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Genetic Mutations Analysis in Tumors: Comprehensive Study

This study investigates novel mutations in genes across different tissues of esophageal and colorectal cancers. It delves into the types of mutations occurring specifically in tumors of CC and ESCC and analyzes genes mutated in multiple tumors. The research includes Sanger sequencing of mutations identified in tumors, with a focus on 515 genes and variant scoring. RNA-seq data from 2 ESCC and 2 CC tumors are analyzed for mutations. Structural variations and high-confidence junctions between genes are examined, along with validation assays using Sanger sequencing.

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Genetic Mutations Analysis in Tumors: Comprehensive Study

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  1. The Number of Genes with Novel Mutations

  2. The Number of Genes with Novel Mutations in Different Combinations of Tissues of CC

  3. The Number of Genes with Novel Mutations in Different Combinations of Tissues of ESCC

  4. The Number of Genes with Different Type of Mutations Occurred Specifically in Tumors of CC

  5. The Number of Genes with Different Type of Mutations Occurred Specifically in Tumors of ESCC

  6. The Number of Genes with Mutations Occurred in Multiple Tumors of ESCC or CC T T or NT

  7. Sanger Sequencing of Mutations Identified in Tumors of ESCC or CC from CGI Data 515 genes in (T or NT) 31 genes from SIFT, Polyphen, and LogRE 15 genes mutated in multiple tumors mapability repeat mask Primer3 41 genes being PCRed/sequenced in DNA from blood, normal, and tumor

  8. RNA-seq of 2 ESCC and 2 CC poly-A RNA isolation library construction will be put on GA2 for sequencing this week

  9. Sanger Sequencing of Mutations 41 genes being PCRed/sequenced in DNA from blood, normal, and tumor 39 assays worked 15 validated 24 Not validated 16: no mutation in tumor 8: heterozygous in B&N

  10. An Example of Validated Mutation blood normal tumor FABP2 L89R in CC0996

  11. An Example of LOH of a Heterozygote blood normal tumor CDKL1 T177M in CC0996

  12. An Example of Absence of the Variant blood normal tumor MED26 E67K in CC0996

  13. Tumor Variant Scores Tumor Scores

  14. Summary of Sequence Reads and BWA Mapping hg18 reference sequence mRNA refseq EST combination of any two exons mapping pipeline splicing junction 108 base pair-end sequences Assemble bam files

  15. Structural Variations highConfidenceJunctionsBeta*.tsv cgatools junctiondiff exclude repeats >= 100 kb 86 translocations both ends within named genes 23 translocations (12 in CC0996 and 11 in E8413) 21 translocations validation assays with Sanger sequencing

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