Common Mutations Drive 12 Different Cancer Types

Cancer types from leukemia to breast cancer, and bladder cancer to lung cancer are all driven by a common set of genes containing driver mutations. Researchers from The Cancer Genome Network (TCGN) sequenced and analyzed genomes of 3,281 tumors from 12 different cancer types and discovered 127 genes that were involved in the initiation or progression of these cancers. This research appears in the October 17, 2013, issue of the journal Nature. 

1000 Genomes, Clan Genomics and Cancer Biomarkers

The publication of human genome blueprint in 2000 was a great block party, summer Olympics coming to town, but the next morning saw most revelers picking up their drunken selves and going back to their old day jobs.  Some kept the flames burning by taking up more and more sequencing of whatever came their way labeled as a model organism.  The human genome blueprint was like a great idea which won a patent but still needed a lot of development work to morph into a cool product.

Post-human genome project

The launching of the 1000 Genomes Project in January 2008 was a true effort to translate the human genome blueprint into something that can really impact clinical practice and health care on a national scale.  The 1000 Genome Project was designed to sequence and catalog genetic variations from different ethnic groups across the globe.  The results of the pilot phase were published in Nature last year.

Webinar Report: Impact of Next Generation/Whole-Genome Sequencing on Companion Diagnostics

Biomarkers are increasingly part of pharmaceutical and clinical strategy.  By some estimates, the success rate of FDA approval of new cancer drugs is 75% if mechanism-of-action and predictive or prognostic biomarkers are clearly defined, whereas it is 25% without the biomarker information.  However, identifying new biomarkers for companion diagnosis (CDx) remains a challenge—the identification of KRAS-type biomarkers is rare, there is a double regulatory hurdle and revenue issues hamper pharmaceutical investment in this area.  Whole-genome sequencing is an important tool in the discovery of biomarkers. 

Diagnostic Trailblazers in San Diego Advancing CDx, PGx and PM Goals in Cancer

Yesterday, I attended a half day symposium on companion diagnostics (CDx) efforts in San Diego which was organized by the SABPA Science & Technology Forum.  CDx is the identification and detection of biomarkers to predict whether a drug will work or not in a given patient.  Two successful marketed products are HercepTest (marketed by Dako) for Herceptin and KRAS tests for Erbitux and Vectibix.  San Diego biotech has a rich history and deep investments in diagnostics.  This was reflected in the lineup of various talks.

Friday Grand Rounds: Russ Altman Introduces Pharmacogenomics Database PharmGKB

Every human cell, with two sets of 23 chromosomes, contains six-billion basepairs of DNA (or three-billion per haploid genome).  Of these three-billion genomic basepairs, each individual shares 99.7% with the rest of the humanity.  It is the three-tenths of a percent that determines the differences between all of us.  This tiny percent, nevertheless, comprises of about a million positions that not only make us unique individuals, but also determine how we respond to environment, succumb to certain diseases, or respond (or not) to certain drugs.  These single nucleotide changes, scattered all over the genome, are called single-nucleotide polymorphism (SNP, pronounced snip) - for example, I may have Adenine at position X, you may have C and my friend may have G at the same position.  Since the complete sequencing of human genome in 2003, the post-genomic goal has been, to answer how this 0.3% of genome determines phenotype.  Pharmacogenomics/Pharmacogenetics (PGx) is the study of how genetic makeup correlates to responses to various drugs.