Nebula Genomics Review: What did we learn from our DNA sequencing?

With so many at-home DNA companies on the market offering the chance to discover your ancestors, potential health concerns, or even half-siblings or paternity relationships, the choice can easily become tedious. Nebula Genomics is changing how at-home DNA testing companies process the 20,000 genes that constitute the human genome.

By offering whole genome sequencing at an affordable price, Nebula Genomics offers the highest level of accuracy for genomic information obtained from a simple swab test.

We put their BASIC package to the test and check if their entry-level offer was up to par with their competitors and was worth the $99 asked for.

What is the history behind Nebula Genomics?

Nebula Genomics was initially incorporated in 2016 by three Harvard researchers: George Church, Dennis Grishin, and Kamal Obbad. The company has offices in San Francisco and Boston.

Pr George Chuch is a Professor of Genetics at Harvard Medical School and is considered a pioneer in “next-generation” sequencing and whole-genome sequencing. 

Financed by numerous Venture Capital funds, including Khosla Ventures, Arch Venture Partners, Fenbushi Capital, Mayfield, F-Prime Capital Partners, GreatPoint Ventures, Hemi Ventures, and Mirae Asset, the start-up rapidly became a major player in the at-home DNA test landscape, mainly due to their reasonably priced offer of whole-genome sequencing.

On August 11, Nebula Genomics was acquired by ProPhase Labs for $14.6 million, which seems like an excellent deal. ProPhase operated CLIA certified laboratories will process Nebula Genomics’samples, resulting in a faster turnaround and ultimately better prices for the clients.

By combining renowned founders, robust science, and the use of high throughout-top-of-the-line sequencers such as the MGI DNBSEQ-T7 DNA, the company changed how personal genome data is processed and handled. In addition, analyzing genetic mutations open the way to a better understanding of the genome.

What are the various tests offered?

Nebula Genomics offers three different types of tests depending on the completeness of the DNA sequencing, sequencing depth, and degree of details of the information provided.

BASIC

• Decode the most critical regions of the DNA,
• Sequencing depth of x 0.4 generating 2 gigabytes of data,
• Basic ancestry report relying on the autosomal DNA,
• Identification of the most common traits and mutations,
• A weekly update of the reports based on the latest scientific articles.

DEEP

• 100% of the DNA decoded
• 30x sequenencing depth (each base is read 30 times)
• Deep ancestry analysis (mitochondrial DNA, Y DNA, autosomal DNA). Processed by Family Tree
• Identification of rare mutations
• Access to Gene Browser and Gene Analysis
• Reports updated weekly

ULTRADEEP

• 100% of the DNA decoded
• 100x sequenencing depth (each base is read 30 times)
• Deep ancestry analysis (mitochondrial DNA, Y DNA, autosomal DNA). Processed by Family Tree
• Identification of rare mutations
• Access to Gene Browser and Gene Analysis
• Reports updated weekly
• Ready for diagnostics

What is the whole DNA test process and waiting time?

The DNA collection process is very standard. After ordering the test on the website, it takes a couple of days to receive the DNA test kit, including a sterile test swab, a collection including some stabilizing agents, a prepaid return envelope, and a simple form summarizing the instruction for collecting the DNA sample.

The first thing to do is to register the unique kit number on the Nebula Genomics website. It is then time to start the DNA collection process. It could not be easier.

After 45 seconds of cheek swabbing:

• Break the tip of the swab in the stabilizing agent vial.
• Put the vial in the envelope.
• Send it back to Nebula Genomic laboratory for sequencing and analysis.

The site claims that it takes between eight and ten weeks to receive the results, which is long. In our case, it took less than four weeks to get the results available on the website, which is a very reasonable timeline.

While waiting for the results, you can fill up surveys in the hope of helping science and also more selfishly to gain credits that can be used to buy tests at a discount.

The surveys are pretty broad and deal with specific topics such as: 

• Alcohol, 
• Basic information,
• Cancer,
• Diet,
• Fitness,
• Health,
• Nebula & EMD Serono study,
• Medications,
• Occupation,
• Rare diseases,
• Sleep,
• Smoking.

Combining answers to the surveys with the individual genetic data makes it possible to find new genetic correlations.

What can you learn from your genomic data?

