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Series GSE72617 Query DataSets for GSE72617
Status Public on Jun 30, 2016
Title Identification of Potentially Pathogenic Variants in the Posterior Polymorphous Corneal Dystrophy 1 Locus
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Purpose: To identify the genetic basis of posterior polymorphous corneal dystrophy 1 (PPCD1).

Methods: Next-generation sequencing was performed on DNA samples from 4 affected and 4 unaffected members of a previously reported family with PPCD1 linked to chromosome 20 between D20S182 and D20S195. Custom capture probes were utilized for targeted region capture of the linked interval. Single nucleotide variants (SNVs) and insertions/deletions (indels) were identified using two bioinformatics pipelines and two annotation databases. Candidate variants met the following criteria: quality score ≥20, read depth ≥5X, heterozygous, novel or rare (minor allele frequency (MAF) ≤ 0.05), present in each affected individual and absent in each unaffected individual. Structural variants were detected with two different microarray platforms to identify indels of varying sizes.

Results: Sequencing reads aligned to the linked region on chromosome 20, and high coverage was obtained across the sequenced region. The majority of identified variants were detected with both pipelines and annotation databases, although unique variants were identified. Twelve SNVs in 10 genes (2 synonymous variants and 10 noncoding variants) and 9 indels in 7 genes met the filtering criteria and were considered candidate variants for PPCD1.

Conclusions: Next-generation sequencing of the PPCD1 interval has identified 17 genes containing novel or rare SNVs and indels that segregate with the affected phenotype in an affected family previously mapped to the PPCD1 locus. We anticipate that screening of these candidate genes in other families previously mapped to the PPCD1 locus will result in the identification of the genetic basis of PPCD1.
 
Overall design Four affected and 4 unaffected individuals from a single family were analyzed for copy number variation within the PPCD1 disease locus.
Array design and analysis is based on genome build hg19.
 
Contributor(s) Le DJ, Frausto RF, Aldave AJ
Citation(s) 27355326
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 EY022082 Identification and Characterization of the Genetic Basis of PPCD UNIVERSITY OF CALIFORNIA LOS ANGELES Aldave
Submission date Sep 01, 2015
Last update date Jul 03, 2016
Contact name Anthony J. Aldave
E-mail(s) Aldave@jsei.ucla.edu
Organization name Stein Eye Institute, UCLA
Department Ophthalmology
Lab Cornea Genetics Laboratory
Street address 200 Stein Plaza DSERC 3-143
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (1)
GPL20879 Agilent-073748 PPCD1 CNV 17.3-34.0 (Probe Name version)
Samples (8)
GSM1866510 PPCD Affected Individual 1
GSM1866511 Unaffected Relative 1
GSM1866512 Unaffected Relative 2
Relations
BioProject PRJNA294630

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE72617_RAW.tar 139.4 Mb (http)(custom) TAR (of TXT)
Raw data provided as supplementary file
Processed data included within Sample table

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