Tag: genomics

Uncategorized

Creative Minds: Studying the Human Genome in 3D

Jesse Dixon

As a kid, Jesse Dixon often listened to his parents at the dinner table discussing how to run experiments and their own research laboratories. His father Jack is an internationally renowned biochemist and the former vice president and chief scientific officer of the Howard Hughes Medical Institute. His mother Claudia Kent Dixon, now retired, did groundbreaking work in the study of lipid molecules that serve as the building blocks of cell membranes.

So, when Jesse Dixon set out to pursue a career, he followed in his parents’ footsteps and chose science. But Dixon, a researcher at the Salk Institute, La Jolla, CA, has charted a different research path by studying genomics, with a focus on understanding chromosomal structure. Dixon has now received a 2016 NIH Director’s Early Independence Award to study the three-dimensional organization of the genome, and how changes in its structure might contribute to diseases such as cancer or even to physical differences among people.

The human body is made up of trillions of cells, each much too small to see without a microscope. And yet, if you could unwind and stretch the DNA contained within the nucleus of any one of those vanishingly small cells, you’d find it’s more than 6 feet long!

How is that possible? It takes a lot of careful folding and packaging. It also requires that the genome is arranged to ensure that the right genes are activated in the right place and at the right time. That’s because DNA is not a disorganized mass of spaghetti in the nucleus.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

In the Journals – April 2017 by Danya Glabau

Critical Public Health

On difference and doubt as tools for critical engagement with public health

Catherine M. Will

This paper argues that critical public health should reengage with public health as practice by drawing on versions of Science and Technology Studies (STS) that ‘de-centre the human’ and by seeking alternative forms of critique to work inspired by Foucault. Based on close reading of work by Annemarie Mol, John Law, Vicky Singleton and others, I demonstrate that these authors pursue a conversation with Foucault but suggest new approaches to studying contemporary public health work in different settings. Proposing that we ‘doubt’ both the unity of public health and its effects, I argue that this version of STS opens up a space to recognise multiplicity; to avoid idealising what is being criticised; and to celebrate or care for public health practices as part of critique. Finally I oppose the view that considering technologies, materials and microbes leads to micro-level analysis or political neutrality, and suggest that it allows us to reframe studies of public health to account for inequalities and to draw attention to weak or retreating states, active markets and the entangled relations of humans and non-humans across the world.

 

Biopolitical precarity in the permeable body: the social lives of people, viruses and their medicines

Elizabeth Mills

This article is based on multi-sited ethnography that traced a dynamic network of actors (activists, policy-makers, health care systems, pharmaceutical companies) and actants (viruses and medicines) that shaped South African women’s access to, and embodiment of, antiretroviral therapies (ARVs).

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

Dueling BRCA Databases: What About the Patient?

The news release Monday morning grabbed my attention:

“Study finds wide gap in quality of BRCA1/2 variant
classification between Myriad Genetics and a common public database.”

Myriad Genetics had been exclusively providing tests, for
$3000+ a pop for full BRCA gene sequencing, for 17 years before the Supreme
Court invalidated key gene patents back in 2013. Since the ruling a dozen or so
competitors have been offering tests for much lower prices. Meanwhile, Myriad
has amassed a far deeper database than anyone else, having been in the business
so much longer. And it’s proprietary.

CLASSIFYING GENE VARIANTS

(NHGRI)

Public databases of variants of health-related genes have
been around for years too. The best known, ClinVar, collects and curates data
from the biomedical literature, expert panels, reports at meetings, testing
laboratories, and individual researchers, without access to Myriad’s database.
ClinVar uses several standard technical criteria to classify variants as
“pathogenic,” “benign,” or “of uncertain significance.” (“Likely pathogenic”
and “likely benign” were used more in the past.)

ClinVar lists 5400 variants just for BRCA1. The criteria
come from population statistics, how a particular mutation alters the encoded
protein, effects on the phenotype (symptoms), and other information.
Bioinformatics meets biochemistry to predict susceptibility. The BRCA1 protein
acts as a hub of sorts where many other proteins that control DNA repair
gather. DNA Science discussed the genes behind breast and ovarian cancers here.

As gene sequences accumulate in the databases and troops of
geneticists and genetic counselors annotate them, the proportion of pathogenic
and benign entries will increase as that of the unsettling “variants of
uncertain significance” — VUS — will decrease.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

Dueling BRCA Databases: What About the Patient?

The news release Monday morning grabbed my attention:

“Study finds wide gap in quality of BRCA1/2 variant
classification between Myriad Genetics and a common public database.”

