Computational protocol: The Role of a Novel TRMT1 Gene Mutation and Rare GRM1 Gene Defect in Intellectual Disability in Two Azeri Families

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Protocol publication

[…] A whole genome scan was performed using SNP Array 6.0 (Affymetrix, Santa Clara, CA, USA) for two or three affected individuals, one unaffected individual and their parents, and the data were analysed using Homozygosity Mapper software[,]. We applied the ALOHOMORA [] software v0.32 which use for converting genotyping data into appropriate format for linkage analysis. The gender-check tool of the ALOHOMORA software was also used to check the gender of selected individuals. Recognition of incompatibility genotypes from genotype data was performed using PedCheck software []. Graphical representation of relationship errors software or GRR [] was used to calculate the relationships between individuals within families. The LOD score was calculated using the MERLIN program based on autosomal recessive mode of inheritance and with complete penetrance and a disease allele prevalence of 0.001 []. The threshold in this research for assessment of the intervals was a LOD score of approximately 2.5. The visualizations of haplotypes in linkage intervals were obtained using Haplopainter software. […]

Pipeline specifications

Software tools ALOHOMORA, PedCheck, Merlin, HaploPainter
Application Population genetic analysis
Organisms Homo sapiens
Diseases Movement Disorders, Oculocerebrorenal Syndrome, Machado-Joseph Disease, Genetic Diseases, Inborn
Chemicals Guanine, S-Adenosylmethionine, Glutamic Acid