Evidence map›Paper›PMID 31839986›Full record

ArticleNPJ genomic medicine2019

Reanalysing genomic data by normalized coverage values uncovers CNVs in bone marrow failure gene panels.

Supanun Lauhasurayotin, Geoff D Cuvelier, Robert J Klaassen, Conrad V Fernandez, Yves D Pastore, Sharon Abish, Meera Rayar, MacGregor Steele, Lawrence Jardine, Vicky R Breakey and 15 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in NPJ genomic medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–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. Autoimmune Neutropenia and Immune-Dysregulation in a Patient Carrying aInternational journal of molecular sciences · 2022
    Article
  2. Review
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

25 authors.

Supanun Lauhasurayotin1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.
Geoff D Cuvelier3Pediatric Hematology-Oncology-Bone Marrow Transplantation, University of Manitoba, Cancer Care Manitoba, Winnipeg, MB Canada.
Robert J Klaassen4Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, ON Canada.
Conrad V Fernandez5Pediatric Hematology/Oncology, IWK Health Centre, Halifax, NS Canada.
Yves D Pastore6CHU Sainte-Justine, Montreal, QC Canada.
Sharon Abish7Pediatric Hematology Oncology, Montreal Children's Hospital, Montreal, QC Canada.
Meera Rayar8Division of Hematology/Oncology, UBC & B.C. Children's Hospital, Vancouver, BC Canada.
MacGregor Steele9Alberta Children's Hospital, Calgary, Canada.
Lawrence Jardine10Children's Hospital, London Health Sciences Centre, London, ON Canada.
Vicky R Breakey11Department of Pediatrics, McMaster University, Hamilton, ON Canada.
Josee Brossard12Centre hospitalier universitaire, Sherbrooke, QC Canada.
Roona Sinha13Royal University Hospital, Saskatoon, SK Canada.
Mariana Silva14Kingston General Hospital, Kingston, ON Canada.
Lisa Goodyear15Pediatric Hematology/Oncology, Janeway Child Health Centre, St. John's, NF Canada.
Jeffrey H Lipton16Allogeneic Blood and Marrow Transplant Program, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON Canada.
Bruno Michon17Centre Hospitalier Universitaire de Quebec, Sainte-Foy, QC Canada.
Catherine Corriveau-Bourque18Pediatrics, University of Alberta, Edmonton, AB Canada.
Lillian Sung19Population Health Sciences, Research Institute, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada.
Iren Shabanova1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.
Hongbing Li1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.
Bozana Zlateska1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.
Santhosh Dhanraj1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.
Michaela Cada2Marrow Failure and Myelodysplasia Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON Canada.
Stephen W Scherer1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.
Yigal Dror1Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON Canada.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Inherited bone marrow failure syndromes (IBMFSs) are genetically heterogeneous disorders with cytopenia. Many IBMFSs also feature physical malformations and an increased risk of cancer. Point mutations can be identified in about half of patients. Copy number variation (CNVs) have been reported; however, the frequency and spectrum of CNVs are unknown. Unfortunately, current genome-wide methods have major limitations since they may miss small CNVs or may have low sensitivity due to low read depths. Herein, we aimed to determine whether reanalysis of NGS panel data by normalized coverage value could identify CNVs and characterize them. To address this aim, DNA from IBMFS patients was analyzed by a NGS panel assay of known IBMFS genes. After analysis for point mutations, heterozygous and homozygous CNVs were searched by normalized read coverage ratios and specific thresholds. Of the 258 tested patients, 91 were found to have pathogenic point variants. NGS sample data from 165 patients without pathogenic point mutations were re-analyzed for CNVs; 10 patients were found to have deletions. Diamond Blackfan anemia genes most commonly exhibited heterozygous deletions, and included

Indexed as

Genetic testingMedical genomics

Identifiers

PMID31839986
PMCPMC6901453

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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.