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% This file was created with JabRef 2.8.
% Encoding: ISO8859_1
@ARTICLE{23andMe2012,
author = {23andMe},
title = {{23andMe Privacy Statement http://www.23andme.com/about/privacy/}},
journal = {23andMe Homepage},
year = {2012},
howpublished = {\url{http://www.23andme.com/about/privacy/}}
}
@ARTICLE{23andMe2011,
author = {23andMe},
title = {{23andMe 2011 State of the Database Address}},
journal = {The Spittoon http://spittoon.23andme.com/2011/06/15/23andme-2011-state-of-the-database-address/},
year = {2011},
number = {June 15},
howpublished = {\url{http://spittoon.23andme.com/2011/06/15/23andme-2011-state-of-the-database-address/}},
type = {Blog}
}
@ARTICLE{prostatecancer,
author = {Abate-Shen, Cory and Shen, Michael M.},
title = {Molecular genetics of prostate cancer},
journal = {Genes \& Development},
year = {2000},
volume = {14},
pages = {2410-2434},
number = {19},
doi = {10.1101/gad.819500},
eprint = {http://genesdev.cshlp.org/content/14/19/2410.full.pdf+html},
url = {http://genesdev.cshlp.org/content/14/19/2410.short}
}
@ARTICLE{Ball24072012,
author = {Ball, Madeleine P. and Thakuria, Joseph V. and Zaranek, Alexander
Wait and Clegg, Tom and Rosenbaum, Abraham M. and Wu, Xiaodi and
Angrist, Misha and Bhak, Jong and Bobe, Jason and Callow, Matthew
J. and Cano, Carlos and Chou, Michael F. and Chung, Wendy K. and
Douglas, Shawn M. and Estep, Preston W. and Gore, Athurva and Hulick,
Peter and Labarga, Alberto and Lee, Je-Hyuk and Lunshof, Jeantine
E. and Kim, Byung Chul and Kim, Jong-Il and Li, Zhe and Murray, Michael
F. and Nilsen, Geoffrey B. and Peters, Brock A. and Raman, Anugraha
M. and Rienhoff, Hugh Y. and Robasky, Kimberly and Wheeler, Matthew
T. and Vandewege, Ward and Vorhaus, Daniel B. and Yang, Joyce L.
and Yang, Luhan and Aach, John and Ashley, Euan A. and Drmanac, Radoje
and Kim, Seong-Jin and Li, Jin Billy and Peshkin, Leonid and Seidman,
Christine E. and Seo, Jeong-Sun and Zhang, Kun and Rehm, Heidi L.
and Church, George M.},
title = {A public resource facilitating clinical use of genomes},
journal = {Proceedings of the National Academy of Sciences},
year = {2012},
volume = {109},
pages = {11920-11927},
number = {30},
abstract = {Rapid advances in DNA sequencing promise to enable new diagnostics
and individualized therapies. Achieving personalized medicine, however,
will require extensive research on highly reidentifiable, integrated
datasets of genomic and health information. To assist with this,
participants in the Personal Genome Project choose to forgo privacy
via our institutional review board- approved “open consent” process.
The contribution of public data and samples facilitates both scientific
discovery and standardization of methods. We present our findings
after enrollment of more than 1,800 participants, including whole-genome
sequencing of 10 pilot participant genomes (the PGP-10). We introduce
the Genome-Environment-Trait Evidence (GET-Evidence) system. This
tool automatically processes genomes and prioritizes both published
and novel variants for interpretation. In the process of reviewing
the presumed healthy PGP-10 genomes, we find numerous literature
references implying serious disease. Although it is sometimes impossible
to rule out a late-onset effect, stringent evidence requirements
can address the high rate of incidental findings. To that end we
develop a peer production system for recording and organizing variant
evaluations according to standard evidence guidelines, creating a
public forum for reaching consensus on interpretation of clinically
relevant variants. Genome analysis becomes a two-step process: using
a prioritized list to record variant evaluations, then automatically
sorting reviewed variants using these annotations. Genome data, health
and trait information, participant samples, and variant interpretations
are all shared in the public domain—we invite others to review
our results using our participant samples and contribute to our interpretations.
We offer our public resource and methods to further personalized
medical research.},
doi = {10.1073/pnas.1201904109},
eprint = {http://www.pnas.org/content/109/30/11920.full.pdf+html},
url = {http://www.pnas.org/content/109/30/11920.abstract}
}
@ARTICLE{Bove2013,
author = {Bove, Riley and Secor, Elizabeth and Healy, Brian C. and Musallam,
Alexander and Vaughan, Timothy and Glanz, Bonnie I. and Greeke, Emily
and Weiner, Howard L. and Chitnis, Tanuja and Wicks, Paul and {De
Jager}, Philip L.},
title = {Evaluation of an online platform for multiple sclerosis research:
patient description, validation of severity scale, and exploration
of BMI effects on disease course.},
journal = {PLoS One},
year = {2013},
volume = {8},
pages = {e59707},
number = {3},
abstract = {To assess the potential of an online platform, PatientsLikeMe.com
(PLM), for research in multiple sclerosis (MS). An investigation
of the role of body mass index (BMI) on MS disease course was conducted
to illustrate the utility of the platform.First, we compared the
demographic characteristics of subjects from PLM and from a regional
MS center. Second, we validated PLM's patient-reported outcome measure
(MS Rating Scale, MSRS) against standard physician-rated tools. Finally,
we analyzed the relation of BMI to the MSRS measure.Compared with
4,039 MS Center patients, the 10,255 PLM members were younger, more
educated, and less often male and white. Disease course was more
often relapsing remitting, with younger symptom onset and shorter
disease duration. Differences were significant because of large sample
sizes but small in absolute terms. MSRS scores for 121 MS Center
patients revealed acceptable agreement between patient-derived and
physician-derived composite scores (weighted kappa = 0.46). The Walking
domain showed the highest weighted kappa (0.73) and correlation (rs
= 0.86) between patient and physician scores. Additionally, there
were good correlations between the patient-reported MSRS composite
and walking scores and physician-derived measures: Expanded Disability
Status Scale (composite rs = 0.61, walking rs = 0.74), Timed 25 Foot
Walk (composite rs = 0.70, walking rs = 0.69), and Ambulation Index
(composite rs = 0.81, walking rs = 0.84). Finally, using PLM data,
we found a modest correlation between BMI and cross-sectional MSRS
(rho = 0.17) and no association between BMI and disease course.The
PLM population is comparable to a clinic population, and its patient-reported
MSRS is correlated with existing clinical instruments. Thus, this
online platform may provide a venue for MS investigations with unique
strengths (frequent data collection, large sample sizes). To illustrate
its applicability, we assessed the role of BMI in MS disease course
but did not find a clinically meaningful role for BMI in this setting.},
doi = {10.1371/journal.pone.0059707},
institution = {Program in Translational NeuroPsychiatric Genomics, Department of
Neurology, Institute for the Neurosciences, Brigham and Women's Hospital,
Boston, Massachusetts, United States of America.},
language = {eng},
medline-pst = {ppublish},
