bioinformatician & genomicist, precision medicine
Are you a lefty? Well, I am. And so was my mom. And her father. AND our daughter. So I was curious to learn how rare genetic factors may contribute to the roughly 10% of us who are left-handed. As reported in GenomeWeb, researchers at the Max Planck Institute for Psycholinguistics in the Netherlands and [ ]
You probably heard that we are running out of static IPv4 addresses. Actually, we ran out in 2011! IPv4 provided 4.3 billion IP addresses, which is not enough to give everyone their own IP address. IPv5 suffered the same fate not enough IP addresses so, enter IPv6, which uses 128-bit addressing compared with IPv4’s 32-bit addressing. Instead [ ]
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 [ ]
After creating FASTQ files from my BAM data and learning how to use Terra, I was finally ready to run the Whole Genome Analysis Pipeline. This collection of workflows, called a workspace, contains the latest GATK Best Practices workflows for whole genome sequence (WGS) data, including pre-processing, germline short variant discovery, and joint variant calling. [ ]
This entry was cross-posted from Terra on April 28, 2021. In April, we celebrate Citizen Science Month, World Autism Day, and National DNA Day. In this guest blog post, all three events come together as KT Pickard, father of a young woman with autism, shares his family s story of personal genomics and citizen science. This past Sunday [ ]
[Update: 2021-01-10: Thank you for your interest in our book club. We are currently closed to new members, but you can watch and subscribe to our meetings on the Genomics in the Cloud Book Club channel on YouTube.] Introducing the Genomics in the Cloud Book Club, an online discussion group. Our 35+ members across 10 [ ]
In this post, I explain how I created FASTQ files from a BAM file using a utility called Picard (no relation, although I pronounce my name the same way). Background In 2014, my wife and I got genomed through Illumina s Understand Your Genome (UYG) program, now managed by Genome Medical. Subsequently, I crowdsourced the sequencing [ ]
In 2014, I uploaded my WGS data to the cloud and made it publicly available. In a previous post, I explained why I moved my WGS data from DNAnexus to Amazon. In this post, I explain the final step: attaching the S3 bucket to a web server. The goal was to replace the ftp server [ ]
Summary: My wife had breast cancer. These posts describe: 1) finding out, 2) genetic testing, 3) radiation therapy, and 4) an incidental finding in the APC gene. Incidental finding in the APC gene Great news! Six months have passed since Kimberly finished radiation therapy for breast cancer. Today, she had a follow-up diagnostic mammogram that [ ]
Summary: My wife had breast cancer. These posts describe: 1) finding out, 2) genetic testing, 3) radiation therapy, and 4) an incidental finding in the APC gene. Radiation therapy One month after surgery, Kimberly began radiation therapy, which is designed to reduce the recurrence of breast cancer after surgery by more than half. We met [ ]