What is a CH Variant Child has a recessive allele from each parent with the variant located at a different position within the same gene How is nucleotide inheritance determined laboratorybased ID: 1044507
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1. Compound Heterozygous (CH) VariantsWhat is a CH Variant? Child has a recessive allele from each parent with the variant located at a different position within the same geneHow is nucleotide inheritance determined?laboratory-based: 10X Genomics or fosmid pool-based strategycomputer-based: SHAPEIT2, Beagle, Eagle2, HapCUT2Why study CH variants? CH variants are understudied in pediatric diseaseMay contribute to early disease onset
2. Idiopathic ScoliosisBackground:Abnormal spine curvature that typically presents in children 10-12 years old (90% of cases)Potential Causes (largely unknown)EnvironmentalGenetic Available Trio DataData Source: Gabriella Miller Kids First Data Resource CenterContains trio data for various pediatric cancers and structural birth defect diseases16 samples with Idiopathic ScoliosisgVCFâs generated from WGS dataImage Source: https://d3b.center/kidsfirst/
3. CH PipelineEach step of the pipeline uses a docker containerWithin each container a python script is executedPython scripts may contain python code only or use numerous programs to complete a taskExample programs:GATKPLINKSAMtoolssummarize biospecimen, clinical and manifest filesparse gVCF filescombine individual triosliftover triosremove multiallelic sites, unplaced sites, and sites with missing genotype informationseparate chromosomes and generate plink files for each triophase with SHAPEIT2revert alt/ref to be congruent with reference and remove sites with Mendel errorsmerge trios into one fileannotateGEMINI database and GEMINI query
4. Pipeline ExampleBuild Docker Image:Run Docker Container:
5. Results(MUC19/MUC16)(MUC19/MUC16/SSPO)(CDC34/INNPP5D/HLA-DRB1)(MUC19/MUC16)(MUC19/MUC16)(MUC19/MUC16)(MUC19/MUC16)(MUC19/MUC16/SSPO)(CDC34/INNPP5D/HLA-DRB1)
6. Future DirectionsFine tune the CH pipelineImplement other phasing softwareProvide test/example data for usersUse the CH pipeline analyze other diseases within the Kids First Data Resource CenterAcknowledgementsPiccolo LabBYU Department of BiologyBYU Office of Research ComputingPoster: P53