Basic Information
This is a experiment guidence.
Databases
- ClinVar
- annotate with existing data
- big (a large amount of data)
- ClinGen
- expert reviewed annotation
- more precise classification
- relatively small (compared with ClinVar)
- ExAC(exon) & gnomAD(whole genome)
- intergred
- ExAC contain data more than gnomAD
- population data, got allele frequence (not variant data)
- input a group of variants, then they can help defining common variants, rare variants
- Focus on interest gene
- MARRVEL
- Interface that integrate various databases
- HGMD
- Disease mutation, demaging mutation …
- Mutation Classification
- GDC
- Data Portal
- dataset of TCGA
- Cancer
- 权威
- ICGC Data Portal
- Data Portal
- Cancer
- 权威
- COSMIC
- DataBase
- from ICGC, GCD, Text mining, other research lab
- data processing
- cancer census gene, cancer cell line
- Statistics and Classification
- CGI
- integreate multiple databases
- discover cancer driver mutation
- 肿瘤异质性 (在这个sample是driver mutation, 另一个sample就不一定是)
- most are rare mutation (appear only once)
- CIVIC
- Clinical, Precision Medicine
- According to Drug Treatment
Annotation Tools
- ANNOVAR
- powerful
- TransVar
- ID Mapping
- OpenCRAVAT
- integrate existing db/tool
- GDC Data Transfer Tool
- GTEx Portal
- 表达
- PMKB
- annotation
- integrate multi db 可以学习其是如何整合多方数据
- VarSome
- need user’s knowledge to inteperate results
- REVEL
- VEST4
- DEOGEN2
- PrimateAI
- dbNSFP
- V4.0
- used by annovar
- keep update
- all human genome possible mutation
- CHASMplus
- ParsSNP
- MutaGene Bscore (non-training)
- MutPred2
- MutFunc
- Interactome INSIDER
- G2S
- PhyreRisk
Q1
Assuming that you are given a data set of human genome exon-sequenceing data, which tools that you have learned during the courses can you use to perform analysis?
- Collect mutation data via some mutation discovery tools
- Crude classification of the mutations and choose corresponding tools
- Annotate these mutation via gnomAD, Annovar etc.