Congratulations to Dr. Somalee Datta, Director of Bioinformatics at Stanford’s Center for Genomics and Personalized Medicine in Palo Alto, CA for winning the 2013 Q2 Causal Variant Challenge. Dr. Datta was randomly selected among the eligible correct entrants to receive a new iPad mini.
Dr. Datta shares some of her reflections on how she approached this specific challenge and the topic of biological analysis and interpretation of genomics data in general:
Looking for causal variant is often described as looking for a particular needle in a stack of needles. So it was really exciting to get the answer right — a mutation in FBN1 consistent with Marfan syndrome.
This particular case started with a description – 31 month old girl born with bilaterally inferiorally displaced lenses. Skeletal exam and cardiac exam, including echocardiogram, are normal. Her height is 75%tile, weight 50%tile. A variant file was also provided as part of the challenge containing millions of variants. The task was to identify which variant best explained the symptoms.
To solve the problem, I applied a series of filters including, a) high confidence variants, b) removing common variants, c) predicted deleterious variants, d) filtered on genotypes and inheritance models, and e) applied the biological context of Marfan syndrome. Application of all these filters allowed me to go from the starting ~2M variants to ~25. With only a handful to review, I could dive deep into each of the relevant gene functions focusing on the path to phenotype and pharmacogenetics which eventually led me to FBN1.
I strongly encourage researchers to participate in such challenges as they offer a great opportunity to get a glimpse of the tough task faced regularly by genetic counselors and clinicians in the field.
Congratulations again, Dr. Datta. And thanks to all who participated in the Ingenuity Causal Variant Challenge. Stay tuned for new and exciting contests coming soon.
For more information on Variant Analysis, click here.