Myriad Genetics had been exclusively providing tests, for
$3000+ a pop for full BRCA gene sequencing, for 17 years before the Supreme
Court invalidated key gene patents back in 2013. Since the ruling a dozen or so
competitors have been offering tests for much lower prices. Meanwhile, Myriad
has amassed a far deeper database than anyone else, having been in the business
so much longer. And it’s proprietary.

CLASSIFYING GENE VARIANTS

(NHGRI)

Public databases of variants of health-related genes have
been around for years too. The best known, ClinVar, collects and curates data
from the biomedical literature, expert panels, reports at meetings, testing
laboratories, and individual researchers, without access to Myriad’s database.
ClinVar uses several standard technical criteria to classify variants as
“pathogenic,” “benign,” or “of uncertain significance.” (“Likely pathogenic”
and “likely benign” were used more in the past.)

ClinVar lists 5400 variants just for BRCA1. The criteria
come from population statistics, how a particular mutation alters the encoded
protein, effects on the phenotype (symptoms), and other information.
Bioinformatics meets biochemistry to predict susceptibility. The BRCA1 protein
acts as a hub of sorts where many other proteins that control DNA repair
gather. DNA Science discussed the genes behind breast and ovarian cancers here.

As gene sequences accumulate in the databases and troops of
geneticists and genetic counselors annotate them, the proportion of pathogenic
and benign entries will increase as that of the unsettling “variants of
uncertain significance” — VUS — will decrease.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

In the Journals–March 2017, Part I by Julia Kowalski

Here is Part I of our March article round-up.

American Anthropologist

A Dog’s Life: Suffering Humanitarianism in Port-au-Prince, Haiti

Greg Beckett

In the Bel Air neighborhood of Port-au-Prince, Haiti, most residents are dependent on humanitarian and foreign assistance for food, services, aid, and jobs. Yet, some residents feel that the conditions under which such aid is provided actively blocks their ability to live a life they find meaningful. In this article, I explore how some Haitians theorize this humanitarian condition through the figure of the dog, an animal that exemplifies, for Haitians, the deep history of violence, dehumanization, and degradation associated with foreign rule. I then contrast this with how foreign aid workers invoke the figure of the dog to illustrate their compassionate care for suffering others. Drawing on research among Bel Air residents and foreign aid workers in the years after a devastating earthquake destroyed much of Port-au-Prince, I show how the figure of the dog is central both to Haitian critiques of humanitarian aid and to the international humanitarian imaginary that responds to forms of suffering it deems cruel.

Biosocieties

“Let’s pull these technologies out of the ivory tower”: The politics, ethos, and ironies of participant-driven genomic research

Michelle L. McGowan, Suparna Choudhury, Eric T. Juengst, Marcie Lambrix, Richard A. Settersten Jr., Jennifer R. Fishman

This paper investigates how groups of ‘citizen scientists’ in non-traditional settings and primarily online networks claim to be challenging conventional genomic research processes and norms. Although these groups are highly diverse, they all distinguish their efforts from traditional university- or industry-based genomic research as being ‘participant-driven’ in one way or another.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

Bioethics & Wine

I
never thought I’d have the opportunity to use this blog title. Never, that is,
until I stumbled across a company called
Vinome, a California
start-up that offers a curated wine service based on a customer’s individual
taste profile. What makes this wine subscription service unique is not its
price (although, at around
$65 a bottle, it’s just a
bit outside of the typical price-per-bottle for many wine club members). At
Vinome, your taste profile includes not only a list of questions about your
preferences, but also information from DNA sequencing from the saliva sample
you provide to the company. The company website proclaims this is “A little
science and a lot of fun,” but
experts are skeptical about whether
there is any science involved at all.

Holding
aside the question of scientific plausibility, companies touting
direct-to-consumer genetic screening for ancestry, medical issues, or just
plain fun include information in the fine print that would give any bioethicist
pause. While the Vinome website requires patrons to check the box indicating “I
have read and understand the Vinome Informed Consent” prior to ordering, that “informed
consent” is only available if the customer
voluntarily
clicks on the informed consent link. Buried at the bottom of the informed
consent screen is a sentence that reads:

 

“You allow
Vinome to retain your data as part of Vinome’s secure research database, for
use by Vinome or its research affiliates, in an effort to improve and expand
services. If any commercial product is developed as a result of the use of your
data, there will be no financial benefit to you.”

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

Bioethics & Wine

I
never thought I’d have the opportunity to use this blog title. Never, that is,
until I stumbled across a company called
Vinome, a California
start-up that offers a curated wine service based on a customer’s individual
taste profile. What makes this wine subscription service unique is not its
price (although, at around
$65 a bottle, it’s just a
bit outside of the typical price-per-bottle for many wine club members). At
Vinome, your taste profile includes not only a list of questions about your
preferences, but also information from DNA sequencing from the saliva sample
you provide to the company. The company website proclaims this is “A little
science and a lot of fun,” but
experts are skeptical about whether
there is any science involved at all.

