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April 30, 2019

Surfing into the genomic future

Filed under: Genetics,Genomics,Human Genome,human-genome-project — Razib Khan @ 7:16 am
The decline in cost per genome

Within genomics circles, the chart above illustrating the crash in sequencing costs since the year 2000 is famous. The reason it is famous is that it shows that genomic technology began to outrun the famous “Moore’s Law”, that computing power doubles every 18 months, around 2008.

The genomic revolution is arguably like no other information revolution of the 21st-century.

In 1983 there were 800 known genes with locations within human chromosomes. This is for all humans. The field of genetics had existed since the first decade of the 20th-century by this point. But the methods of the 20th-century were laborious, and not well suited to human genetics (we are a slow reproducing organism that one cannot experiment upon).

20th-century human genetics

Since the turn of the century, the sequencing of hundreds of thousands of human genomes has transformed our understanding of the landscape of inheritance. In 1983 scientists had no sense of how many genes humans had. They guessed 100,000, a suspiciously round number.

We now know that humans have 19,000 genes. We have also cataloged, more or less, all 3,000,000,000 positions in the genome. Genomics has finally allowed scientists to grasp the scale of variation among humans on the DNA level. To put a specific number to that variation (~100,000,000 polymorphisms), and assign specific places within the genome.

A “map: filled with “Here Be Dragons” has been transformed into something that one can perform a scientific GPS upon.

21st-century human genomics

Fundamentally the discipline of genetics has always been one of the transmission of information across the generations, but the emergence of “next-generation sequencing” (NGS) resulted in such a gusher of data that genomics and computer science have developed symbiotically in this century. For many researchers, the size of genomes is measured as often in computer memory as it is in base-length or classical recombination map-length.

But all of this fancy technology wasn’t developed so that computer scientists could work on interesting algorithms and data-mining techniques.

Though genomics has applications to basic science, as well as animal breeding and crop development, the original rationale for the Human Genome Project was to further the goal of human health and longevity. This promise has arguably been a disappointment. We have not won the war on cancer, nor has healthcare at the point-of-delivery been transformed.

But how likely were the promises in the first place? What could a single human genome tell us? Rather than be a pot-of-gold at the end of the rainbow, the first genome is more likely a map that points us to the future.

The growth of “personal” genomics

Many futurists contend that the transformative power of technology is often overestimated in the short-term, but underestimated in the long-term. Humans don’t anticipate what the broader market will respond to through reflection. Rather, there needs to be a trial and error process.

The internet exploded on the scene in the 1990s. It certainly transformed communication, but initial attempts to provide services and goods failed as the “dot-com bubble” collapsed. But the ashes of such failures gave rise to a whole new economy, which has transformed our lives in ways we can’t imagine account for. Remember anonymity before Google and social media?

The first decade after the first human genome saw little progress because it was fundamentally a blue-sky technology restricted to academic laboratories. The second decade of genomics has seen the explosion of the consumer market, from 100,000 users to 30,000,000 as of 2019.

Millions of consumers and dozens of companies means that the dynamic and adaptive power of the market will shape the future of genomics. The current “killer app” is genealogy, for fun and forensics. But as the whole American population gets whole-genome sequenced in the next generation the opportunities for personalization will open up. Instead of a single sequence, one can imagine consumers getting sequenced repeatedly over their lifetime, from different tissues, as healthcare professionals track the mutational arc of one’s life. And from the genome, consumer firms will explore the microbiome, the epigenome, and the transcriptome.

Information science will flood genetic science.

And once science becomes a technology, breaking out of the laboratory, the outcomes and changes can be unpredictable. Even protean.

In the years after 2000 what we would call “smartphones” existed, but they were luxury goods in the age of the “candy bar” and “flip” phone. The rivals to Apple were skeptical about the iPhone when it came out. But it turned out that the iPhone created an industry, and transformed many others (remember cheap digital cameras and paper maps?). Nevertheless, even Steve Jobs did not anticipate the proliferation of “apps”, and their centrality to the modern smartphone experience.

Apple’s ecosystem of applications developed organically, and its magnitude and importance were not anticipated. Jobs and his executive team clearly viewed the iPhone as a phone that had deluxe music functionality. As it turns out, Jobs had unveiled the next iteration of the computer! Today, a smartphone is really a computer with some phone functionality.

The genomic future likely will exhibit the same arc.

Genomics will transform our lives. That I can state with confidence. But how it will transform our lives, if I hazarded a guess I’d surely be wrong. History is more surprising than anything our imaginations can come up with.

Surfing into the genomic future was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

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