8 Whole Genome Sequencing Companies for Precision Health

Earlier this year, we picked apart the 23andMe stock offering for genetic testing. The financial picture looked stagnant, with 23andMe (ME) trying to build interest in the company’s FDA-authorized health insights and a subscription service that provides access to additional reports as they become available. As we noted in the article, the company’s most valuable asset is its genetics database. Pharmaceutical companies like GlaxoSmithKline (GSK), which invested $300 million in 23andMe about three years ago, can leverage the genetics data from millions of people to develop more precise therapeutics in areas like oncology and cardiovascular disease. But the genetic tests from 23andMe and other DNA companies only scratch the surface of what we can learn about hereditary conditions like cancer and heart disease. To see the whole picture, you need whole genome sequencing (WGS).

What is Whole Genome Sequencing?

The kind of genetic tests offered by 23andMe and others is usually referred to as genotyping, which looks for specific variations in genes across less than 1% of the human genome’s four-letter alphabet. Most of these direct-to-consumer genetic tests rely on single nucleotide polymorphisms (SNPs) to act as biomarkers to locate genes associated with disease. SNPs are sort of like typos that occur when a cell divides and copies its DNA to new cells. It’s these typos or variations that genetic tests can use to identify potential problems. But the tests are quite limited in scope. For example, 23andMe can only pick out three of the thousands of mutations in the BRCA genes associated with breast cancer

Illustration showing volume of data produced by whole genome sequencing versus genotyping.
Do you want the Cliff Notes of your genome or the encyclopedia set? Credit: Veritas Genetics

Whole genome sequencing, on the other hand, looks at all 3.2 billion base pairs (or 6.4 billion, depending on if you count both sets of chromosomes) in the human genome. As you might imagine, this provides a much bigger picture to identify genetic variations associated with disease. In the analogy above, genotyping is the equivalent of reading a short novel versus a 4,200-book library dedicated to your health. 

Whole Genome Sequencing Companies

It originally took 13 years and nearly $3 billion to sequence the first human genome. Today, it can be done for $1,000 or less in just a day using next-generation sequencing (NGS), which involves sequencing millions of small fragments of DNA in parallel. Illumina (ILMN) is the company that pioneered genome sequencing at scale, and its machines remain the gold standard, with the stock bouncing back strongly after falling at the end of last year

A number of genetic testing companies now offer whole genome sequencing by leveraging NGS technology (usually from Illumina) either directly to consumers or through healthcare providers. These tests provide a deep dive into a patient’s genetics. This not only enables doctors to treat disease through gene-editing, but empowers patients to potentially prevent disease by providing personalized insights into their genetic makeup. While genetics may predispose someone to certain chronic diseases like breast cancer, environment and lifestyle also play a role. The idea is that if we know where our genetic landmines exist, we can avoid them and live much longer lives.

Playing the Long Game

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That’s certainly the goal of the company topping our list – Human Longevity. We’ve been following the San Diego-based startup since 2014, largely because it was co-founded by leading geneticist J. Craig Venter. Founded in 2013, Human Longevity has raised $330 million from a host of big names, including Illumina, GE (GE), and Celgene, which was acquired by Bristol-Myers Squibb at the end of 2019. The company has struggled despite its pedigree as one of the top longevity companies in the biotech world. Human Longevity has developed a diagnostic platform it calls Health Nucleus, which uses whole-genome sequencing, brain and body MRI imaging, a cardiac CT calcium scan, metabolomics, advanced blood tests, and more, to provide health insights. 

Health Nucleus platform by the numbers.
We were never good at math, but that looks about right. Credit: Human Longevity

A 2020 study published in the journal PNAS showed that Health Nucleus provided “clinically significant findings associated with age-related chronic conditions.”

The Church of George

Another one of the world’s leading geneticists, George Church, is also a serial entrepreneur who has founded a whole bunch of genetics companies, several of which offer whole-genome sequencing.

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Founded in 2014, Veritas Genetics was the first company to break the $1000 barrier for whole genome sequencing. The Boston area startup has raised nearly $62 million from investors mostly based in Boston and China. The company’s genome interpretation engine uses its own machine learning tools, as well as Google’s DeepVariant, a deep-learning technology developed partly by Verily Sciences to reconstruct genome sequences. Veritas Genetics’ flagship product, myGenome, provides several different kinds of health insights. For example, there is a section of the report that identifies more than 59 genes deemed medically actionable that are associated with cardiovascular health, cancer, and metabolic health, among others. There are also sections devoted to genetic risks and carrier status for various genetic conditions, as well as offerings like traits and ancestry. And it’s now available for only $599, with a doctor’s authorization.

