the COVID-19 pandemic recedes further into the global rearview mirror, life science research—and in particular, the tools that fuel it—continues to forge ahead. The past couple of iterations of The Scientist’s annual Top 10 Innovations featured many products that directly addressed the (hopefully) once-in-a-generation disease outbreak, but also highlighted technological advances that pressed forward even in the face of that massive global disruption.
This year’s winners reaffirm that the research enterprise has not only persevered but gained momentum as the world emerges from the worst that SARS-CoV-2 threw at us. These include technology that can sequence a human genome for $100, highly sensitive imaging platforms for studying individual cells and subcellular compartments, and an assay system that facilitates protein discovery. There are also several tools with a clinical focus, such as personalized sequencing panels to detect residual cancer cells left after tumor removal, a software tracking system for overseeing gene and cell therapies from bench to bedside, and a DNA processing tool that improves technicians’ ability to analyze fetal DNA in a mother’s blood.
We are happy to announce the new products that our panel of independent judges has chosen as this year’s Top 10 Innovations.
NeXT Personal™ Personalis
Small quantities of cancer cells can linger in the body after tumor removal, a phenomenon known as minimal or molecular residual disease (MRD) that, if left undetected, can lead to recurrence. Personalis’s NeXT Personal™ assay, unveiled in December 2021, uses a patient’s own tumors to detect, quantify, and monitor circulating tumor DNA in order to spot MRD and track responses to therapy.
Using 1 mm3 of tumor tissue sampled from a patient, Personalis’s lab performs whole genome sequencing to identify up to 1,800 single-nucleotide variants. These patient-specific mutations are used to design a panel of primers targeting those regions for sequencing in future blood biopsies. The assay also includes primers for other known cancer-related genes, says Dan Norton, associate director for product management at Personalis. “We can see if there are other variants emerging that have a precision therapy associated that may be more effective for that patient.”
Medical oncologist Jonathan Loree of BC Cancer and the University of British Columbia began partnering with Personalis in August to use NeXT Personal in a study of patients who’d had tumors removed from their pancreases or colons, testing the technology’s ability to diagnose disease recurrence “earlier when there is a window of opportunity for patients to still be cured,” he says in an email to The Scientist. Loree says that if the assay could replace conventional diagnostic CT scans and blood tests, “[t]hat has the potential to save money [and] improve outcomes.”
NeXT Personal is currently used in research only, with plans to expand to clinical trial settings next year, Norton says. Personalis declined to provide a cost for NeXT Personal, explaining that the price varies depending on user needs.
KAMDAR: “NeXT Personal offers [the potential to] address a number of tumors that are not fully analyzed by other technologies to help identify and manage a patient’s disease.”
CosMx™ Spatial Molecular Imager NanoString Technologies
The platform, developed by NanoString Technologies, Inc., allows users to follow a standard protocol to prepare and hybridize specific probes and antibodies to their samples, which can be frozen tissue slices or formalin-fixed, paraffin-embedded slices. In the automated instrument, reporter sets hybridize and are imaged, then the fluorescent dyes are cleaved with UV light and washed off before the next reporter set hybridizes with the sample, allowing researchers to image multiple targets in one sample.
The CosMx SMI, priced at US$295,000, contains a high-resolution microscope and “allows researchers to visualize and quantify 1,000 RNA and 100 protein targets at a subcellular resolution across more than 1 million cells,” Vikram Devgan, senior director of Spatial Genomics Business at NanoString, says in an email to The Scientist. He adds that users can also purchase the AtoMx™ Spatial Informatics Platform, a subscription-based software produced by NanoString, to visualize and analyze the data generated by the CosMx.
“The CosMx is the only instrument that has provided us with the opportunity to simultaneously visualize thousands of genes, at subcellular resolution, and across all cells in a tissue,” says Miranda Orr, an Alzheimer’s disease researcher at Wake Forest University School of Medicine in North Carolina who, after using another NanoString product, bought the CosMx SMI. “We are able to develop maps of the brain at an unprecedented resolution.”
QIAN:“This will transform the in situ spatial biology and molecular pathology fields.”
UG100™ Ultima Genomics
Thus far, only early-access customers have had the chance to use the company’s new platform, called UG100™, but Ultima Genomics expects to release the product to the broader market in the first half of 2023. Compared to other sequencers, UG100 has several advantages, including higher speed, better efficiency, and less waste, says Josh Lauer, the company’s chief commercial officer.
Lauer attributes many benefits of the UG100 to a unique feature: a circular, open flow cell. Reagents are applied directly to a spinning silicon wafer that distributes them more efficiently than reagents pumped through a traditional flow cell, Lauer explains. In addition, the revolving design increases the speed of data collection and imaging, enabling Ultima’s sequencer to complete one run in about 20 hours, which he says is about twice as fast as existing technologies. “Much like a CD player, this enables ultra-high-speed scanning of genetic material.”
“I'm excited about the throughput of the platform, as well as the cost,” says Reuben Saunders, a genetics graduate student at the Whitehead Institute who collaborated with Ultima Genomics to use its UG100 in recent research. “It’s heralding an exciting era where very large-scale experiments . . . will become accessible methods that can really drive advancements in our understanding of genetics and cell biology.”
Lauer says the $100 per genome cost includes wafers and chemical reagents, but Ultima Genomics declined to release the price of the refrigerator-sized hardware that performs the sequencing.
RAO: “This is the first under $100 genome, and they have achieved it with an innovative use of technology.”
You must be logged in to post a comment.