Bioinformatics Seminar - Prediction potential and pitfalls in pervasive population personal genomics: Interpreting newborn genomes with Notes on privacy timebombs in functional genomics data

Speaker: Steven Brenner , Berkeley

Date: Monday, October 02, 2023

Time: 11:30 AM to 1:00 PM Note: all times are in the Eastern Time Zone

Public: Yes


Event Type: Seminar

Room Description: G882

Host: Bonnie Berger, CSAIL MIT

Contact: Shuvom Sadhuka,

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Reminder Subject: TALK: Bioinformatics Seminar: Steven Brenner, "TBA", October 2, 2023

Plans to sequence everyone in the developed world at birth were developed three decades ago. This is now plausible, and companies offer newborn sequencing as an option to parents—sometimes as an alternative to newborn screening (NBS) which identifies rare, treatable conditions that require urgent intervention. Yet the benefits and risks remain largely unknown. We probed the potential and pitfalls of performing pervasive population-scale public health sequencing of newborns. To do so, we drew upon an unparalleled NBS public health resource and used inborn errors of metabolism (IEMs) as a model system for human genetics.

We obtained archived residual dried blood spots and data for nearly all IEM cases from the 4.5 million infants born in California during an 8.5 year period. We found that exome analysis alone was insufficiently sensitive or specific to be a primary screen for most NBS IEMs. However, as a secondary test for infants, exomes could reduce false-positive results, facilitate timely case resolution and in some instances even suggest more appropriate or specific diagnosis. Sequence-based NBS could also be the foundation of a learning public health system identifying additional disorders.

As genomic data become increasingly mainstream, privacy risks have garnered increasing attention. Forensic cases using previously unidentifiable DNA have direct implications for research data. We found that consumer genomics and biological discovery activate latent privacy risk in ’omics data, including data scrubbed of any genetic variation information. I will briefly discuss how data previously deemed safe by privacy researchers for unrestricted sharing now appear to be at risk of potential re-identification.

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Created by Jose Abola Email at Thursday, September 28, 2023 at 9:52 AM.