owner = {drsnuggles},
pii = {PONE-D-12-37775},
pmid = {23527256},
timestamp = {2013.05.30},
url = {http://dx.doi.org/10.1371/journal.pone.0059707}
}
@ARTICLE{Brown1999,
author = {Brown, Patrick O. and Botstein, David},
title = {{ Exploring the new world of the genomewith DNA microarray}},
journal = {nature genetics supplement},
year = {1999},
volume = {21},
pages = {33--37}
}
@ARTICLE{Cariaso2011,
author = {Cariaso, Michael and Lennon, Greg},
title = {SNPedia: a wiki supporting personal genome annotation, interpretation
and analysis},
journal = {Nucleic Acids Research},
year = {2011},
abstract = {SNPedia (http://www.SNPedia.com) is a wiki resource of the functional
consequences of human genetic variation as published in peer-reviewed
studies. Online since 2006 and freely available for personal use,
SNPedia has focused on the medical, phenotypic and genealogical associations
of single nucleotide polymorphisms. Entries are formatted to allow
associations to be assigned to single genotypes as well as sets of
genotypes (genosets). In this article, we discuss the growth of this
resource and its use by affiliated software to create personal genome
reports.},
doi = {10.1093/nar/gkr798},
eprint = {http://nar.oxfordjournals.org/content/early/2011/12/02/nar.gkr798.full.pdf+html},
url = {http://nar.oxfordjournals.org/content/early/2011/12/02/nar.gkr798.abstract}
}
@ARTICLE{Caulfield2011,
author = {Caulfield, Timothy and McGuire, Amy L},
title = {Direct-to-Consumer Genetic Testing: Perceptions, Problems and Policy
Responses},
journal = {Annual Review of Medicine},
year = {2011},
volume = {63},
pages = {1.1-1.11},
doi = {10.1146/annurev-med-062110-123753}
}
@ARTICLE{Danecek01082011,
author = {Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers, Cornelis
A. and Banks, Eric and DePristo, Mark A. and Handsaker, Robert E.
and Lunter, Gerton and Marth, Gabor T. and Sherry, Stephen T. and
McVean, Gilean and Durbin, Richard and 1000 Genomes Project Analysis
Group},
title = {The variant call format and VCFtools},
journal = {Bioinformatics},
year = {2011},
volume = {27},
pages = {2156-2158},
number = {15},
abstract = {Summary: The variant call format (VCF) is a generic format for storing
DNA polymorphism data such as SNPs, insertions, deletions and structural
variants, together with rich annotations. VCF is usually stored in
a compressed manner and can be indexed for fast data retrieval of
variants from a range of positions on the reference genome. The format
was developed for the 1000 Genomes Project, and has also been adopted
by other projects such as UK10K, dbSNP and the NHLBI Exome Project.
VCFtools is a software suite that implements various utilities for
processing VCF files, including validation, merging, comparing and
also provides a general Perl API.Availability: http://vcftools.sourceforge.netContact:
doi = {10.1093/bioinformatics/btr330},
eprint = {http://bioinformatics.oxfordjournals.org/content/27/15/2156.full.pdf+html},
url = {http://bioinformatics.oxfordjournals.org/content/27/15/2156.abstract}
}
@ARTICLE{Darst2013,
author = {Darst, Burcu F. and Madlensky, Lisa and Schork, Nicholas J. and Topol,
Eric J. and Bloss, Cinnamon S.},
title = {Characteristics of Genomic Test Consumers Who Spontaneously Share
Results With Their Health Care Provider.},
journal = {Health Commun},
year = {2013},
month = {Feb},
abstract = {The purpose of this study was to evaluate the characteristics of direct-to-consumer
(DTC) genomic test consumers who spontaneously shared their test
results with their health care provider. Utilizing data from the
Scripps Genomic Health Initiative, we compared demographic, behavioral,
and attitudinal characteristics of DTC genomic test consumers who
shared their results with their physician or health care provider
versus those who did not share. We also compared genomic risk estimates
between the two groups. Of 2,024 individuals assessed at approximately
6 months post testing, 540 individuals (26.5\%) reported sharing
their results with their physician or health care provider. Those
who shared were older (p < .001), had a higher income (p = .01),
were more likely to be married (p = .005), and were more likely to
identify with a religion (p = .004). As assessed prior to undergoing
testing, sharers also reported higher levels of exercise (p = .003),
lower fat intake (p = .02), fewer overall concerns about testing
(p = .001), and fewer concerns related to the privacy of their genomic
information (p = .03). The genomic disease risk estimates disclosed
were not associated with sharing. Thus, in a DTC genomic testing
context, physicians and other health care providers may be more likely
to encounter patients who are more health conscious and have fewer
concerns about the privacy of their genomic information. Genomic
risk itself does not appear to be a primary determinant of sharing
behavior among consumers.},
doi = {10.1080/10410236.2012.717216},
institution = {a Scripps Genomic Medicine , Scripps Translational Science Institute,
Scripps Health.},
language = {eng},
medline-pst = {aheadofprint},
owner = {drsnuggles},
pmid = {23384116},
timestamp = {2013.05.30},
url = {http://dx.doi.org/10.1080/10410236.2012.717216}
}
@ARTICLE{CrowdsourcingReview2010,
author = {Dickinson, Janis L. and Zuckerberg, Benjamin and Bonter, David N.},
title = {{Citizen Science as an Ecological Research Tool: Challenges and Benefits}},
journal = {The Annual Review of Ecology, Evolution, and Systematics},
year = {2010},
volume = {41},
pages = {149--172},
citeulike-article-id = {10239704},
keywords = {citizen, nrc, science},
posted-at = {2012-01-18 15:45:27},
priority = {2}
}
@ARTICLE{Do2011,
author = {Chuong B Do and Joyce Y Tung and Elizabeth Dorfman and Amy K Kiefer
and Emily M Drabant and Uta Francke and Joanna L Mountain and Samuel
M Goldman and Caroline M Tanner and J. William Langston and Anne
Wojcicki and Nicholas Eriksson},
title = {Web-based genome-wide association study identifies two novel loci
and a substantial genetic component for Parkinson's disease.},
journal = {PLoS Genet},
year = {2011},
volume = {7},
pages = {e1002141},
number = {6},
month = {Jun},
abstract = {Although the causes of Parkinson's disease (PD) are thought to be
primarily environmental, recent studies suggest that a number of
genes influence susceptibility. Using targeted case recruitment and
online survey instruments, we conducted the largest case-control
genome-wide association study (GWAS) of PD based on a single collection
of individuals to date (3,426 cases and 29,624 controls). We discovered
two novel, genome-wide significant associations with PD-rs6812193
near SCARB2 (p = 7.6 × 10(-10), OR = 0.84) and rs11868035 near SREBF1/RAI1
(p = 5.6 × 10(-8), OR = 0.85)-both replicated in an independent
cohort. We also replicated 20 previously discovered genetic associations
(including LRRK2, GBA, SNCA, MAPT, GAK, and the HLA region), providing
support for our novel study design. Relying on a recently proposed
method based on genome-wide sharing estimates between distantly related
individuals, we estimated the heritability of PD to be at least 0.27.
