On DNA Testing

Dated Sep 18, 2018; last modified on Thu, 02 Sep 2021

The human genome has sequences of nucleotide base pairs that are repeated over and over again. At each locus of interest, a person has two sets of repeats inherited from each parent. Each possible difference at a locus is an allele. The combinations of the possible differences at multiple loci form a DNA profile that can be used to tie suspects to a crime scene.

The Accuracy of DNA Testing is Wanting

74/108 crime labs erroneously incriminated a suspect during a mock study. The reported match statistic for whether the match was coincidental varied over 100 trillion-fold.

There are methods (e.g. TrueAllele ) to reanalyze old DNA mixture data using software without the need for lab testing. This could help correct convictions made on faulty DNA tests.

Your genome isn’t private. Maybe it never was

Golden State Killer case, 2018: Investigators upload sample from 30-year old rape kit to GEDmatch, a genealogy site for finding relatives. Investigators then pieced out family trees, rough age and location down to a single man. Neither he or any of his immediate relatives had made their DNA public.

Given the increasing success of consumer genetics companies, 1 in 25 American adults is in some company’s database, anyone can track down your identity if they have access to your genetic info (think hair strand).

Furthermore, \(\approx\) 38 genetic variants give good predictions on facial structure.

Advancements in Genetic Sequencing (and the Role in COVID-19)

The advent of commercial genome sequencing is compared to the invention of the microscope. The National Human Genome Research Insitute invested $200m over 15 years in startups trying to lower the cost and raise the speed of whole-genome sequencing. Many failed, but Solexa’s optical sequencing technique proved successful, and was eventually absorbed into Illumina - the de facto leader in the industry.

The HIV genome has 10k letters. SARS-CoV-2 genome has 30k. The human genome has 3b. The seminal Sanger sequencing of the 1970s was labourious: ~35 base pairs in a year. Fast forward to 2010, and we could do 500k letters a day. And now, 3b pairs can be done overnight.

Illumina’s NovaSeq 6000s go for ~$1m a pop. In 2014, Illumina announced the $1k genome. In summer 2020, the sequencing cost for a genome was $600. Oxford Nanopore also has an electrical-based (as opposed to optical) and portable, albeit less accurate sequencer.

In Jan 2020, a Sydney virologist, with the consent of the Chinese scientist, uploaded the COVID-19 genome sequence to virological.org . Teams from all over the world could analyze the sequences and upload new ones, and hypothesize mutations and spreads.

Genetic surveillance is a popular trend in the community. The idea is to monitor samples and then identify hidden pathways of transmission and curb the spread of infection.

References

  1. The Dangers of DNA Testing. Hampikian, Greg. Boise State University. https://www.nytimes.com/2018/09/21/opinion/the-dangers-of-dna-testing.html . Sep 21, 2018.
  2. Your genome isn't private. Maybe it never was. Tessa Alexanian. https://www.eastbaybiosecurity.org/blog/defcon-biohacking-genetic-privacy . 2018-09-19.
  3. Genome-wide mapping of global-to-local genetic effects on human facial shape. Claes, P.; Roosenboom, J.; White, J.D. Nature. https://doi.org/10.1038/s41588-018-0057-4 . 2018-02-19.
  4. Genome Sequencing and Covid-19: How Scientists Are Tracking the Virus. Gertner, Jon. https://www.nytimes.com/interactive/2021/03/25/magazine/genome-sequencing-covid-variants.html . Mar 25, 2021.