To paraphrase Forest Gump, Genomic sequencing is just like a box of chocolate. You never know what you will discover. With 6.4 billion base pairs and 20,000 genes, the entire genome is a huge box of chocolate. 

Whole-genome sequencing allows gaining access to a flow of genetic variants that need to be organized. Thanks to the power of bioinformatics.

The reports we received from Nebula Genomics cover:

• well established genetic traits that define our appearance, personality, body, and nutrition,
• ancestry information,
• personalized DNA reports based on the latest scientific discoveries,
• gene analysis to identify genetic variants and mutations,
• genome browser to check the raw sequencing data.

For the Basic test we conducted, we only had access to the traits, basic ancestry information, and personalized DNA reports. So it was certainly enough as an appetizer but remained somehow limited.

Whole-genome sequencing is undoubtedly a better choice to get more information about the genetic variants and provide real value to personal genome sequencing.

Ancestry

The ancestry report that comes with the BASIC package is pretty rough as the world is only divided into 25 regions (East Asia, Northeast Asia, Southeast Asia, Central Asia, North-central Asia, Southern Africa, Western Africa, Central Africa, Eastern Africa, Northern Africa, Central India subcontinent, Southern India subcontinent, Oceania, Bengal, Eastern Mediterranean, Anatolia, Caucasus, Iranian Plateau, Middle East, Southwestern Europe, Northern Italy, Northeast Europe, Scandinavia, Finland, Northern, and Central Europe, Northern British Isle, Ashkenazi Jewish, and Americas). 

For the Americas, no distinctions are made between North and South America. 

Our test was conducted on my wife, who is Japanese. So you can imagine her deception when the results only stated that she was just from East Asia without any more details.

Genome sequencing has the potential to provide many more details about ancestry analysis. The Deep and Ultra Deep whole-genome sequencing packages make the most of the partnership of Nebula Genomics with Family Tree DNA to make the most of the most comprehensive family database available.

The 30x sequencing depth, meaning that the same region is read an average of 30 times for extra accuracy, offers an analysis of the Y chromosome DNA for exploring the paternal lineage and mitochondrial DNA for the maternal lineage, while the Basic sequencing only allows to scratch the surface with no real added value for those interested in genetic genealogy.

Traits report

The traits reports are much more informative than the ancestry ones.

They are divided into four categories are based on well-established genetic traits. Interestingly, the reports are regularly updated.

Appearance & Hormones

Only four variants were identified, including one for testosterone levels, which is surprising considering the DNA sample was from a woman.

We somehow learned that my wife was prone to dry earwax, freckles (which are rare in the Japanese population), and thick hair (which is true.)

Each trait characteristic can be expanded to learn more about the genes and variants supporting the results. We also appreciated the possibility of accessing the scientific paper on which the result is based. 

Behavior & Perception

Behavior and Perception variants are standards in DNA data analyses but add a bit of fun to what can become a dry report for non-genetic aficionados.

The genetic variants will provide information on:

• Alcool sensitivity
• Asparagus metabolite odor: Always interesting to know if you are genetically programmed to detect the smell of asparagus in urine.
• Caffeine use: An excellent excuse to have a second cup
• Cilantro preference
• Misophonia: Sensitivity to chewing sounds
• Nicotine response
• Pain sensitivity
• Snacking behavior: Another good excuse to treat yourself with snacks based on your personal genomic data.

Body & Athletism

The body & Athletism trait report will explore how your body will potentially react. In addition, a lot of genetic information is provided that may help the way you treat your body.

Genome sequencing will never provide black and white results. Most of the time, you will obtain a probability of developing a condition or the risk of developing a disease. 

The trait analysis is not different, and carrying a genetic variant for high blood pressure does not mean that you will systematically develop hypertension. Still, it means that genetically you may be more prone to a specific condition. 

Armed with this knowledge, it will then be up to you to treat your health and body in a way that will balance the genetic risks. In that sense, the data provided by Nebula Genomics carry much value, and it may help you treat your health more holistically.

The body & Athletism will concentrate on:

• Blood pressure
• Height
• Jimmy’s legs
• Longevity
• Muscle strength
• Muscle volume
• Nearsightedness
• Obesity
• Physical conditioning
• Skin Sensitivity
• Sleep depth

Nutrition & Diet

This trait report was exciting and amusing as it describes the potential taste for sweets or will detect genetically based food allergies or intolerance.