Finally, using sparse regression techniques, we constructed predictive
models that account for 6\%-7\% of the total variance in liability
and that suggest the presence of true associations just beyond genome-wide
significance, as confirmed through both internal and external cross-validation.
These results indicate a substantial, but by no means total, contribution
of genetics underlying susceptibility to both early-onset and late-onset
PD, suggesting that, despite the novel associations discovered here
and elsewhere, the majority of the genetic component for Parkinson's
disease remains to be discovered.},
doi = {10.1371/journal.pgen.1002141},
institution = {23andMe, Mountain View, California, United States of America. [email protected]},
keywords = {Databases, Factual; Genetic Loci, genetics; Genetic Predisposition
to Disease; Genome-Wide Association Study; Heredity, genetics; Humans;
Internet; Parkinson Disease, genetics; Polymorphism, Single Nucleotide,
genetics; Risk Assessment},
language = {eng},
medline-pst = {ppublish},
owner = {drsnuggles},
pii = {PGENETICS-D-11-00444},
pmid = {21738487},
timestamp = {2011.12.13},
url = {http://dx.doi.org/10.1371/journal.pgen.1002141}
}
@ARTICLE{Dowell2001,
author = {Dowell, Robin and Jokerst, Rodney and Day, Allen and Eddy, Sean and
Stein, Lincoln},
title = {The Distributed Annotation System},
journal = {BMC Bioinformatics},
year = {2001},
volume = {2},
pages = {7},
number = {1},
abstract = {BACKGROUND:Currently, most genome annotation is curated by centralized
groups with limited resources. Efforts to share annotations transparently
among multiple groups have not yet been satisfactory.RESULTS:Here
we introduce a concept called the Distributed Annotation System (DAS).
DAS allows sequence annotations to be decentralized among multiple
third-party annotators and integrated on an as-needed basis by client-side
software. The communication between client and servers in DAS is
defined by the DAS XML specification. Annotations are displayed in
layers, one per server. Any client or server adhering to the DAS
XML specification can participate in the system; we describe a simple
prototype client and server example.CONCLUSIONS:The DAS specification
is being used experimentally by Ensembl, WormBase, and the Berkeley
Drosophila Genome Project. Continued success will depend on the readiness
of the research community to adopt DAS and provide annotations. All
components are freely available from the project website http://www.biodas.org/
webcite.},
doi = {10.1186/1471-2105-2-7},
issn = {1471-2105},
pubmedid = {11667947},
url = {http://www.biomedcentral.com/1471-2105/2/7}
}
@ARTICLE{Eiben2012,
author = {Eiben, Christopher B. and Siegel, Justin B. and Bale, Jacob B. and
Cooper, Seth and Khatib, Firas and Shen, Betty W. and Players, Foldit
and Stoddard, Barry L. and Popovic, Zoran and Baker, David},
title = {Increased Diels-Alderase activity through backbone remodeling guided
by Foldit players.},
journal = {Nat Biotechnol},
year = {2012},
volume = {30},
pages = {190--192},
number = {2},
month = {Feb},
abstract = {Computational enzyme design holds promise for the production of renewable
fuels, drugs and chemicals. De novo enzyme design has generated catalysts
for several reactions, but with lower catalytic efficiencies than
naturally occurring enzymes. Here we report the use of game-driven
crowdsourcing to enhance the activity of a computationally designed
enzyme through the functional remodeling of its structure. Players
of the online game Foldit were challenged to remodel the backbone
of a computationally designed bimolecular Diels-Alderase to enable
additional interactions with substrates. Several iterations of design
and characterization generated a 24-residue helix-turn-helix motif,
including a 13-residue insertion, that increased enzyme activity
>18-fold. X-ray crystallography showed that the large insertion adopts
a helix-turn-helix structure positioned as in the Foldit model. These
results demonstrate that human creativity can extend beyond the macroscopic
challenges encountered in everyday life to molecular-scale design
problems.},
doi = {10.1038/nbt.2109},
institution = {Department of Biochemistry, University of Washington, Seattle, Washington,
USA.},
keywords = {Algorithms; Catalysis; Computational Biology; Crystallography, X-Ray;
Enzymes, chemical synthesis/chemistry; Helix-Turn-Helix Motifs; Humans;
Models, Molecular; Protein Engineering, methods; Structure-Activity
Relationship; Substrate Specificity; Video Games},
language = {eng},
medline-pst = {epublish},
owner = {drsnuggles},
pii = {nbt.2109},
pmid = {22267011},
timestamp = {2013.06.01},
url = {http://dx.doi.org/10.1038/nbt.2109}
}
@ARTICLE{Eriksson2010,
author = {Nicholas Eriksson and J. Michael Macpherson and Joyce Y Tung and
Lawrence S Hon and Brian Naughton and Serge Saxonov and Linda Avey
and Anne Wojcicki and Itsik Pe'er and Joanna Mountain},
title = {Web-based, participant-driven studies yield novel genetic associations
for common traits.},
journal = {PLoS Genet},
year = {2010},
volume = {6},
pages = {e1000993},
number = {6},
month = {Jun},
abstract = {Despite the recent rapid growth in genome-wide data, much of human
variation remains entirely unexplained. A significant challenge in
the pursuit of the genetic basis for variation in common human traits
is the efficient, coordinated collection of genotype and phenotype
data. We have developed a novel research framework that facilitates
the parallel study of a wide assortment of traits within a single