Holding
aside the question of scientific plausibility, companies touting
direct-to-consumer genetic screening for ancestry, medical issues, or just
plain fun include information in the fine print that would give any bioethicist
pause. While the Vinome website requires patrons to check the box indicating “I
have read and understand the Vinome Informed Consent” prior to ordering, that “informed
consent” is only available if the customer
voluntarily
clicks on the informed consent link. Buried at the bottom of the informed
consent screen is a sentence that reads:

 

“You allow
Vinome to retain your data as part of Vinome’s secure research database, for
use by Vinome or its research affiliates, in an effort to improve and expand
services. If any commercial product is developed as a result of the use of your
data, there will be no financial benefit to you.”

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

H3Africa: Fostering Collaboration

Caption: Pioneers in building Africa’s genomic research capacity; front, Charlotte Osafo (l) and Yemi Raji; back, David Burke (l) and Tom Glover.
Credit: University of Michigan, Ann Arbor

About a year ago, Tom Glover began sifting through a stack of applications from prospective students hoping to be admitted into the Master’s Degree Program in Human Genetics at the University of Michigan, Ann Arbor. Glover, the program’s director, got about halfway through the stack when he noticed applications from two physicians in West Africa: Charlotte Osafo from Ghana, and Yemi Raji from Nigeria. Both were kidney specialists in their 40s, and neither had formal training in genomics or molecular biology, which are normally requirements for entry into the program.

Glover’s first instinct was to disregard the applications. But he noticed the doctors were affiliated with the Human Heredity and Health in Africa (H3Africa) Initiative, which is co-supported by the Wellcome Trust and the National Institutes of Health Common Fund, and aims in part to build the expertise to carry out genomics research across the continent of Africa. (I am proud to have had a personal hand in the initial steps that led to the founding of H3Africa.) Glover held onto the two applications and, after much internal discussion, Osafo and Raji were admitted to the Master’s Program. But there were important stipulations: they had to arrive early to undergo “boot camp” in genomics and molecular biology and also extend their coursework over an extra term.

Both agreed and were soon put through the paces of performing basic lab techniques, hearing about the latest in DNA sequencing, learning the basics of designing genomic studies, and immersing themselves in their courses.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

The 14 day rule – A brief update

In early December, this blog commented upon the 7 December 2016 conference at University College London, which debated rethinking the ethics whether or not to increase the UK’s restriction on experimentation on human embryos from 14 to 28 days. One result of that conference is that the Progress Educational Trust (the sponsor of the original conference) has since submitted a request to the House of Commons Science and Technology Committee to open a new Parliamentary inquiry. That Committee’s response (in typical bureaucratic fashion) was to table the request until their current inquiry of genomics and genome editing was complete (see number 6 in their report).

In my Internet stalking of this issue, I came across a mid-January 2017 BBC Radio 4 two-part telecast coverage of the issue by Matthew Hill, which I commend to you. Each is approximately 30 minutes. Part 1 provides background information primarily regarding the general history of IVF in the UK in general and the history of the 14 day rule in particular, all done via present day interviews of the actual historical figures (or recorded interviews done at the time the events were transpiring). Note that the first 2 minutes are unrelated to the topic. Part 2 is similar, though concentrates upon the key persons in the current debate of moving from the present 14 day limit to a proposed new 28 day limit for embryo experimentation. If you don’t have time or inclination to listen to the whole series, consider the following snippets (time in minutes from start of each recording):

  • Part 1 – 12:00 – 15:00 – Baroness Mary Warnock discusses why she and the Warnock Committee settled on 14 days (arbritary, but a fixed number of days made more sense than a point in embryologic development that varied slightly from embryo to embryo).

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.

Uncategorized

Genomics Reveal Surprises about Florida Zika Outbreak

March 6, 2017

(Medscape) – The Zika virus outbreak in the United States in 2016 was caused by multiple infected travelers arriving in South Florida, not by a single “patient zero,” genomic research has revealed. “From an epidemiologic standpoint, it’s important to understand we had multiple introductions. It’s not something that happened once — it happened over and over,” said Kristian Andersen, PhD, of Scripps Translational Science Institute in La Jolla, California.

The views, opinions and positions expressed by these authors and blogs are theirs and do not necessarily represent that of the Bioethics Research Library and Kennedy Institute of Ethics or Georgetown University.