Posts Tagged ‘x78qt’

‘Sanitizing’ functional genomics data may prevent privacy breaches | Spectrum | Autism Research News

January 8, 2021

Researchers simulate privacy leaks in functional genomics studies — ScienceDaily

November 15, 2020

Q&A: A New Tool for Ensuring Genetic Privacy | The Scientist Magazine(R)

November 15, 2020

Yale team finds way to protect genetic privacy in research | YaleNews

November 15, 2020

Covid-19 vaccine distribution agreement with pharmacies, measles cases hit 23-year high, & participation in cancer trials

November 15, 2020

Lab Chat: Cleaning up genetic data to protect privacy but get maximum use

As research using genetic data has accelerated in recent decades, scientists are trying to find ways to get the most out of the data while still preserving individuals’ privacy. In a new study, experts describe a program that allows them to “sanitize” and blur out any identifying genetic variants in available data. I spoke with Mark Gerstein and Gamze Gursoy, two authors of the study and bioinformatics researchers at Yale, to learn more:

What is the current problem with privacy, and which datasets have this problem? Gerstein: There is this binary view of privacy — either the data is locked or not locked. It’s hard to aggregate data when it’s locked down and what we’re trying to do in the paper is measure the amount of private information in there so we can just remove that [and access the rest].
Gursoy: Some examples of databases with this problem are the Cancer Genome Atlas, and even the one we manage, called PsychENCODE [for understanding the genetics of psychiatric disorders].

How did you cover up the private data?
Gursoy: We have a reference genome that represents everyone — but there is 1% that’s unique to each of us. So, if you see an “A” in the genetic code of the reference genome, but a “G” in the data you have, you change it to the “A.”
Gerstein: When you use Google’s Street View, the people on the street are unimportant to the information you’re trying to get about stores, etc. The Google car takes pictures of people’s faces, but then finds people in the images and blurs them out. Our process is similar. “}}

Insights & Outcomes: a new spin on quantum research, and the biology of sex | YaleNews

August 3, 2020
ENCODE and the dance between genes and DNA/RNA
Since 2003, the lab of Yale’s Mark Gerstein has played a major role in an international effort to catalog data on the complex interactions between genes and the segments of DNA and RNA that regulate their functions. The latest findings of the ENCODE project were published July 29 in 30 papers, four spearheaded by Gerstein’s lab, in a variety of scientific journals. Jing Zhang and Donghoon Lee from Gerstein’s lab have created a video illustrating science’s evolving understanding of the complex regulatory networks that can contribute to cancer and other diseases. The latest findings by the Gerstein lab and other major ENCODE contributors can be found on the Gerstein lab website. “}}

DNAaaahahaha: Twins’ 23andMe, Ancestry, etc genetic tests vary wildly, surprising no one • The Register

January 19, 2019

Inauguration of the Yale Center for Biomedical Data Science

January 30, 2018

Is Genetic Privacy a Myth?

October 28, 2017

But it’s the very specificity of genomic data that threatens privacy. Although most genomic databases strip away any information linking a name to a genome, such information is very hard to keep anonymous. “I’m not convinced you can truly de-identify the data,” says Mark Gerstein, a Yale professor who studies large genetic databases and is a fierce privacy advocate. He is concerned about whether even the most cutting-edge protections can safeguard personal data. “I am not a believer that large-scale technical solutions or ‘super-encryption’ will solely work,” he says. “There also needs to be a process for credentialing the individuals who access this data.”

Threats to privacy could multiply once there is an active market for genetic data. Wood speculates that it could be valuable to life insurance companies, which could use it to raise your premiums; or it could become a tool for those who want to prove or disprove paternity. White nationalist groups, who have become preoccupied with genetic testing, might find a way to weaponize the ancestry data the tests can show. It would not be the first time genetic information was used against a race or races. “Genetics has a very troubled history, from Darwin on,” says Yale’s Mark Gerstein.

Yet Columbia’s Yaniv Erlich and others, including Church, fear differential privacy could compromise biomedical research, with smudged data making it harder to get clear results. Mark Gerstein at Yale believes that scientists would be better off testing hypotheses on small amounts of publicly available but pure data, even if it’s not representative of the overall population, rather than using larger quantities of imperfect data.

Is Genetic Privacy a Myth?
Genetic tests and genome sequencing are generating terabytes of sensitive private data. How can they be kept safe?

Shedding light on the dark proteome

April 24, 2017

“The dark proteome could be an evolutionary playground for trying out new folds

Ultimately one would expect particularly useful variations to get fixed at the genetic level. But it needn’t be where that variation begins. What’s more, organisms needn’t be quite so dependent for their molecular repertoire on their evolutionary heritage. O’Donoghue thinks that all organisms probably have a significant fraction of proteins unique just to them.

‘The fact that the dark matter of the proteome has less evolutionary constraint than the other bits of proteome may suggest that it’s under less selection,’ says Gerstein. ‘This is perhaps because it’s more flexible structurally, but also in a sense more flexible in terms of accommodating various amino-acid changes compared to the structurally inflexible and fixed parts of the crystallised proteome.’ This adds momentum to the picture of genomics as a rather more fluid affair than is suggested by the old picture of identical proteins being
mass-produced from a fixed genetic template.

Gerstein feels that studying the dark proteome opens up a host of interesting questions. For example, although known bacteria have a smaller dark proteome than eukaryotes, there’s a huge ‘dark
microbiome’ of unculturable bacteria. Might that be more full of dark proteins – perhaps useful ones?

And what about us? ‘How does the human dark proteome compare to that of eukaryotes as a whole?’ Gerstein wonders. How well, really, do we know ourselves?”

Shedding light on the dark proteome