Tag: whole-genome-sequencing

Which pharmacogenes have real prescribing evidence, what the GeneSight and PRIME Care trials found, and how to call the alleles yourself.

Pharmacokinetic genotyping of CYP2C19 and CYP2D6 has real clinical guidelines behind it. Panels that claim to predict which antidepressant will work do not. Here is how to get an accurate diplotype call from your own sequencing data.

A practical guide to DeepMind's AlphaGenome model: what it outputs, how to call the API on your own variants, and how to check its predictions.

A practical guide to running ANNOVAR on a personal whole-genome VCF: which databases to download, the exact table_annovar.pl command, how to normalize input, and how transcript choice changes the answer.

A working guide to genotype-guided drug response: which genes carry the signal, how to call star alleles yourself, and where arrays fail.

A step-by-step guide to going from FASTQ or CRAM to a filtered, annotated germline VCF on one human genome using BWA-MEM2, GATK4 HaplotypeCaller, and hard filters, with the failure modes that matter at n=1.

A technically specific guide to choosing a whole-genome test: what files you should demand, what coverage and platform choices change, and how to analyze the data yourself.

A technical walkthrough of pharmacogenetic star-allele calling from whole-genome data: which genes have real evidence, why CYP2D6 breaks most pipelines, and how to read a diplotype-to-phenotype report without over-trusting it.

A working pipeline for calling deletions, duplications, inversions, and insertions from your own short-read whole-genome sequencing data, including which callers to run, how to merge them, and how to judge whether a call is real.

A specific, opinionated toolchain for a single person's whole-genome, RNA-seq, proteomics, and CGM data: the tools we would run, the flags that matter, and the failure modes that silently corrupt results.

Psychiatric pharmacogenetics is mostly two genes, CYP2C19 and CYP2D6, plus two HLA alleles. Here is what the evidence supports, how to call those genes from whole-genome data with PharmCAT and Cyrius, and where the commercial panels overreach.

A survey of the labs selling pharmacogenomic testing, what their panels genotype, how strong the clinical evidence is, and how to reproduce (and extend) those calls from your own whole-genome data with PharmCAT, Cyrius, and Aldy.

In the US, most clinical genetic tests require a provider's order, but the requirement is procedural and there are several ways to satisfy it. Here is how ordering works, what to specify, and what files to demand back.

Pharmacogenetic testing predicts how fast you metabolize certain antidepressants. How to call the star alleles yourself, and where the calls fail.

A technical account of pharmacogenetic panels, whole-genome sequencing, and the files they produce: coverage requirements, star-allele calling, CYP2D6 copy number, and where prices land in 2026.

Pharmacogenomic testing resolves star alleles in about a dozen drug-metabolism genes and maps them to CPIC phenotypes. Here is what panels cover, why CYP2D6 is the hard part, and how to generate diplotype calls from your own sequencing data.

How to get pharmacogenomic (PGx) results at home, why sequencing beats the saliva-kit panels for most genes, and how to run PharmCAT, Aldy, and HLA typing over your own data without over-reading the output.

A technical guide to preventive genetic testing: which variants have actionable evidence, why sequencing depth and file format matter, and how to work with your own VCF without over-reading it.

A working guide to producing star-allele diplotypes and CPIC phenotypes from your own sequencing data with PharmCAT, Cyrius, and PyPGx, and to reading a commercial PGx report critically.

Whole-genome sequencing processed with PharmCAT and Cyrius gives you more pharmacogenetic information than any branded psychiatric panel, and you keep the data. Here is how to run it and what the evidence supports.

Pharmacogenetic testing reliably predicts how you metabolize a few dozen drugs, and says almost nothing about which antidepressant will work. Here is what the genes cover, how to call the star alleles yourself from whole-genome data, and where the calls break.

A technical comparison of PGx testing companies, what their panels genotype, where they fail on CYP2D6 and DPYD, and how to produce CPIC-grade diplotype calls yourself from whole-genome sequencing.

A plain answer to what a genome is, what whole-genome sequencing produces, and how to work with your own FASTQ, CRAM, and VCF files without fooling yourself.

Why genotyping arrays like 23andMe and AncestryDNA answer a narrow question, what whole-genome sequencing gives you instead, and how to work with the files yourself.

Pharmacogenomic panels like myDNA and GeneSight genotype a short list of variants and return a color-coded report. Here is what those genes do, how to call the same star alleles yourself from whole-genome sequencing, and where the evidence stops.