Tag Archives: whole exome sequencing

Vocab Rehab

Our word choices in speech and writing are often reflexive rather than reflective. Some words become so engrained into our vocabulary that we use them out of habit rather than after careful consideration. We think we are communicating clearly because everybody “knows” what a particular word means so we don’t pause to consider what the word might really mean or suggest. This can be particularly true of professional vocabulary, wherein we are inculcated with a set of specialized terms and word choices early in our training that are later reinforced throughout our careers by journal articles, books, and at educational meetings.

Even the rhythm and meter of spoken language can silently work their way into professional oral presentations. The next time you attend a multi-day conference pay attention to how the speakers at the end of the conference may unconsciously repeat the speech patterns of the speakers from the previous days. I first noticed this phenomenon about 10 years ago at an annual genetic counseling education conference during which a few speakers at the beginning of the conference frequently used a high-rising terminal (i.e., a rise in pitch at the end of a sentence). By the last day of the meeting it seemed like every speaker was raising their pitch at the end of too many sentences and it was starting to drive me crazy (I’ve since adapted). The “right” way to speak or write is the one that we encounter most often and most recently by respected members of our professional and social circles.

Reflexive vocabulary usage can sometimes mislead or confuse. Let me offer two examples of  vocabulary used by – but not unique to – the medical genetics community that in my view need some reconsidering and revision: whole exome/genome sequencing and gender neutral pronouns (for related discussions, see my prior postings about the words “psychosocial.” and “mutation“).

Whole Genome/Whole Exome Sequencing – These are inaccurate and misleading terms. The descriptor “whole” suggests that the entire genome or the entire exome is being sequenced. In fact, the analysis usually includes a lot of the genome or a lot of the exome – but not the entirety of either.  They don’t quite go the whole nine yards. The limits of some “whole” techniques and platforms become even more salient when you understand that they may not reliably detect some of the most common DNA-based disorders such as Down syndrome, fragile X syndrome, and alpha-thalassemia. I suggest that we drop the word “whole” and simply call it genome sequencing or exome sequencing, a practice I’ve already seen in some journal articles. But it should include a descriptor that indicates which technology was used to sequence the genome – short read, long read, optical mapping, etc. Each has its strengths and limitations and knowing which technique was used informs us as to which conditions are reliably or unreliably detected.

Incidentally, genome was coined (as genom) in 1920 by the German botanist Hans Winkler. Until the discovery that most DNA was non-coding, the word genome implied the sum of an organism’s genes. Now that we know that only a smidgen of an organism’s DNA are genes as we understand them today, the 20th century sense of genome does not align with the current sense of genome that refers to the entirety of an organism’s coding and non-coding DNA. Exome, on the other hand,  arose out of 21st century technology. The earliest article I could find in PubMed that used exome in it’s title or abstract was a 2008 publication about J. Craig Venter’s exome (Venter was the senior author).

Gender Neutral Pronouns and Verb Agreement – I wholeheartedly support the use of gender neutral or third gender pronouns in English, even if I think a few of them like zie, zir, and ver will not likely catch on. The vagaries of language evolution could ultimately prove me wrong but no matter how conscientious and respectful you try to be, these neologisms entail learning new words that have no clear etymology to guide the user or listener as to their meaning. However, pronouns such as “they” or “them” as a singular subjective or objective pronoun or “their” as a singular possessive pronoun have gained more linguistic traction. These pronouns have historical usage as a a singular form. Take the sentence I wonder who left their mobile phone on their seat in the auditorium? Whoever it is, they are not going to be happy when they realize it. “They” is a pronoun substitute for the singular “that person.” This sentence would have been perfectly clear and acceptable in just about all English dialects well before gender neutral pronouns became a subject of debate and discussion. Further, “they” and “them” do not have a linguistic history of denoting a specific gender.

My question, though, is not about which pronouns will survive the test of time but rather which verb form to use with that pronoun. Does it call for the plural or the singular verb form, as in “They are” or “They is?” I vote for “They is.”

I confess to being a bit of a fanatic about the arcana of grammar and syntax, but I am not a language tyrant. Language evolves so quickly that the “rules” desperately try to keep up with usage. Good writers instinctively know the rules and then go about flaunting and manipulating them. I am not trying to be snobbishly picky when I raise the question of pronoun/verb agreement. There are two important issues raised by verb choice in this situation, one of meaning and one of value judgment. “They is” clearly communicates the meaning of one, and only one, person rather than a group of people. The value judgment implied by using the singular verb  is implicit acceptance and acknowledgment of the person’s choice to not identify as being of male, female, or any gender. The slightly jarring effect of hearing a singular verb follow a typically plural pronoun makes “they” stand out in the sentence. It’s not just any old use of “they.” It’s a special case that reflects and honors the desires of that person.

Yeah, I know. “They is” just sounds plain wrong. But it only sounds wrong because we are used to having heard it another way for our entire lives. If the singular verb is used more frequently and consistently, the dissonance will fade. I remember the endless discussions about whether one should use a singular or plural verb with the word “data.” Now, it’s like Who Cares? “Date are” and “Data is” both now sound equally fine and either form is considered acceptable by most authoritative usage guides. Rule-obsessed grammarians can argue all they want; the rest of us just get on with our linguistic lives.

