Evidence map›Paper›PMID 25457163›Full record

ArticleClinical genetics2015

Exome sequencing in 32 patients with anophthalmia/microphthalmia and developmental eye defects.

A M Slavotinek, S T Garcia, G Chandratillake, T Bardakjian, E Ullah, D Wu, K Umeda, R Lao, P L-F Tang, E Wan and 17 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
42citing papers in PubMed, 1 pooled it
4.7field-weighted citation impact, top 5% 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

42 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.

  1. Pooled it
  2. Article
  3. Article
  4. Article
  5. Article
  6. Article
  7. Review
  8. Article
  9. Article
  10. Protein truncating splice site variant inInternational journal of ophthalmology · 2025
    Article
  11. Review
  12. Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta.Genetics in medicine : official journal of the American College of Medical Genetics · 2023
    Article
  13. Article
  14. International journal of molecular sciences · 2021
    Article
  15. Observational
  16. Updating the Genetic Landscape of Inherited Retinal Dystrophies.Frontiers in cell and developmental biology · 2021
    Article
  17. Rare heterozygous GDF6 variants in patients with renal anomalies.European journal of human genetics : EJHG · 2020
    Article
  18. Article
  19. Role of carotenoids and retinoids during heart development.Biochimica et biophysica acta. Molecular and cell biology of lipids · 2020
    Review
  20. 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

27 authors at 5 institutions in 2 countries.

A M SlavotinekDepartment of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
S T GarciaPersonalis, Inc., Menlo Park, CA, USA.
G ChandratillakePersonalis, Inc., Menlo Park, CA, USA.
T BardakjianDivision of Medical Genetics, Einstein Medical Center, Philadelphia, PA, USA.
E UllahDepartment of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
D WuDepartment of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
K UmedaDepartment of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
R LaoCardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
P L-F TangCardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
E WanCardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
L MadireddyDepartment of Neurology, University of California San Francisco, San Francisco, CA, USA.
S LyalinaDepartment of Neurology, University of California San Francisco, San Francisco, CA, USA.
B A MendelsohnDepartment of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
S DuganDivision of Medical Genetics, Children's Hospitals & Clinics, Minneapolis, MN, USA.
J TirchPersonalis, Inc., Menlo Park, CA, USA.
R TischlerPersonalis, Inc., Menlo Park, CA, USA.
J HarrisPersonalis, Inc., Menlo Park, CA, USA.
M J ClarkPersonalis, Inc., Menlo Park, CA, USA.
S ChervitzPersonalis, Inc., Menlo Park, CA, USA.
A PatwardhanPersonalis, Inc., Menlo Park, CA, USA.
J M WestPersonalis, Inc., Menlo Park, CA, USA.
P UrsellDepartment of Pathology, University of California San Francisco, San Francisco, CA, USA.
A de Alba CampomanesDepartment of Ophthalmology, University of California San Francisco, San Francisco, CA, USA.
A SchneiderDivision of Medical Genetics, Einstein Medical Center, Philadelphia, PA, USA.
P-Y KwokCardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA.
S BaranziniDepartment of Neurology, University of California San Francisco, San Francisco, CA, USA.
R O ChenPersonalis, Inc., Menlo Park, CA, USA.
Personalis (United States) · USUniversity of California, San Francisco · USUniversity of San Francisco · USEinstein Medical Center Philadelphia · USChildren's Minnesota · US

Funding

Integrative Program in Complex Biological System (ipCBS)T32EB009383 · NIBIB · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI MARSHALL, WALLACE, WEINER, ORION D · 2009 to 2022
$3.2M
Gene Discovery in Human Anopthalmia/MicropthalmiaR21EY022779 · NEI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SLAVOTINEK, ANNE M. · 2012 to 2013
$421k
NEI NIH HHS R21 EY022779NIBIB NIH HHS T32 EB009383
6 · The paper itself

Abstract

Anophthalmia/microphthalmia (A/M) is a genetically heterogeneous birth defect for which the etiology is unknown in more than 50% of patients. We used exome sequencing with the ACE Exome(TM) (Personalis, Inc; 18 cases) and UCSF Genomics Core (21 cases) to sequence 28 patients with A/M and four patients with varied developmental eye defects. In the 28 patients with A/M, we identified de novo mutations in three patients (OTX2, p.(Gln91His), RARB, p.Arg387Cys and GDF6, p.Ala249Glu) and inherited mutations in STRA6 in two patients. In patients with developmental eye defects, a female with cataracts and cardiomyopathy had a de novo COL4A1 mutation, p.(Gly773Arg), expanding the phenotype associated with COL4A1 to include cardiomyopathy. A male with a chorioretinal defect, microcephaly, seizures and sensorineural deafness had two PNPT1 mutations, p.(Ala507Ser) and c.401-1G>A, and we describe eye defects associated with this gene for the first time. Exome sequencing was efficient for identifying mutations in pathogenic genes for which there is no clinical testing available and for identifying cases that expand phenotypic spectra, such as the PNPT1 and COL4A1-associated disorders described here.

Indexed as

MutationAnophthalmosCollagen Type IVDNA Mutational AnalysisExomeExoribonucleasesEye AbnormalitiesFemaleHumansInfantMaleMembrane ProteinsMicrophthalmosMitochondrial ProteinsOtx Transcription FactorsReceptors, Retinoic AcidCOL4A1 protein, humanCollagen Type IVExoribonucleasesMembrane ProteinsMitochondrial ProteinsOTX2 protein, humanOtx Transcription FactorsPNPT1 protein, humanReceptors, Retinoic Acidretinoic acid receptor betaSTRA6 protein, humananophthalmia/microphthalmiaCOL4A1exome sequencingFBLN1PNPT1

Identifiers

PMID25457163
PMCPMC4452457
OpenAlexW1886835423

What OpenQuestion holds

Textmetadata
LicenceTDM
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.