Since the year is drawing to a close, I went back and looked at my most popular posts on MassGenomics 2013. Because of my new responsibilities this year, I’d hoped to be able to post a new article once every two weeks. I barely made that goal: 26 posts in 2013, not counting this one. When I ranked these by page views (an inherently biased metric, but still a useful one) some trends quickly emerged.
Next-gen Sequencing in Practice
Perhaps unsurprisingly, the most popular articles concerned practical considerations and challenges for the next-gen sequencing community, including:
- False Positives from Next-Gen Sequencing, in which I discuss some of the common artifacts we encounter when applying NGS to the complex human genomes in large cohorts.
- Remaining Challenges of Next-Gen Sequencing, where I discuss some of the hurdles that still face investigators and bioinformaticians.
- Data Sharing, Embargo, and Big Science, my commentary on large-scale submission and embargo of sequencing data as part of “big science” projects.
The Role of Rare Variants in Human Disease
With NGS of large cohorts ramping up this year, there has been a growing recognition of the importance of rare variants (as well as common variants) in susceptibility to disease.
- Rare Variants in Human Disease, a review of the contribution of rare variation to both rare disorders and common disease.
- Genetics of Blindness: Inherited Retinal Diseases, an overview of many of the inherited forms of blindness including retinitis pigmentosa.
- Breast Cancer Susceptibility: The Role of Rare Variants, covering a PLoS ONE study of familial breast cancer
I attended two scientific meetings (ARVO and ASHG) this year, and wistfully followed a third (AGBT) via twitter. Here were my takes on their themes.
- Human Genetics: Emerging Themes from ASHG, my personal account of highlights from the American Society of Human Genetics meeting in Boston, MA.
- AGBT: Sequencing’s Debutante Ball or Déjà Vu, my remote account of the hype of the Advances in Genome Biology & Technology meeting this year, versus previous years.
Genetics Education and Policy
I tackled a few of the many community and ethical issues that are becoming more prominent as NGS becomes commonplace in research and clinical settings.
- Common Human Genetics Myths, where I dispel some of the common misconceptions about what’s heritable and what’s urban legend.
- Identifying Samples from Genomics Data, a summary of Yaniv Erlich’s “genome hacking” to identify CEPH sample contributors.
- Science Shutdown: The Government’s Impact on U.S. Research, which I wrote in appreciation of the important roles government employees play in our research.
Noncoding and Regulatory Variation
Although I’m a fan of exome sequencing, I’ve long championed the view that a significant portion of phenotypically-relevant variation lies outside the exons of protein-coding genes.
- Searching for Functional Noncoding Variation, an introduction to how and why we might identify important genetic variants outside of genes.
- Functional Validation of Genomic Discoveries, motivation and strategies for experimental confirmation of genetic/genomic findings.
- Functional Variation Uncovered by Transcriptome Sequencing, a demonstration of using RNA-seq to uncover regulatory variants.
Self-knowledge and Shameless Self-Promotion
Lastly, I offer you some fodder for New Year’s Resolutions: starting your own research-oriented blog, and the benefits of personal genetics testing with 23andMe.
- How and Why to Start a Science Blog, a crash course in setting up your own platform for writing about your research.
- Personal Genetics: Sending Off for 23andMe Genotyping, my foray into personal genetics with 23andMe’s service.
- Personal Genetics: Risk Alleles from 23andMe, about the risk alleles included on 23andMe’s custom chip, and how they present the information.
- Tracing My Genetic Ancestry with 23andMe, in which my genetics pretty much matched my genealogy.
I wish all of you a safe and productive 2014!