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After celebrating its 18th birthday, the team at Complete Genomics is more committed than ever to providing the sequencing community with affordable sequencing solutions. It comes as no surprise as their Co-founder and Chief Scientific Officer Dr. Radoje (Rade) Drmanac has a long history of paving the way for the advancement of genomics. From working on the Human Genome Project to his various genomic startups, Drmanac has always had the goal of improving genomics research and technologies.
After what seemed like a delayed start from lengthy legal battles and an acquisition from MGI, Complete Genomics has proven that they’re ready to keep driving innovations in genomics. With several instrument launches and new uses for their technologies, they have firmly established the company as a formidable player in the sequencing industry. The company's dedication to cutting-edge technology, coupled with their robust sequencing platform and comprehensive service model, has garnered significant attention and trust from researchers, clinicians, and biotech companies alike.
Complete Genomics is all about, “driving higher-quality, new standards, more complete genomes, and better tools for monitoring our health and preventing disease,” explained Drmanac. “Many times, people think that because we provide lower costs, it's all about being cheaper, but actually it's all about affordability and quality. It's always important not to cut corners on quality. We want to cut costs but keep quality.”
Drmanac also highlighted Complete Genomics’ mission to provide users with more than just sequencers. “Complete Genomics is providing the whole workflow.” They currently offer users library preps, various automation solutions, an array of sequencers, and different analysis packages to give users everything they need to take full advantage of their full-circle frontend to backend instruments. “When you have this massive data set, we provide the tools that are efficient to use this enormous number of reads and map them efficiently, and do variant calling,” added Drmanac. He emphasized the difficulty to scale without having all of these tools available.
Available sequencing technologies
The array of sequencing instruments available from Complete Genomics is one of the widest selections from any provider. This includes ultra-small portable sequencers like their DNBSEQ-E25 up to their production-scale sequencers such as the DNBSEQ-T20x2, which currently offers the highest throughput in the industry. It’s capable of sequencing 50,000 whole genomes a year at 30x coverage, according to Drmanac.
Complete Genomics also utilizes a clever way to name each instrument. “All our naming is actually throughput per day,” said Drmanac. “But it's a fair way to measure throughput because different runs can take different times. Sometimes a run takes one day, sometimes two days, sometimes half a day like G99’s complete run in 12 hours.” This means popular instruments like the DNBSEQ-T7 are capable of producing 7 terabases (Tb) of data per day.
The current lineup of Complete Genomics’ instruments includes:
- DNBSEQ-E25
- DNBSEQ-G99
- DNBSEQ-G400
- DNBSEQ-T7
- DNBSEQ-T20x2
DNBSEQ
As explained by Drmanac, all of Complete Genomics’ platforms use DNBSEQ (DNA nanoball sequencing) technology. The preparation of the samples for this process begins with denaturing the target dsDNA containing specific adapters to form ssDNA. Next, the ssDNA undergoes DNA single-strand circularization, where the target ssDNA forms a nicked circle, which is repaired into a single-stranded circle. Then DNA nanoballs (DNBs) are generated through rolling circle replication (RCR) using the single-stranded circular DNA as a template. The DNBs are loaded onto a patterned array chip that has uniform binding sites to bind a single DNB at each spot.
After loading, sequencing primers hybridize to the adapter region of the DNBs, and fluorescently labeled dNTP probes are incorporated with DNA polymerase. Unbound dNTPs will be washed away, and the fluorescence signal during the image capture is converted into a digital signal. Proprietary base-calling software is used to determine the base information according to signal intensities. Once the first strand has been sequenced, the addition of second-strand generation primers and a polymerase with strand displacement activity initiates the synthesis of the second strand. This process extends the new primer until it displaces the original sequenced strand, resulting in a longer single-stranded template optimized for attachment to the original DNB. Using the same sequencing chemistry as the first strand, the second-strand sequencing produces a stronger signal and higher sequencing accuracy due to the increased number of inserted DNA copies in the new template.
An important distinction of the DNBSEQ technology is the PCR-free nature of the process. Drmanac often refers to this technology as “real PCR-free WGS (whole genome sequencing)” since there is no PCR anywhere in the workflow. “We cannot create clonal errors, he stated. “Because of that, our whole genome sequencing has two to three times fewer indel [insertion and deletion] errors than sequencing based on PCR clusters because PCR clusters have clonal errors.”