The report will provide information on:

• hunger response
• Lactose intolerance
• Sweet tooth
• Vitamin B12 levels
• Vitamin C levels
• Vitamin D levels

Nebula Library

The Nebula Library reports are probably what we think genome sequencing brings the most value. For just $99, we had access to a wealth of scientific knowledge. 

We received 272 personalized reports based on the latest scientific discoveries, detailing the percentile of the population we fail into for various disease risks or behavioral or physical inherited traits. 

New reports are also added daily based on the latest articles published, which means that your results will always be accurate and up to date.

It is easy to spend hours browsing through the data. The results can be sorted by polygenic score, showing the percentile in which we fell. Falling in the 100th percentile is a clear indication that you should pay attention.

As we mentioned, genetic testing results are a matter of probabilities, and personal genomic companies are always careful not to provide definitive answers, at least for DNA tests aimed at the public.

We learned a lot of exciting elements. For example, my wife has a 100% percentile genetic predisposition for being thin, having a high level of vitamin D, suffering from insomnia, being ambidextrous, and suffering from high blood pressure and high level of HDL cholesterol. 

The interface provides an easy way to sort the results using tags that will group the results in categories such as addiction, aging, alcoholism, allergy, appearance, autoimmunity, behavior, bladder, blood, bone, brain, breast, cancer, dementia, development, diet, eyes, gallbladder, heart, hormones, infection, inflammation, intelligence, intestines, joints, kidneys, liver, lung, metabolism, mind, mouth, muscles, nose, obesity, pancreas, pelvis, pregnancy, prostate, senses, sex, skin, sleep, spine, stomach, taste, thyroid, uterus, vasculature.

For the heart only, 23 reports were generated covering numerous elements from Atrial Fibrillation to cholesterol levels, cardiomyopathy, and PR interval. If you are interested in a specific topic, Nebula genomics provides an unprecedented way to analyze your data and know more about your genetic predisposition. 

Trait, SNP, or gene can even search the results of the DNA sequencing.

Each characteristic can be expanded to know more about it and check your personal data and variants. 

As an example, we downloaded the report on the genetic predisposition of my wife for high cholesterol. She doesn’t have high cholesterol, but her genetic makeup predisposes her to it. 

The whole list of variants is presented, with your genotype, effect size, variant frequency, and overall significance. The variants contributing positively to the effect are highlighted in green, while those negatively correlated are highlighted in blue. I can see myself spending hours digging into the genome sequencing data. On top of that, new variants and added as science progresses. DNA sequencing is just the first step-no need to be a geneticist to enjoy the presented reports and are easily understandable.

The Gene Analysis and Gene Browser are only available for the DEEP and ULTRADEEP analyses. We certainly regret not being able to have access to them.

Data sharing

Genomic data sharing is the main point of concern for privacy and healthcare cyberattacks. One of the strong points of Nebula Genomics is its concern with the privacy of the DNA data and the use of blockchain technology to protect your DNA test results.

Whole-genome sequencing produces a vast amount of data – up to 300 Gb for the Ultra-Deep analysis- that can be shared with your doctor or even with another company that can potentially detect mutations not included in the Nebula Genomics database.

Hence the DNA testing raw data can be downloaded in various raw formats compatible with your intended use: BAM, BAI, FASTQ, and VCF. Note that the larger dataset is only stored for 14 days. The DNA data is still available afterward, but it will require a maximum time of 48 hours to be prepared. 

Is the Nebula Genomics test worth it?

In this Nebula Genomic review, we hope to have convinced you that we enjoyed this genetic test. We tested the entry-level version, and even for just $99, we appreciated what we learned from this DNA testing kit.

Whole-genome sequencing offers a whole new level of accuracy that was unachievable just a couple of years ago. In addition, the DNA collection and processing time was efficient and straightforward. 

Even though this entry-level test is certainly not recommended for those interested in tracking their ancestors and potentially make new family connections, the healthcare part of the results was well presented, relatively complete, and informative.

For those starting the genetic exploration journey, Nebula Genomics has a lot to offer. However, we somehow recommend a more comprehensive test to make the most of the power of next-generation sequencers and do not feel frustrated with just creaming the surface of what your DNA has to offer.