Privacy issues when looking for a needle in a genomic haystack


Fri Mar 20, 2015


Amalio Telenti
Human Longevity Inc.





Very rare single nucleotide variants are the most prevalent form of genetic diversity in the human population. Such variants are generally refered to as Variants of Unknown Significance (VUS). It is expected that VUS will attract increasing attention of the medical services as possibly associated with clinical disease or disease predisposition.

The considerations above call for specific solutions to identify the few individuals that may share a very rare variant (eg. 5 individuals among 100.000 or 1 million population). These individuals are likely to be found across different studies, populations, and countries. The required tools would be those that search for those rare variants, recover and condense available metadata, and trigger additional phenotyping.

The conditions to search for unique individuals, with a need for broad phenotype information, represent a unique challenge to privacy, and to researcher and institutional research privileges. The current web seminar will discuss approaches for the secured analysis of phenotypes associated with rare variants– with an emphasis on crowdsourcing strategies that provide phenotype detail through cooperative efforts between database owners and individuals querying for unique VUS.  These aim at establishing a fair, privacy-preserving trade between a professional database that contains a relational genotype-phenotype database with limited capacity to attribute phenotype detail to the rarest of VUS, and the external interested party (typically a genetic counselor) that searches additional information on a given novel VUS and is prepared to release a limited amount of phenotype detail through the query procedure.



A. Telenti, MD (Infectious Diseases) and PhD (Microbiology) trained in internal medicine and infectious diseases at the Mayo Clinic, Rochester, MN, USA. He did research in microbiology and genetics at the University of Berne, Switzerland, at the Albert Einstein College of Medicine (Bronx, NY, USA), and Ragon Institute of MGH, MIT and Harvard (Boston, MA, USA). Between 2007 and 2014 he was the Director of the Institute of Microbiology at the University Hospital in Lausanne (CHUV). He is currently scientist at the Medical Genomics group at the J. Craig Venter Institute in La Jolla, CA, USA, and head of functional biology at Human Longevity Inc., a genomics company that aims at sequencing 1 million individuals by 2020. Dr Telenti’s first main contributions have been on the genetics of tuberculosis drug resistance. This knowledge is the basis for current rapid diagnostic tools worldwide. In the last decade he led several major initiatives for the study of genetic susceptibility to HIV and HCV, as well as for the understanding of the genetic of innate immunity responses. Dr. Telenti was senior, co-senior author or member of the writing committee of the first large genome analyses investigating human susceptibility to HIV-1 and hepatitis C virus (Fellay et al, Science 2007, Loeuillet et al, PloS Biol 2008, Fellay et al PLoS Pathogen 2009, International HIV Controllers Consortium, Science 2010, Rauch et al. Gastroenterology 2010). His laboratory also completed the largest genome-wide transcriptome analysis in HIV disease (Rotger et al, PLoS Pathogens 2010, Mohammadi et al, PLoS Pathogens 2013 and 2014), the first comparative transcriptome study between HIV-infected humans, and SIV-infected primates (Rotger et al J Clin Invest 2011), and the first host-to-pathogen, genome-to-genome analysis (Bartha et al. eLife 2013). The laboratory has been very active in the field of pharmacogenetics, and of protection of genomic information in the clinical setting. He has received many national and international awards, including the prestigious Cloëtta Award, one of the highest distinctions in medicine in Switzerland. In 2012, he was elected member of the Swiss Academy of Medical Sciences.