Genome Diary

Purification of 4-year-old deceased relative hair DNA for Whole Genome Sequencing


With thanks to Samuel Benavides from Mingo.

On March 22nd 2017 we posted in Personal Genomics Zone a blog post that described our plans to sequence the genome of my aunt who passed 4 years ago. We mentioned that the purpose of this sequencing experiment was, to perform a direct-to-consumer Whole Genome Sequencing (WGS) of a deceased relative. To our knowledge, we do not know of other study trying to understand the extent to which the sequencing of a deceased relative can contribute to the understanding of the genomes of a family of living relatives. We are also interested in exploring the implications of sequencing the genomes of the deceased as a way of enriching and surmounting the current restrictions to access genome data. This is particularly relevant at this moment in the light of current disputes between the family of Henrietta Lacks (the unconsented donor of the well-studied HeLa cells) and the research community.

To sequence the genome of my relative we were able to retrieve 36 hairs from a comb. These hairs had naturally fallen hence the amount of tissue surrounding their roots would be reduced. In addition, the sample being at least four years old, some further DNA degradation was to be expected. An initial test was performed with hair from another living person. This preliminary test yielded 65 ng/μl of DNA, for a total of 20 μl.

On March 27th 2017, we performed the extraction of DNA from the my relative’s sample by selecting 7 of the 36 bulbs. We selected these bulbs ensuring the highest possible uniformity in colour and shape. After performing the extraction, we found that the DNA was very degraded, having obtained only 0.452 ng for a total of 16 μl, compared to the minimum of 500 required by our provider to perform WGS.

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Materials

  • Type of sample:
    • Capillary bulb (selected from the total of those provided by the user)
  • Amount of starting sample:
    • 7 capillary bulbs (0.5-1 cm in length taken from the bulb)
  • Positive extraction control:
    • 7 capillary bulbs (0.5-1 cm length taken from the bulb)
  • Extraction protocol:
    • Isolation of DNA from forensic samples (lysis and purification), performed with QIAcube extraction equipment (QIAGEN)
    • Processing samples on 4/17/2017
  • Recommended extraction kit:
    • QIAamp DNA Micro Kit (QIAGEN)

Results

Spectrophotometric

(NanoVue PlusTM)

Fluorimetric

(Qubit dsDNA HS)

Concentration (ng/μl)

Concentration (ng/μl) A260/A280 (Absorbance)
Relative’s Sample 53.5 3.057 0.452
+ Control 82.5 1.988 38.8

Table 1: Results from DNA extraction of 7 hairs from my deceased relative. Only 0.452 ng/μl are obtained from a total of 16 μl, which makes the total amount of DNA extracted >7ng.

The amount of DNA that we could isolate (in excess of 7ng) is clearly insufficient, hence we are going to perform PCR to amplify the DNA. We also found that the absorbance of the sample is higher than expected. We think that this is because the hairs were dyed. To ensure that the dye does not interfere with the PCR by inhibiting it, we are going to perform a separate PCR. After that, we will perform another PCR to reach the needed amount so we can proceed with WGS. If this amplification does not give us DNA of sufficient quality, we will perform a second extraction procedure with the remaining hair sample.

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