cohort. The approach takes advantage of the interactivity of the
Web both to gather data and to present genetic information to research
participants, while taking care to correct for the population structure
inherent to this study design. Here we report initial results from
a participant-driven study of 22 traits. Replications of associations
(in the genes OCA2, HERC2, SLC45A2, SLC24A4, IRF4, TYR, TYRP1, ASIP,
and MC1R) for hair color, eye color, and freckling validate the Web-based,
self-reporting paradigm. The identification of novel associations
for hair morphology (rs17646946, near TCHH; rs7349332, near WNT10A;
and rs1556547, near OFCC1), freckling (rs2153271, in BNC2), the ability
to smell the methanethiol produced after eating asparagus (rs4481887,
near OR2M7), and photic sneeze reflex (rs10427255, near ZEB2, and
rs11856995, near NR2F2) illustrates the power of the approach.},
doi = {10.1371/journal.pgen.1000993},
institution = {23andMe, Mountain View, California, United States of America. [email protected]},
keywords = {Chromosomes, Human; Genetic Variation; Genome-Wide Association Study,
methods; Genomics; Genotype; Hair; Humans; Internet; Models, Genetic;
Phenotype},
language = {eng},
medline-pst = {epublish},
owner = {drsnuggles},
pmid = {20585627},
timestamp = {2011.12.13},
url = {http://dx.doi.org/10.1371/journal.pgen.1000993}
}
@ARTICLE{Finn2007,
author = {Finn, Robert D. and Stalker, James W. and Jackson, David K. and Kulesha,
Eugene and Clements, Jody and Pettett, Roger},
title = {ProServer: a simple, extensible Perl DAS server},
journal = {Bioinformatics},
year = {2007},
volume = {23},
pages = {1568-1570},
number = {12},
abstract = {Summary: The increasing size and complexity of biological databases
has led to a growing trend to federate rather than duplicate them.
In order to share data between federated databases, protocols for
the exchange mechanism must be developed. One such data exchange
protocol that is widely used is the Distributed Annotation System
(DAS). For example, DAS has enabled small experimental groups to
integrate their data into the Ensembl genome browser. We have developed
ProServer, a simple, lightweight, Perl-based DAS server that does
not depend on a separate HTTP server. The ProServer package is easily
extensible, allowing data to be served from almost any underlying
data model. Recent additions to the DAS protocol have enabled both
structure and alignment (sequence and structural) data to be exchanged.
ProServer allows both of these data types to be served.Availability:
ProServer can be downloaded from http://www.sanger.ac.uk/proserver/
or CPAN http://search.cpan.org/~rpettett/. Details on the system
requirements and installation of ProServer can be found at http://www.sanger.ac.uk/proserver/.Contact:
[email protected] Materials: DasClientExamples.pdf},
doi = {10.1093/bioinformatics/btl650},
eprint = {http://bioinformatics.oxfordjournals.org/content/23/12/1568.full.pdf+html},
url = {http://bioinformatics.oxfordjournals.org/content/23/12/1568.abstract}
}
@ARTICLE{fitbit,
author = {FitbitInc},
title = {{Fitbit http://www.fitbit.com}},
journal = {Fitbit Homepage},
year = {2012},
howpublished = {\url{http://www.23andme.com/about/privacy/}}
}
@ARTICLE{GelMoreno2011,
author = {Gel Moreno, Bernat and Jenkinson, Andrew and Jimenez, Rafael and
Messeguer Peypoch, Xavier and Hermjakob, Henning},
title = {easyDAS: Automatic creation of DAS servers},
journal = {BMC Bioinformatics},
year = {2011},
volume = {12},
pages = {23},
number = {1},
abstract = {BACKGROUND:The Distributed Annotation System (DAS) has proven to be
a successful way to publish and share biological data. Although there
are more than 750 active registered servers from around 50 organizations,
setting up a DAS server comprises a fair amount of work, making it
difficult for many research groups to share their biological annotations.
Given the clear advantage that the generalized sharing of relevant
biological data is for the research community it would be desirable
to facilitate the sharing process.RESULTS:Here we present easyDAS,
a web-based system enabling anyone to publish biological annotations
with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas
webcite is capable of reading different standard data file formats,
process the data and create a new publicly available DAS source in
a completely automated way. The created sources are hosted on the
EBI systems and can take advantage of its high storage capacity and
network connection, freeing the data provider from any network management
work. easyDAS is an open source project under the GNU LGPL license.CONCLUSIONS:easyDAS
is an automated DAS source creation system which can help many researchers
in sharing their biological data, potentially increasing the amount
of relevant biological data available to the scientific community.},
doi = {10.1186/1471-2105-12-23},
issn = {1471-2105},
pubmedid = {21244646},
url = {http://www.biomedcentral.com/1471-2105/12/23}
}
@ARTICLE{Gollust2012,
author = {Gollust, S. E. and Gordon, E. S. and Zayac, C. and Griffin, G. and
Christman, M. F. and Pyeritz, R. E. and Wawak, L. and Bernhardt,
B. A.},
title = {Motivations and perceptions of early adopters of personalized genomics:
perspectives from research participants.},
journal = {Public Health Genomics},
year = {2012},
volume = {15},
pages = {22--30},
number = {1},
abstract = {To predict the potential public health impact of personal genomics,
empirical research on public perceptions of these services is needed.
