How to sequence your own DNA at home

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I have now sequenced my own genome 5 times with an Oxford Nanopore Technologies MinION. This means collecting them from a swab, prepping them for sequencing, running them through a sequencer, then doing analysis over them.

Cheek cells are easily accessible and replenish pretty quickly. They are not used for cancer diagnosis, inflammation, or what genes are being activated in other parts of the body (like if you have hives on your chest and want to test what genes are being expressed in the cells that are inflamed), since you would want to collect the cells having problems and compare them against other normal versions of those cells.

To sequence the cells, I bought lab materials and consumables to sequence my own genome at home. It took me about two months to get everything together to do a full end to end high quality run. Likewise, the costs are still out of reach for the average person but they are decreasing (exponentially!) and we will eventually have affordable technology, like a cell phone or AI, telling us about our DNA + RNA expression real-time.

What can I even do with my own genome?

Before we actually spend all this time and money on sequencing, what can we actually do with our genome? The genome is not magic by itself - it is the reference layer. Once I have a VCF, I can run it through tools like VEP, ClinVar, gnomAD, PharmGKB (highly recommend), Gene Inspector, or Claude, and start asking:

• Which variants do I have?
• Which genes and pathways are affected?
• Which medicines might I metabolize differently?
• What rare variants should I take seriously?
• Where does the model know nothing yet?

This last part matters - the information produced is not yet diagnosis-level, and it is definitely not "edit yourself with CRISPR because an AI said so." The near-term value is turning a static genome into something queryable, but the "edit yourself with CRISPR" will most likely follow. DNA is the stable reference, RNA is the current state, and we will eventually integrate all biosensor data into one 'model' of yourself.

Here are a list of links and Twitter posts to help:

• Genetic variants from first principles: TLDR these genes, and the combinations of them, compound into real physical diseases. We will probably map these in the next decade
• Pass your genome + RNA to any of these models: https://www.biotender.online/bio-model-install-guide/
• Give your genome to Claude Code - message me if you want me to set this up for you
• Take it to a doctor if you metabolize particular drugs differently
• Patrick Collison post on using agents to talk to his genome

Protocol Steps

This is intended to be read by AI - please just copy and paste the URL of this and have ChatGPT walk you through it. If you have AR glasses, even better, since the AI can walk you through the whole protocol.

Hardware

• Oxford Nanopore Technologies MinION ($7.5k)
• Laptop/workstation for MinKNOW (any PC should be fine)
• 100GB+ storage for outputs
• GPU for Dorado basecalling
• Vortex ($50)
• Heat block ($250)
• Centrifuge ($400 used on eBay)

Consumables

• SQK-LSK114 Ligation Sequencing Kit V14 for DNA
• EXP-WSH004 Flow Cell Wash Kit
• EXP-CTL001 Control material
• PBS 1x
• Isohelix Buccal swabs

Reagents

• DNA extraction kit - NEB Monarch HMW DNA Extraction Kit for Cells & Blood ($87 for 5 runs)
  • Nuclei Prep Buffer
  • Nuclei Lysis Buffer
  • RNase A
  • Proteinase K
  • Precipitation Enhancer
  • DNA Capture Beads
  • gDNA Wash Buffer
  • Elution Buffer II
  • Bead retainers / Monarch collection parts from kit
• DNA library-prep reagents - NEBNext Companion Module v2 / repair-end prep reagents ($760 for 24 reactions)
  • FFPE DNA Repair Buffer
  • FFPE DNA Repair Mix
  • Ultra II End-prep Reaction Buffer
  • Ultra II End-prep Enzyme Mix
  • NEBNext Quick T4 DNA Ligase
  • Oxford Nanopore SQK-LSK114 ($720 for 6 reactions)
  • Long Fragment Buffer / LFB
  • Elution Buffer / EB
  • Ligation Adapter / LA
  • Ligation Buffer / LNB
  • Sequencing Buffer / SB
  • Library Beads / LIB
• Flow cell priming reagents
  • Flow Cell Flush / FCF
  • Flow Cell Tether / FCT
  • BSA
• AMPure XP beads
• 80% ethanol
• Nuclease-free water ($32 for 25mL)
• DNA quantity measurement
  • Qubit fluorometer
  • Qubit dsDNA BR or HS Assay Kit

