ID

45830

Description

Principal Investigator: Margaret M. DeAngelis, PhD, John A. Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of Utah, School of Medicine, Salt Lake City, UT, USA MeSH: Macular Degeneration,Geographic Atrophy,Wet Macular Degeneration https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001039 Advanced age-related macular degeneration (AMD) is the leading cause of blindness in the elderly, with limited therapeutic options. To further our understanding of AMD genetics, we examined the contribution of common and rare genetic variation in the International AMD Genomics Consortium that included ~50,000 samples of 26 AMD case - control cohorts that were jointly genotyped. Analyzing 16,144 patients with late stage AMD and 17,832 controls, we identified 52 independently associated common and rare variants distributed across 34 loci. Besides these single variant signals, we also observed gene-based enrichment of very rare coding variants (frequency 0.1%) in cases that implicated causal roles for *CFH*, *CFI* and *TIMP3* in three of the known AMD risk loci. Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.

Link

dbGaP study = phs001039

Keywords

Versions (1)
  1. 8/1/23 8/1/23 - Simon Heim
Copyright Holder

Margaret M. DeAngelis, PhD, John A. Moran Eye Center, Department of Ophthalmology and Visual Sciences, University of Utah, School of Medicine, Salt Lake City, UT, USA

Uploaded on

August 1, 2023

DOI

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License

Creative Commons BY 4.0
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dbGaP phs001039 International AMD Genomics Consortium - Exome Chip Experiment

English

Eligibility Criteria

5 forms  
Inclusion and exclusion criteria
Description

Inclusion and exclusion criteria

Alias
UMLS CUI [1,1]
C1512693
UMLS CUI [1,2]
C0680251
*Inclusion criteria*:
Description

*Inclusion criteria*:

Data type

boolean

Alias
UMLS CUI [1,1]
C1512693
Cases: Avanced AMD cases with GA and/or CNV in at least one eye and age at first diagnosis >= 50 years, intermediate AMD cases with pigmentary changes in the RPE or more than five macular drusen greater than 63μm and age at first diagnosis >= 50 years.
Description

Cases: Avanced AMD cases with GA and/or CNV in at least one eye and age at first diagnosis >= 50 years, intermediate AMD cases with pigmentary changes in the RPE or more than five macular drusen greater than 63μm and age at first diagnosis >= 50 years.

Data type

boolean

Alias
UMLS CUI [1,1]
C1706256
UMLS CUI [1,2]
C5687385
UMLS CUI [1,3]
C0600518
UMLS CUI [1,4]
C1536085
UMLS CUI [1,5]
C0420617
UMLS CUI [1,6]
C0015392
UMLS CUI [1,7]
C1828181
UMLS CUI [2,1]
C1706256
UMLS CUI [2,2]
C5230245
UMLS CUI [2,3]
C4015287
UMLS CUI [2,4]
C0035322
UMLS CUI [2,5]
C0677628
UMLS CUI [2,6]
C0456389
UMLS CUI [2,7]
C1828181
Controls: Without known advanced or intermediate AMD.
Description

Controls: Without known advanced or intermediate AMD.

Data type

boolean

Alias
UMLS CUI [1,1]
C0009932
UMLS CUI [1,2]
C0686906
UMLS CUI [1,3]
C5230245
UMLS CUI [1,4]
C5687385
Recruitment and ascertainment strategies varied by study.
Description

Recruitment and ascertainment strategies varied by study.

Data type

boolean

Alias
UMLS CUI [1,1]
C2949735
UMLS CUI [1,2]
C0679199
UMLS CUI [1,3]
C3846158
UMLS CUI [1,4]
C0679199
UMLS CUI [1,5]
C0947630
*Exclusion criteria* (cases and controls):Duplicated and related individuals (kinship coefficient Φ >= 0.0884, i.e. 3<sup>rd</sup> degree relatives or closer)
Description

*Exclusion criteria* (cases and controls):Duplicated and related individuals (kinship coefficient Φ >= 0.0884, i.e. 3<sup>rd</sup> degree relatives or closer)

Data type

boolean

Alias
UMLS CUI [1,1]
C0680251
UMLS CUI [1,2]
C1706256
UMLS CUI [1,3]
C4553389
UMLS CUI [1,4]
C0445223
UMLS CUI [1,5]
C0237401
UMLS CUI [1,6]
C0870772
UMLS CUI [1,7]
C3639750
UMLS CUI [1,8]
C1519210
UMLS CUI [1,9]
C1517194
Subjects with discrepancies between reported gender and sex chromosomal information or with atypical sex chromosome configurations
Description