In this study, 'early adopters' of personal genomics were surveyed
to assess their motivations, perceptions and intentions.Participants
were recruited from everyone who registered to attend an enrollment
event for the Coriell Personalized Medicine Collaborative, a United
States-based (Camden, N.J.) research study of the utility of personalized
medicine, between March 31, 2009 and April 1, 2010 (n = 369). Participants
completed an Internet-based survey about their motivations, awareness
of personalized medicine, perceptions of study risks and benefits,
and intentions to share results with health care providers.Respondents
were motivated to participate for their own curiosity and to find
out their disease risk to improve their health. Fewer than 10\% expressed
deterministic perspectives about genetic risk, but 32\% had misperceptions
about the research study or personal genomic testing. Most respondents
perceived the study to have health-related benefits. Nearly all (92\%)
intended to share their results with physicians, primarily to request
specific medical recommendations.Early adopters of personal genomics
are prospectively enthusiastic about using genomic profiling information
to improve their health, in close consultation with their physicians.
This suggests that early users (i.e. through direct-to-consumer companies
or research) may follow up with the health care system. Further research
should address whether intentions to seek care match actual behaviors.},
doi = {10.1159/000327296},
institution = {Division of Health Policy and Management, University of Minnesota
School of Public Health, Minneapolis, MN, USA. [email protected]},
keywords = {Adolescent; Adult; Aged; Consumer Participation; Female; Genetic Predisposition
to Disease; Genomics; Humans; Individualized Medicine; Information
Dissemination; Male; Middle Aged; Motivation; Perception; Prospective
Studies; Young Adult},
language = {eng},
medline-pst = {ppublish},
owner = {drsnuggles},
pii = {000327296},
pmid = {21654153},
timestamp = {2013.05.30},
url = {http://dx.doi.org/10.1159/000327296}
}
@ARTICLE{Hauskeller2011,
author = {Hauskeller, C.},
title = {{Direct to consumer genetic testing}},
journal = {Bmj},
year = {2011},
volume = {342},
pages = {d2317--d2317},
number = {apr21 1},
month = apr,
doi = {10.1136/bmj.d2317},
file = {:Users/bastian/Documents/Paper/Hauskeller/Bmj/0.pdf:pdf},
issn = {0959-8138},
url = {http://www.bmj.com/cgi/doi/10.1136/bmj.d2317}
}
@ARTICLE{Hindorff2009,
author = {Hindorff, Lucia A. and Sethupathy, Praveen and Junkins, Heather A.
and Ramos, Erin M. and Mehta, Jayashri P. and Collins, Francis S.
and Manolio, Teri A.},
title = {Potential etiologic and functional implications of genome-wide association
loci for human diseases and traits},
journal = {Proceedings of the National Academy of Sciences},
year = {2009},
volume = {106},
pages = {9362-9367},
number = {23},
abstract = {We have developed an online catalog of SNP-trait associations from
published genome-wide association studies for use in investigating
genomic characteristics of trait/disease-associated SNPs (TASs).
Reported TASs were common [median risk allele frequency 36%, interquartile
range (IQR) 21%−53%] and were associated with modest effect sizes
[median odds ratio (OR) 1.33, IQR 1.20–1.61]. Among 20 genomic
annotation sets, reported TASs were significantly overrepresented
only in nonsynonymous sites [OR = 3.9 (2.2−7.0), p = 3.5 × 10−7]
and 5kb-promoter regions [OR = 2.3 (1.5−3.6), p = 3 × 10−4]
compared to SNPs randomly selected from genotyping arrays. Although
88% of TASs were intronic (45%) or intergenic (43%), TASs were not
overrepresented in introns and were significantly depleted in intergenic
regions [OR = 0.44 (0.34−0.58), p = 2.0 × 10−9]. Only slightly
more TASs than expected by chance were predicted to be in regions
under positive selection [OR = 1.3 (0.8−2.1), p = 0.2]. This new
online resource, together with bioinformatic predictions of the underlying
functionality at trait/disease-associated loci, is well-suited to
guide future investigations of the role of common variants in complex
disease etiology.},
doi = {10.1073/pnas.0903103106},
eprint = {http://www.pnas.org/content/106/23/9362.full.pdf+html},
url = {http://www.pnas.org/content/106/23/9362.abstract}
}
@ARTICLE{Hogarth2008,
author = {Hogarth, Stuart and Javitt, Gail and Melzer, David},
title = {{The current landscape for direct-to-consumer genetic testing: legal,
ethical, and policy issues.}},
journal = {Annual review of genomics and human genetics},
year = {2008},
volume = {9},
pages = {161--82},
month = jan,
abstract = {This review surveys the developing market for direct-to-consumer (DTC)
genetic tests and examines the range of companies and tests available,
the regulatory landscape, the concerns raised about DTC testing,
and the calls for enhanced oversight. We provide a comparative overview
of the situation, particularly in the United States and Europe, by
exploring the regulatory frameworks for medical devices and clinical
laboratories. We also discuss a variety of other mechanisms such
as general controls on advertising and consumer law mechanisms.},
doi = {10.1146/annurev.genom.9.081307.164319},
file = {:Users/bastian/Documents/Paper/Hogarth, Javitt, Melzer/Annual review of genomics and human genetics/annurev\%2Egenom\%2E9\%2E081307\%2E164319.pdf:pdf},
issn = {1527-8204},
keywords = {Advertising as Topic,Europe,Genetic Techniques,Genetic Techniques:
economics,Genetic Techniques: ethics,Genetics, Medical,Genetics,
Medical: economics,Genetics, Medical: ethics,Genetics, Medical: legislation
\& jurisprudence,Humans,Marketing of Health Services,Public Policy,United
States},
pmid = {18767961},
url = {http://www.ncbi.nlm.nih.gov/pubmed/18767961}
}
@ARTICLE{Jenkinson2008,
author = {Jenkinson, Andrew and Albrecht, Mario and Birney, Ewan and Blankenburg,
Hagen and Down, Thomas and Finn, Robert and Hermjakob, Henning and
Hubbard, Tim and Jimenez, Rafael and Jones, Philip and Kahari, Andreas
and Kulesha, Eugene and Macias, Jose and Reeves, Gabrielle and Prlic,
Andreas},
title = {Integrating biological data - the Distributed Annotation System},
journal = {BMC Bioinformatics},
year = {2008},
volume = {9},
pages = {S3},
number = {Suppl 8},
abstract = {BACKGROUND:The Distributed Annotation System (DAS) is a widely adopted
protocol for dynamically integrating a wide range of biological data
from geographically diverse sources. DAS continues to expand its
applicability and evolve in response to new challenges facing integrative
bioinformatics.RESULTS:Here we describe the various infrastructure
components of DAS and present a new extended version of the DAS specification.