No doubt some of you will disagree with my suggestions. So I open up the discussion to the Good Readers. What do you think? And is there other vocabulary that needs reconsidering and discussion?

 

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A Diagnosis Is Not The End Of The Odyssey

by Robert Resta, Jennifer A. Sullivan, Allyn McConkie-Rosell

Allyn McConkie-Rosell, Ph.D., CGC, is a Professor in the Division of Medical Genetics at Duke University Medical Center. Jennifer A. Sullivan, MS, CGC is a
Senior Genetic Counselor in the Division of Medical Genetics at Duke University Medical Center. Robert Resta, MS, CGC, is a genetic counselor at Swedish Medical Center in Seattle and a frequent contributor to The DNA Exchange.

The Diagnostic Odyssey – that meandering, lengthy, and frustrating quest for a diagnosis. Genetic counselors, medical geneticists, and patients with rare disorders and their families are achingly familiar with it. The allusion to Homer’s Odyssey is apt. Odysseus’s decade of wanderings are replete with perils, disappointment, love, wonder, whimsical gods, adventure, and frustration. Surely some specialist somewhere in the world can tell me what condition my child has been born with, and I will brave the wine dark seas for as long as I must to find that expert! Genetic testing technologies like whole exome/genome sequencing have shortened the quest for many patients, though perhaps not as often as one would have hoped.

The label Diagnostic Odyssey suggests that the diagnosis is the end of the odyssey. And therein lies the problem. Many families and patients discover that a diagnosis does not necessarily allow them to settle down happily with Penelope in the kingdom of Ithaca. A successful diagnostic workup may be the end of the odyssey for clinicians, but for patients and families the diagnostic quest is just one phase in the life cycle of genetic disorders.

A diagnosis may answer some questions such as cause and recurrence risk, but it can also create a whole new set of issues. For patients diagnosed with ultra-rare conditions, families may be faced with frustration from a lack of available knowledge about treatment or prognosis. Even if medical interventions are possible, finding and accessing those resources, and getting health insurers to pay for them, can be a major undertaking. Or a condition’s rarity may make it impossible to form an effective patient/family community to provide advocacy and support. The diagnostic odyssey may result in some patients feeling like diagnostic oddities.

If a newly diagnosed syndrome turns out to be untreatable or life-shortening, parents may lose all hope and descend into existential despair. A non-diagnosis at least holds the glimmer of a chance for a treatment or cure out there somewhere. Patients who have a diagnosis changed from a previous incorrect diagnosis may lose the sense of identity and support supplied by the disease community that they had been involved with for years.

The label Diagnostic Odyssey focuses on one medical aspect of a condition. Clinicians can take much-deserved professional satisfaction in having finally solved a long-standing mystery. But for many families, living with a genetic condition is not a temporally demarcated event and, above all, not only a medical experience. Patients will also still need to implement strategies and solutions to the social, educational, lifestyle, and psychological ramifications of the disorder. It is an ongoing journey, one that continues to unfold as patients age and develop new symptoms, family structures evolve over time, medical treatment advances, and sociocultural changes re-shape attitudes toward inclusivity and the availability of resources. A genetic condition, named or not, will continually present new challenges throughout the entire life of a patient.

We do not mean to imply that a diagnosis is unimportant. We recognize the emotional and potential medical value of finally “putting a name on it.” But the name just points the ship in a new direction to unexplored regions with different threats, problems, and rewards.

Perhaps the Diagnostic Odyssey label needs to be retired or renamed to more accurately reflect its role in the process of living with, and adapting to, genetic conditions. So we turn to the Good Readers of The DNA Exchange to offer their suggestions – what do you think?


Genetic Counselor Talent Show Friday, November 16th

Are you attending the 2018 Annual Education Conference of the National Society of Genetic Counselors in Atlanta next week? Worried that days of  PowerPoint presentations and polite applause will make you forget what fun is? Want to have a blast one evening and see your genetic counseling colleagues in a very different light? Then attend the Genetic Support Foundation’s GC’s Got Talent  2018 genetic counselor talent show on Friday evening November 16th. Cancel all your other evening plans for Friday, November 16th. Trust me – there will be nothing even close for entertainment. With Yours Truly, Bob Resta, as Master of Ceremonies, how could anything beat it? Can you dance, sing, or play an instrument? Are you a Slam Poet? Then show off your talents to your colleagues! Or, if like me, you have Zero Talent, then join me as part of the Story Telling Crew. I have a goofy and weird story to tell. But we all also have poignant, tragic, comic – or all of the above – tales to tell. If I can do it, then you can do it. If you wish to impress your colleagues with your talent, send an email to info@geneticsupport.org to sign up. Show up et regarder les bon temps rouler.

For more information, visit: https://geneticsupportfoundation.org/gc2018

 

 

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