SAN FRANCISCO (GenomeWeb) – After receiving approval from the China Food and Drug Administration for a sequencing-based HPV test that relies on self-sampling technology for screening women for cervical cancer, BGI is targeting the test at women in rural areas of China.
Na Liu, BGI Genomics' vice president, said that the CFDA approved the test in June to run on the BGISEQ-100, one of BGI's internally developed CFDA-approved sequencers that is based on semiconductor sequencing technology similar to that of Thermo Fisher's Ion Torrent.
BGI has sequenced around 2 million patient samples, most of which have been physician collected rather than self collected, and has found an HPV positive rate of around 10 percent, Liu said. Samples are tested both at BGI — at clinical testing facilities it has throughout China — as well as at some local hospitals.
The self-sampling version costs around 199 RMB ($30), Liu said, and many of the local governments in China have allocated funds to pay for it, adding that China's Health Commission and Planning Commission have started focusing on health prevention measures for breast and cervical cancer in the country. In areas that do not have funding, individuals can purchase test kits on the website and even pay through the social media application WeChat. "It allows people to obtain the test and do the sampling fairly easily without going to the hospital," Liu said.
Researchers published a validation of the assay in 2014 in the American Journal of Clinical Pathology.
In the study, the researchers describe the targeted NGS HPV genotyping assay, which uses unique primers to amplify portions of the L1 gene, which codes the major HPV virus capsid protein; and a pair of primers to amplify a portion of the human beta-globin gene, which acts as an internal quality control. In addition, the assay includes PCR primers that provide a unique primer index, so that samples can be multiplexed.
The team compared self-sampling to physician-collected samples and analysis via next-generation sequencing with hybrid capture and mass spectrometry-based testing, and showed that self-collected samples run on either the PGM or Illumina's MiSeq instrument produced comparable results to physician-collected samples and to samples analyzed by the other technologies.
In addition, the researchers demonstrated that they could multiplex 1,440 samples per 4.5-hour run on the PGM and 1,248 samples per 27-hour run on the MiSeq.
Liu said that following the validation study, the CFDA spent several years evaluating the test before ultimately approving it this year to run on the BGISEQ-100. The assay relies on self-sampling technology invented by Jerome Belinson, a professor of surgery at the Cleveland Clinic and president of Preventive Oncology International.
Belinson first began working on self-sampling for HPV testing in 1997. He said that testing from self-sampling initially resulted in 15 percent to 20 percent lower sensitivity than sampling done by a physician. He along with collaborators had been trying to figure out why and ultimately determined that if they used PCR as a method for testing the samples, the sensitivity would be comparable to that of a physician-collected sample. However, initial PCR technology was too expensive and slow to be clinically relevant for broad population screening.
In 2009, Belinson, along with researchers at Peking University and BGI, launched a 10,000-patient clinical trial testing self-collection and physician-collected cervical samples and testing using Hologic's Cervista HPV assay, Qiagen's Digene assay, and a BGI-designed MALDI-TOF assay.
The results of that trial were published in the American Journal of Clinical Pathology in 2011 and showed that self-collection combined with BGI's MALDI-TOF assay was as sensitive as Qiagen's and Hologic's assays, but had a much higher throughput, at 4,500 samples per day.
Following that study, the BGI group began building up its sequencing capacity, and Belinson's team continued to work on the front-end steps to make the process more amenable for self-collection.
Belinson said that one key piece was figuring out how to make self-collected samples transportable. He first worked with GE Healthcare's FTA elute sample collection cards — cards that enabled nucleic acid samples to be stored at room temperature. When a sample is applied to the card, the card changes colors, indicating that the sample is there. Reagents on the card "lyse the cells, stabilize the DNA, and make it noninfectious," Belinson said. Such cards are more amenable to self-sampling because individuals do not have to handle liquids and the cards themselves are easier to mail. Belinson and his team ultimately designed a version of such a card for HPV testing and he is now working to modify the card to simplify the process even further.
Belinson hopes to make his self-sampling techniques available in other countries, including the US. As CEO of Medworks, a nonprofit that provides free medical and healthcare services to the uninsured and underinsured, Belinson said that self-sampling technology could enable the organization to offer cancer screening in medically underserved communities.
Liu said that self-sampling to screen for HPV would be particularly important in China because "of the difficulty of carrying out the screening in rural areas with limited healthcare resources. With limited medical resources, the coverage of disease screening is demanding, while self-sampling techniques free up doctors from sampling and provide a new choice for cervical cancer screening."
In addition, she said, self-sampling technology and NGS are a good combination because typically, very few cells are obtained through self-sampling, so "we need a technology with high sensitivity."
Sequencing offers an added advantage over other testing methods in that it is very high throughput and can "not only confirm whether the infection is positive, but also identify the virus subtype accurately," Liu said.
Liu said that the BGI team is using this added information about virus subtype for research purposes and said that it could potentially help guide the development of an HPV vaccine "that is more efficient and suitable for the Chinese population."
In addition, she said that while the clinical tests run so far have shown that the overall positive rate is about 10 percent, HPV prevalence seems to vary between provinces. For instance, in the Jiangsu province, about 12 percent of samples were HPV positive while in the province just north, Shandong, only 7 percent of samples were positive. Liu said that so far, it is unclear why prevalence varies between provinces, but that BGI researchers planned to further study those differences.
Liu said that BGI is also working on developing a pharmacogenomics test and a hereditary cancer risk test that both use self-sampling technology, although she declined to disclose the timeline for launching such tests.