Evidence map›Paper›PMID 27440996›Full record

ArticleMolecular vision2016

Variation in PTCHD2, CRISP3, NAP1L4, FSCB, and AP3B2 associated with spherical equivalent.

Fei Chen, Priya Duggal, Barbara E K Klein, Kristine E Lee, Barbara Truitt, Ronald Klein, Sudha K Iyengar, Alison P Klein

Open access · greenAbstract read

PubMed Full text at PMC

In one paragraph

Article in Molecular vision, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it

0cells of the map it votes in

8citing papers in PubMed

1.0field-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

8 citing papers in PubMed, 14 citations in OpenAlex.

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The sleep quality- and myopia-linked PDE11A-Y727C variant impacts neural physiology by reducing catalytic activity and altering subcellular compartmentalization of the enzyme.bioRxiv : the preprint server for biology · 2023
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Rare variant analyses across multiethnic cohorts identify novel genes for refractive error.Communications biology · 2023
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Genetic Variants Associated With Human Eye Size Are Distinct From Those Conferring Susceptibility to Myopia.Investigative ophthalmology & visual science · 2021
Article
MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery: application to lens development and cataract.Human genetics · 2020
Article
Association analysis of exome variants and refraction, axial length, and corneal curvature in a European-American population.Human mutation · 2018
Article
Refraction and Change in Refraction Over a 20-Year Period in the Beaver Dam Eye Study.Investigative ophthalmology & visual science · 2018
Article
Müller glia-derived PRSS56 is required to sustain ocular axial growth and prevent refractive error.PLoS genetics · 2018
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 at 2 institutions in 1 country.

Fei ChenDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD.

Priya DuggalDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD.

Barbara E K KleinDepartment of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI.

Kristine E LeeDepartment of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI.

Barbara TruittDepartment of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH.

Ronald KleinDepartment of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI.

Sudha K IyengarDepartment of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH.

Alison P KleinDepartment of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD; Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD.

Case Western Reserve University · USJohns Hopkins University · US

Funding

Identification of quantitative ocular trait genes in the Beaver Dam EyeR01EY021531 · NEI · JOHNS HOPKINS UNIVERSITY · PI DUGGAL, PRIYA, KLEIN, ALISON P · 2011 to 2013

$1.2M

NEI NIH HHS R01 EY021531Wellcome Trust

6 · The paper itself

Abstract

purposeOcular refraction is measured in spherical equivalent as the power of the external lens required to focus images on the retina. Myopia (nearsightedness) and hyperopia (farsightedness) are the most common refractive errors, and the leading causes of visual impairment and blindness in the world. The goal of this study is to identify rare and low-frequency variants that influence spherical equivalent.

methodsWe conducted variant-level and gene-level quantitative trait association analyses for mean spherical equivalent, using data from 1,560 individuals in the Beaver Dam Eye Study. Genotyping was conducted using the Illumina exome array. We analyzed 34,976 single nucleotide variants and 11,571 autosomal genes across the genome, using single-variant tests as well as gene-based tests.

resultsSpherical equivalent was significantly associated with five genes in gene-based analysis: PTCHD2 at 1p36.22 (p = 3.6 × 10(-7)), CRISP3 at 6p12.3 (p = 4.3 × 10(-6)), NAP1L4 at 11p15.5 (p = 3.6 × 10(-6)), FSCB at 14q21.2 (p = 1.5 × 10(-7)), and AP3B2 at 15q25.2 (p = 1.6 × 10(-7)). The variant-based tests identified evidence suggestive of association with two novel variants in linkage disequilibrium (pairwise r(2) = 0.80) in the TCTE1 gene region at 6p21.1 (rs2297336, minor allele frequency (MAF) = 14.1%, β = -0.62 p = 3.7 × 10(-6); rs324146, MAF = 16.9%, β = -0.55, p = 1.4 × 10(-5)). In addition to these novel findings, we successfully replicated a previously reported association with rs634990 near GJD2 at 15q14 (MAF = 47%, β = -0.29, p=1.8 × 10(-3)). We also found evidence of association with spherical equivalent on 2q37.1 in PRSS56 at rs1550094 (MAF = 31%, β = -0.33, p = 1.7 × 10(-3)), a region previously associated with myopia.

conclusionsWe identified several novel candidate genes that may play a role in the control of spherical equivalent. However, further studies are needed to replicate these findings. In addition, our results contribute to the increasing evidence that variation in the GJD2 and PRSS56 genes influence the development of refractive errors. Identifying that variation in these genes is associated with spherical equivalent may provide further insight into the etiology of myopia and consequent vision loss.

Indexed as

Polymorphism, Single NucleotideAdaptor Protein Complex 3Adaptor Protein Complex beta SubunitsAdultAgedAged, 80 and overCalcium-Binding ProteinsExomeEye ProteinsFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyGenotyping TechniquesHumansLinkage DisequilibriumMaleAdaptor Protein Complex 3Adaptor Protein Complex beta SubunitsAP3B2 protein, humanCalcium-Binding ProteinsCRISP3 protein, humanDISP3 protein, humanEye ProteinsMembrane ProteinsNAP1L4 protein, humanNuclear ProteinsSalivary Proteins and PeptidesSeminal Plasma Proteins

Identifiers

PMID27440996

PMCPMC4945165

OpenAlexW2506221664

What OpenQuestion holds

Textmetadata

LicenceCC BY-NC-ND

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.