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Chinese Group Develops Melt Curve-PCR Assay for Beta-Thalassemia Genotyping


This article has been updated from a previous version to update the name of Zeesan Biotech.

By Ben Butkus

Scientists from China's Xiamen University and other Chinese academic institutions have developed a fast, low-cost assay based on PCR and melting curve analysis to genotype 24 β-thalassemia mutations common in Chinese populations with 100 percent sensitivity and specificity, according to a recently published research study.

The researchers, along with a startup company called Zeesan Biotech, have submitted the test to Chinese regulatory officials for approval as a widespread prenatal diagnostic and screening tool for β-thalassemia; and have begun developing additional assays based on the method for various cancer and infectious disease mutation panels.

Zeesan "has been granted an exclusive right to commercialize this assay," Qingge Li, a corresponding author on the study and a researcher at Xiamen University, told PCR Insider in an e-mail this week.

Xiamen University has applied for two patents on the assay, according to Li: One, an international patent, covers the assay technique; while the other, a Chinese patent application, is a product patent focused on the diagnostic kit, called MeltPro HBB.

"This assay is now being submitted by Zeesan Biotech to [China's State Food and Drug Administration] for approval, which will take one year or so to get finalized," Li added. "This assay will be used for pre-marriage and pre-pregnancy screenings as well as for prenatal diagnostics in China. In [the] southern part of China, where [β-thalassemia] is highly prevalent, the MeltPro HBB assay can be used for widespread carrier screening."

Details on the MeltPro HBB assay and its performance in a large double-blind, multicenter validation study were published in the July edition of the Journal of Molecular Diagnostics.

Beta-thalassemia is an autosomal recessive form of hemoglobinopathy and is one of the most widespread life-shortening genetic diseases in humans, according to the study's authors. Although the disease is problematic worldwide, its incidence is especially high in certain countries in the Mediterranean, Africa, the Middle East, India, and Southeast Asia.

Incidence is especially high in southern China, where studies have shown that nearly 7 percent of the population in the Guangxi province, and 1 percent to 6 percent of the population elsewhere in the region, are β-thalassemia carriers.

To combat this, the Chinese government is currently instituting a population-based screening program to try and reduce the birth rate of fetuses with the disease in endemic regions, the study's authors wrote. Part of the goal of this program is to offer for free a simple, reliable, and cost-effective genetic test to screen for carriers and provide appropriate genetic counseling.

The Xiamen University researchers and their colleagues have spent several years attempting to uncover the mutations in the hemoglobin-β gene, or HBB, that cause β-thalassemia in endemic regions of China.

So far, they have identified 45 SNPs and small deletions in the gene, and have previously developed several assays in hopes that one would be ideal for widespread clinical screening. The most popular, reverse dot blot, or RDB, analysis, is currently the only method approved in China, and although it is cost-effective, its throughput is too low and variability to high to use in screening campaigns, the researchers wrote.

However, with the development of MeltPro HBB, the researchers may have finally hit pay dirt. MeltPro HBB is a qualitative in vitro diagnostic assay designed to genotype a panel of 24 of the SNPs and small indels in the HBB gene.

The test uses a proprietary, multicolored, self-quenched, probe-based melting curve analysis that can be performed with most standard real-time PCR instruments commonly found in clinical laboratories, according to the researchers.

More specifically, the assay uses asymmetric PCR with two primers to generate excess single-stranded amplicons for probe hybridization, followed by melting curve analysis using four-color real-time PCR. One of the main advantages of the assay, according to the researchers, is that it can be performed in one step on one machine, with a high degree of reproducibility.

In their JMD study, Li and colleagues evaluated MeltPro HBB in 1,022 pre-typed genomic DNA samples, including 909 clinical cases of β-thalassemia, collected from six hospitals in the Guangdong and Guangxi provinces from November 2008 to April 2010. The double-blind assay yielded 100 percent sensitivity and specificity for all included mutations, the researchers reported.

