Computational protocol: Mutations in CDK5RAP2 cause Seckel syndrome

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Protocol publication

[…] We performed genome-wide linkage analysis in two families (SK-1 and SK-2) using the Affymetrix GeneChip® Human Mapping 250K Sty Array (Affymetrix, Santa Clara, CA). We verified sample genders by counting heterozygous SNPs on the X chromosome. Relationship errors were evaluated with the help of the program Graphical Relationship Representation (Abecasis et al. ). The program PedCheck was applied to detect Mendelian errors (O’Connell and Weeks ) and data for SNPs with such errors were removed from the data set. Non-Mendelian errors were identified by using the program MERLIN (Abecasis et al. ) and unlikely genotypes for related samples were deleted. Linkage analysis was performed assuming autosomal recessive inheritance, full penetrance and a disease gene frequency of 0.0001. Multipoint LOD scores were calculated using the program ALLEGRO (Gudbjartsson et al. ). Haplotypes were reconstructed with ALLEGRO and presented graphically with HaploPainter (Thiele and Nürnberg ). All data handling was performed using the graphical user interface ALOHOMORA (Ruschendorf and Nürnberg ). […]

Pipeline specifications

Software tools PedCheck, Merlin, Allegro, HaploPainter, ALOHOMORA
Application Population genetic analysis
Organisms Homo sapiens
Diseases Congenital Abnormalities, Microcephaly, Movement Disorders, Genetic Diseases, Inborn