Genomics and the Social Web: A Timeline

(As posted on www.hernaturehisnurture.com)

I thought I’d share this timeline that I put together recently for a presentation on the social asepcts of genomics. Although clearly not an exhaustive list of events, I still find it interesting to see the major milestones in genomics side-by-side the evolution of the social web.  Not only does this provide a potential explanation for why the genomics industry has developed the way that it has, but it helps to illustrate the relationship between genomics and social media: openness, connectivity, patient autonomy and citizen science.

 

(click on image for larger view)

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“Family History In Times of Siege (1945)” by Robert Resta

A full schedule, impatient with patients,

committing the mistake

of heading straight to

matters of fact

But they must tell their stories first

Facts only matter

in the setting of the heart.

§

An incendiary March night,

standing in a meadow,

looking up in little girl wonder

In the distance

Tokyo vaporizing

into hot white ash, carried by a vortex

of burning wind, transformed into

a snowfall from Hell

that calmly floated down, and covered the grass

as far as her eyes could see.

§

August, family and neighbors

crowding the barn

surrounding the only radio in the village

a silent circle of heads

weighted with shame and shock

listening to the Great Emperor

surrender their country to strangers

from across the ocean

But she was secretly relieved

Never again would her asthmatic airway

be inflamed by sirens and the musty air

of a stifling underground shelter

her mother pulling her by a stiffened arm,

protesting, in the purple dark of night

as the world exploded around her.

§

Across the Axis, a tiny girl

cried in a Dresden bunker,

unaware that her desperate mother

had raced back

to coax a stubborn father to join them

 

in the safety of the depths

Her family history erased forever

by a carpet of bombs

that rolled down the street

to arrive at the door of her house

precisely as her mother opened it

to plead with him to run for his life.

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Guest Post: What Makes You Who You Are?

By Anne Madeo

Anne Madeo is a genetic counselor who has worked for the National Institutes of Health for the past 11 years.  The views expressed here are her own and do not necessarily represent the views of the National Institutes of Health or the U.S. Department of Health and Human Services.

A few months ago, Bob Resta mused on clients’ responses to queries about ethnicity and what they tell us about the client. A recent conversation on the Nat’l. Society of Genetic Counselors’ listserv about ancestry testing and sex verification got me thinking about a similar issue in a different light.

What defines who we are on a fundamental level? Am I a woman because I wear dresses? Am I a woman because I have two X chromosomes? Am I woman simply because I say I am and that is how I feel on a gut level? Am I a woman if I have two X chromosomes and identify as a female, but I have a point mutation in a gene that increases testosterone production but not so much that in utero or postnatally I have male external genitalia? In the final question we might say that I am clearly female. But in the case of high-level performance athletics, my increased testosterone might provide such an advantage over women with typical human female hormone production that I shouldn’t be allowed to compete as a woman. In a recent decision, the International Amateur Athletic Federation (IAAF) side-stepped the issue of determining somebody’s sex and ruled that if a woman’s androgen levels are within the range of a typical male, she will not be allowed to compete as a woman in IAAF-regulated competitions. Should we should start testing athletes for mutations that predispose them to excel at sprinting and handicap the athletes that have these alleles to make the playing field even?

What about ethnicity or race? Am I Italian-American because I celebrate the Feast of the Seven Fishes on Christmas Eve? Am I Italian American because my paternal great grandparents immigrated here from Italy? Am I Italian-American because I say I am and it is how I’ve been raised and feel? Am I Italian-American because my DNA testing demonstrates that I’m a descendant of both Michelangelo and Leonardo da Vinci? I think most students of genetics would say that no, that last idea doesn’t make me Italian-American. We’re probably all distantly related to some famous individual or the other from the past. I could be Queen Victoria or Genghis Khan’s distant relative. (I doubt many people request testing to see if they’re related to Josef Stalin.)

So, can we use genetics to determine what racial or ethnic group we belong to? Although I usually assume that people with training in molecular or clinical genetics would say no, that’s clearly not always true. The postmodern interpretation of race is that it is a social construct. We determine our race and it is determined for us through family, societal and cultural cues. So, can I identify as Native American if my maternal great great grandmother was Native American and that’s the identity my family has always embraced? It seems that some would say yes, that if your experience is Native American and that is how you identify then you are Native American. But the extreme of the post-modern argument is that I, an individual with no known to me African heritage could claim that I am African-American simply because like most Americans I likely have some African ancestry. What say those who decry postmodernism? The extreme of the position that race and ethnicity are not culturally determined but the result of ancestry is the one-drop rule and the perception that light-skinned multi-racial individuals who identify as “white” are passing.