Version 1.53E incorporates several recent developments, including
its extension to serve new data types and an ontology for protein
features.CONCLUSION:Our extensions to the DAS protocol have facilitated
the integration of new data types, and our improvements to the existing
DAS infrastructure have addressed recent challenges. The steadily
increasing numbers of available data sources demonstrates further
adoption of the DAS protocol.},
doi = {10.1186/1471-2105-9-S8-S3},
issn = {1471-2105},
pubmedid = {18673527},
url = {http://www.biomedcentral.com/1471-2105/9/S8/S3}
}
@ARTICLE{Joh2011,
author = {Joh, Elizabeth E},
title = {{Ethics watch: DNA theft: your genetic information at risk.}},
journal = {Nature reviews. Genetics},
year = {2011},
volume = {12},
pages = {3113},
number = {October},
month = oct,
doi = {10.1038/nrg3113},
file = {:Users/bastian/Documents/Paper/Joh/Nature reviews. Genetics/nrg3113.pdf:pdf},
issn = {1471-0064},
pmid = {22025003},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22025003}
}
@ARTICLE{Johnson2009,
author = {Johnson, Andrew and O'Donnell, Christopher},
title = {An Open Access Database of Genome-wide Association Results},
journal = {BMC Medical Genetics},
year = {2009},
volume = {10},
pages = {6},
number = {1},
abstract = {BACKGROUND:The number of genome-wide association studies (GWAS) is
growing rapidly leading to the discovery and replication of many
new disease loci. Combining results from multiple GWAS datasets may
potentially strengthen previous conclusions and suggest new disease
loci, pathways or pleiotropic genes. However, no database or centralized
resource currently exists that contains anywhere near the full scope
of GWAS results.METHODS:We collected available results from 118 GWAS
articles into a database of 56,411 significant SNP-phenotype associations
and accompanying information, making this database freely available
here. In doing so, we met and describe here a number of challenges
to creating an open access database of GWAS results. Through preliminary
analyses and characterization of available GWAS, we demonstrate the
potential to gain new insights by querying a database across GWAS.RESULTS:Using
a genomic bin-based density analysis to search for highly associated
regions of the genome, positive control loci (e.g., MHC loci) were
detected with high sensitivity. Likewise, an analysis of highly repeated
SNPs across GWAS identified replicated loci (e.g., APOE, LPL). At
the same time we identified novel, highly suggestive loci for a variety
of traits that did not meet genome-wide significant thresholds in
prior analyses, in some cases with strong support from the primary
medical genetics literature (SLC16A7, CSMD1, OAS1), suggesting these
genes merit further study. Additional adjustment for linkage disequilibrium
within most regions with a high density of GWAS associations did
not materially alter our findings. Having a centralized database
with standardized gene annotation also allowed us to examine the
representation of functional gene categories (gene ontologies) containing
one or more associations among top GWAS results. Genes relating to
cell adhesion functions were highly over-represented among significant
associations (p < 4.6 x 10-14), a finding which was not perturbed
by a sensitivity analysis.CONCLUSION:We provide access to a full
gene-annotated GWAS database which could be used for further querying,
analyses or integration with other genomic information. We make a
number of general observations. Of reported associated SNPs, 40%
lie within the boundaries of a RefSeq gene and 68% are within 60
kb of one, indicating a bias toward gene-centricity in the findings.
We found considerable heterogeneity in information available from
GWAS suggesting the wider community could benefit from standardization
and centralization of results reporting.},
doi = {10.1186/1471-2350-10-6},
issn = {1471-2350},
pubmedid = {19161620},
url = {http://www.biomedcentral.com/1471-2350/10/6}
}
@ARTICLE{Klein2005,
author = {Klein, Robert J. and Zeiss, Caroline and Chew, Emily Y. and Tsai,
Jen-Yue and Sackler, Richard S. and Haynes, Chad and Henning, Alice
K. and SanGiovanni, John Paul and Mane, Shrikant M. and Mayne, Susan
T. and Bracken, Michael B. and Ferris, Frederick L. and Ott, Jurg
and Barnstable, Colin and Hoh, Josephine},
title = {Complement Factor H Polymorphism in Age-Related Macular Degeneration},
journal = {Science},
year = {2005},
volume = {308},
pages = {385-389},
number = {5720},
abstract = {Age-related macular degeneration (AMD) is a major cause of blindness
in the elderly. We report a genome-wide screen of 96 cases and 50
controls for polymorphisms associated with AMD. Among 116,204 single-nucleotide
polymorphisms genotyped, an intronic and common variant in the complement
factor H gene (CFH) is strongly associated with AMD (nominal P value
<10-7). In individuals homozygous for the risk allele, the likelihood
of AMD is increased by a factor of 7.4 (95% confidence interval 2.9
to 19). Resequencing revealed a polymorphism in linkage disequilibrium
with the risk allele representing a tyrosine-histidine change at
amino acid 402. This polymorphism is in a region of CFH that binds
heparin and C-reactive protein. The CFH gene is located on chromosome
1 in a region repeatedly linked to AMD in family-based studies.},
doi = {10.1126/science.1109557},
eprint = {http://www.sciencemag.org/content/308/5720/385.full.pdf},
url = {http://www.sciencemag.org/content/308/5720/385.abstract}
}
@ARTICLE{Lee2009,
author = {Lee, Sandra Soo-Jin and Crawley, LaVera},
title = {Research 2.0: social networking and direct-to-consumer (DTC) genomics.},
journal = {Am J Bioeth},
