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1.
Figure 1

Figure 1. Exploratory integrative sequencing of tumors for personalized oncology. From: Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study.

A, The MI-ONCOSEQ study recruits cancer patients and provides up-front genetic counseling. Patients are tracked through a biospecimen and clinical database. B, A multi-disciplinary Sequencing Tumor Board was instituted including expertise in clinical oncology, genomics, bioinformatics, pathology, bioethics, and genetics. C, Clinically relevant timeframe from tumor biopsy to available results. D, Integration of whole genome sequencing (blue), whole exome capture sequencing for 1-2% of the genome (red), and transcriptome or messenger RNA sequencing (green). Each sequencing strategy can be integrated (bottom) for analysis of tumor aberrations including structural rearrangements, copy number alteration, point mutations, and gene expression.

Sameek Roychowdhury, et al. Sci Transl Med. 2011 November 30;3(111):111ra121-111ra121.
2.
Figure 3

Figure 3. Aberrations reported in Patient 4 (Melanoma). From: Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study.

Patient 4 is a 48-year-old woman with metastatic melanoma. A, Multiple skin metastases and sites of biopsy. B, Representative histology from skin biopsy demonstrates dermal proliferation of ovoid to spindle cells with frequent prominent nucleoli. C, Summary of mutations reveals an activating HRAS mutation and an ETS transcription factor (ELK1) mutation. Wildtype genes included BRAF, CKIT, MEK, and NRAS. D, Copy number landscape across chromosomes derived from whole genome and exome sequencing. E, Circos plot derived from whole genome sequencing depicts structural variations including deletions (green), interchromosomal (orange) and intrachromosomal (blue) rearrangements. F, RNA-seq data support a possible rearrangement involving CDKN2C, WIPI1, and FSHR, and is predicted to inactivate CDKN2C. G, Integrative analysis identifies the activating HRAS mutation.

Sameek Roychowdhury, et al. Sci Transl Med. 2011 November 30;3(111):111ra121-111ra121.
3.
Figure 2

Figure 2. Integrative sequencing of a patient with metastatic colorectal cancer enrolled on the MI-ONCOSEQ protocol. From: Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study.

Patient 3 is a 46-year-old man with metastatic colorectal cancer and the first patient enrolled. A, CT scan abdomen demonstrates liver metastases and biopsy site. B, Representative histology from liver biopsy demonstrates poorly differentiated adenocarcinoma and estimated tumor content 60-70%. C, Summary of genetic aberrations identified includes an activating point mutation of NRAS, an inactivating point mutation of TP53, and amplification of CDK8. Wildtype genes included KRAS and BRAF. D, Integrated copy number analysis based on exome and whole genome data. E, Amplification in region of chromosome 13q including CDK8 is displayed as estimated copy number based on integrative analysis of whole genome (green) and exome (orange) data. F, CDK8 is highly expressed based on RNA-seq compared with benign or other cancer samples. G, Schema shows integrative analysis used to identify activating NRAS mutation with number of variant reads on right. H, Schema of probable inactivating rearrangement involving PPP2R3B based on integrative analysis of RNA-seq and whole genome data.

Sameek Roychowdhury, et al. Sci Transl Med. 2011 November 30;3(111):111ra121-111ra121.

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