nucleotide variantsWhole exome sequencing

Identifiers

PMID37391719
PMCPMC10314602

What OpenQuestion holds

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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.