Computational protocol: Complex genetic architecture in severe hypobetalipoproteinemia

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Protocol publication

[…] Targeted next-generation sequencing of genomic DNA comprised all known dyslipidemia genes, including MTTP (ABL gene), APOB (FHBL gene), PCSK9 and SAR1B (chylomicron retention disease gene) [, ]. VarSeq software prioritized possible or likely pathogenic rare variants of using the Online Mendelian Inheritance in Man database (https://www.ncbi.nlm.nih.gov/omim/). Prediction algorithms such as the Combined Annotation Dependent Depletion (CADD; 7; http://cadd.gs.washington.edu/); Sorting Intolerant From Tolerant (SIFT; 8; http://sift.jcvi.org/); and Polymorphism Phenotyping tool version 2 (PolyPhen-2; 9; http://genetics.bwh.harvard.edu/pph2/). Minor allele frequencies were compared against those cited for African subpopulations in the Exome Aggregation Consortium database (ExAC; 10; http://exac.broadinstitute.org/). All rare variants were confirmed by Sanger sequencing. Segregation of variants across three generations was demonstrated by genotyping family members using Sanger sequencing. […]

Pipeline specifications

Software tools VarSeq, CADD, SIFT, PolyPhen
Databases OMIM
Application WGS analysis
Organisms Homo sapiens
Diseases Abetalipoproteinemia, Blood Coagulation Disorders, Hypobetalipoproteinemias, Muscular Diseases, Nervous System Diseases, Retinal Diseases, Neoplasms, Adipose Tissue, Genetic Diseases, Inborn, Hypobetalipoproteinemia, Familial, Apolipoprotein B