Genotype data were available for 527 Ashkenazi Jewish individuals (64 extended families) selected due to their strong information content for linkage studies of myopia from among the 105 Ashkenazi Jewish families included in the Penn Family Study. Details of the recruitment of these families has been previously described [14 (link)]. This study followed the tenets of the Declaration of Helsinki and informed consent was obtained from all subjects after explanation of the nature of the study and any potential consequences. This study was approved by the institutional review boards of the University of Pennsylvania and the National Human Genome Research Institute. All subjects were genotyped with the Illumina ExomePlus array by the Center for Inherited Disease Research (CIDR) at Johns Hopkins University.
Exomeplus array
Manufactured by Illumina
Sourced in United States
The ExomePlus array is a comprehensive genetic analysis tool designed to interrogate the protein-coding regions of the human genome, known as the exome. It provides high-resolution coverage of the exome, enabling the detection of genetic variations that may be associated with various health conditions or traits.
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Lab products found in correlation
2 protocols using exomeplus array
1
Genotyping Ashkenazi Jewish Families for Myopia
2
Genotyping and Pedigree Analysis of DNA Samples
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Five hundred seventeen subject DNA samples were genotyped using an Illumina ExomePlus array at the Center for Inherited Disease Research (CIDR) at Johns Hopkins University (Baltimore, MD, USA). Variants were filtered to a mean call rate of 99%, and any variant with a quality score of 0.15 or less was set to missing. Monomorphic markers were removed using PLINK.37 (link) Sib-pair38 was used to identify Mendelian inconsistencies. Markers with a Mendelian inconsistency in a single family were removed from that family; markers with multiple Mendelian error were removed from all families. PLINK and Prest-Plus39 (link) were used to verify familial relationships by calculating identity by descent (IBD) values.
Ten ungenotyped individuals were added to the data set to connect disjointed pedigrees. The existence of these individuals was confirmed by family history, but they were either unwilling or unavailable to participate. Their phenotypes and genotypes were coded as unknown.
The single-nucleotide polymorphism (SNP) data was merged with a previous set of 367 microsatellite genotypes; 493 individuals from the exome-based array had microsatellite data. The final data set consisted of 527 individuals with 98,631 markers.
Ten ungenotyped individuals were added to the data set to connect disjointed pedigrees. The existence of these individuals was confirmed by family history, but they were either unwilling or unavailable to participate. Their phenotypes and genotypes were coded as unknown.
The single-nucleotide polymorphism (SNP) data was merged with a previous set of 367 microsatellite genotypes; 493 individuals from the exome-based array had microsatellite data. The final data set consisted of 527 individuals with 98,631 markers.
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