The obvious answer to all this is that who we are is determined by a complex mix of genetics, family, cultural and individual influences. Which still leaves us with the question—how do we decide ‘who’ or ‘what’ somebody is? Or, is that the right question to ask?

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Guest Post: The Feminine Tightrope Walk

By Myra I. Roche, M.S., C.G.C.

Myra I. Roche, M.S., C.G.C. is an Associate Professor in Pediatrics, Director of Pediatric Genetic Counseling Services, and an investigator in the Center for Genomics and Society at UNC, Chapel Hill.  Her research interests include parents’ understandings of genetic information and their genetic counseling experiences following acceptance of newborn screening for fragile X syndrome.  She co-edited An Ethics Casebook for Genetic Counselors: Ethical Discourse for the Practice of Genetic Counseling, serves on the JGC editorial board, and was chair of the ABGC Certification Exam Committee.  She has worked at UNC for the past 25 years, living in the same house for the last 24.  Her favorite past-time is walking.

“Women are notoriously bad at asking for raises, and as 95% of our field is women, we have suffered the consequences.”

This statement recently appeared on the NSGC listserv with a plea for participation in a salary survey, an extremely important task for a young, thinly-populated profession like genetic counseling. What struck me hard, though, was the echo of a well-worn misconception promising a simple explanation for the pay discrepancy between the genders. The answer: women just aren’t good enough- at being men. This evaluation of women’s negotiating skills is not new and is best summed up by Professor Henry Higgins’ exasperated rhetorical question, “Why can’t a woman be more like a man?” But shouldn’t we be suspicious when righting an inequality requires the “have nots” get better at imitating the “haves”? The fault lines here are clearly drawn.

Yes, the playing (and paying) field between the genders remains uneven. Sorry to be the one to bring this up for the 15 billionth time. Currently women make, on average, 77 cents for every dollar a man makes. Analyzing salaries across genders is full of pitfalls but even after several corrections, the disparity remains (pdf). If you don’t know the facts, see this National Committee on Pay Equity Quiz.

Admonitions that women have only themselves to blame are old but the twist, “thanks for dragging me down with you”, strikes a new, blatant tone that is shocking. If women would just stiffen up their collective lips, stride into their bosses’ offices carrying their weight in unequivocal salary data to prove they are underpaid, well, what’s been stopping them? But if poor negotiating is the culprit, how can it be that women, long stereotyped as being superior wheedlers (particularly of men) to get their way, would inexplicably fail to wield these same skills when more money is the goal. Is this simply a lack of gumption?

As every good negotiator knows you have to be ready and able to walk when the answer is no. To walk, you need options. And good shoes. Women have had fewer options than men because they can become pregnant- something that was, until only an evolutionary blink ago, uncontrollable. This monthly roulette, combined with fewer educational and financial resources, left them less able to walk away because they were barefoot, pregnant, or both.

Looking up from our respective grindstones, we see that women, ages 23- 30, have, apparently, arrived. In those who are college-educated and, not accidentally, without children, we find our proof of principle. Their salaries are comparable, or even exceed, their male counterparts.

Have they figured out how to act like men? Do they have more gumption? Or, do they just have better walking shoes?

Some have argued that women are very savvy negotiators because they understand how risky it is to ignore the social costs implicit in these transactions. When shown a video of a man or a woman asking for a raise, judges of both genders agreed that, yes, certainly, the man should get a raise. But the woman, speaking from the identical script? Nope, and furthermore, we don’t like her either because she is way too pushy. For a woman. Same script, opposite decisions.

For a women wanting a raise, Henry Higgins’ advice was dead wrong. Don’t act more like a man. Act more like a (stereotypical) woman. Be warm and friendly, show more concern for others than yourself, and figure out how to make the raise your team leader’s idea, not yours. Tellingly, women’s reluctance to negotiate for higher pay occurred only when the judge was a man.

Is more money always, unequivocally, without a doubt, better? For many women the answer is clearly no. Certainly not always better than being socially ostracized otherwise what else could be stopping them? As women walk toward more money, they are, at the same time, often walking away. Away from their safety net of people who individually and collectively support them. Add in children, elderly parents, and lots of other factors and the tightrope beings to sway even more, making walking a very precarious choice.

