Scott Edmunds

**The Human Genetics Massive: \#ASHG15 in Baltimore  
**

[![](http://gigasciencejournal.com/blog/wp-content/uploads/2015/10/IMG_0353-262x300.jpg){.alignleft
.size-medium .wp-image-1611 loading="lazy" decoding="async" width="262"
height="300"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2015/10/IMG_0353-262x300.jpg 262w, http://gigasciencejournal.com/blog/wp-content/uploads/2015/10/IMG_0353.jpg 558w"
sizes="(max-width: 262px) 100vw, 262px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2015/10/IMG_0353.jpg)This
week the human genetics "tribe" (as NIH Director Francis Collins
referred to "his people" here) have muscled out the Eastside and
Westside crews to take over the Baltimore waterfront for the yearly
American Society of Human Genetics (#ASHG15) meeting. The *GigaScience*
editors have attended this, the worlds largest human genetics meeting
many times over the years, but standing in the cavernous auditorium this
year really got the point across how large this meeting and the field as
a whole has grown. Pushing well over 6,000 attendees this year, in his
Presidential address Neil Risch said that while this was the 5^th^ time
in Baltimore and joint top venue for hosting it, this would likely be
the last time it is hosted here for some time as it has outgrown the
[self proclaimed "Greatest City in
America"](http://www.redorbit.com/news/business/511672/baltimores_new_bait_the_city_is_about_to_unveil_a/).
The explosion of people working in the field has mirrored the explosion
of material for them to work on generated by next (and now next-next)
sequencing technologies, and while over the society's long history,
membership has changed with the technological and molecular trends
---moving from clinicians towards scientists--- as this genomic data now
starts to become routine for clinical applications, membership trends
are likely to start moving back the other way.

The ASHG president has much to do with this increase in data scales,
with his seminal paper on ["The Future of Genetic Studies of Complex
Human Diseases"](http://www.sciencemag.org/content/273/5281/1516.long)
published nearly two decades ago predicting and promoting the rise of
cohort and genome wide association studies (GWAS). This paper was
mentioned numerous times in the opening Presidential Symposium on
"Genomic Epidemiology at Scale", not least by Francis Collins in his
talk on the [US Precision Medicine
Initiative](http://www.nih.gov/precisionmedicine/). Announced at the US
State of the Union Address this year, this initiative is building a US
national research cohort of over one million people. Lots of these
participants will be gathered by combining and integrating data from
ongoing projects from Kaiser Permanente and the US Veteran Affairs, but
on top of "synthetic cohorts", to make the wider population as a whole
represented large numbers of volunteers are needed. It was great to see
the NIH Director stress the importance of data sharing; both with
patients who should have the right to access their own data, and with
any researchers with a good research idea who should be able to access
it. Sharing is essential to empower and engage patients, and to enable
the connections and sample sizes needed for this type of precision
medicine to work. The NIH are currently working on a new federal policy
on biospecimens. Topically for the Baltimore audience, these policies
are being drafted with the family of [Henrietta Lack's (of HeLa cell
fame)](https://en.wikipedia.org/wiki/Henrietta_Lacks) in mind, and the
fact that many of the family were present at the meeting got a large
round of applause.

The importance of engaging with patients was passionately presented in
the "art of science communication" track by "BRCActivist " and
"Previvor" Andrea Downing (AKA [Brave
Bosom](http://www.bravebosom.com/)). Andrea became an ePatient activist
after being diagnosed with a BRCA mutation, and trying to understand the
implications and uncertainty surrounding her 87% risk of breast cancer.
She very eloquently stressed to the audience that actionable genes are
not actionable when you don't have access to the information or medical
care you need. As a [vocal campaigner
against](http://forward.com/culture/203739/genetics-lab-refuses-to-share-data-that-could-save/)
Myriad, while their gene patents are now over, there is still a big
data-sharing problem with most of the useful genetic data still in the
propriety databases of former patent holders. Patients are keen to
participate and join studies, undergoing batteries of tests and filling
out incredibly long surveys, but in most cases getting no information
back in return. Even when receiving results there is no translation of
their implications to patients. Information is behind paywalls, a
majority of cases have no access to genetic councilors, and their
regular doctors are not trained and experienced enough to help.