year = {2009},
volume = {9},
pages = {35--44},
number = {6-7},
__markedentry = {[drsnuggles:6]},
abstract = {The convergence of increasingly efficient high throughput sequencing
technology and ubiquitous Internet use by the public has fueled the
proliferation of companies that provide personal genetic information
(PGI) direct-to-consumers. Companies such as 23andme (Mountain View,
CA) and Navigenics (Foster City, CA) are emblematic of a growing
market for PGI that some argue represents a paradigm shift in how
the public values this information and incorporates it into how they
behave and plan for their futures. This new class of social networking
business ventures that market the science of the personal genome
illustrates the new trend in collaborative science. In addition to
fostering a consumer empowerment movement, it promotes the trend
of democratizing information--openly sharing of data with all interested
parties, not just the biomedical researcher--for the purposes of
pooling data (increasing statistical power) and escalating the innovation
process. This target article discusses the need for new approaches
to studying DTC genomics using social network analysis to identify
the impact of obtaining, sharing, and using PGI. As a locus of biosociality,
DTC personal genomics forges social relationships based on beliefs
of common genetic susceptibility that links risk, disease, and group
identity. Ethical issues related to the reframing of DTC personal
genomic consumers as advocates and research subjects and the creation
of new social formations around health research may be identified
through social network analysis.},
doi = {10.1080/15265160902874452},
institution = {Stanford Center for Biomedical Ethics, Stanford University Medical
School, Palo Alto, CA 94304, USA. [email protected]},
keywords = {Biotechnology, ethics/trends; Consumer Participation, trends; Databases,
Genetic; Decision Making, ethics; Genetic Predisposition to Disease;
Genetic Privacy, ethics; Genetic Testing, ethics; Genome, Human;
Genomics, ethics; Humans; Internet; Marketing of Health Services,
ethics/methods; Private Sector, ethics/trends; Public Opinion; Public
Policy, trends; Social Support},
language = {eng},
medline-pst = {ppublish},
owner = {drsnuggles},
pii = {911997739},
pmid = {19998112},
timestamp = {2013.06.03},
url = {http://dx.doi.org/10.1080/15265160902874452}
}
@ARTICLE{parkinsons,
author = {Lill, , Christina M. AND Roehr, , Johannes T. AND McQueen, , Matthew
B. AND Kavvoura, , Fotini K. AND Bagade, , Sachin AND Schjeide, ,
Brit-Maren M. AND Schjeide, , Leif M. AND Meissner, , Esther AND
Zauft, , Ute AND Allen, , Nicole C. AND Liu, , Tian AND Schilling,
, Marcel AND Anderson, , Kari J. AND Beecham, , Gary AND Berg, ,
Daniela AND Biernacka, , Joanna M. AND Brice, , Alexis AND DeStefano,
, Anita L. AND Do, , Chuong B. AND Eriksson, , Nicholas AND Factor,
, Stewart A. AND Farrer, , Matthew J. AND Foroud, , Tatiana AND Gasser,
, Thomas AND Hamza, , Taye AND Hardy, , John A. AND Heutink, , Peter
AND Hill-Burns, , Erin M. AND Klein, , Christine AND Latourelle,
, Jeanne C. AND Maraganore, , Demetrius M. AND Martin, , Eden R.
AND Martinez, , Maria AND Myers, , Richard H. AND Nalls, , Michael
A. AND Pankratz, , Nathan AND Payami, , Haydeh AND Satake, , Wataru
AND Scott, , William K. AND Sharma, , Manu AND Singleton, , Andrew
B. AND Stefansson, , Kari AND Toda, , Tatsushi AND Tung, , Joyce
Y. AND Vance, , Jeffery AND Wood, , Nick W. AND Zabetian, , Cyrus
P. AND Young, , Peter AND Tanzi, , Rudolph E. AND Khoury, , Muin
J. AND Zipp, , Frauke AND Lehrach, , Hans AND Ioannidis, , John P.
A. AND Bertram, , Lars AND 23andMe, The Genetic Epidemiology of Parkinson's
Disease (GEO-PD) Consortium, The International Parkinson's Disease
Genomics Consortium (IPDGC), The Parkinson's Disease GWAS Consortium,
The Wellcome Trust Case Control Consortium 2 (WTCCC2)},
title = {Comprehensive Research Synopsis and Systematic Meta-Analyses in Parkinson's
Disease Genetics: The PDGene Database},
journal = {PLoS Genet},
year = {2012},
volume = {8},
pages = {e1002548},
number = {3},
month = {03},
abstract = {<title>Author Summary</title> <p>The genetic basis of Parkinson's
disease is complex, i.e. it is determined by a number of different
disease-causing and disease-predisposing genes. Especially the latter
have proven difficult to find, evidenced by more than 800 published
genetic association studies, typically showing discrepant results.
To facilitate the interpretation of this large and continuously increasing
body of data, we have created a freely available online database
(“PDGene”: <ext-link xmlns:xlink="http://www.w3.org/1999/xlink"
ext-link-type="uri" xlink:href="http://www.pdgene.org" xlink:type="simple">http://www.pdgene.org</ext-link>)
which provides an exhaustive account of all published genetic association
studies in PD. One particularly useful feature is the calculation
and display of up-to-date summary statistics of published data for
overlapping DNA sequence variants (polymorphisms). These meta-analyses
revealed eleven gene loci that showed a statistically very significant
(<italic>P</italic><5×10<sup>−8</sup>; a.k.a. genome-wide significance)
association with risk for PD: <italic>BST1</italic>, <italic>CCDC62/HIP1R</italic>,
<italic>DGKQ/GAK</italic>, <italic>GBA</italic>, <italic>LRRK2</italic>,
<italic>MAPT</italic>, <italic>MCCC1/LAMP3</italic>, PARK16, <italic>SNCA</italic>,
<italic>STK39</italic>, <italic>SYT11/RAB25</italic>. In addition
and purely by data-mining, we identified one novel PD susceptibility
locus in a gene called <italic>ITGA8</italic> (rs7077361, <italic>P</italic> = 1.3×10<sup>−8</sup>).
