What’s the Answer? (clinical cancer genomics)

Biostars is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.

This week’s highlighted question sort of pairs with my post from yesterday about the cancer genomics challenge. Despite all the chatter about what will be possible with tumor sequencing, one of the Biostars community members wants to know what we really know, and what we’ve really seen so far on this topic for treating specific individuals. It’s a nice summary type of question that brings together a bunch of the knowledge from folks who are on the front lines and thinking/reading/working on this issue. Biostars works well in this type of chatter, kind of like an international lab meeting.

Forum: Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing

What papers are you aware of that attempt the following: (1) Whole genome, exome and/or transcriptome sequencing of (2) live patient tumor samples in an attempt to (3) guide clinical decision making for cancer. The omic events could provide diagnostic, prognostic or treatment response predictions. This approach is widely referred to as personalized medicine, individualized medicine, precision medicine, or precision oncology. There are many reviews describing this idea and many examples that make use of targeted panels (one to hundreds of molecular events). I’m looking for proof-of-principle papers, describing the paradigm where researchers (or tumor genome boards) attempt to use omic NGS data to alter or inform clinical care. These could be N-of-1 case reports or overviews describing experiences with small to large cohorts.

Here is a prototypical example in which an oral adenocarcinoma was sequenced by whole genome and transcriptome sequencing and analysis done to suggest a particular target/pathway for therapy that might not otherwise by considered in this disease type at the time. http://genomebiology.com/content/11/8/R82

[then the post is updated with many examples of the types of papers]

Obi Griffith

In a fast-moving area, with so much literature and/or data getting published in places that might be outside of the PubMed reach at this point, it’s a nice way to collect useful input. Go have a look at the ensuing discussion.