Subjects with discrepancies between reported gender and sex chromosomal information or with atypical sex chromosome configurations

Data type

boolean

Alias
UMLS CUI [1,1]
C1290905
UMLS CUI [1,2]
C0017249
UMLS CUI [1,3]
C1562251
UMLS CUI [1,4]
C0036868
Subjects with genotyping call rates < 98.5%
Description

Subjects with genotyping call rates < 98.5%

Data type

boolean

Alias
UMLS CUI [1,1]
C1285573
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Similar models

Eligibility Criteria

5 forms
Name
Type
Description | Question | Decode (Coded Value)
Data type
Alias
Item Group
Inclusion and exclusion criteria
C1512693 (UMLS CUI [1,1])
C0680251 (UMLS CUI [1,2])
*Inclusion criteria*:
Item
*Inclusion criteria*:
boolean
C1512693 (UMLS CUI [1,1])
Cases: Avanced AMD cases with GA and/or CNV in at least one eye and age at first diagnosis >= 50 years, intermediate AMD cases with pigmentary changes in the RPE or more than five macular drusen greater than 63μm and age at first diagnosis >= 50 years.
Item
Cases: Avanced AMD cases with GA and/or CNV in at least one eye and age at first diagnosis >= 50 years, intermediate AMD cases with pigmentary changes in the RPE or more than five macular drusen greater than 63μm and age at first diagnosis >= 50 years.
boolean
C1706256 (UMLS CUI [1,1])
C5687385 (UMLS CUI [1,2])
C0600518 (UMLS CUI [1,3])
C1536085 (UMLS CUI [1,4])
C0420617 (UMLS CUI [1,5])
C0015392 (UMLS CUI [1,6])
C1828181 (UMLS CUI [1,7])
C1706256 (UMLS CUI [2,1])
C5230245 (UMLS CUI [2,2])
C4015287 (UMLS CUI [2,3])
C0035322 (UMLS CUI [2,4])
C0677628 (UMLS CUI [2,5])
C0456389 (UMLS CUI [2,6])
C1828181 (UMLS CUI [2,7])
Controls: Without known advanced or intermediate AMD.
Item
Controls: Without known advanced or intermediate AMD.
boolean
C0009932 (UMLS CUI [1,1])
C0686906 (UMLS CUI [1,2])
C5230245 (UMLS CUI [1,3])
C5687385 (UMLS CUI [1,4])
Recruitment and ascertainment strategies varied by study.
Item
Recruitment and ascertainment strategies varied by study.
boolean
C2949735 (UMLS CUI [1,1])
C0679199 (UMLS CUI [1,2])
C3846158 (UMLS CUI [1,3])
C0679199 (UMLS CUI [1,4])
C0947630 (UMLS CUI [1,5])
*Exclusion criteria* (cases and controls):Duplicated and related individuals (kinship coefficient Φ >= 0.0884, i.e. 3<sup>rd</sup> degree relatives or closer)
Item
*Exclusion criteria* (cases and controls):Duplicated and related individuals (kinship coefficient Φ >= 0.0884, i.e. 3<sup>rd</sup> degree relatives or closer)
boolean
C0680251 (UMLS CUI [1,1])
C1706256 (UMLS CUI [1,2])
C4553389 (UMLS CUI [1,3])
C0445223 (UMLS CUI [1,4])
C0237401 (UMLS CUI [1,5])
C0870772 (UMLS CUI [1,6])
C3639750 (UMLS CUI [1,7])
C1519210 (UMLS CUI [1,8])
C1517194 (UMLS CUI [1,9])
Subjects with discrepancies between reported gender and sex chromosomal information or with atypical sex chromosome configurations
Item
Subjects with discrepancies between reported gender and sex chromosomal information or with atypical sex chromosome configurations
boolean
C1290905 (UMLS CUI [1,1])
C0017249 (UMLS CUI [1,2])
C1562251 (UMLS CUI [1,3])
C0036868 (UMLS CUI [1,4])
Subjects with genotyping call rates < 98.5%
Item
Subjects with genotyping call rates < 98.5%
boolean
C1285573 (UMLS CUI [1,1])
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