1. SNP and Genomic analysis SNP/genomic signature Clinical sampling Personalized chemotherapy Personalized Targeted therapy Personalized RNA therapy Personalized radiation therapy drugs Targeted molecules siRNA Labeling radiation Fig. 1

2. Higher expression of transcripts and SNVs in tumor RNA-seq (normal and tumor) Pairing DNA-sample (normal and tumor) WES (Tumor) Whole genomic DNA-Seq Captured exome for DNA-Seq Pairing RNA-sample (normal and tumor) WGS (Tumor) Fig. 2 ABCABC Initial materials NGS technique NGS database

3. FASTQ data input with IGenome Groomer With QC cut of 30 Tophat/ Tophat2 (38) QC report 2 files Cufflink Assembly transcripts Gene expression (FPKM) Transcript expression (FPKM) BWA GATK Add or replace groups (picard) (38) Fasta (hg19) Realigner target creator SAM filter (38) Rmsup () Variant calling variScan Add or replace groups () Mpileup with fasta VCF filtering and annotatopn Fig. 3

4. Targeted Fragment amplification PCR Strand displacement amplification Allelic discrimination reaction Primer extension Specific cleavage Ligation Pyrosequencing Allele specific product identification Mass spectrometry Electrophoresis FI/FRET/FP hybridization Fig. 4 ABCABC

5. A B Fig. 5

6. Gene targets SNVs combined with GES Global SNPs and SNVs Disease network data combined SNPs predicted gene expression combined SNVs Both transcriptome and SNVs Fig. 6 ABCABC Local SNPs detection SNP detection mining SNP signatures Gene targets

7. Targeted molecule In silico validation Ex vivo validation In vivo validation In vitro verification SNP confirmation Gene expression related SNP Indirect verification Direct validation Gene and SNPs signature indirect direct Fig. 7

8. A B Fig. 8