They also compared results of the assay to RDB analysis or bidirectional sequencing: Because RDB analysis detects 17 mutations, 15 of which are detected by MeltPro HBB, the remainder of the 24 mutations were determined using the sequencing method. The researchers reported that the concordance rate between MeltPro HBB and RDB or DNA sequencing was 99.4 percent only because of the two mutations that are picked up in RDB analysis but not in MeltPro HBB.

One of the major advantages of the new assay, Li told PCR Insider, is that it is truly homogenous, which eliminates the need for post-PCR processing and the risk for contamination. In addition, Li said that with a panel of 24 mutations, MeltPro HBB "covers the largest number of mutations thus far" for β-thalassemia testing.

The researchers also conducted their study with an eye toward desirable traits for clinical application of the assay, such as reproducibility, limit of detection, throughput, and cost. For instance, they found that reproducibility of the test between different lab technicians was 100 percent in all aspects; and that the assay could detect mutations in as little as 10 picograms of sample DNA.

In addition, the researchers found that they could perform an entire genotyping test in about three hours when their protocol involved a single step of adding gDNA to two reaction tubes for each assay.

"It is conceivable that by using one four-color, 96-well real-time PCR instrument, supported by a sufficient number of standard thermal cyclers, more than 1,000 samples can be analyzed within one workday," the researchers wrote. In contrast, RDB analysis would take at least 10 workdays to process the same number of samples.

Lastly, the cost of running MeltPro HBB is approximately $2 per sample, compared with about $5 per sample for RDB analysis and $10 per sample for sequencing, the authors wrote.

In an accompanying commentary on the study in JMD, Daniel Sabath and Harvey Greisman of the departments of laboratory medicine and medicine at the University of Washington School of Medicine in Seattle, note that the Xiamen University study is "an excellent example of a real-world validation of a molecular diagnostic test."

Sabath and Greisman wrote that particularly impressive aspects of the study included the assay throughput and the fact that reproducibility was so high — particularly in light of the fact that "the DNA samples used came from six laboratories using five different DNA isolation methods;" and that in each of these laboratories, "two technicians performed the testing and a third analyzed the data and performed quality assurance."

However, while the commentators agreed that assays like MeltPro HBB might be "very important for genetic counseling and prenatal diagnosis in the southern Chinese population (quite a large population, it should be noted)," it may have limited utility for alleles present in other populations.

Nevertheless, "one could envision melting curve assays designed for other populations with a similar skewed allele distribution;" and the multiplex method "could be envisioned to screen other genes like [cystic fibrosis transmembrane conductance regulator] or the BRCA genes for modest numbers of more common mutations, perhaps followed by reflexive next-generation sequencing for detection of less common variants," Sabath and Greisman wrote.

Indeed, Li and colleagues at Zeesan are already eyeing such applications of their method. In particular, Li said, the collaborators are working on assays for multidrug-resistant tuberculosis, extreme drug-resistant tuberculosis, drug-resistant hepatitis B, human papillomavirus genotyping, and glucose-6-phosphate dehydrogenase deficiency.

"MDR TB will be commercialized first early next year followed by XDR TB, drug-resistant HBV detection, and HPV genotyping," Li said. "The last one will be the G6PD genotyping assay, which should be commercialized in 2013 according to our schedule." All of these assays essentially use the same method as the MeltPro HBB assay, he said.

In general, Li said, the assays' homogeneity and ability to multiplex are expected to be key differentiators in the marketplace. "People will find that a much [higher] number of mutations or genotypes can be detected in a single reaction. For example, 15 high-risk HPV [mutations] can be simultaneously quantified and identified, even when they are mixed together in a single tube, within one hour," he said.

And while Sabath and Greisman raised the prospect of similar assays for BRCA and CFTR mutations, those "are not under study by us right now," Li said. "The reason is that these two genes are very rarely studied in China and we hope to find collaborations with Western companies" to develop such assays, he added.

Have topics you'd like to see covered in PCR Insider? Contact the editor at bbutkus [at] genomeweb [.] com.