**Its all about the data. The human genetics data re-up  
**As Lea Starita pointed out in her later plenary (and also obvious from
walking through the exhibitor area), since the Myriad patent on BRCA
gene testing has been over turned, genetic testing has exploded, with
lower costs leading to more companies testing more genes. Unfortunately
less characterized genes than BRCA1/2 need new technologies to screen
variants of unknown significance, and there are huge challenges to scale
out to new genes. Matchmaking and sharing of data between patients is
needed to properly understand phenotypes, and genetic data needs to
break out of the proprietary silos highlighted by Andrea Downing to
enable this. Many of the problems are due to the perceived legal and
ethical issues surrounding genetic data because of the possibility of
re-identification, but many tools and schemes are trying to address this
issue to open this data up. [The Global Alliance for Genomes and
Health](http://genomicsandhealth.org/) (of which we at *GigaScience* are
members) have tried to address this niche through secure ways of sharing
variant information through their [Matchmaker
Exchange](http://www.matchmakerexchange.org/), [BRCA
challenge](http://brcaexchange.org/) and [Beacon
Projects](http://ga4gh.org/#/beacon). Nicely, they had both an
information session and a booth at ASHG.

At *GigaScience*, we continue to experiment with and improve new ways of
sharing our human genomic data, both by setting up our own Beacon (with
some initial test data at <http://giga-beacon.org/>), making it easier
to access any of our data held in external controlled access databases
(e.g. [this example in GigaDB](dx.doi.org/10.5524/100112) making the
data access committee application more straightforward), and through the
[newly
announced](https://www.genomeweb.com/informatics/repositive-gigascience-partner-improve-access-genomic-data)
collaboration with [Repositive](https://repositive.io/) indexing our
human genomic data. Experimenting with this further, we are [hosting a
workshop](https://www.facebook.com/events/1064128190288114/) with
Repositive and OpenSNP on the 26^th^ of October in Hong Kong.

[![](http://gigasciencejournal.com/blog/wp-content/uploads/2015/10/makerbaydnalogo.jpg){.aligncenter
.size-full .wp-image-1612 loading="lazy" decoding="async" width="717"
height="385"
srcset="http://gigasciencejournal.com/blog/wp-content/uploads/2015/10/makerbaydnalogo.jpg 717w, http://gigasciencejournal.com/blog/wp-content/uploads/2015/10/makerbaydnalogo-300x161.jpg 300w"
sizes="(max-width: 717px) 100vw, 717px"}](http://gigasciencejournal.com/blog/wp-content/uploads/2015/10/makerbaydnalogo.jpg)Aimed
at researchers struggling to find the data they need to power their
research, this workshop will demonstrate a number of ways of searching
for, finding and accessing human genomics data that has been consented
for research use. In a similar manner to our ["Bring You Own Data
Parties"](http://blogs.biomedcentral.com/gigablog/2014/08/22/aint-no-party-like-a-bring-your-own-data-party/),
we will cover how data that you have in your lab can be made as useful
as possible for yourself and your colleagues, and how this data may be
the starting point for finding your next research collaboration.
Representatives of Repositive, OpenSNP, and *GigaScience* will providing
hands-on training on using tools and data resources such as openSNP,
1000 Genomes, Global Alliance Beacons and GigaDB. This will be followed
by a more general interest evening lecture on "Hacking the human genome"
(see the event page
[here](https://www.facebook.com/events/2197362690286603/)). Both events
are free and are hosted by [MakerBay](http://www.makerbay.org/), and you
can sign up on the [eventbright
page](https://www.eventbrite.hk/e/genome-hackathon-makerbay-tickets-18836695062)
if you want to attend.

The post [Sharing Genomic Data in the Precision Medicine
Era](http://gigasciencejournal.com/blog/sharing-genomic-data-precision-medicine-era/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


**The Human Genetics Massive: #ASHG15 in Baltimore **  This week the human genetics “tribe” (as NIH Director Francis Collins referred to “his people” here) have muscled out the Eastside and Westside crews to take over the Baltimore waterfront for the yearly American Society of Human Genetics (#ASHG15) meeting.

Sharing Genomic Data in the Precision Medicine Era

![ASHG
poster](http://farm7.static.flickr.com/6095/6257004528_50ab42fb3d_m.jpg){decoding="async"
style="width: 106px; height: 161px;" align="left" border="0" hspace="4"
vspace="4"}[*GigaScience*](http://www.gigasciencejournal.com "GigaScience homepage"){target="_blank"
rel="noopener"} was on hand to witness plenty of lively discussion last
week at the annual [American Society of Human
Genetics](http://www.ashg.org/ "ASHG"){target="_blank" rel="noopener"}
jamboree: the [International Conference of Human
Genetics](http://www.ichg2011.org/ "ICHG 2011 meeting"){target="_blank"
rel="noopener"} in Montreal. As always, the meeting had a strong medical
genetics presence but the rapid growth and uptake of genomics
technologies in the field produced much fascinating work on display this
year. However, some amongst the heavy clinical contingent were obviously
uncomfortable with the lack of clinical validation of much of this work
and debate was heated in many of the plenary debate sessions. This can
be followed if you are patient enough to trawl the \>4700 tweets
utilizing the hashtag
[\#ichg2011](http://twitter.com/?lang=en&logged_out=1#!/search/%23ichg2011 "#ICHG2011")
or, fortunately, a growing number of ICHG 2011
[webcasts](http://www.ashg.org/press/multimedia.shtml "ASHG webcasts"){target="_blank"
rel="noopener"}.