Bench equipment

• Microcentrifuge
• Vortex mixer
• Heat block / dry bath
• Magnetic rack for 1.5/2 mL tubes
• Tube racks
• Ice bucket / cold block
• Freezer at -20°C
• Fridge at 4°C
• Pipettes

Plastics / Lab Pro-style consumables

• Sterile flocked cheek swabs
• 1.5 mL microcentrifuge tubes
• 2.0 mL microcentrifuge tubes
• DNA LoBind 1.5 mL tubes
• RNA LoBind tubes
• 0.2 mL PCR tubes
• Qubit assay tubes
• Pipette sterile filtered tips
• Wide-bore P200 tips
• Tube labels / lab marker
• Gloves

Software stack

• MinKNOW
• Dorado
• minimap2
• samtools
• mosdepth
• NanoPlot or pycoQC
• Clair3
• DeepVariant, optional
• Ensembl VEP
• ClinVar
• gnomAD
• PharmGKB
• dbSNP, optional
• Python/R
• SQLite/Postgres for query layer later

End-to-end DNA sequencing protocol

The goal is to go from 2 cheek-swab samples → MinION sequencing.

0. Setup

• Gloves on.
• Clean bench.
• Label tubes: Cheek sample, Extracted DNA, End-prep, Ligation, Final library, Priming mix, Loading mix
• Bring AMPure XP beads to room temperature.
• Keep enzyme mixes cold.
• Set heat block to 56°C.
• Keep Nuclei Prep Buffer cold.
• Confirm gDNA Wash Buffer already has ethanol added.
• Confirm you have isopropanol for DNA binding.
• Confirm you have fresh 80% ethanol for AMPure cleanup.
• Confirm you have the corrected ONT reagents:
  • FFPE DNA Repair Buffer v2
  • FFPE DNA Repair Mix
  • N-Prep Enzyme Mix
  • Salt-T4 DNA Ligase
  • LNB
  • LA
  • LFB
  • EB
  • SB
  • LIB
  • FCF
  • FCT

1. Collect cheek cells

Goal: get as much cheek-cell material as possible into PBS.

• Rinse mouth with water.
• Wait 10 minutes.
• Do not brush teeth.
• Do not use mouthwash.
• Scrape inside cheek firmly for 60 seconds.
• Add 1 mL cold PBS to labeled tube.
• Put swab head into PBS.
• Vortex 10 seconds.
• Press swab against tube wall to squeeze liquid out.
• Remove and discard swab.

What good looks like: PBS may look slightly cloudy.

2. Pellet cheek cells

Goal: concentrate cells and remove excess PBS.

• Spin at 2,000 × g for 30 seconds.
• Look for a small white/off-white pellet or smear.
• Remove most PBS with P1000.
• Remove more PBS carefully with P200.
• Leave 50–100 µL above the pellet.
• Flick gently to resuspend the pellet. Do not aspirate the pellet.

3. Prepare Monarch lysis solutions for one sample

Nuclei Prep Solution

• 165 µL Nuclei Prep Buffer
• 5.5 µL RNase A

Mix gently. Keep cold. You will use 150 µL.

Nuclei Lysis Solution

• 165 µL Nuclei Lysis Buffer
• 11 µL Proteinase K

Mix gently. Keep at room temperature. You will use 150 µL.

The extra volume is intentional so pipetting error does not leave you short.

4. Lyse cells

Goal: break open cells and digest proteins while preserving long genomic DNA.

• Add 150 µL Nuclei Prep Solution to the resuspended cheek-cell pellet.
• Pipette up/down gently 10 times.
• Incubate 2 minutes at room temperature.
• Add 150 µL Nuclei Lysis Solution.
• Invert tube gently 10 times.
• Do not vortex.
• Incubate at 56°C for 10 minutes.

What good looks like: The liquid may become more viscous. Do not vortex after lysis. At this point, the priority is preserving high molecular weight DNA.

5. Bind DNA to Monarch capture beads

Goal: precipitate genomic DNA onto the large Monarch capture beads.

