README.md

Data Analysis for : Diverse Genes with Germline Variants Converging on p53 Network May Predispose to Solid Tumors in Children, Adolescents, and Young Adults

• This github dir contains the data analysis jupyter notebooks, scripts and data tables accompaning the paper : Diverse Genes with Germline Variants Converging on p53 Network May Predispose to Solid Tumors in Children, Adolescents, and Young Adults
  • GermLine Analysis of Children, Adolescents, and Young Adults (C-AYA) with SolidTumor
• Authors : Sara Akhavanfard, Roshan Padmanabhan, Lamis Yehia, Feixiong Cheng, Charis Eng

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Contents

IVA Filteration Parameters

• CCF_CAYA_IVA_variant_filtertion_params
• StJude CAYA IVA variant filteration params

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Analysis

Known Cancer Predisposing Genes (KCPG)

• KCPG_woAR_Oncoplot
• KCPG_Heatmap
• KCPG_LollipopPlots
• KCPG_woAR_TT-AdrenocorticalCarcinoma_Oncoplot
• KCPG_woAR_TT-Carcinoma_Oncoplot
• KCPG_woAR_TT-CentralNervousSystem_Oncoplot
• KCPG_woAR_TT-EwingsSarcoma_Oncoplot
• KCPG_woAR_TT-GermCellTumor_Oncoplot
• KCPG_woAR_TT-HighGradeGlioma_Oncoplot
• KCPG_woAR_TT-LowGradeGlioma_Oncoplot
• KCPG_woAR_TT-Neuroblastoma_Oncoplot
• KCPG_woAR_TT-Osteosarcoma_Oncoplot
• KCPG_woAR_TT-OtherSolidTumor_Oncoplot
• KCPG_woAR_TT-Retinoblastoma_Oncoplot
• KCPG_woAR_TT-Rhabdomyosarcoma_Oncoplot
• KCPG_woAR_TT-SoftTissueSarcoma_Oncoplot
• KCPG_woAR_TT-Wilmstumor_Oncoplot

Candidate Genes

• CandidateGenes_Oncoplot
• CandidateGenes_Heatmap
• CandidateGenes_LollipopPlots
• CandidateGenes_TT-AdrenocorticalCarcinoma_Oncoplot
• CandidateGenes_TT-Carcinoma_Oncoplot
• CandidateGenes_TT-CentralNervousSystem_Oncoplot
• CandidateGenes_TT-EwingsSarcoma_Oncoplot
• CandidateGenes_TT-GermCellTumor_Oncoplot
• CandidateGenes_TT-HighGradeGlioma_Oncoplot
• CandidateGenes_TT-LowGradeGlioma_Oncoplot
• CandidateGenes_TT-Neuroblastoma_Oncoplot
• CandidateGenes_TT-Osteosarcoma_Oncoplot
• CandidateGenes_TT-OtherSolidTumor_Oncoplot
• CandidateGenes_TT-Retinoblastoma_Oncoplot
• CandidateGenes_TT-Rhabdomyosarcoma_Oncoplot
• CandidateGenes_TT-SoftTissueSarcoma_Oncoplot
• CandidateGenes_TT-Wilmstumor_Oncoplot

C-AYA Patiants with solid tumors vs NonTCGA-ExAC controls

• Freq_Plot_of_CAYA_vs_NonTCGA-ExAc

Congential Heart Defects (CHD) Related Genes / Variants

• CHD_only_monoallelic_Oncoplots
• CHD_monoallelic_Heatmap

Scripts

• includes inhouse scipts to process and anlayze the data

Data

• table dir contain the supplimentary excel files
• Browse the data at SRA RunSelector
• Summary List for project PRJNA559601 here

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