Common applications
Due to their extensive line of instruments and products, Complete Genomics’ sequencers could be used for nearly any sequencing application. However, one application that they particularly excel at is large-scale sequencing projects. “When you have high throughput and that affordable price, you can do lots of population-scale whole genome sequencing,” explained Drmanac, referring to the DNBSEQ-T7’s and DNBSEQ-T20’s high output. He envisions their potential to be used in national genome projects, similar to the ongoing sequencing of newborn genomes in England.
These powerful devices enable deep sequencing of blood, cell-free DNA, or extensive single-cell sequencing applications. “We enable prevention and treatments before it's too late, but all of that depends on affordable sequencing,” said Drmanac. With lower sequencing costs, increased throughput, and haplotyping capabilities, he believes users can also utilize these sequencers for routine health screenings.
Complete Genomics also has a range of low-med throughput sequencers such as the DNBSEQ-E25 and DNBSEQ-G99 which are perfect for common applications like targeted sequencing, methylation studies, small genome sequencing, low-pass whole-genome sequencing, and transcriptome work.
Advances and the future
The largest introduction for Complete Genomics this year has been the launch of their DNBSEQ-400, T7, and G99 sequencers, and will launch DNBSEQ-T20x2 in H2, 2023. As previously mentioned, DNBSEQ-T20x2 is the largest sequencer to date, and in addition to the improved scalability, the cost for WGS is low. “For the first time in the industry, we have a sub $100 WGS price and, for the first time in the industry, the price includes instrument depreciation,” said Drmanac. The machine was designed to reuse reagents by performing sequencing on slides that can be dipped into the reagents, which saves considerable amounts of money to scale their experiments.
“We also recognize that in addition to large projects that the T20x2 covers, there are lots of laboratories that are limited by the sequencing price and flexibility of instruments,” added Drmanac. “So, we have a new standard for most of the labs; we call it the DNBSEQ-T7 instrument.” The system was announced to the U.S. market in January, 2023 but was available in other markets for a number of years. “What is nice about this instrument is that it has four flow cells, it's flexible. You can run one flow cell at a time. If you don't have enough samples, you don't need to wait for the other three and you can put the other flow cells in at any time. In the middle of the run, in the middle of the night, anytime, just plug it in.” After its release, Complete Genomics announced the price of $150 per genome or $1.5 per gigabase. Drmanac believes this type of flexibility is crucial for different labs and allows smaller labs to expand their applications to do more genomes at a flexible rate but with deeper sequencing.
Single-tube long fragment reads (stLFR) technology has been created and used by Complete Genomics for a number of years1, but it has really come into the spotlight with the low costs created by their large-scale sequencers. This technology uses transposons to insert unique barcodes throughout long stretches of DNA, allowing them to be easily sequenced using their short-read sequencers but assembled to provide important long-read information. Put simply by Drmanac, “What the single-tube LFR allows in an efficient way is to produce whole genome sequencing with haplotype phasing information and reduce the number of the so-called blind spots.” Drmanac emphasized that stLFR is very important for providing users with complete and affordable phased genomes and that because it’s a library prep, it’s available to use on any of their instruments.
Another important addition to the Complete Genomics lineup is the DNBSEQ-G99 sequencer. As a benchtop sequencer, it’s capable of performing many routine sequencing applications at a very fast pace. This includes completing a pair-end 150-cycle (total of 300 cycles with up to 48Gb) sequencing run in 12 hours. Users can also obtain a report after the first 2.5 hours of the run to begin assessing the data. This is crucial for applications like pathogen detection that require a fast turnaround.
Driven by Drmanac's radiant optimism and steadfast commitment to advancing human health, Complete Genomics is at the forefront of revolutionizing DNA sequencing. “Our goal is really to enable everybody to live a healthier, longer, and more productive life,” he said. With a clear goal of making sequencing a routine application for healthcare, the company is tirelessly working to lower the cost of sequencing and build a future where the benefits of genomics are within reach for all.
References:
- Wang O, Chin R, Cheng X, et al. Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assembly. Genome Research. 2019;29(5):798-808. doi:https://doi.org/10.1101/gr.245126.118