899 W. Evelyn Ave Mountain View, CA January 24th, 2019 - 23andMe Research
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899 W. Evelyn Ave
January 24th, 2019
Mountain View, CA
Welcome
Genetic data is of limited value
without its longtime partner,
phenotypic data
When we talk about the potential value of human genetic research, many people immediately focus on the rapidly increasing volume of genetic data that is now available for study. But as anyone in the field knows, genetic data is of limited value without its longtime partner, phenotypic data. For human genetics to have a real impact, we need to be good at collecting phenotypes — the set of individual characteristics resulting from the interaction of its genotype with the environment However, to talk about phenotypic data collection as a single thing is not entirely sensible, as the world of phenotypic data is incredibly broad and diverse — from disease diagnosis to biometrics, to diet and exercise habits. In addition, in order for the collection of phenotypes to scale up to the level at which we can perform adequately powered studies, the collection methods need to be efficient and cost-effective. This is currently not true for many (most) phenotypes. Fortunately, there is hope! In the same way that technology has made communication and information sharing increasingly accessible, cheap, and easy, it can do the same for data collection. Mobile apps, consumer devices, APIs to live datasets — all of these have the ability to generate high-quality data for research at scale. The key will be to bring the phenotype experts, technologists, and researchers together to work out smart solutions, and there’s no better place for that to happen than the Bay Area. This is why we are hosting the inaugural Future of Phenotyping conference — to bring together scientists from our community who are developing and using the next generation of phenotyping methods. By sharing ideas, we hope to inspire and accelerate the work that will help people live better, healthier lives. Sincerely, Joyce Tung Vice President, Research 23andMe, Inc.
Schedule
Posting about Future of Phenotyping on Twitter?
Use #Pheno199:15 AM Introduction
Geoff Benton, Ph.D. | Director of Health R&D at 23andMe, Inc.
9:30 AM Keynote Talks
Steve Hershman, Ph.D. | Director of mHealth at Stanford University School of Medicine
Greg Sommer, Ph.D. | Founder and CSO of Sandstone Diagnostics, Inc.
Akash Kumar, M.D., Ph.D. | Pediatric Genetics Resident at Stanford University School of
Medicine
Maayan Cohen | CEO and Co-Founder of Hello Heart, Inc.
Ryan Hays | Research Assistant at Torous Lab/Beth Israel Deaconess Medical Center, Harvard
Medical School
Matthew McIntyre, Ph.D. | Senior Scientist, Data Collection at 23andMe, Inc.
12:00 PM Lunch
Choose a theme:
Apps and Wearables • Longitudinal Engagement • Medical Records at Scale
1:30 PM 23andMe Info Sessions
Choose a focus:
Working at 23andMe • Collaborating with 23andMe
2:10 PM 23andMe Lightning Talks
Yunru (Claire) Huang, Ph.D. | Scientist, Biostatistics
Stella Aslibekyan, Ph.D. | Genetic Epidemiologist
Karl Heilbron, D.Phil. | Post-Doctoral Computational Biologist
Liz Babalola | Scientist, Data Collection
3:00 PM Panel Discussion
Moderator: Sarah Laskey, Ph.D. | Scientist, Health R&D at 23andMe, Inc.
Geoff Benton, Ph.D. | Director of Health R&D at 23andMe, Inc.
Julia Hu | Founder and CEO of Lark Technologies, Inc.
Scarlet Shore | Product Manager and Platform Lead at Verily Life Sciences LLC.
Steve Hershman, Ph.D. | Director of mHealth at Stanford University School of Medicine
4:00 PM Happy HourKeynote Talks
Crowdsourcing genotypes for association studies:
Results from the MyHeart Counts ResearchKit study
Steven Hershman, Ph.D.
Director of mHealth at Stanford University School of Medicine
MyHeart Counts is an open-enrollment, smartphone-based research study that uses
ResearchKit to collect data about physical activity and cardiac risk factors to aid scientists
studying the prevention and treatment of heart disease. More than 60,000 users in the
United States, Hong Kong and the United Kingdom have discovered the app in the
iOS App Store and proceed to agree to participate in the study. The free app enables
users to complete tasks and answer surveys from iPhone while capturing a dataprint of
their lifestyle in order to compute a summary of each user’s heart health and areas for
improvement.
On March 20, 2016 we released version 1.7.0 of MyHeart Counts, which included an
activity that enabled existing 23andMe customers to complete a simple informed consent
process and grant us access to their genotypes. Credentials are sent to the mHealth server,
developed and run by Stanford’s Office of Information Resources and Technology, which
then pulls genotype data from 23andMe servers in a way that is de-identified, yet linkable
to the rest of the study data.
To date, 1,071 distinct citizen scientists have granted us with us access to their 23andMe
data. Such data can be used to validate self-reported responses. For example, we are able
to use PCA to separate individuals into groups that separated based on their reported
ethnicities. By correlating participants genotypes to their app data, we are able to study
the interaction of genetic variation, activity levels, fitness and cardiovascular health
outcomes to better understand what keeps hearts healthy. Our findings validate previously
reported associations as well as discover new ones.
