Evidence map›Paper›PMID 30084993›Full record

ArticleBioinformatics (Oxford, England)2019

Detection of de novo copy number deletions from targeted sequencing of trios.

Jack M Fu, Elizabeth J Leslie, Alan F Scott, Jeffrey C Murray, Mary L Marazita, Terri H Beaty, Robert B Scharpf, Ingo Ruczinski

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

8 authors.

Jack M FuDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Elizabeth J LeslieDepartment of Human Genetics, Emory University, Atlanta, GA, USA.
Alan F ScottDepartment of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Jeffrey C MurrayDepartment of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
Mary L MarazitaDepartment of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA.
Terri H BeatyDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
Robert B ScharpfDepartment of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
Ingo RuczinskiDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.

Funding

Extending the Phenotype of Nonsyndromic Orofacial CleftsR01DE016148 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L., WEINBERG, SETH M · 2004 to 2018
$19.7M
Molecular Genetic Epidemiology of Cleft Lip and PalateR37DE008559 · NIDCR · UNIVERSITY OF IOWA · PI MURRAY, JEFFREY C · 2004 to 2013
$6.8M
Human genomics analysis interface for FaceBase 2U01DE024425 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI MARAZITA, MARY L. · 2014 to 2018
$1.2M
GENETIC MAPPING STUDIES OF ORAL-FACIAL CLEFTS IN CHINAR01DE009886 · NIDCR · VIRGINIA COMMONWEALTH UNIVERSITY · PI MARAZITA, MARY L · 1992 to 2002
$1.0M
Genetics of Craniofacial Disorders and Related PhenotypesR00DE025060 · NIDCR · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI LESLIE-CLARKSON, ELIZABETH JANE · 2017 to 2019
$732k
Methods, software, and analyses of genomic data in multiplex oral cleft familiesR03DE025279 · NIDCR · JOHNS HOPKINS UNIVERSITY · PI RUCZINSKI, INGO · 2015 to 2016
$486k
Sequencing of significant signals from cleft lip GWASU01HG005925 · NHGRI · UNIVERSITY OF IOWA · PI MURRAY, JEFFREY C · 2010 to 2010
$238k
NHGRI NIH HHS U01 HG005925NIDCR NIH HHS R00 DE025060NIDCR NIH HHS R01 DE009886NIDCR NIH HHS R01 DE016148NIDCR NIH HHS R03 DE025279NIDCR NIH HHS R37 DE008559NIDCR NIH HHS U01 DE024425
6 · The paper itself

Abstract

motivationDe novo copy number deletions have been implicated in many diseases, but there is no formal method to date that identifies de novo deletions in parent-offspring trios from capture-based sequencing platforms.

resultsWe developed Minimum Distance for Targeted Sequencing (MDTS) to fill this void. MDTS has similar sensitivity (recall), but a much lower false positive rate compared to less specific CNV callers, resulting in a much higher positive predictive value (precision). MDTS also exhibited much better scalability. AVAILABILITY AND IMPLEMENTATION: MDTS is freely available as open source software from the Bioconductor repository. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

AlgorithmsDNA Copy Number VariationsSequence DeletionSoftwareComputational Biology

Identifiers

PMID30084993
PMCPMC6378941

What OpenQuestion holds

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Registered trials

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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.