The scene was set in the opening "[Whole Genome Sequencing: To Do It or
Not to Do
It?](http://www.ichg2011.org/cgi-bin/ichg11s?title=whole%20genome%20sequencing&sort=ptimes&sbutton=Detail&absno=90155&sid=62543 "WGS panel"){target="_blank"
rel="noopener"}" panel (involving the always controversial James Watson
memorably talking about "Genetic Losers") and the technology v. medicine
debate was particularly polarized in the "[Current and Emerging
Sequencing
Technologies](http://www.ichg2011.org/cgi-bin/ichg11s?abst=current%20and%20emerging%20sequencing&sort=ptimes&sbutton=Detail&absno=90182&sid=62543 "Technologies panel"){target="_blank"
rel="noopener"}" panel the following day (nicely
[summarized](http://www.genetic-inference.co.uk/blog/2011/10/ichg2011-debating-the-future-of-genome-sequencing-is-medicine/ "Luke Jostins: future of genome sequencing"){target="_blank"
rel="noopener"} by Luke Jostins in his blog). Whilst there was a
consensus that sequencing will become a standard tool in the diagnosis
of genetic diseases, the second panel was divided on whether this
approach should be a purely targeted one, restricted to finding the
pathogenic mutations causing a disease. Some of the more clinically
focused members argued that medical genome sequencing was "hype", held
back by the lack of genetic councilors, lack of clear policies from
healthcare providers and insurance companies, and a very poor level of
genetic training of clinicians in general.

The concerns raised have much merit but the circular arguments and calls
for further debate didn't really acknowledge that technological advances
and events on the ground are threatening to make them redundant.  It was
obvious that panelists such as [Rade
Drmanac](http://www.rdrmanac.com/ "Rade Drmanac website"){target="_blank"
rel="noopener"} from Complete Genomics were going to argue against
genomics technology in the clinic, but some of the clinicians on the
board provided evidence that many physicians are already using them on a
large scale. [Joris
Veltman](http://www.genomicdisorders.nl/joris "Joris Veltman"){target="_blank"
rel="noopener"} provided examples from his recent work using exome
sequencing rather than single gene tests on 500 individuals, and our
[editorial
board](http://www.gigasciencejournal.com/about/edboard "GigaScience editorial board"){target="_blank"
rel="noopener"} member Ming Qi also admitted to doing similar work in
the clinic. With one lucky attendee at the conference
[winning](http://spittoon.23andme.com/2011/10/07/23andme-ichgashg-2011-mixer/ "Exome draw"){target="_blank"
rel="noopener"} the chance to have their exome sequenced from 23 & Me
(market value of 999 USD from 23 & Me -- or
[BGI](http://bgiamericas.com/human-exome-sequencing-staring-at-999/ "BGI $999 exome"){target="_blank"
rel="noopener"}), many on Twitter pointed out that the market will
likely decide the debates' outcome.