Yes, definitely, arm yourself with all the salary data you can, stride briskly into that office, and try to convince your boss that it was her idea. I applaud your efforts even as I keep my fingers crossed. I hope you get the raise you believe will make you happier. But sometime soon, put yourself in someone else’s shoes. Maybe more money will make you happier. But for women in other shoes, the figures may add up differently. No need to shame others who have done their own math and calculated that the timing is wrong, they can’t afford to waste precious social capital or, frankly, their feet hurt. To imply that colleagues who are not actively negotiating their salary are somehow responsible for anyone’s inadequate income smacks of nothing more than just shoddy reasoning.

Acknowledgment: Thanks to Elana Jones for her insightful editorial comments.

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Taking Exception to Genetic Exceptionalism

A recent situation in Ontario has prompted the discussion about whether or not it is appropriate for geneticists to act as gatekeepers of genetic testing. Essentially a policy change was made on the provincial level that would only allow for out-of-province funding for genetic tests when the test is ordered by a certified Canadian College of Medical Genetics (CCMG) geneticist. This change removed the ability of oncologists, cardiologists, neurologists and non-CCMG certified geneticists from ordering genetic tests as part of a diagnostic work-up for his or her patient. And, as a trickle-down effect, it hurt genetic counsellors working in specialty clinics with non-geneticists. For my US colleagues, I would loosely compare this situation to an insurance company only approving to cover the cost of genetic testing if that test was ordered by a geneticist certified by a specific certifying body. (As a side note: has anyone heard of this happening?)

For me, any discussion about the genetics community acting as ‘gatekeepers’ to genetic information naturally leads to a conversation about genetic exceptionalism. Defined as ‘the belief that genetic information is special and should be treated differently from other medical information,’ genetic exceptionalism is a natural topic for genetic counsellors, as we are specifically trained to communicate the unique nature of genetic testing to patients. In our training we learn over and over again about the potential harm (psychological, insurance) that can come from genetic testing for someone who was not properly informed about the test ahead of time. I graduated from my training program in 2008 believing that everyone undergoing a genetic test should have a genetics consultation first. And then I started at my first job.

Working in the adult genetics world I’ve increasingly felt that the field of genetics is actually very similar to other specialties, especially with respect to the diagnostic work-up. For example, if a drug-infusion study used by a cardiologist to assess for Brugada syndrome comes back negative, it reduces the likelihood of Brugada syndrome in that patient but doesn’t rule it out completely. How is this different from a negative genetic test result in which the mutation detection rate is only 75%? In genetics we commonly worry about how other specialists might interpret the ambiguity of a variant of unknown clinical significance. But I’d argue that this is no different than a brain MRI with non-specific equivocal changes. Most specialties (if not all) work with ambiguous results and data every day. So why is an ambiguous genetic test result so different?

I believe that we are firmly in an era where we need to promote collaboration and excluding other physicians from ordering genetic tests is likely to alienate specialties, rather than bring them together. Everyone agrees that increased genetics education in medical students and continuing education for practicing physicians is an important priority. But what better way to educate than through collaboration on a case? And yes, there is an important place for the traditional genetics and genetic counselling model, but applying the same model to every genetic test is short-sighted. While a handful of genetic tests represent ‘exceptional’ information and should be treated differently, the majority do not.

So, are genetic tests different enough from other medical tests that geneticists (or the genetics community) should act as gatekeepers of the information? In my opinion, the answer is a resounding no.

As for the Ontario policy, immediately following the release of the news, the genetics and non-genetics community was up-in-arms. Having no inside knowledge on the situation, it seems from the outside that this uproar was heard by the government, and the policy change has been put on hold, for now.

I know this is a loaded topic. For those who disagree with me, please share your comments below as I think this is an important debate for us to have out loud. While this shift for me occurred largely because of my work experience, I have a hunch that given the increase in use of genetic testing and the applicability of new genomic information, even seasoned counsellors may have altered their viewpoint on the ‘exceptionalism’ of genetics in the past few years. I’m interested to know: what is your opinion and has it shifted over time? Please cast your (anonymous) vote to my (very non-scientific) poll below.

