18 posts
How to use R and Bioconductor as the annotation, statistics, and integration layer for a personal molecular dataset: VCFs, RNA-seq counts, proteomics, and continuous glucose data, with the parts you should not do in R.
A technical account of the privacy properties of consumer and clinical DNA testing: what data exists, who holds it, what re-identification attacks work, and a concrete setup for keeping your own sequence data under your control.
Genetic Genie's methylation panel reads about two dozen genotypes out of a consumer array file. This guide shows how to extract and verify those calls yourself, what they can and cannot tell you, and how to measure actual DNA methylation if that is what you were after.
Pharmacogenomic panels marketed for ADHD medication selection rest on thin evidence for stimulants. Here is what the genotypes predict, which variants have real pharmacokinetic support, and how to extract them from your own sequencing data.
How to run a genome-wide association study in R end to end, from VCF to QC to association testing to polygenic scores, and what you can and cannot do with a single genome.
HIPAA compliance is a property of the entity holding your data, not of a sequencing assay. Here is what HIPAA does and does not cover for genetic data, what to read in a lab's contract instead, and how to take custody of your own FASTQ, BAM, and VCF files.
Dehydration concentrates plasma by a few percent, which is far too small to explain most ALT and AST elevations. Here is what usually causes them, how to draw a clean measurement, and how to read enzymes against your own genomic and proteomic baseline.
A practical comparison of Oxford Nanopore, Illumina, Element, PacBio, and Sanger for sequencing one person's genome: why we would choose nanopore long reads, what to ask a provider for, and the pipeline we would run on the output.
A FoundMyFitness report is a literature annotation layer on top of a consumer genotyping array. Here's how to audit the underlying file, rebuild the analysis yourself, and understand where array data runs out.
A working guide to the free DNA upload sites worth using, what each one does with your file, and how to run the same annotation, polygenic scoring, and relative-matching analyses yourself on your own machine.
A step-by-step method for pulling rs1801133 and rs1801131 out of a 23andMe, AncestryDNA, or WGS file yourself, getting the strand right, and understanding what the result does and does not tell you.
A working guide to interpreting raw genotype files from 23andMe or Ancestry, converting them to VCF, annotating variants, and knowing where array data stops being useful.
A working guide to taking a 23andMe/Ancestry export or a whole-genome FASTQ, converting it to an annotated VCF, filtering it sensibly, and knowing which results are real.
A technical account of whole genome sequencing as a data product: coverage and chemistry, file formats, a pipeline we would run, and the questions a genome can and cannot answer.
Celebrate World DNA Day on April 25. Learn its history, significance, and get ideas for your lab to engage with the future of DNA engineering and genomics.
Explore next generation DNA sequencing technologies. Learn about platforms, workflows, and selection criteria for biotech & pharma R&D applications in 2026.
Get a comprehensive whole exome sequencing review for R&D teams. Explore WES methodology, bioinformatics, limitations, & data integration with models.
An overview of how in-silico approaches are accelerating the drug development pipeline, reducing costs, and improving success rates in clinical trials.