ASHG 2015, Day 2: Top questions on the minds of NGS users

ASHG

Day 2 of ASHG 2015 opened with a very interesting session on ASHG/ESHG Building Bridges, which focused on perceptions of clinical sequencing in the US and the EU. The 4-member panel included researchers from Columbia University, the US Food and Drug Administration (FDA), the Cyprus Institute of Neurology and Genetics and Our Lady’s Children’s Hospital, Dublin. The discussion revealed that in the US, the current focus is on making next-generation sequencing (NGS) a cost-effective tool and increasing its utility in clinical settings. There was a special emphasis on the fact that the NGS field is very young and we are still collecting data. Our knowledge on genetic variance and its role in disease will, naturally, become clearer as more data is gathered. Dr. Mansfield from the FDA discussed a plan to develop well-curated data for NGS analysis, along with an open-source bioinformatics tool that will be available for public use at no cost. In the EU, the approach to NGS leans toward caution. There’s a lot of emphasis on what to do with unsolicited findings, extensive patient counseling before testing and informed consent, in addition to making clinical accreditation mandatory for labs dealing with NGS. As of now, in the EU there are no specific regulations for NGS. There were many insightful questions from the audience as well, regarding the use of genetic testing as a pre-screening tool for drug trials and training programs for both physicians and patients about NGS applications.

During the afternoon, QIAGEN offered an educational program on NGS titled, “NGS Diagnostic Odyssey: From Bench to Bedside.” Yuval Itan, Ph.D. of Rockefeller University discussed how bioinformatic solutions transform NGS results into actionable hereditary disease insights. Ben Solomon, M.D. of Inova spoke on “Solving Diagnostic Odysseys in the Neonatal Intensive Care Unit Achieving Valuable Insight from a Single Cell Genome.” The event was a full house with some great follow-up discussion.

In the evening, the poster sessions ran from 4:30 p.m. to 7 p.m. The sessions featured many interesting posters on applying NGS for analysis of genetic variance and its association with diseases. Check at the end of this post for QIAGEN’s upcoming poster sessions!

As I spoke to researchers and attended various sessions, I found that there were some common concerns on the minds of many researchers who are working on NGS. The first is the cost of doing these experiments. Even though the cost of NGS to analyze a single sample has dropped significantly in the last couple of years, it is still a key factor – after all, even lowered costs add up as one increases sample size. Another concern was about genetic variability and what to do with variations of unknown significance. One speaker mentioned that only 2% of all genetic variance is useful for understanding disease. If that’s the case, is the cost of NGS technology justified? Another concern was accuracy of data interpretation, especially when we associate genetic variance with disease. How can this be standardized?

So when you are designing your NGS experiments, what are your thoughts about cost, data analysis and interpretation? Let us know. To learn more about NGS, attend our webinar series on “Next-Generation Sequencing: overview of technology, application, data analysis and interpretation.” Sign up today!

More information on QIAGEN’s presence at ASHG 2015:

Booth 1621: Meet our experts on solutions for research with exosomes, FFPE, circulating nucleic acids and single cells.
Booth 1622: Meet our Bioinformatics team and ask for a demo of IVA, HGMD, the Biomedical Workbench, and QIAGEN Clinical Insight!

Thursday’s posters from QIAGEN (11 a.m.–1 p.m., Convention Center Hall E, Level 1):

– Rapid extraction of high yield, high quality DNA from tissue samples. Dominic O’Neil, 1901 T. Abstract here.
– An automatic end-to-end solution for disease-causing variant detection in rare and hereditary diseases with a high case solve rate and a much reduced false positive rate. Anika Joecker, 1610T, 12:00 p.m.–1:00 p.m.
– Genomic Crowdsourcing: Allele Frequency Community Provides Expansive, Ethnically Diverse, Freely Available Community Resource for Allele Frequency Annotation. Dan Richards, 1592T,12:00 p.m.–1:00 p.m.
– Ingenuity Variant Analysis, Leveraging the Knowledge Base and HGMD®, achieves over 30x enrichment in biologically relevant variants from whole genome and exome sequence data from patients with rare disease. Sohela Shah, 1913T,  11:00 a.m.–12:00 p.m.

Friday’s poster from QIAGEN (10:45 a.m.–12:45 p.m., Convention Center Hall E, Level 1):

– Development of a quantitative targeted RNA-seq methodology for use in differential gene expression analysis by Melanie Hussong, Matt Fosbrink and Eric Lader, 3191F. Check out the abstract here!

 

 

Krishnan Allampallam, Ph.D.

Senior Global Marketing Manager, Translational Sciences

Dr. Krishnan Allampallam has spent over 10 years in the biotechnology industry. Before beginning his career in biotech, Dr. Allampallam worked on pathophysiology of myelodysplastic syndrome and authored and co-authored multiple publications, abstracts and book chapters. He received his Ph.D. from University of Toledo Medical Center in 1996 and did post-doctoral research at The Cleveland Clinic and Rush University Medical Center. He has been at QIAGEN since 2008.

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