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p + q = Solved, Being the True Story of How the Chromosome Got Its Name

A few weeks ago I discussed different stories we have come to tell about the origins of the convention of using “p” and “q” to identify the chromosomal short and long arms, respectively (L’histoire de p et q: Urban Legends of Cytogenetics). That posting created quite a bit of discussion, particularly on the Cytogenetics Listserv. Several cytogenetics colleagues forwarded a comment from their listserv that should stand as the definitive story of how p & q became established as official cytogenetic nomenclature.

The True Version was related by someone who was in the room when the decision was made. In my previous post I alluded to the Battle of Hastings. That imagery was apparently not far off from the truth; one conference attendee reported that at times the session seemed like World War 2 1/2. As I had suspected, the 1966 Chicago Conference* was the scene of the crime. The suspects included some important figures in the history of medical genetics: Klaus Patau, Jérôme Lejeune, and Lionel Penrose.

Klaus Patau first described the clinical and cytogenetic basis of trisomy 13 in 1960, along with his wife Eeva Therman (the Finnish cytogeneticist who was sometimes called Mrs. X Chromosome), the great dysmorphologist Dave Smith, and two other authors. Patau originally worked at Germany’s Kaiser Wilhelm Institute and then went on to a long and illustrious career at the University of Wisconsin at Madison.

France’s Jérôme Jean Louis Marie Lejeune is known for his lifelong devotion to the study and care of people with Down syndrome. He was a devout Catholic and a friend and advisor to Pope John Paul II. In 1959, Lejeune, along with Raymond Turpin and Marthe Gautier, were the first to report the underlying cytogenetics of Down syndrome. Gautier, a physician who worked in Turpin’s laboratory at the Centre National de la Recherche Scientifique in Paris, first thought of the idea to karyotype a patient with Down syndrome patient and noted the presence of an extra chromosome in the cells cultured from a skin biopsy.  Lejeune identified the culprit as the twenty-first chromosome. Decades before, several scientists had suggested that Down syndrome might have a cytogenetic basis, including Petrus Waardenburg, Guido Fanconi, and Lionel Penrose, but the technology was not available at the time to test the theory.

Lionel Penrose, the longtime Galton Chair at the Galton Laboratory at University College London, was one of those great polymaths that England seems to be a breeding ground for. He was a psychiatrist, chess master, mathematician, medical geneticist, and, among other things, proposed a method (now called Penrose’s Law) for fairly allocating votes among countries in international organizations like the UN. He statistically established the association between advancing maternal age and an increased risk of Down syndrome.

Back in Chicago, the nomenclature session lasted many hours. Initially, “s” and “l” were recommended for the chromosomal short and long arms. Patau countered with “k” for kurz (German for “short”). Lejeune strongly argued for “p” for petite. This was followed by arguments about naming the long arm, with the concern that “l” could easily be confused for the number 1. In the wee hours of the morning, Penrose entered the room, wanting to know why the session had not yet ended. After hearing about the difficulties, he offered p & q because they were linguistically neutral, and because p + q = 1, evoking the idea that a short arm and a long arm together make one whole unit.

So it turns out that the True Story is closest to Version 4, what I labeled The Hardy-Weinberg version in my earlier post, but it also contains elements of Version 1 (The French Connection) and Version 2 (Francophones vs. Anglophones). Alas and alack, Version 3 (The NY Typesetter’s Error) appears to have no basis in truth, though it is still a good story. Interestingly, the results of the Voting Poll in my previous posting indicated that most people thought The French Connection was the correct story (garnering about 62% of the 211 votes cast by April 30th), whereas the Hardy-Weinberg story came in a distant third at about 11%, with The Francophones vs. The Anglophones attracting 19%, and the New York Typesetter’s Error coming in last with about 8% of the vote.

I guess that when it comes to history, there’s no such thing as The Truth, only distorted versions of it that over time become mistaken for the real thing. Of course, what is really interesting about history is not The Truth so much as the fact that we need to tell stories about our past, and those stories reflect complex personal, psychological, educational, and sociological factors.

* – Chicago Conference (1966): Standardization in Human Cytogenetics: Birth Defects. Original Article Series, Vol 2, No 2, New York, The National Foundation (1966).

Thank you to my colleagues from the Cytogenetics Listserv for forwarding the communication, and to the many readers of the DNA Exchange who took the time vote on The True Story and share their own stories.

