README.md

1. AACR Project GENIE

   

   AACR Project GENIE:https://www.synapse.org/#!Synapse:syn7222066/wiki/405659

   Suehnholz S P, Nissan M H, Zhang H, et al. Quantifying the Expanding Landscape of Clinical Actionability for Patients with Cancer[J]. Cancer Discovery, 2023.

2. GDC DNA-Seq analysis pipeline

   DNA-Seq analysis is implemented across six main procedures

   Genome Alignment
   Alignment Co-Cleaning
   Somatic Variant Calling
   Variant Annotation
   Mutation Aggregation
   Aggregated Mutation Masking
   

3. Menzel M, Ossowski S, Kral S, et al. Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients[J]. NPJ Precision Oncology, 2023, 7(1): 106.

   

4. Cortés-Ciriano I, Gulhan D C, Lee J J K, et al. Computational analysis of cancer genome sequencing data[J]. Nature Reviews Genetics, 2022, 23(5): 298-314.

5. Schwartzberg L, Kim E S, Liu D, et al. Precision oncology: who, how, what, when, and when not?[J]. American Society of Clinical Oncology Educational Book, 2017, 37: 160-169.

6. FoundationOne 与MSK-IMPACT资料

   FoundationOne CDx.pdf De novo request for evaluation of automatic class III designation for the MSK-IMPACT.pdf MSK-IMPACT数据库 MSK-IMPACT数据分析Pipeline Chalmers Z R, Connelly C F, Fabrizio D, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden[J]. Genome medicine, 2017, 9: 1-14. Cheng D T, Prasad M, Chekaluk Y, et al. Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing[J]. BMC medical genomics, 2017, 10(1): 1-9. Zehir A, Benayed R, Shah R H, et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients[J]. Nature medicine, 2017, 23(6): 703-713.

7. somatic机器学习

8. Example of Hierarchy of Evidence of Genomic Alterations