In patient 1, ROH were identified using HomozygosityMapper and applying default settings (32 (link)). ROH of less than 3 kb adjacent to each other were merged manually, reducing ROH from 71 to 67. In patient 2, ROH were initially mapped by genome–wide single-nucleotide polymorphism (SNP) chip analysis (HumanCytoSNP-12 BeadChip platform; Illumina). ROH (> 1 Mb) were identified using PLINK software (33 (link)) integrated in ViVar (34 (link)) and ranked according to length and number of consecutive homozygous SNPs. For both patients 1 and 2, ROH were determined with AutoMap (35 (link)) using VCF files from both patients (hg38). After identification of individual ROH, shared ROH (based on coordinates) were determined (Figure 2C and Supplemental Table 1). To define the shared ROH on chromosome 6 and the common haplotype containing the CEP162 variant, all WES variants on chromosome 6 were considered, irrespective of their zygosity (Figure 2C).
Nuzhat N., Van Schil K., Liakopoulos S., Bauwens M., Rey A.D., Käseberg S., Jäger M., Willer J.R., Winter J., Truong H.M., Gruartmoner N., Van Heetvelde M., Wolf J., Merget R., Grasshoff-Derr S., Van Dorpe J., Hoorens A., Stöhr H., Mansard L., Roux A.F., Langmann T., Dannhausen K., Rosenkranz D., Wissing K.M., Van Lint M., Rossmann H., Häuser F., Nürnberg P., Thiele H., Zechner U., Pearring J.N., De Baere E, & Bolz H.J. (2023). CEP162 deficiency causes human retinal degeneration and reveals a dual role in ciliogenesis and neurogenesis. The Journal of Clinical Investigation, 133(8), e161156.
Corresponding Organization : University Hospital Cologne
Other organizations :
Goethe University Frankfurt, University Medical Center of the Johannes Gutenberg University Mainz, Johannes Gutenberg University Mainz, University of Giessen, Bürgerhospital Frankfurt am Main, University of Regensburg, Institut de Génétique Moléculaire de Montpellier, Université de Montpellier, University of Cologne
Applying default settings (32 (link)) in HomozygosityMapper to identify ROH in patient 1
Merging ROH of less than 3 kb adjacent to each other manually, reducing ROH from 71 to 67 in patient 1
Using PLINK software (33 (link)) integrated in ViVar (34 (link)) to identify ROH (> 1 Mb) in patient 2
Ranking ROH according to length and number of consecutive homozygous SNPs in patient 2
Using AutoMap (35 (link)) to determine ROH using VCF files from both patients (hg38) in both patients 1 and 2
dependent variables
Identification of ROH in patient 1 and patient 2
control variables
Not explicitly mentioned
controls
Not explicitly mentioned
Annotations
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