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Example Case

An example analysis of a DNA file

Recently someone shared their Sequencing.com DNA file with me along with permissions to do a writeup going over what we found in their DNA. Hopefully this writeup can serve as an example when investigating your own DNA.

DNA files

Sequencing.com DNA files contain a vcf, but not the index. Supposedly if you email support they will generate you one. Alternatively I used Genome Browse to generate it for me locally. (from
Sequencing.com Guide: How to Obtain TBI and BAI files : r/sequencing_com)

  1. Download and install Genome Browse (by Golden Helix).
  2. Open the app: Genome Browse.
  3. When prompted, select the genome: Homo Sapiens (Human) GRCh38 (Dec 2013)
  4. Go to File > Plot
  5. Select the folder with your dna file at the top of the “Add Data Sources” dialog
  6. In the Filter: select *, (Any type), (Any assembly)
  7. Select your downloaded VCF file
  8. Click “Plot & Close”
  9. Genome Browse will automatically create the appropriate index file (TBI for VCF, BAI for BAM) in the same folder as your original file.

Gene.iobio

With the VCF and index files use https://gene.iobio.io/ to explore the DNA file.

  1. Goto https://gene.iobio.io/
  2. Click Load your DATA
  3. Click “Choose files” next to the “Enter vcf URL”
  4. Select the foo.vcf.gz and the foo.vcf.gz.tbi files.
  5. Click LOAD

Estrogen Metabolism

These days I always look at CYP1B1 first to see what I

NCAH

They very much matched the phenotype of someone with NCAH having all the symptoms. In “Phenotype” I search for “congenital adrenal hyperplasia” CYP21A2 jumps right out with the following with rs7755898 C;T (Stop gain) or the nonclassic form of Congenital adrenal hyperplasia due to 21-hydroxylase deficiency - Wikipedia. They had several smaller variants associated with salt wasting, but I didn’t know if they were on the chromosome with the stop gain CYP21A2 or not, but overall very much confirms what symptoms, etc already were showing.