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Asper Biotech Applies Arrayed Primer Extension Technology to Prenatal Testing


By Justin Petrone

This story was originally posted Sept. 10

Asper Biotech has introduced array-based prenatal testing for fetuses with increased nuchal translucency but normal karyotype.

Nuchal translucency is a collection of fluid under the skin at the back of a fetus' neck. It can be measured using ultrasound during the first trimester of pregnancy. For cases where increased nuchal translucency is detected, yet no genetic disorder can be immediately identified via karyotyping, Asper is now offering a targeted array-based genotyping service, according to the Estonian firm's CEO.

Eneli Oitmaa told BioArray News last week that the company's test, based on its arrayed primer extension, or APEX, technology, allows doctors to advise patients who are at risk because of hereditary factors and helps parents make relevant decisions in family planning.

According to the firm's website, the indication for such genetic testing is a fetal nuchal translucency of 3 millimeters or more during weeks 11 to 14 of gestation. Before referring a case to genetic testing, Asper recommends that geneticists exclude fetal aneuploidy.

The test is available as a diagnostic package service, which includes DNA extraction, genotyping, and additional validation of the APEX-based analysis findings by dideoxy sequencing, followed by interpretation and the delivery of a results report. The sample material for testing is DNA separated from fetal chorionic cells or amniocytes. Asper is able to provide results within three weeks.

Oitmaa said that Asper only offers the test through healthcare professionals such as gynecologists, clinical geneticists, and genetic counselors. She said that Tartu-based Asper rolled out the service last year, and has since offered it globally, with customers in the EU as well as the US.

"We develop and offer our tests, including the NT test, globally as well as in Estonia," she said of the firm's strategy. Oitmaa declined to name any of Asper's clients.

Arrayed primer extension involves hybridizing probes arrayed on slides and performing a primer extension reaction in which DNA polymerase extends the hybridized primers by adding a base that is complementary to the nucleotide of interest. The incorporated bases are then detected and alleles determined.

While researchers can develop their own APEX genotyping assays to look at up to 1,000 SNPs per array, a newer APEX method, called APEX-2 has been developed at the Estonian Biocenter, also located in Tartu.

APEX-2 is based on single-tube multiplex PCR followed by arrayed primer extension reaction and allows users to conduct custom genotyping of up to 1,000 SNPs "more cost-effectively," according to its inventors. Asper Biotech obtained a license to the APEX-2 technology in 2008 (BAN 8/5/2008).

Oitmaa said that Asper is using the APEX-1 technology in its prenatal testing service. Still, scientists from Asper were co-authors of a paper published last year in Prenatal Diagnosis describing how they used quantitative APEX-2 microarrays to diagnose Down syndrome.

According to the paper, the Asper scientists set out to develop a high-throughput, microarray-based prenatal diagnostic test to detect trisomy 21. They reported that the resulting T21 APEX-2 assay could discriminate between trisomy and euploid DNA samples by comparing the signal intensities of allelic fractions of heterozygous SNPs after APEX reaction.

After preliminary validation using DNA samples from Down syndrome patients, they analyzed DNA samples from cultured and uncultured amniocytes and chorionic villus for 90 SNPs with high heterozygosity from the 21(q21.1q22.2) region.

The authors determined that 90 SNPs were "sufficient for reliable discrimination between T21 and euploid DNA samples." Using 134 clinical samples, they claimed the sensitivity and the specificity of the assay were 100 percent.

Oitmaa said this week that Asper "does not have any specific plans to develop an APEX-based test for Down syndrome at this moment, although we do not exclude the possibility in the future."

Asper is one of an increasing number of companies and laboratories that offer array-based screening in the prenatal and in vitro fertilization setting, though the offerings and technologies vary. In May, Pacific Reproductive Center, a Southern California fertility medical practice, said that it would use BlueGnome comparative genomic hybridization arrays to screen embryos prior to implantation during in vitro fertilization cycles (BAN 5/17/2011).

And in March, PerkinElmer's Signature Genomic Laboratories launched its CGH-based Precision prenatal-testing panel, which it claimed can detect 15 common and severe chromosomal disorders. The assay is intended for women undergoing invasive testing for advanced maternal age or parental concern (BAN 3/8/2011).

Oitmaa said that APEX differs from other array-based methods used in prenatal testing, such as CGH arrays or high-density SNP-genotyping chips, in that it is used explicitly for mutation screening and "enables targeted analysis of nucleotide changes, indels, and short repeats that cause genetic disorders."

By comparison, she characterized CGH as useful for detecting genomic copy-number variations, and SNP arrays as suitable for "whole genome studies, for determining disease-susceptibility loci, copy-number variations, and for loss-of-heterozygousity studies."

She described the APEX assay as "flexible and easily customized" and with a "short" sample turnaround time. Oitmaa added that the recent Prenatal Diagnosis paper confirmed that APEX "is also applicable for copy number variation detection" and compared to array CGH requires "less sample amount for analysis, shorter turnaround time," and can be offered at a lower price per test.

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.