Offerings from Veritas' myGenome platform.
Credit: Veritas Intercontinental
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An offshoot of Veritas Genetics, Madrid-based Veritas Intercontinental was founded in 2018 and has separately raised more than $25 million, including a nearly $6 million Series A one year ago. In addition to whole genome sequencing, Veritas Intercontinental also delves into whole exome sequencing (WES), which is the portion of the genome involved in coding for proteins. Most known genetic mutations that cause disease occur in exons, so the company offers specific genetic tests for cancer. There’s even one that assesses risk for developing medical complications associated with COVID-19 infection. Veritas Intercontinental’s services portfolio also includes non-invasive prenatal testing (NIPT), a technique that analyzes DNA in the mother’s blood to determine if the child is the Antichrist at risk of genetic abnormalities. 

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Nebula Genomics is another George Church whole genomics company that we’ve covered before, most recently in our list of genomics startups that investors should watch. Founded in 2016, San Francisco-based Nebula Genomics has raised $4.3 million. It offers several tiers of tests, ranging from $99 for typical ancestry analytics to $999 for the whole shebang. The company differentiates itself by emphasizing privacy and security for its customers’ DNA by using blockchain to keep prying eyes away. Its most recent foray into fringe cutting-edge technologies involves non-fungible tokens (NFTs). More specifically, the company is auctioning the whole genome of its co-founder, professor Church. That’s got to be worth something, right?

AI and WGS for Cancer Detection

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Cancer is one of the primary targets of precision medicine today, and whole genome sequencing can help identify the numerous gene variants that put people at risk. A New York-based company called C2i Genomics goes further by leveraging WGS technology to track cancer progression from a liquid biopsy. Founded in 2019, the startup has raised $112 million, including a $100 million Series B in April. Based on technology developed at Cornell University and the New York Genome Center, C2i Genomics combines AI pattern recognition and whole genome sequencing to detect residual signs of cancer after a tumor has been removed. The company claims its test is 100X more sensitive than competing technologies. 

C2i Genomics platform.
Credit: C2i Genomics

C2i Genomics’ platform is cloud-based, leveraging existing genome sequencers anywhere on the planet, meaning the company can offer its WGS-based screens at any location in the world. The company is still in the clinical stage, as it continues to prove the technology.

WGS for Rare Diseases

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Founded in 2014 and based in the Boston area, Variantyx has raised $38 million in funding, including a $20 million Series C in March that included IBM (IBM). The startup calls its whole genome sequencing testing platform Genomic Unity, which focuses on rare inherited and neurological disorders. The brains behind the operation is something called Genomic Intelligence, which uses algorithms and Big Data to analyze and interpret the genomic data. Thanks to the new funding, the company plans to expand its WGS technology to tumor diagnostics.

Low-Pass Sequencing

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Founded in 2015, New Yawk-based Gencove has raised $6.2 million, including a $1.8 million Series A in March. The company is developing a type of whole genome sequencing called low-pass sequencing. Instead of sequencing a single sample multiple times as in WGS, numerous samples are sequenced less than once. It’s sort of the difference between today’s best high-resolution smartphone camera and a super cheap flip phone camera. In this case, the pixels required to create a comparable picture using the latter are added through a computational method called imputation. 

Screenshot of genomics data provided by Gencove.
Screenshot of genomics data provided by Gencove. Credit: Gencove

Gencove scientists published a paper earlier this year that claimed the company’s low-pass sequencing technique produced more accurate polygenic risk scores for coronary artery disease and breast cancer than Illumina’s Global Screening Array, a tool for genetic risk screening of large global populations. In addition to humans, Gencove is developing its low-pass WGS for industrial-scale applications, including identifying genetic variations in livestock and pets. 

Whole Genome Sequencing as SaaS

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Founded in 2016, Dante Labs is a whole genomics sequencing company based in the UK. It has raised an undisclosed amount of funding since 2018, including a mystery Series A in 2019. The company offers both clinical and consumer WGS testing through its Immensa platform, which uses “machine learning to advance the interpretation of the human genome with every analysis.” It has performed more than 30,000 whole genome sequences to date using a software as a solution (SaaS) model. The company recently acquired another UK startup called Cambridge Cancer Genomics, which had raised $8 million for its machine learning platform focused on applying genomics data to precision cancer treatment. The plan is to combine their technologies to develop an end-to-end, genomics-based diagnostics platform for oncology.

Overview of Dante Labs.
Overview of Dante Labs. Credit: Dante Labs

Like other WGS companies, Dante Labs has also pushed into COVID-19 testing and analysis. Earlier this year, it invested more than $40 million to run a global surveillance program to identify new variants of the SARS-CoV-2 virus.

Conclusion

The breadth and depth of this list of whole genome sequencing companies really illustrates how close we are to fulfilling the promise of the Human Genome Project that was completed less than 20 years ago. We can now sequence whole human genomes for less than $1,000. That enables us to identify genetic variants that pose a risk to our health at scale, leading to precision health solutions in oncology and more. Not to mention gene-editing techniques will soon be able to edit out bad mutations, potentially prolonging our lives, which comes with its own risks and opportunities. Whole genome sequencing is definitely an area investors should continue to monitor.

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