Computational protocol: The genotypic and phenotypic spectrum of PIGA deficiency

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Protocol publication

[…] With a profound IDD and an abnormal biochemical phenotype, this patient met the inclusion requirements for our TIDEX (Treatable Intellectual Disability Endeavour exome sequencing) gene discovery study. We isolated genomic DNA samples from the peripheral blood of the patient as well as parents and two unaffected male siblings using standard techniques. WES was performed for the index patient and his unaffected parents using the Agilent SureSelect kit and Illumina HiSeq 2000 (Perkin-Elmer, Santa Clara, California, USA). An in-house designed bioinformatics pipeline [] was used to align the reads to the human reference genome version hg19 and to identify and assess rare variants for their potential to disrupt protein function. The candidate variants were further confirmed using Sanger re-sequencing in all the family members. Deleteriousness of the candidate variants was assessed using Combined Annotation–Dependent Depletion (CADD) scores [], PolyPhen-2 ( [] and SIFT (Sorting Intolerant From Tolerant; ( []. Protein alignment was generated using T-Coffee ( [] and analyzed using GeneDoc Only those variants predicted to be “functional” (missense, nonsense and frameshift changes, as well as in-frame deletions and splice-site effects) were subsequently screened under a series of inheritance models. […]

Pipeline specifications

Software tools CADD, PolyPhen, SIFT, T-Coffee
Applications WGS analysis, WES analysis
Organisms Homo sapiens
Diseases Congenital Abnormalities, Abnormalities, Multiple, Contracture, Deficiency Diseases, Heart Arrest, Hemoglobinuria, Paroxysmal, Hyperlipoproteinemia Type I, Liver Diseases, Maple Syrup Urine Disease, Spasms, Infantile, Genetic Diseases, X-Linked, Dyslipidemias
Chemicals Phosphatidylinositols, Glycosylphosphatidylinositols