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New Genome App from NYGC, Columbia U Team Targets Never-Been-Sequenced Individuals

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NEW YORK (GenomeWeb) – Seeking to reach members of the population who want to be part of genetic studies but do not have access to their genomic data, researchers from the New York Genome Center and Columbia University are offering sequencing services and a free app for smart phones called Seeq.

For $50, interested individuals receive a specimen collection kit for providing a saliva sample which they then mail to the NYGC. They also install the free Seeq app, available for both Android and Apple operating systems, through which the app developers will share some basic analysis results as well as recruit participants for research.

Joseph Pickrell, an NYGC core member, adjunct assistant professor at Columbia, and one of Seeq's developers, told GenomeWeb that his team began developing Seeq, now in beta testing, about a year ago in response to growing interest from the general population to participate in genomics-based research projects as well as interest in what their genes can tell them about their ancestry, personality traits and quirks, and other details.

That interest has prompted many people to avail themselves of the services of direct-to-consumer companies such as 23andMe and Ancestry.com. It has also encouraged them to participate in efforts such as DNA.Land, a non-profit effort launched last year by researchers from Columbia and NYGC, and GenomeConnect, which enables patients with rare diseases to contribute de-identified genotype and phenotype information to public databases. Furthermore, at least one company, Portable Genomics, is looking to help patients profit from the use of their genomic data by brokering revenue-sharing arrangements with for-profit and non-profit companies and research organizations who want access to patient data for research studies.

Seeq targets individuals who have not had their genomes analyzed by DTC testing services, Pickrell said, and offers them an opportunity to both participate in research and learn something about themselves. It uses a similar approach to DNA.Land's in the sense that both resources offer ancestry among other kinds of information to users who can also contribute those datasets to academic research projects. The main difference is that DNA.Land targets individuals who have already had their genomes sequenced by DTC companies and asks them to contribute those datasets to research. According to the most recent numbers from the DNA.Land site, 29,205 people have contributed their genomes to the project so far. The projects will eventually connect to each other, said Pickrell, who is also involved with the DNA.Land project, and Seeq users will be able to seamlessly transfer their data from Seeq to DNA.Land if they so choose.

In order to purchase the spit kit, Seeq users have to go through a four-step consent process to agree to participate in research. Full details of consent protocols are provided here. When Pickrell's team receives Seeq users' samples, it performs shotgun sequencing on them and then analyzes the data using two algorithms. The first is a bespoke implementation of a population genetics algorithm called Structure that was developed by researchers in the statistics department of the University of Oxford. The version of the software used by the Seeq team, called Ancestry, infers an individual's ancestry works by mapping their sequence reads to genome data from different populations around the world and then modeling the test individual as a mixture of the populations. Like DNA.Land users, Seeq app users get approximate information about where their ancestors might have lived a few centuries ago. 

The Seeq researchers also use the Kraken software, developed by researchers at Johns Hopkins University, to analyze submitted samples and characterize the mouth microbiome of Seeq participant. Not only do they offer insights into the bacteria, viruses, and other microbes in individual's mouth, they also return information about the food that person ate around the time that the sample was collected. It takes six to eight weeks to go from saliva sample to result in the Seeq app.  

In addition to sharing their information with NYGC, Seeq users can share their information with researchers at other institutions if they choose to, Pickrell told GenomeWeb. They can request the raw sequence from the NYGC researchers who will provide a link where users can download their Bam files. Pickrell's lab does not share Seeq users' data with any third parties, however, they are willing to work with researchers from institutions who want to include responses from Seeq participants in their studies. In fact, Pickrell said that the team has begun reaching out to some large research consortia to gauge their interest in using the app for their studies. "We've had a lot of interest from researchers who also are interested in these sorts of things who don't have the internal expertise to run a lab or write an app," he said.

For now, his lab is using the app for its own research studies. For example, some researchers are interested in studying the genetics of sleep patterns. To help with that, the Seeq team has added a questionnaire to the app through which they hope to gather useful information from participants for the study, he said. They have also added questionnaires that are aimed at gathering information for studies on things like personality and food preferences as well as in studies focused on microbiome genetics. Users are free to withdraw from any research studies they previously consented to at any time.

Pickrell told GenomeWeb that his team plans to publish details of some internal pilots they did as part of Seeq's development in the near future. Prior to starting the beta, they tested the Seeq app on data from individuals from the 1000 Genomes project "to make sure we could correctly infer their ancestry and impute missing variants" as well as on a larger sample of individuals who self-reported their ancestry "to make sure our algorithms performed well in a more real-world situation," he said.

The Seeq beta will likely last for several months. It will officially end "once we are confident that all the major kinks and bugs have been worked out," Pickrell said. Over the course of the beta, he and his colleagues will gather feedback from app users about features that they would like to see in future iterations of the app and will try to implement them where possible, he said. They already have some new features that they hope to roll out in the coming months. For example, Pickrell said that some users have expressed interest in using their genetic sequences to find unknown and distant relatives — this is information that DNA.Land users receive as part of their results. 

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