These results show that it is possible to crowdsource genotypes and phenotypes using an
open-enrollment, smartphone-based investigation for the purpose of completing genome
wide association studies (GWAS).Sperm Count - The Sixth Vital Sign?
Greg Sommer, Ph.D.
Founder and CSO of Sandstone Diagnostics, Inc.
Male fertility is in crisis. The fertility rate has hit an all-time low in the US, and recent studies have
shown that the average sperm count has plummeted by over 50% over the past 4 decades and
shows no signs of leveling off. Researchers have also established a clear link between men’s
reproductive health and overall health: men who have a low sperm count and fertility issues are at
significantly higher risk of developing chronic diseases such as cardiovascular disease, diabetes, and
cancer.
Launched in 2017, Sandstone’s Trak Male Fertility Testing System is opening new insights into male
reproductive health by allowing men to measure and track their sperm count and semen volume at
home. Based on Sandstone’s patented CentriFluidic technology, the Trak System is a comprehensive
at-home testing kit that provides the most precise sperm count measurement available along with
convenient longitudinal tracking to see changes over time as men pursue health, lifestyle, and
medical interventions that impact sperm production.
In addition to consumer use, Trak is currently deployed in several private and NIH-funded studies
investigating health and lifestyle factors that impact sperm production and fertility outcomes.
Previously, male fertility studies relied on men to repeatedly visit a centralized laboratory for semen
analysis. By enabling testing and reporting from home, Trak has dramatically improved the cost,
convenience, and scope for fertility studies.
Working with leading Urologists who specialize in male reproductive health, we have also built a
personalized phenotypic assessment questionnaire to help men understand risks to their fertility
and get recommendations for how to improve. With nearly 20,000 entries to date, Trak’s fertility
assessment questionnaire is unlocking new insights into how health and lifestyle factors impact
sperm count and fertility, and clearly emphasizes that sperm count is a marker for overall health.
This talk will provide an overview of the current understandings
and gaps around male reproductive health, including the
phenotypes associated with impaired fertility in men. This
talk will also cover the genetic tests clinically used in male
infertility diagnoses. Finally, we will discuss why sperm count is
increasingly viewed as a new marker for overall health in men,
and may soon be considered a Sixth Vital Sign for men.Facial Measurements for Genetic Evaluation
Using a Mobile Phone
Akash Kumar, M.D., Ph.D.
Pediatric Genetics Resident, Stanford University School of Medicine
Conventional dysmorphology involves measuring specific facial features to aid in identifying
individuals with rare diseases. Future approaches may leverage computer assisted evaluation of
facial images. However, 2D-image-based techniques are limited by artifacts related to projection
distortion and head pose affecting measurement accuracy. Capturing 3D images can circumvent
these limitations, but many current devices are bulky and difficult to use.
Infrared-based sensors used for facial recognition in mobile phones (e.g. iPhone
X) can now capture 3D images and their inherent portability and ubiquity may
overcome major limitations of current 3D technologies. Before use in clinical
practice, evaluation of their measurements under ideal and clinical circumstances
is needed to identify and address sources of error.
Under ideal circumstances, a mannequin head labeled with markers was used
to examine accuracy of the 3dMD system (3dMD, Atlanta GA) as compared
to an iPhone X face-capturing application. Three facial images were captured
using both devices. Facial meshes from 3dMD and iPhone X were overlaid and
aligned using a computational algorithm. Point-point distances of facial landmarks
(palpebral fissure length, inner/outer canthal distance, ear length, mouth width)
were calculated in triplicate for each image using MeshLab software. Error was
calculated by comparing point-point distances and comparing the alignment of
each facial mesh.
Alignment and comparison of the mesh obtained from 3dMD and the iPhone X revealed a global
alignment error of 0.42-0.60mm. The average differences in linear measurements from 3dMD and
the iPhone X ranged from 0.07-1.47mm for various landmarks with measurements of lateral features
more error prone than measurement of features in the anterior face. Additional studies in humans
are underway.
In this pilot study, the accuracy of an iPhone X facial scanner was evaluated for use in a genetics
clinic. The ease of use and portability of the system are clear advantages. Limitations include the
need for cooperation during scanning as well as reduced accuracy over specific facial landmarks.
Additional studies are needed before the platform can be adopted as an addition to manual
anthropometry and 2D photography.Improving Hypertension and Heart Health Using
Smartphone Technology: A clinical study review
Maayan Cohen
CEO and Co-Founder of Hello Heart, Inc.
This session will review the clinical outcomes of using gamification and smartphones
to increase engagement in patient health. Published in Health Information Science
and Systems, the 2017 study, “Improving Patient Engagement in Self-Measured Blood
Pressure Monitoring Using a Mobile Health Technology,” demonstrated improved
patient engagement in cardiac patients. Hello Heart’s solution demonstrated a
meaningful blood pressure drop for 50% of patients.
