Learn Basic Info

  • Biomarkers can be classified into four types: diagnostic, prognostic, predictive, and therapeutic

    Biomarkers can be classified into four types: diagnostic, prognostic, predictive, and therapeutic. A diagnostic biomarker allows the early detection of the cancer in a noninvasive way and thus the secondary prevention of the cancer. A predictive biomarker allows predicting the response of the patient to a targeted therapy and so defining subpopulations of patients that are likely going to benefit from a specific therapy. A prognostic biomarker is a clinical or biological characteristic that provides information on the likely course of the disease; it gives information about the outcome of the patient [14, 17, 18]. A therapeutic biomarker is generally a protein that could be used as target for a therapy [18].

    The above description comes from the paper: The following quto comes from the paper: Carlomagno N, Incollingo P, Tammaro V, et al. Diagnostic, Predictive, Prognostic, and Therapeutic Molecular Biomarkers in Third Millennium: A Breakthrough in Gastric Cancer. Biomed Res Int. 2017;2017:7869802. doi:10.1155/2017/7869802

  • Sample GenBank Record

    This page presents an annotated sample GenBank record (accession number U49845) in its GenBank Flat File format. You can see the corresponding live record for U49845, and see examples of other records that show a range of biological features.

    It describe a lot of basic concepts like: Locus, Sequence length, accession number and version and son on.

  • Standards - definitions, symbols, nucleotides, codons, amino acids (v2.0)

    Describe the the symble meaning used to reprent DNA, Potein…

    Such as NM_005465.7:c.*4943_*4946del, here NM_ means protein-coding RNA(mRNA) Here’s a new version of standards that used in HGVS:https://hgvs-nomenclature.org/stable/background/standards/

    Here’s also a good paper describe the standards : A beginner’s guide to mutation nomenclature using the HGVS recommendations

  • Ensembl Variation - Calculated variant consequences

    Based on the Consequences of the variant to check the impact.

Databases to Annotate the variants

  • CIViC

    You can use this website to check the Gene basic information and get the AMP/ASCO/CAP Category if this variant has this infor in the web. This web is aimed to create an open source that other people can use and share. And it alos has the API.

  • CKB

    You can use this website to check the variant evidence including the tumor type, therapy, guidlines, clinical trials. Illumina uses this database.

  • OncoKB

    OncoKB™ is a precision oncology knowledge base developed at Memorial Sloan Kettering Cancer Center that contains biological and clinical information about genomic alterations in cancer.

  • Genome Nexus

    Genome Nexus is free and available under an open source license. Genome Nexus is a resource that integrates annotations from multiple sources to help with the interpretation and annotation of genomic variants in cancer. It can be installed in a local environment or private cloud, and integrated with local resources

  • Cancer HotSpots

    This resource is maintained by the Kravis Center for Molecular Oncology at Memorial Sloan Kettering Cancer Center. It provides information about statistically significantly recurrent mutations identified in large scale cancer genomics data.

    Single residue and in-frame indel mutation hotspots identified in 24,592 tumor samples by the algorithm described in [Chang et al. 2017] and [Chang et al. 2016]

  • OncoTree

    Show the Tumor Types that is used by MSKCC. You can search the tumor types.

  • My Cancer Genome

    To check Biomarker and diesase associated clinical trials

ICGC Data Portal

It contains the gene profile

NIH resources

In NIH, some good resources that about:

  1. DNA-Seq analysis pipeline
  2. copy number variation (CNV) pipeline

If you have time, then it’s a good place to go through some basic concepts and workflow. The good point it that, it has the command line to tell you how to use the software.

How to install illumina bcl-convert software in Ubuntu

illumina has bcl-convert packages for centos. We have ubuntu OS. thus there is the solution to use the centos package in ubuntu.

rpm2cpio ./bcl-convert-3.9.3-2.el7.x86_64.rpm | cpio -idmv

- resource description for dbsnp and clinvar

- dbsnp resourec donwload

- clinvar resource donwload

对VCF的详细解释说明

生物星球

这里面的文章很不错，介绍了生物信息的相关知识，可以作为基因测序的知识入门。

生物星球-solid tumor 介绍

FDA drugs

This website contain the FDA drugs and biomarkers

PharmGKB website

This website contain detailed information about drug labeling. Need to read the infor in detail

How to define the Tier Level

Clinical Annotation Levels of Evidence