Also on display at the meeting were many examples of larger and larger
projects utilizing exomic or even whole genome sequencing. Announcements
were made at the meeting from [Autism
Speaks](http://www.autismspeaks.org/ "Autism speaks"){target="_blank"
rel="noopener"} and our colleagues at the
[BGI](http://en.genomics.cn/navigation/index.action "BGI"){target="_blank"
rel="noopener"} about a new
[project](http://en.genomics.cn/navigation/show_news.action?newsContent.id=8936 "10K autism announcement"){target="_blank"
rel="noopener"} to sequence 10,000 individuals with Autism spectrum
disorders. Initial data was presented by [Tim
Spector](http://www.kcl.ac.uk/medicine/research/divisions/gmm/sections/clusters/cdc/spector/tspector.aspx "Tim Spector"){target="_blank"
rel="noopener"} of his EpiTwin
[project](http://www.twinsuk.ac.uk/pressr0910.html "Epitwin release"){target="_blank"
rel="noopener"}, a BGI collaboration to sequence the epigenome of 5,000
twins. [Cisca
Wijmenga](http://www.rug.nl/umcg/faculteit/disciplinegroepen/medischegenetica/research/employees/cvciscawijmenga?lang=en "Cisca Wijmenga"){target="_blank"
rel="noopener"} also
[presented](http://www.ichg2011.org/cgi-bin/ichg11s?author=Wijmenga&sort=ptimes&sbutton=Detail&absno=21382&sid=559730 "Genome of the Netherlands poster"){target="_blank"
rel="noopener"} an overview of the "[Genome of the
Netherlands](http://www.nlgenome.nl/wiki/GonlStart "GoNL"){target="_blank"
rel="noopener"}", another BGI collaboration that has already sequenced
250 Dutch trios. With many similar scale projects presented at the
meeting
[such](http://www.ichg2011.org/cgi-bin/ichg11s?author=Schork&sort=ptimes&sbutton=Detail&absno=90018&sid=559730 "Schork presentation"){target="_blank"
rel="noopener"} as [Nick
Schork](http://psychiatry.ucsd.edu/faculty/nschork.html "Nick Schork"){target="_blank"
rel="noopener"}'s work with Complete Genomics to produce 1000 human
reference genomes of the
"[Wellderly](http://ir.completegenomics.com/releasedetail.cfm?ReleaseID=610178 "Wellderly PR"){target="_blank"
rel="noopener"}", it's clear that the field is having to deal with
bigger and bigger datasets. A nice visual representation of this was
shown by Cisca Wijmenga when she presented a slide showing the number of
discs needed to transfer 770 whole genomes worth of GoNL project data
from BGI back to the Netherlands.

The particularly challenging issues of scale remain. Hints of future
ways this is likely to be tackled included an
[announcement](http://techcrunch.com/2011/10/12/dnanexus-raises-15-million-teams-with-google-to-host-massive-dna-database/ "DNA nexus SRA announcement"){target="_blank"
rel="noopener"} at the meeting from
[DNAnexus](https://dnanexus.com/ "DNAnexus"){target="_blank"
rel="noopener"} about their tie-in with Google to host a mirror of the
([no longer
defunct](http://www.ncbi.nlm.nih.gov/About/news/13Oct2011.html "NCBI announcement"){target="_blank"
rel="noopener"}) [Short Read
Archive](http://www.ncbi.nlm.nih.gov/sra "SRA"){target="_blank"
rel="noopener"} in the cloud. The prickly topic of patient data security
also needs resolving, and there were promising posters on display trying
to improve utility and security of this type of data with tools such as
[MedSavant](http://genomesavant.com/medsavant/ "MedSavant"){target="_blank"
rel="noopener"} by [Marc
Fiume](http://www.ichg2011.org/cgi-bin/ichg11s?abst=medsavant&sort=ptimes&sbutton=Detail&absno=11169&sid=559730 "Marc Fiume poster"){target="_blank"
rel="noopener"} and GWAS data encryption protocols from [Itsik
Pe'er](http://www.ichg2011.org/cgi-bin/ichg11s?abst=encryption&sort=ptimes&sbutton=Detail&absno=22106&sid=559730 "Itsik Pe'er poster"){target="_blank"
rel="noopener"}. All of these issues surrounding data handling are very
relevant to the scope of
[*GigaScience*](http://www.gigasciencejournal.com "GigaScience homepage"){target="_blank"
rel="noopener"}, and we are currently commissioning papers covering the
many issues surrounding the handling of medical data. If you have an
interesting point of view you would like to put forward as a commentary
or review in this area or if you have useful research or tools relating
to this, please contact us at <editorial@gigasciencejournal.com> about
[submitting](http://www.gigasciencejournal.com/manuscript "submission system"){target="_blank"
rel="noopener"} to the journal. Whilst there is a huge amount still to
resolve and do, these areas are of great interest and we are keen to
follow and be part of the debate in the future.

The post [ICHG2011: Genetics and Genomics Gets
Personal](http://gigasciencejournal.com/blog/ichg2011-genetics-and-genomics-gets-personal/){rel="nofollow"}
appeared first on
[GigaBlog](http://gigasciencejournal.com/blog){rel="nofollow"}.


<em>
 GigaScience
</em>
was on hand to witness plenty of lively discussion last week at the annual American Society of Human Genetics jamboree: the International Conference of Human Genetics in Montreal. As always, the meeting had a strong medical genetics presence but the rapid growth and uptake of genomics technologies in the field produced much fascinating work on display this year.

Messaggi di Rogue Scholar

Sharing Genomic Data in the Precision Medicine Era

ICHG2011: Genetics and Genomics Gets Personal