• Add 75 µL Precipitation Enhancer.
• Invert gently 8–10 times.
• Add 2 DNA Capture Beads.
• Add 275 µL isopropanol.
• Invert slowly 30 times.
• Do not vortex.

Important: The beads now carry the DNA. Do not lose the beads. Do not use ethanol here.

6. Wash DNA-bound beads

Goal: wash contaminants away while keeping DNA bound to the capture beads.

• Let beads settle briefly.
• Remove liquid carefully without removing beads.
• Add 500 µL gDNA Wash Buffer.
• Invert gently 2–3 times.
• Remove wash buffer carefully.
• Add another 500 µL gDNA Wash Buffer.
• Invert gently 2–3 times.
• Remove wash buffer carefully.
• Remove as much residual wash as practical without touching or removing beads.

Critical: gDNA Wash Buffer must already have ethanol added.

7. Elute genomic DNA

Goal: release purified genomic DNA from the Monarch capture beads.

• Put bead retainer into Monarch collection tube.
• Transfer/pour beads into the retainer.
• Pulse spin ≤1 second.
• Move beads to a clean Monarch tube.
• Add 100 µL Elution Buffer II.
• Incubate at 56°C for 5 minutes.
• Put bead retainer over a clean DNA LoBind tube labeled "Extracted DNA".
• Transfer eluate + beads into bead retainer.
• Spin at 12,000 × g for 30 seconds.
• Keep the eluate.

The eluate is the purified genomic DNA. Do not discard the eluate.

8. Measure quantity of DNA with a Fluorometer

Goal: measure whether there is enough DNA to justify ONT library prep.

Use: 1x dsDNA High Sensitivity. Do not select the older non-1X dsDNA HS workflow if using the premixed 1X reagent.

Standards

• Standard #1: 190 µL 1X dsDNA HS working solution + 10 µL Standard #1
• Standard #2: 190 µL 1X dsDNA HS working solution + 10 µL Standard #2

Sample, first attempt

• 198 µL 1X dsDNA HS working solution + 2 µL DNA

On Qubit, enter: Sample volume = 2 µL

If too low
Use more DNA in a fresh Qubit tube:

• 190 µL 1X dsDNA HS working solution + 10 µL DNA

On Qubit, enter: Sample volume = 10 µL

Do not just add 8 µL to the old 198 + 2 tube, because that makes 208 µL total and breaks the assay math.

Record:

• Genomic DNA concentration:
• Remaining DNA volume:
• Estimated total DNA:

Calculate: total DNA ng = Qubit concentration ng/µL × remaining volume µL

Pause point
This is the best place to pause. For a same-day break: Store extracted DNA at 4°C / fridge.

Before storing:

• Make sure the DNA is in a clearly labeled DNA LoBind tube.
• Quick spin.
• Do not vortex.
• Close tube tightly.
• Put it in the fridge.

Resume at Step 10.

9. Prepare DNA input for repair/end-prep

Goal: prepare 47 µL DNA input. Ideal target: 1,000 ng DNA in 47 µL.

Calculate:

• DNA volume needed = 1000 ng / Qubit concentration ng/µL
• Then: water volume = 47 µL - DNA volume

If the DNA is too dilute and 1,000 ng cannot fit into 47 µL, use the maximum possible volume:

• 47 µL extracted DNA
• 0 µL water

For the first low-input run: 0.296 ng/µL × 47 µL = ~13.9 ng DNA. That was far below the recommended input, but useful as an end-to-end practice run.

10. Repair / end-prep

Goal: repair DNA and prepare the ends for adapter ligation.

Use the actual v2 reagents:

• FFPE DNA Repair Buffer v2
• FFPE DNA Repair Mix
• N-Prep Enzyme Mix / Ultra II End Prep Enzyme Mix

Do not use Salt-T4 DNA Ligase in this step. It is used later.

If not using DCS, replace the optional 1 µL DCS with 1 µL nuclease-free water.

