Evidence map›Paper›PMID 27769252›Full record

ArticleBMC urology2016

Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism.

Yanping Wang, Jin Li, Thomas F Kolon, Alicia Olivant Fisher, T Ernesto Figueroa, Ahmad H BaniHani, Jennifer A Hagerty, Ricardo Gonzalez, Paul H Noh, Rosetta M Chiavacci and 8 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC urology, 2016. 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
0.9field-weighted citation impact, top 22% 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

1 citing paper in PubMed, 4 citations in OpenAlex.

  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

18 authors at 4 institutions in 3 countries.

Yanping WangNemours Biomedical Research, Nemours /Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
Jin LiCenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Thomas F KolonDivision of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Alicia Olivant FisherNemours Biomedical Research, Nemours /Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
T Ernesto FigueroaDivision of Urology, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
Ahmad H BaniHaniDivision of Urology, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
Jennifer A HagertyDivision of Urology, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
Ricardo GonzalezDivision of Urology, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
Paul H NohDivision of Urology, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
Rosetta M ChiavacciCenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Kisha R HardenCenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Debra J AbramsCenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Deborah StableyNemours Biomedical Research, Nemours /Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
Cecilia E KimCenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Katia Sol-ChurchNemours Biomedical Research, Nemours /Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.
Hakon HakonarsonCenter for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Marcella DevotoDivision of Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
Julia Spencer BartholdNemours Biomedical Research, Nemours /Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA. Julia.Barthold@nemours.org.
Alfred I. duPont Hospital for Children · USChildren's Hospital of Philadelphia · USKinderkrankenhaus auf der Bult · DEUniversity of Pennsylvania · US

Funding

Predictive Modeling & Optimal Control Framework for Model-Based Epidemic Response in DelawareP20GM103446 · NIGMS · UNIVERSITY OF DELAWARE · PI MELINDA K DUNCAN · 2012 to 2026
$67.2M
Center for Pediatric ResearchP20GM103464 · NIGMS · NEMOURS CHILDREN'S HOSPITAL, DELAWARE · PI SHAFFER, THOMAS H · 2012 to 2014
$5.6M
Center for Pediatric Research Pilot ProgramP30GM114736 · NIGMS · NEMOURS CHILDREN'S HOSPITAL, DELAWARE · PI SHAFFER, THOMAS H · 2015 to 2019
$5.1M
Genetic Basis of CryptorchidismR01HD060769 · NICHD · NEMOURS CHILDREN'S HOSPITAL, DELAWARE · PI BARTHOLD, JULIA SPENCER · 2010 to 2014
$2.0M
NICHD NIH HHS R01 HD060769NIGMS NIH HHS P20 GM103446NIGMS NIH HHS P20 GM103464NIGMS NIH HHS P30 GM114736
6 · The paper itself

Abstract

backgroundCopy number variation (CNV) is a potential contributing factor to many genetic diseases. Here we investigated the potential association of CNV with nonsyndromic cryptorchidism, the most common male congenital genitourinary defect, in a Caucasian population.

methodsGenome wide genotyping were performed in 559 cases and 1772 controls (Group 1) using Illumina HumanHap550 v1, HumanHap550 v3 or Human610-Quad platforms and in 353 cases and 1149 controls (Group 2) using the Illumina Human OmniExpress 12v1 or Human OmniExpress 12v1-1. Signal intensity data including log R ratio (LRR) and B allele frequency (BAF) for each single nucleotide polymorphism (SNP) were used for CNV detection using PennCNV software. After sample quality control, gene- and CNV-based association tests were performed using cleaned data from Group 1 (493 cases and 1586 controls) and Group 2 (307 cases and 1102 controls) using ParseCNV software. Meta-analysis was performed using gene-based test results as input to identify significant genes, and CNVs in or around significant genes were identified in CNV-based association test results. Called CNVs passing quality control and signal intensity visualization examination were considered for validation using TaqMan CNV assays and QuantStudio® 3D Digital PCR System.

resultsThe meta-analysis identified 373 genome wide significant (p < 5X10

conclusionsOur data do not support that structural variation is a major cause of nonsyndromic cryptorchidism.

Indexed as

DNA Copy Number VariationsCryptorchidismGenome-Wide Association StudyHumansMaleSoftwareWhite PeopleCNVCryptorchidismGenetics

Identifiers

PMID27769252
PMCPMC5073740
OpenAlexW2538771084

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.