Original resource: http://www.genomeweb.com/sequencing/indias-supratech-micropath-developing-ngs-based-tests-pgs-newborn-dx-cancer

NEW YORK (GenomeWeb) – Supratech Micropath, a reference and diagnostic lab in the state of Gujarat, India, is developing next-generation sequencing-based tests for preimplantation genetic screening and diagnosis, newborn diagnosis, and cancer.

The laboratory is CAP accredited and certified by India's National Accreditation Board for Testing and Calibration Laboratories. It has been offering molecular testing five years ago using PCR, Sanger sequencing, FISH, and other technologies. This year it began offering NGS tests that it markets as research-use only, and is aiming to market them for clinical use in 2015.

Parth Shah, a research scientist at Supratech Micropath, told Clinical Sequencing News that the lab has developed preimplantation tests and cancer panels on Thermo Fisher's Ion Torrent PGM. The lab currently has one PGM machine and runs around 20 to 30 tests per month, he said.

Shah said that the lab decided to go with the PGM over an Illumina system because of the cost and also because an Illumina system would have had too much throughput for the lab's needs. "In India, people are much happier with small panels," he said. And with the higher throughput of the Illumina system, the lab would need many more samples in order to fill the machine, which would have made turnaround times prohibitively long. Additionally, Shah said that Thermo Fisher has more clinical support available in India.

Thus far, he said that the lab has experienced some issues in calling variants in homopolymeric regions, but added that chemistry improvements are helping to resolve those issues. In addition, he said that the lab can now readily identify those errors, so the overall sensitivity of the assays is still very high.

The first NGS test the lab developed was a preimplantation aneuploidy test, which uses low-coverage whole-genome sequencing of single cells to look for chromosomal aneuploidies in embryos before they are implanted, Shah said. The group plans to publish its method in a journal this year.

Currently, most insurance plans in India do not cover these tests, Shah said, so patients pay out of pocket. The PGS test cost varies depending on how many embryos are screened, but is around $250 per embryo when eight are screened. The lab returns information about chromosomal aneuploidies, but will not give sex chromosome information unless there is an abnormality.

Supratech is also developing preimplantation genetic diagnostic tests for blood disorders like hemophilia and beta thalassemia, as well as for glycogen storage disorders, urea cycle disorders, muscular dystrophy, neuromuscular disorders, and lysosomal disorders.

These panels include between 20 and 30 genes each, said Shah, and can be used for both preimplantaion or newborn diagnoses.

In the realm of cancer, Shah said that the lab is offering a comprehensive AmpliSeq panel of around 400 genes, a 50-gene hotspot AmpliSeq panel, and smaller panels of fewer than 10 genes for specific types of cancer like lung or colon.

For the comprehensive and hotspot panels, the lab started with the Ion AmpliSeq kits and then "customized them for our own purposes," Shah said, adding or subtracting genes as necessary. "Where we find that the AmpliSeq panels are not sufficient, we develop our own amplicons and make them a part of those panels in order to expand them," he added.

In addition, in order to cater to oncologists in India that are not familiar with broad genomic testing and want to just analyze a few genes, Supratech offers a targeted lung cancer panel and a targeted colon cancer panel that each have only a handful of genes — fewer than 10 — but are sequenced to 1,000-fold coverage. Prices for the cancer panels also vary, but Supratech charges around 20,000 rupees ($328) for the hotspot panel, Shah said.

Thus far, Shah said the majority of tests run have been for inherited diseases and PGS. For cancer, the benefits are less obvious, and the test results more difficult for the clinician to interpret. In addition, a Sanger-based EGFR test will cost around $120, Shah said, so although a 50-gene panel test is more efficient from a cost-per-gene standpoint, physicians are not as interested in those other genes.

However, Shah said, he expects that cancer test volumes will pick up as more data accrues around the actionability of cancer genes and as physicians become more comfortable with the data.

In the future, the lab plans to develop assays to detect pathogens from body fluids, Shah said. He added that scientists from Supratech are working to validate a protocol established by a group at the University of California, Los Angeles on pathogen detection. In addition, he said the lab is working to develop a cancer panel for fusion transcripts. Currently, the lab has several PCR-based assays for gene fusions in cancer, but would like to incorporate all of those into an NGS assay.

NGS (next generation sequencing)-based preimplantation genetic screening has become another powerful platform in IVF realm. 

Array based	Sequencing based
It provides   vastly improved resolution and detection capability and more consistent results compared to traditional karyotyping, the American College of Medical Genetics (ACMG) recommends microarrays as the first approach for postnatal cytogenomic screening.	NGS offers complimentary chromosome aberration testing that can add additional mutational and higher-resolution data beyond the CNV (copy number variation) and AOH (absence of heterozygosity) capabilities of microarrays. With higher levels of functional resolution, NGS is ideal for measuring chromosome inversions, balanced translocations, and disease-associated point mutations.

(reference: Illumina. inc)