Evidence map›Paper›PMID 28868155›Full record

ArticleNPJ genomic medicine2016

Missense-depleted regions in population exomes implicate ras superfamily nucleotide-binding protein alteration in patients with brain malformation.

Xiaoyan Ge, Henry Gong, Kevin Dumas, Jessica Litwin, Joanna J Phillips, Quinten Waisfisz, Marjan M Weiss, Yvonne Hendriks, Kyra E Stuurman, Stanley F Nelson and 4 more

Open access · goldAbstract read
In one paragraph

Article in NPJ genomic medicine, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed
3.9field-weighted citation impact, top 6% of its field
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

37 citing papers in PubMed, 56 citations in OpenAlex.

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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

14 authors at 3 institutions in 2 countries.

Xiaoyan GeDepartment of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA.
Henry GongDepartment of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA.
Kevin DumasDepartment of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA.
Jessica LitwinDepartment of Neurology, University of California San Francisco, San Francisco, CA, USA.
Joanna J PhillipsDepartment of Neurologic Surgery, University of California San Francisco, San Francisco, CA, USA.
Quinten WaisfiszDepartment of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
Marjan M WeissDepartment of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
Yvonne HendriksDepartment of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
Kyra E StuurmanDepartment of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
Stanley F NelsonDepartments of Pathology and Laboratory Medicine, Pediatrics, and Human Genetics, Divisions of Medical Genetics and Molecular Diagnostics, University of California Los Angeles, Los Angeles, CA, USA.
Wayne W GrodyDepartment of Pathology and Laboratory Medicine and Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA.
Hane LeeDepartment of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA.
Pui-Yan KwokInstitute for Human Genetics, University of California San Francisco, San Francisco, CA, USA.
Joseph Tc ShiehDepartment of Pediatrics, Division of Medical Genetics, University of California San Francisco, San Francisco, CA, USA.
University of California, San Francisco · USAmsterdam UMC Location VUmc · NLUniversity of California, Los Angeles · US

Funding

Comprehensive Sequencing and Analysis of Variation in NHLBI CohortsUC2HL102925 · NHLBI · BROAD INSTITUTE, INC. · PI ALTSHULER, DAVID, GABRIEL, STACEY · 2010 to 2010
$14.7M
Northwest Genomics CenterUC2HL102926 · NHLBI · UNIVERSITY OF WASHINGTON · PI GREEN, PHILIP P, NICKERSON, DEBORAH A · 2010 to 2010
$14.0M
Northwest Genomics CenterRC2HL102926 · NHLBI · UNIVERSITY OF WASHINGTON · PI GREEN, PHILIP P, NICKERSON, DEBORAH A · 2009 to 2009
$11.0M
Comprehensive Sequencing and Analysis of Variation in NHLBI CohortsRC2HL102925 · NHLBI · BROAD INSTITUTE, INC. · PI ALTSHULER, DAVID, GABRIEL, STACEY · 2009 to 2009
$10.2M
PREDOCTORAL TRAINING IN BIOMEDICAL SCIENCEST32GM008568 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANSEL, KARL MARK · 1995 to 2019
$6.3M
ARRA - NHLBI Lung Cohorts Sequencing ProjectRC2HL102923 · NHLBI · UNIVERSITY OF WASHINGTON · PI BAMSHAD, MICHAEL JOSEPH, BARNES, KATHLEEN C · 2009 to 2009
$2.6M
ARRA - NHLBI Lung Cohorts Sequencing ProjectUC2HL102923 · NHLBI · UNIVERSITY OF WASHINGTON · PI BAMSHAD, MICHAEL JOSEPH, BARNES, KATHLEEN C · 2010 to 2010
$2.6M
WHI Sequencing Project (WHISP)UC2HL102924 · NHLBI · OHIO STATE UNIVERSITY · PI CARLSON, CHRISTOPHER S, JACKSON, REBECCA D · 2010 to 2010
$2.4M
WHI Sequencing Project (WHISP)RC2HL102924 · NHLBI · OHIO STATE UNIVERSITY · PI CARLSON, CHRISTOPHER S, JACKSON, REBECCA D · 2009 to 2009
$2.1M
Human Exome Sequencing in Six Well-Phenotyped NHLBI CohortsUC2HL103010 · NHLBI · UNIVERSITY OF VIRGINIA · PI RICH, STEPHEN S. · 2010 to 2010
$1.5M
Human Exome Sequencing in Six Well-Phenotyped NHLBI CohortsRC2HL103010 · NHLBI · UNIVERSITY OF VIRGINIA · PI RICH, STEPHEN S. · 2009 to 2009
$817k
Role of MicroRNA-499 in the HeartK08HL092970 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SHIEH, JOSEPH T · 2009 to 2013
$627k
NHLBI NIH HHS K08 HL092970NHLBI NIH HHS RC2 HL102923NHLBI NIH HHS RC2 HL102924NHLBI NIH HHS RC2 HL102925NHLBI NIH HHS RC2 HL102926NHLBI NIH HHS RC2 HL103010NHLBI NIH HHS UC2 HL102923NHLBI NIH HHS UC2 HL102924NHLBI NIH HHS UC2 HL102925NHLBI NIH HHS UC2 HL102926NHLBI NIH HHS UC2 HL103010NIGMS NIH HHS T32 GM008568
6 · The paper itself

Abstract

Genomic sequence interpretation can miss clinically relevant missense variants for several reasons. Rare missense variants are numerous in the exome and difficult to prioritise. Affected genes may also not have existing disease association. To improve variant prioritisation, we leverage population exome data to identify intragenic missense-depleted regions (MDRs) genome-wide that may be important in disease. We then use missense depletion analyses to help prioritise undiagnosed disease exome variants. We demonstrate application of this strategy to identify a novel gene association for human brain malformation. We identified

Indexed as

ARF1brain malformationExome sequencingGDP/GTPMDRmissense-depletionnucleotide-bindingRAS superfamilyvariant prioritization

Identifiers

PMID28868155
PMCPMC5576364
OpenAlexW2593518041

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.