Genomic alterations in the RB pathway indicate prognostic outcomes of early-stage lung adenocarcinoma
Our lab utilizes whole-genome and whole-exome sequencing data from cancer patients to detect potentially interesting driver mutations involved in cancer progression. Recent efforts have included the world's largest genomic research into lung adenocarcinoma patients. By studying the prognostic effect of mutations from early-stage lung adenocarcinoma patients, we showed that patients with mutations in the RB pathway exhibited significantly higher mortality rate than patients without. The study proposed that mutations in the RB pathway could potentially serve as a useful biomarker for the diagnosis and treatment of early-stage lung adenocarcinoma.
(Global mutational landscape of the 170 lung adenocarcinoma patients (Choi et al. 2015))
WGS-based SNV/small indel discovery and analysis pipeline
Single nucleotide variants (SNVs) and small insertions/deletions (indels) have been shown to be the source of various genetic diseases. The accurate detection of SNVs and indels have been an important area of study for various research efforts on diseases and genetic conditions. Despite the various number of methodologies developed over the years for the detection of SNVs and indels, the lack of a standardized method in which the results can be integrated have presented difficulties. Currently, our lab is interested in combining and standardizing the many SNV/small indel detection pipelines as well as developing tools to better detect them from genomic data.
(Flowchart for discovery of SNV and small indel)
Developement of accurate somatic variation detection tool
Our lab is making efforts to develop an improved method for the detection of genetic variants in cancer genomics. Currently, tools such as Mutect and others have been developed but are still lacking in accuracy. Our lab is interested in improving the software algorithms in variant detection to develop an improved detection tool for the discovery of genetic variants.
(Schematic outline of somatic variant callling, plot by Dr. Yongdeuk Hwang)
References
1. Choi, S., Kim, H. R., Sung, C. O., Kim, J., Kim, S., Ahn, S. M., ... Baek, D. & Jang, S. J. Genomic alterations in the RB pathway indicate prognostic outcomes of early-stage lung adenocarcinoma. Clinical Cancer Research (2015).
2. Ahn, S. M., Jang, S. J., Shim, J. H., Kim, D., ... Baek, D., ... Choi, S., ... Kim, J., Kim, S., ... Kong, G. Genomic portrait of resectable hepatocellular carcinomas: implications of RB1 and FGF19 aberrations for patient stratification. Hepatology (2014)