Digital Phenotyping Towards Advancing
Relapse Prediction in Serious Mental Illnesses
Ryan Hays
Research Assistant, Torous Lab/Beth Israel Deaconess Medical Center,
Harvard Medical School
Digital phenotyping, defined as the moment-by-moment quantification of the
individual-level human phenotype in-situ using data from personal digital devices, is
an emerging tool in the field of psychiatric research. Traditionally, patient observation
has been reserved to infrequent clinical visits using “gold standard” paper-and-pencil
tests; with digital phenotyping, researchers and clinicians can now continually observe
patients with serious mental illness (SMI) through the collection both active and passive
social and behavioral data.
Using LAMP, a digital phenotyping platform designed with behavioral health in mind, we are
currently performing a 90-day longitudinal study in patients with schizophrenia, bipolar disorder, and
major depressive disorder. Our platform measures and quantifies the lived experiences of those with
mental illness across cognition, depressive/psychotic/anxiety symptoms, physical activity and more
in a temporally dense and longitudinal manner. By combining these numerous parallel data streams,
we will discuss clinically-relevant insights into relapse prediction, app usability, patient
engagement, and digital health ethics.Validity of the Cold Pressor Test and Pain Sensitivity
Questionnaire via Online Self-Administration
Matthew McIntyre, Ph.D.
Senior Scientist, Data Collection at 23andMe, Inc.
Research participants from the customer base of 23andMe were invited to participate in an online
version of a pain sensitivity questionnaire (PSQ) as well as a cold pressor test which is used in
clinical assessments of pain. Overall our online version of the PSQ performed similarly to the
original pen-and-paper version. Convergent validity of the PSQ total was demonstrated by internal
consistency and consistent discrimination between more and less painful items. Criterion validity was
demonstrated by correlation with pain sensitivity as measured by the cold pressor test (CPT).
Within the same cohort we performed a cold pressor test using
a layperson description and household equipment. Comparison
with published reports from controlled studies revealed similar
distributions of cold pain tolerance times (i.e., time elapsed
before removing the hand from the water). Of those who elected
to participate in the CPT, a large majority of participants did not
report issues with the test procedure or noncompliance to the
instructions (97%). We confirmed a large sex difference in CPT
thresholds in line with published data, such that women removed
their hands from the water at a median of 52.3 seconds, which
was 31.0 seconds earlier than the median for men (Kruskal-Wallis
statistic, p < 0.0001), but other factors like age or current pain
treatment were, at most, weakly associated, and inconsistent
between men and women.
We introduced a new paradigm for performing pain testing, called testing@home, that showed
comparable results to studies conducted under controlled conditions and supervision of a
healthcare professional.Lunch
Choose a theme
Apps and Wearables Longitudinal Engagement Medical Records at Scale
23andMe Info Session
Choose a focus
Working at 23andMe Collaborating with 23andMe
Timeless - 4th Floor LunchroomLightning Talks
Brain games: Implementation and research
insights of online cognitive assessments
Yunru (Claire) Huang, Ph.D.
Scientist, Biostatistics
Studies suggest complicated relationships among genetics, aging and brain
functions. This talk will describe our five cognitive games, which measure specific
aspects of brain aptitude, as well as discuss the performance of over 40,000 23andMe
consented research participants.
Using 23andMe data to explore the phenomes of
Parkinson’s disease and cognitive function
Stella Aslibekyan, Ph.D. Genetic Epidemiologist
Karl Heilbron, D.Phil. Post-Doctoral Computational Biologist
The 23andMe database contains a wealth of phenotypes derived from online
surveys and games. Using these data, we comprehensively characterized the
phenomes of both Parkinson’s disease and cognitive game performance.
Hear me out: Implementing a web-based
hearing assessment
Liz Babalola
Scientist, Biostatistics
Hearing loss has been associated with social isolation, depression, cognitive decline
and reduced physical well-being among older adults. This project aims to identify the
environmental and genetic factors contributing to age-related hearing impairment in the
23andMe cohort using an online validated digits-in-noise test.Panel Discussion
Future opportunities and challenges in phenotyping large cohorts
Moderator:
Sarah Laskey, Ph.D.
Scientist, Health R&D at
23andMe, Inc.
Steven Hershman, Ph.D. Julia Hu
Director of mHealth at Stanford Founder and CEO of
University School of Medicine Lark Technologies, Inc.
Geoff Benton, Ph.D. Scarlet Shore
Director of Health R&D at Product Manager and Platform Lead
23andMe, Inc. at Verily Life Sciences LLC
Happy HourResources
Interested in…
...collaborating with 23andMe? Please visit:
https://research.23andme.com/collaborate/
...careers at 23andMe? Please visit:
https://www.23andme.com/careers/
...23andMe publications? Please visit:
https://research.23andme.com/publications/
...latest news from 23andMe? Follow @23andMeResearch on Twitter
Let us know what you thought of Future of Phenotyping!
Fill out a survey at https://research.23andme.com/phenosurvey/
by 1/28 for the chance to win a free 23andMe kit.Notes
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