Tag Archives: precision medicine

Paper: Multi-omics analysis of renal clear cell carcinoma progression

In August 2021, I joined Amazon Web Services (AWS) as an industry specialist, completing a personal, 12-year goal to work in precision medicine. At AWS, I work with leading-edge customers in areas such as cancer detection, disease diagnostics, clinical trials, population health, and drug discovery. All the cool stuff!

In our spare time, we wrote a paper to investigate how mRNA, microRNA, and protein expression levels change as kidney cancer patients progress to different disease stages.

Here’s the preprint abstract on medRxiv (Nov 2022):

Renal clear cell carcinoma (RCC), the most common type of kidney cancer, lacks a well-defined collection of biomarkers for tracking disease progression. Although complementary diagnostic and prognostic RCC biomarkers may be beneficial for guiding therapeutic selection and informing clinical outcomes, patients currently have a poor prognosis due to limited early detection. Without a priori biomarker knowledge or histopathology information, we used machine learning (ML) techniques to investigate how mRNA, microRNA, and protein expression levels change as a patient progresses to different stages of RCC. The novel combination of big data with ML enables researchers to generate hypothesis-free models in a fraction of the time used in traditional clinical trials. Ranked genes that are most predictive of survival and disease progression can be used for target discovery and downstream analysis in precision medicine. We extracted clinical information for normal and RCC patients along with their related expression profiles in RCC tissues from three publicly-available datasets: 1. The Cancer Genome Atlas (TCGA), 2. Genotype-Tissue Expression (GTEx) project, 3. Clinical Proteomic Tumor Analysis Consortium (CPTAC).

The code for this study is available on GitHub, and we are actively submitting the paper for peer review.


Today I joined All of Us, a research community of one million people to lead the way for individualized prevention, treatment, and care for, well, all of us. This project was previously known as the Precision Medicine Initiative.

Many of you know that our family has used whole genome sequencing to look for clues in our daughter’s autism. This blog shares that journey. I have also published peer-reviewed papers to explore the reasons why people share personal health information. Through this research, I am convinced that information sharing will contribute to a learning healthcare system to improve care and lower costs.

It just takes people like you and me to #JoinAllofUs and lead by example.




Big data: From medical imaging to genomics

KT & Kimberly Pickard

In 2006, a Scientific American article written by George Church, “Genomics for All,” rekindled my interest in genomics. I went back to school in 2009 to contemplate the business of genomic medicine, and celebrated my MBA by writing a Wikipedia entry for the word, “Exome.” I was hooked.

We started our odyssey by genotyping our family using 23andMe, and later my wife and I had our whole genomes sequenced. Realizing that genomics were starting to yield clinically useful information, we crowdsourced the sequencing of our kid’s genomes to look for genetic clues in their autism. We found interesting results, gave talks and wrote papers.


Along the way, I realized that medical imaging and genomics are highly complementary: genomics informs or identifies conditions, and radiology localizes them. Sarah-Jane Dawson pointed this out at a Future of Genomic Medicine conference in 2014.

DIY genomics, autism, and coffee on Mendelspod

I have been a long-time listener to the intelligent and informative podcasts on Mendelspod, a site that connects people and ideas in life sciences. (Most nights you can find me listening to Mendelspod while I do the dishes.) I tuned-in sometime in 2012 and created a mental map of the industry by listening to every podcast I could find. A steady diet of listening to the latest developments in the industry has allowed me to talk about genomics with ease at meetups, tweetups and conferences. (OK, going back to school helped, too.) Somewhere along the way I decided that I would do something worthy of being interviewed on the show.

Well, last week I got my wish when my interview was posted on Mendelspod. I talked about our crowdfunded family trio sequencing project, autism, and even “coming out” of the research closet after being invited to speak at a conference in China last year. We explored parallels between my career in medical imaging and the future of genomic medicine (more in this blog post).

We concluded the interview by talking about Genomics Coffee, a (now defunct) discussion group that met in San Francisco.

Many thanks to Theral Timpson and Ayanna Monteverdi, co-producers of Mendelspod, for their great show.

DIY Genomics at MindEx 2015

I recently presented results from our DIY genomics project at MindEx 2015 held at Harvard’s very Hogwarts-looking Sanders Theatre.

Hosted by the Mind First Foundation, this conference enabled participants in the Personal Genome Project to hear first-hand how their health data could be used in research, especially mental health research. The second day of the conference, the “PGPalooza,” let PGP participants directly interact with researchers to select projects of interest and have their questions answered immediately.

James Tao graciously edited this 25-minute video of my talk about family trio sequencing and autism:

Also, special thanks to Alex Hoekstra, co-founder of Mind First, for the invitation to this event.

Additional resources: Video Slides