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Application Case Study

NIPT / NIPS

The Customer

Sequenom, Inc. (NASDAQ: SQNM) is committed to enabling healthier lives through the development of innovative products and services. Sequenom Laboratories, a CAP-accredited and CLIA-certified molecular diagnostics laboratory, has developed a broad range of laboratory tests, with a focus principally on prenatal care and has the most comprehensive portfolio of products for noninvasive prenatal applications. These molecular genetic laboratory-developed tests provide early patient management information for obstetricians, geneticists, and maternal fetal medicine specialists. Sequenom Laboratories is changing the landscape in genetic diagnostics using proprietary cutting edge technologies.

The Challenge

For Sequenom, a leader in noninvasive prenatal testing (NIPT) with about 40% market share, faster analysis at lower cost is of the essence

NIPT uses maternal blood, which contains short fragments of circulating fetal DNA. If mapping a single genome is like piecing together a telephone book, then NIPT is like putting together two telephone books, which share at least half of the constituent phone numbers, when there are a dozen copies of Mom’s phone book for every one of Baby’s. Nonetheless, Sequenom has found ways to piece together a low-coverage sequence of the fetal genome, enough to identify aneuploidy as well as some microdeletions. The company advertises diagnostic capability for a panel of fourteen genetic disorders, from Down syndrome (trisomy 21) to Prader-Willi/Angelman syndrome (deletion in 15q).

The first and only NIPT that identifies genome-wide deletions or duplications of 7 Mb and greater, and also detects select microdeletions. The first and most comprehensive noninvasive prenatal test (NIPT) of its kind for women at high risk for fetal chromosomal abnormalities. The first noninvasive prenatal test (NIPT) of its kind utilizing common trisomy information mirrored after serum screening content. Comprehensive, customizable expanded carrier test that screens for >250 diseases and >2,000 disease-causing mutations. Analyzes 136 mutations and 5 variants proven to be clinically relevant to cystic fibrosis (CF). The only noninvasive prenatal test of its kind that detects fetal RHD genotype in RhD-sensitized mothers. A high-resolution, genome-wide microarray assessment of patient sample from a chorionic villus sampling (CVS) or amniocentesis specimen.

“Edico Genome’s DRAGEN chip analyzes the large amounts of sequencing data we generate in a rapid and cost-effective manner, without compromising accuracy,” said Tim Burcham, Ph.D., Vice President, Informatics and Software of Sequenom, Inc. “This has the potential to improve the analysis of next-generation sequencing data, by reducing analysis time and storage costs, and potentially improving turnaround time.”

Sequenom’s flagship MaterniT21 Plus test currently has a five-day turnaround time from receipt of a maternal blood sample.

The Solution

The two companies recently completed a proof-of-concept study, comparing results between Sequenom Laboratories’ (a wholly owned subsidiary of Sequenom, Inc.) current analysis pipeline and the results using DRAGEN.

The Results

“Edico Genome’s DRAGEN chip analyzes the large amounts of sequencing data we generate in a rapid and cost-effective manner, without compromising accuracy,” said Tim Burcham, Ph.D., Vice President, Informatics and Software of Sequenom, Inc.

Results from the collaborators’ study comparing standard software used by Sequenom Laboratories and the DRAGEN processer were provided as a poster presentation at the American Society of Human Genetics (ASHG) annual meeting in October 2014 as part of the Bioinformatics and Genomic Technology session (1675M).