Pere Mir Pardo, Ph.D.
Lab Manager, IGENOMIX, Valencia
IGENOMIX helps deliver healthy babies – from the lab, rather than the labor ward, and the Labcyte Echo® Liquid Handlers have enabled the Valencia-based company to do so more quickly, accurately and efficiently.
Since January 2017, IGENOMIX has performed 4,905 carrier screening tests for 311 couples in protocols incorporating automated Labcyte liquid handling. Genetic mutations were found in 92% of the samples, and 29 of the couples were referred to genetic counseling to discuss the risk that those mutations might result in diseases in their offspring.
As IGENOMIX Lab Manager, next-generation sequencing based expanded CGT (compatibility genetic test) analysis constitutes a powerful tool to predict risk for Mendelian diseases, and the Echo system makes the test more affordable and available to a higher number of patients.explained in this webinar,
IGENOMIX is an international leader in fertility and reproductive testing, with labs in 11 countries - and growing. It offers several tests across the reproductive spectrum, from preconception to preimplantation to prenatal, with a mission to increase pregnancy success.
Its menu of offerings include the ERA (Endometrial receptivity analysis) test to identify a woman’s personal window of implantation; a PGS (preimplantation genetic screening) test to select chromosomally normal embryos; the NACE non-invasive alternative to amniocentesis; and the POC (products of conception) test, which evaluates all 24 chromosomes to detect miscarriage and/or disease-causing aneuploidy in fetal tissues from previous pregnancies.
One of the company’s most popular tests is the CGT, a genetic test which enables the determination of a person’s carrier status for more than 600 diseases and 15,000 mutations through massive sequencing. In addition to wide-scale next-generation sequencing, IGENOMIX offers complementary tests to detect diseases such as spinal muscular atrophy, hemophilia and Fragile X Syndrome. The tests enable couples to make informed decisions about family planning, such as whether to pursue reproduction naturally or via assisted reproductive techniques.
The Echo 525 Liquid Handler has proved indispensable in Mir Pardo’s Valencia lab as his team performs these tests. Used in both sample and library preparation, the Echo system has sliced an entire day off the six-day turnaround time previously required to manually extract DNA, prepare two plates of 96 samples, create libraries, process, sequence and analyze.
LIbrary preparation, for example, is a multi-step process, and Mir Pardo’s team employs the Echo system repeatedly to simplify it. The first step, tagmentation of the genomic DNA, requires different types of reagents dispensed using different calibrations. The Echo system can do this one by one, across a 384-well source plate.
“After the Echo dispenser dispenses them directly to the sample plate where we have the DNA dilutions, we can take the samples to the thermal cycler,” Pardo said. “After the protocol of the thermal cycler, the same plate can be introduced directly to the Echo system, which will dispense a new reagent, the STOP tagment reagent.”
Following clean-up with magnetic beads, PCR amplification begins. Additional dispensing is required, followed by another turn at the thermal cycler, a second clean-up, and a final quantification.
DNA dilution is also made much easier with the Echo system’s precise dispensing of water onto sample plates, and it eliminates the need for serial dilutions to reach the desired DNA concentration, Mir Pardo said.
“Using the Echo technology, we are able to move directly from the initial genomic DNA quantification to the final step of 5 nanograms per microliter.”
Some of the non-NGS genetic tests require MLPA-based protocols that are quite sensitive to DNA quantity and quality. The precision provided by the Echo system is a big boon in these cases, offering very stable results that are not easily obtained manually, Mir Pardo said.
Mir Pardo said he has been very happy with the performance of the Echo system, and now uses it for sample plate preparation for every protocol requiring sample dilution.
“We have already introduced it for some PCR-based protocols out of the CGT panel, and we plan to use the Echo system for every protocol of NGS library preparation in the company,” Mir Pardo said.