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L’histoire de p et q: Urban Myths of Cytogenetics

Karyotypes are sooooo 20th century. Time was when a ripe crop of G-banded chromosomes promised a fruitful harvest of genetic secrets. But nowadays a Giemsa-stained karyotype seems like a quaint low resolution black and white TV set – those cute little D & G groups even have rabbit-ear antennas – compared with the bright, sexy colors of FISH, the fine oligonucleotide detail of microarrays, and the dense volumes of data of generated by high throughput DNA sequencing.

But before all that trypsin, calf serum, and Giemsa stain sails off in a T-25 culture flask to navigate the seas of our mythic memories, some cytogenetic stories need to be told. The tale I want to relate started with an email from Debbie Collins, one of our Kansas City genetic counseling colleagues.

“I went to a lecture today,” Debbie’s email began, “and learned how the chromosome’s short and long arms came to be called p & q.” She then related a story that was completely different than what I had always held to be true.

Debbie’s email got me into a Rudyard Kipling frame of mind. Just how did the chromosome get its name? As it turns out, probably neither Debbie’s story nor my story is true. I searched for the “real” answer in standard genetics textbooks and PubMed, but to no avail. So I unscientifically queried geneticists and cytogeneticists of various stripes and ages about how they thought “p” & “q” came to be the official chromosomal designations. Here are their stories, with annotations by me:

1)    The French Connection. This was the most popular version in my unofficial survey.  In this story, “p” stands for petite, the French word for “short.” The long arm came to be called “q” because “q” follows “p” in the alphabet. But that seems inconsistent. Why would one chromosomal arm be named after a word and the other arm named after a letter? It would be more logical to call the long arm “g” for grande, French for “big” or “large.”

2)    Francophones vs. Anglophones. In this version, the French in fact wanted to go avec “p” et “g”. Mais l’English speaking contingent objected to the French conquering the entire chromosome, apparently still harboring some nationalistic resentment nine centuries after The Norman Conquest. The Anglophones held out for “q” because, they claimed, “q” follows “p” (see The French Connection above). But really “q” appears English and also had the quality of making “p” evoke English rather than French. Even though it gave the appearance of a civilized linguistic compromise in which both sides got to name half of a chromosome, victoire pour les Anglais. Hastings avenged!

3)    The New York Typesetter’s Error. This is the version Debbie Collins related to me. The 1971 Paris conferees recommended “p” and “g” á la petite et grande. The nomenclature was reported in 1972 in Birth Defects: Original Article Series, which was published in New York City. A mythical typesetter inadvertently confused “g” for “q”.  The mistake was noticed after the issue had gone to press, too late for correction.

Great story, which caters to our stereotypes of New Yorkers’ penchant for giving language a unique twist. Sadly, though, it is not likely true. First off, I’ve never met a cytogeneticist who was not pathologically detail-oriented, and there is no way they would ever let an error like that get beyond the earliest stages. But more tellingly, although the Paris Conference indeed recommended “p” and “q”, these designations were in use at least 5 years before the 1971 meeting.

4)    The Hardy-Weinberg Equilbrium. As one source quoted to me, all geneticists know that p + q = 1. This has nice poetic and historical resonance . But it sounds too pat to be true. Somehow, I can’t imagine a sober-minded committee thinking this up, and then everyone agreeing to it (or perhaps they weren’t sober). Besides, what does cytogenetics have to do with the Hardy-Weinberg Law?

After spending an inordinate amount of time on PubMed, I think that I have narrowed down the start of the p/q story to the Chicago Conference in 1966, also published in Birth Defects: Original Article Series (I have to admit, though, that I have been unable to obtain a copy of this publication. If anybody is willing to send me an electronic or print copy, I would be forever indebted). The 1960 Denver Conference, by the way, makes no reference to “p” & “q.”

Which story do you think is true?  History is essentially the stories about our past that we have come to believe to be true. So let us choose our history systematically and democratically, rather than leaving it to the confabulations of story tellers or the biased views of the powerful. We can create the truth by popular vote, rather than simply relying on bothersome facts. Use the polling box below to vote for your favorite story so we can settle on the official History of Chromosome Nomenclature. Please, no stuffing the ballot box to ensure that your favorite theory wins; I have ways of finding this out and I will hunt you down. It would also be fun to hear other theories that I may have overlooked, so please use the Comments section to add to the list of Urban Legends of Cytogenetics.

See the follow-up to this posting on the DNA Exchange: “p+q = Solved, Being The True Story of How the Chromosome Got Its Name.”

Thanks to Debbie Collins, Alex Minna Stern, and Nathaniel Comfort for helpful discussions.


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