Reaction

• 47 µL DNA
• 1 µL nuclease-free water
• 7 µL FFPE DNA Repair Buffer v2
• 2 µL FFPE DNA Repair Mix
• 3 µL N-Prep Enzyme Mix
• Total = 60 µL

Steps

• Add 47 µL DNA to a 0.2 mL thin-walled PCR tube labeled "End-prep".
• Add 1 µL nuclease-free water.
• Add 7 µL FFPE DNA Repair Buffer v2.
• Pipette mix 10–20 times.
• Add 2 µL FFPE DNA Repair Mix.
• Pipette mix 10–20 times.
• Add 3 µL N-Prep Enzyme Mix.
• Pipette mix 10–20 times.
• Quick spin.

Incubate:

• 20°C for 5 minutes
• 65°C for 5 minutes

Then place on ice.

11. AMPure cleanup after repair/end-prep

Goal: clean the repaired/end-prepped DNA.

Input: 60 µL repair/end-prep reaction

• Resuspend AMPure XP beads until uniformly brown.
• Add 60 µL AMPure XP beads to the 60 µL reaction.
• Mix gently by pipetting 10 times.
• Incubate 5 minutes at room temperature.
• Put tube on magnet.
• Wait until solution clears.
• Remove and discard supernatant without touching beads.

Wash 1

• Keep tube on magnet.
• Add 200 µL fresh 80% ethanol.
• Remove ethanol.

Wash 2

• Add another 200 µL fresh 80% ethanol.
• Remove ethanol.

Dry

• Remove residual ethanol with P10/P20.
• Air dry briefly, about 30 seconds.
• Do not overdry.
• Do not let beads crack.

Elute

• Remove tube from magnet.
• Add 61 µL nuclease-free water.
• Resuspend beads gently.
• Incubate 5–10 minutes at room temperature.
• Put tube back on magnet.
• Wait until clear.
• Transfer 60 µL clear eluate to a clean DNA LoBind tube labeled "Ligation".
• Do not transfer beads.

12. Adapter ligation

Goal: attach ONT sequencing adapters.

Use the actual reagents:

• LNB
• LA
• Salt-T4 DNA Ligase

Reaction

• 60 µL repaired/end-prepped DNA
• 25 µL LNB
• 10 µL Salt-T4 DNA Ligase
• 5 µL LA
• Total = 100 µL

Steps

• Use a clean DNA LoBind tube labeled "Ligation".
• Mix LNB slowly by pipetting before adding. It is viscous.
• Add 60 µL repaired/end-prepped DNA.
• Add 25 µL LNB.
• Add 10 µL Salt-T4 DNA Ligase.
• Add 5 µL LA.
• Mix gently by pipetting 10–15 times.
• Do not vortex.
• Quick spin.
• Incubate 10 minutes at room temperature.

Before incubation, say/check: DNA, LNB, Salt-T4 DNA Ligase, LA.

Failure points:

• Forgetting LA = no sequenceable library.
• Forgetting Salt-T4 DNA Ligase = adapter ligation fails.
• Poorly mixed LNB = bad ligation chemistry.
• Vortexing = unnecessary DNA shearing.

13. Adapter-ligated library cleanup

Goal: remove free adapters, ligase, salts, and small fragments while keeping adapter-ligated DNA.

Important: This cleanup uses LFB, not ethanol.

Input: 100 µL ligation reaction

• Resuspend AMPure XP beads fully.
• Add 40 µL AMPure XP beads to the 100 µL ligation reaction.
• Mix gently by pipetting 10 times.
• Incubate 5 minutes at room temperature.
• Place tube on magnet.
• Wait until solution clears.
• Keep tube on magnet.
• Remove and discard supernatant carefully.
• Do not touch bead pellet.

Wash 1

• Add 250 µL LFB to beads.
• Remove tube from magnet.
• Gently resuspend beads by flicking or slow pipetting.
• Put tube back on magnet.
• Wait until clear.
• Remove and discard LFB.

Wash 2

• Add another 250 µL LFB.
• Remove tube from magnet.
• Gently resuspend beads.
• Put tube back on magnet.
• Wait until clear.
• Remove and discard LFB.
• Remove residual LFB with P10/P20.
• Do not overdry.

Elute

• Add 25 µL EB.
• Remove tube from magnet.
• Resuspend gently.
• Incubate 10 minutes at room temperature.
• Put