In 2016, the PLOS Genetics Research Prize was awarded to Naranjo, Smith et al., for their work on a complex trait adaptation. Hunter Fraser, the corresponding author of the winning article and Associate Professor at Stanford University, tells us about the challenges he faced bringing the research to fruition and what winning the prize meant to him.
I was thrilled beyond words to start my job as an Assistant Professor in 2009. The previous two years had been tough—I had been fired from a postdoc position and then laid off from an industry job just 18 months later—so I was eager to turn things around. I was bursting with ideas for how to study the evolution of gene expression, but was missing just one ingredient: data.
During my ill-fated postdoc, I had devised an approach to use allele-specific gene expression data to identify lineage-specific selection on gene expression (see our paper’s Introduction for details). I wanted to use high-throughput sequencing of cDNA from inter-species hybrids for this, since sequence reads overlapping with heterozygous genetic variants (of which there are many in hybrids) could be used to measure the mRNA level of each allele. However, my advisor did not believe this would work, as this was before any publications of high-throughput cDNA sequencing (now known as RNA-seq). Without his support, I was unable to collect the data I so desperately wanted, and moved on to an industry position soon after that.
Fast forward to 2009: After being laid off in a “corporate restructuring,” I was chomping at the bit to start my faculty position. Things went slowly at first—I was busy buying equipment, writing grants, meeting new colleagues, and searching for my first lab hire, so those allele-specific expression (ASE) data I needed were still just a tantalizing mirage. However, I was overjoyed when I came across a paper (Tirosh et al., Science 2009) that generated exactly the type of ASE data that I wanted, from…