We note that our continuously updated database represents the most
comprehensive research synopsis of genetic association studies in
PD to date. In addition to vastly facilitating the work of other
PD geneticists, our approach may serve as a valuable example for
other complex diseases.</p>},
doi = {10.1371/journal.pgen.1002548},
publisher = {Public Library of Science},
url = {http://dx.doi.org/10.1371%2Fjournal.pgen.1002548}
}
@ARTICLE{GalaxyZoo,
author = {Lintott, Chris J. and Schawinski, Kevin and Slosar, Anže and Land,
Kate and Bamford, Steven and Thomas, Daniel and Raddick, M. Jordan
and Nichol, Robert C. and Szalay, Alex and Andreescu, Dan and Murray,
Phil and Vandenberg, Jan},
title = {Galaxy Zoo: morphologies derived from visual inspection of galaxies
from the Sloan Digital Sky Survey},
journal = {Monthly Notices of the Royal Astronomical Society},
year = {2008},
volume = {389},
pages = {1179-1189},
number = {3},
abstract = {In order to understand the formation and subsequent evolution of galaxies
one must first distinguish between the two main morphological classes
of massive systems: spirals and early-type systems. This paper introduces
a project, Galaxy Zoo, which provides visual morphological classifications
for nearly one million galaxies, extracted from the Sloan Digital
Sky Survey (SDSS). This achievement was made possible by inviting
the general public to visually inspect and classify these galaxies
via the internet. The project has obtained more than 4 × 107 individual
classifications made by ∼105 participants. We discuss the motivation
and strategy for this project, and detail how the classifications
were performed and processed. We find that Galaxy Zoo results are
consistent with those for subsets of SDSS galaxies classified by
professional astronomers, thus demonstrating that our data provide
a robust morphological catalogue. Obtaining morphologies by direct
visual inspection avoids introducing biases associated with proxies
for morphology such as colour, concentration or structural parameters.
In addition, this catalogue can be used to directly compare SDSS
morphologies with older data sets. The colour–magnitude diagrams
for each morphological class are shown, and we illustrate how these
distributions differ from those inferred using colour alone as a
proxy for morphology.},
doi = {10.1111/j.1365-2966.2008.13689.x},
eprint = {http://mnras.oxfordjournals.org/content/389/3/1179.full.pdf+html},
url = {http://mnras.oxfordjournals.org/content/389/3/1179.abstract}
}
@ARTICLE{McGowan2010,
author = {McGowan, Michelle L. and Fishman, Jennifer R. and Lambrix, Marcie
A.},
title = {Personal genomics and individual identities: motivations and moral
imperatives of early users.},
journal = {New Genet Soc},
year = {2010},
volume = {29},
pages = {261--290},
number = {3},
month = {Sep},
abstract = {Since 2007, consumer genomics companies have marketed personal genome
scanning services to assess users' genetic predispositions to a variety
of complex diseases and traits. This study investigates early users'
reasons for utilizing personal genome services, their evaluation
of the technology, how they interpret the results, and how they incorporate
the results into health-related decision-making. The analysis contextualizes
early users' relationships to the technology, the knowledge generated
by it, and how it mediates their relationship to their own health
and to biomedicine more broadly. The results reveal that early users
approach personal genome scanning with both optimism for genomic
research and scepticism about the technology's current capabilities,
which runs contrary to concerns that consumers may be ill equipped
to interpret and understand genome scan results. These findings provide
important qualitative insight into early users' conceptualizations
of personal genomic risk assessment and illuminate their involvement
in configuring this technology in the making.},
doi = {10.1080/14636778.2010.507485},
institution = {Department of Bioethics, Case Western Reserve University, Cleveland,
US.},
language = {eng},
medline-pst = {ppublish},
owner = {drsnuggles},
pmid = {21076647},
timestamp = {2013.05.30},
url = {http://dx.doi.org/10.1080/14636778.2010.507485}
}
@ARTICLE{10.1371.journal.pone.0031470,
author = {Mei, , Hao AND Chen, , Wei AND Jiang, , Fan AND He, , Jiang AND Srinivasan,
, Sathanur AND Smith, , Erin N. AND Schork, , Nicholas AND Murray,
, Sarah AND Berenson, , Gerald S.},
title = {Longitudinal Replication Studies of GWAS Risk SNPs Influencing Body
Mass Index over the Course of Childhood and Adulthood},
journal = {PLoS ONE},
year = {2012},
volume = {7},
pages = {e31470},
number = {2},
month = {02},
abstract = {<p>Genome-wide association studies (GWAS) have identified multiple
common variants associated with body mass index (BMI). In this study,
we tested 23 genotyped GWAS-significant SNPs (p-value<5*10-8)
for longitudinal associations with BMI during childhood (3–17 years)
and adulthood (18–45 years) for 658 subjects. We also proposed
a heuristic forward search for the best joint effect model to explain
the longitudinal BMI variation. After using false discovery rate
(FDR) to adjust for multiple tests, childhood and adulthood BMI were
found to be significantly associated with six SNPs each (q-value<0.05),
with one SNP associated with both BMI measurements: KCTD15 rs29941
(q-value<7.6*10-4). These 12 SNPs are located at or near genes
either expressed in the brain (BDNF, KCTD15, TMEM18, MTCH2, and FTO)
or implicated in cell apoptosis and proliferation (FAIM2, MAP2K5,
and TFAP2B). The longitudinal effects of FAIM2 rs7138803 on childhood
BMI and MAP2K5 rs2241423 on adulthood BMI decreased as age increased
(q-value<0.05). The FTO candidate SNPs, rs6499640 at the 5 ′-end
and rs1121980 and rs8050136 downstream, were associated with childhood
and adulthood BMI, respectively, and the risk effects of rs6499640
and rs1121980 increased as birth weight decreased. The best joint
effect model for childhood and adulthood BMI contained 14 and 15
SNPs each, with 11 in common, and the percentage of explained variance
increased from 0.17% and 9.0*10<sup>−6</sup>% to 2.22% and 2.71%,
respectively. In summary, this study evidenced the presence of long-term
major effects of genes on obesity development, implicated in pathways
related to neural development and cell metabolism, and different
sets of genes associated with childhood and adulthood BMI, respectively.
The gene effects can vary with age and be modified by prenatal development.
The best joint effect model indicated that multiple variants with
effects that are weak or absent alone can nevertheless jointly exert
a large longitudinal effect on BMI.</p>},
doi = {10.1371/journal.pone.0031470},
publisher = {Public Library of Science},
url = {http://dx.doi.org/10.1371%2Fjournal.pone.0031470}