Computational protocol: A deep intronic CLRN1 (USH3A) founder mutation generates an aberrant exon and underlies severe Usher syndrome on the Arabian Peninsula

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Protocol publication

[…] DNA was extracted from peripheral blood samples using standard methods. DNA samples of the parents and the four affected siblings (family as displayed in Fig. ) were analyzed for genome wide linkage using the Infinium CoreExome-24 v1.1 BeadChip (Illumina Inc., San Diego, CA) according to the manufacturer’s protocol. Subsequent data handling was performed using the graphical user interface ALOHOMORA. Relationship errors were identified by using the program Graphical Relationship Representation. The program PedCheck was applied to find Mendelian errors and data for SNPs with such errors were removed from the data set. Non-Mendelian errors were identified by using the program MERLIN and unlikely genotypes for related samples were deleted. Linkage analysis was performed assuming autosomal-recessive inheritance, full penetrance, consanguinity, and a disease gene frequency of 0.0001. Multipoint LOD scores were calculated using the program Allegro. Haplotypes were reconstructed with Allegro and presented graphically with HaploPainter. Regions of homozygosity by descent (HBD) were annotated with their positions corresponding to NCBI Build 37. […]

Pipeline specifications

Software tools ALOHOMORA, PedCheck, Merlin, Allegro, HaploPainter
Application Population genetic analysis
Diseases Retinal Dystrophies