Why 23andMe is Not for Me — Yet

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(NHGRI)

(NHGRI)

A year ago I posted Direct-to-Consumer Genetic Testing: A New View, describing the unveiling of dtc testing at the  American Society of Human Genetics meeting back in 2007 – to shock and antagonism – and my change of heart after learning of two friends grateful for their results from 23andMe.

On November 22, FDA sent 23andMe a letter warning that their “Personal Genome Service,” marketed as “information,” is in fact a medical device and in violation of the Federal Food, Drug and Cosmetic Act. Reading the letter I recalled FDA’s letter blasting the researcher under whose watch an 18-year-old died in a clinical trial for gene therapy. That letter was a valentine compared to FDA’s blistering admonishment to 23andMe, which has been very late in complying with many requests for information.

The company has many fans. Yet still I haven’t had my own DNA tested, except for ancestry, which confirmed what grandma told me. 23andMe does what it calls genotyping, a hodgepodge of tests for genes and markers, not exome or genome sequencing.

I got grief for posting Why I Don’t Want to Know My Genome Sequence, also a year ago, from dtc enthusiasts. But since then, I’ve learned that not wanting to know is not unusual among geneticists.

(Dept. of Energy)

(Dept. of Energy)

A LESSON FROM THE “INCIDENTAL FINDINGS” SITUATION?
At the ASHG annual meeting in Boston last month, a wonderful talk by Anna Middleton, PhD, a research associate at the Wellcome Trust Sanger Institute in Cambridge, UK, confirmed what I’d noticed about my colleagues. Her work as an ethics researcher and genetic counselor has shown that people’s feelings about how much they want to know about their DNA tracks not so much with age, religion, income level or geography, but with profession.

The talk was part of a session on incidental findings: having a test to diagnose one condition, and finding unexpected evidence of another. (See “Incidental findings from genome sequencing: nuances and caveats” from Scientific American blogs.) Direct-to-consumer testing, of course, isn’t the same as a research study in a clinical setting; multiple findings are intended, not incidental. But the issue of how to handle complex genetic information is similar.

Dr. Middleton and her colleagues recruited nearly 7,000 people from 91 countries, most of whom admitted to knowing nothing about genetics, to take an online survey presenting 10 vignettes about ethical issues raised by genomics. One scenario was deciding which incidental findings a researcher should impart. At the meeting, she reported on the responses from 533 genetic health professionals (clinical geneticists and genetic counselors), 607 genomics researchers, and 843 other health professionals. She found that the three groups tend to be much more conservative about how much data to provide than others, with the genetic health professionals the most hesitant.

“We asked, ‘should research participants receive information on hundreds of conditions at once?’ Genetic health professionals were more likely to say no. Are they being protective about these data? Are they unrealistically overly concerned?” she asked the crowd. Reportable conditions should be those for which a person is at high risk and for which treatment or prevention strategies exist, many health professionals agreed. They should be “actionable.”

Dr. Middleton speculated that some genetics health professionals are concerned about practical matters, such as the time it would take to research and explain the potential impact of dozens of gene variants identified in the genome of a patient. But I think a more important reason for hesitancy among some geneticists, including myself, is the incomplete health picture our genomes paint, for now. And that brings me back to the FDA and its warning to 23andMe.

(Jane Ades, NHGRI)

(Jane Ades, NHGRI)

ARE FALSE NEGATIVES AND POSITIVES POSSIBLE?
The agency is requiring that 23andMe provide evidence of validation of their tests. But that won’t be enough to ensure that false negatives and positives don’t happen, because of the nature of a gene.

Consider just one, BRCA1. When mutant it elevates risk of developing any of several types of cancer – it doesn’t directly cause cancer. Angelina Jolie had a well-known mutation, and that was enough to convince her to have prophylactic surgery. She’s in an ethnic group in which that mutation is associated with a very high risk. If she were from another background, the risk would be lower, and perhaps she wouldn’t have had the surgery. If she never developed the cancer, would her test result have been a false positive? Not really. A mutation is a mutation. But a genotype does not always translate into a phenotype. And how can there even be a false positive if what one is inheriting is risk, not a “yes” or “no”?

If a person takes a 23andMe test for the most common BRCA1 mutations, which was possible until recently, and learns she doesn’t have any of them, she might not read all that 23andMe has to say and assume she can’t develop a BRCA1-associated cancer. But she can. The entire gene must be sequenced to rule out risk, and that requires a much costlier test. Is that result of not having any of the most common mutations then a false negative? Not really. Again, a DNA sequence is a DNA sequence. (Then there are the mysterious VOUS – “variants of uncertain significance” – a gene sequence that’s not the “wild type” or normal, but a variant that hasn’t been associated with developing cancer.)

Why doesn’t a BRCA1 sequence mean the same thing to everyone, just as a word is read the same way by everyone? Because a gene does not act in a vacuum. Genes influence each other’s expression. What happens to inheriting two apoE4 alleles, which hikes the risk of Alzheimer’s 15-fold, if a person also inherits a variant of a different gene (APP) that protects against the condition?

Until we (or an algorithm) decipher all possible interactions among all gene variants, detecting mutations for some genes provides incomplete information. I’d like to wait until we know more before mailing my spit to a dtc company, although ironically the more of us who do so, the sooner we’ll figure it all out. And while I think people have a right to know their DNA sequences if they want to, I fear that many people who are not familiar with how genes interact may take the results too seriously, especially the bad ones.

Abstract_pillsA genome sequence and even the smattering of tests that 23andMe offers are a new kind of information, different from a cholesterol level or a spot on an x-ray, and perhaps outside the comfort zone of some if not many physicians. FDA may have to adapt and find a new way to handle the information in genomes. I hope that the agency and the direct-to-consumer company in its crosshairs can find a way to work together — for the benefit of us all.

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Another Blind Boy Sees the Light, Thanks to Gene Therapy

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FFB posterA funny thing happened on the way to this week’s blog post. I’d planned a guest post from a father who very recently observed his young son seeing for the first time thanks to gene therapy. I’d read the father’s blog from a link on Facebook . The boy is participating in a phase 3 clinical trial (efficacy) of gene therapy for Leber congenital amaurosis type 2 (LCA2). My book The Forever Fix: Gene Therapy and the Boy Who Saved It chronicles one of the first participants in the phase 1/2 trial who had his first eye treated in 2008 — he’s now on a poster for the Foundation Fighting Blindness and sees so well that he can hunt turkeys (he lives near me in the wilds of upstate NY. I don’t hunt).

The phase 3 trial, according to Facebook posts, has a rather unusual design. Participants are randomized to have two eyes done days apart, or the gene therapy in a year, to serve as a control group. When I couldn’t find any news releases or media reports to corroborate the design, and the description on clinicaltrials.gov curiously lacked detail, I emailed someone directly involved in the trial.

Early Tuesday morning I got a call – too important for an email – from the clinical trial director, asking me not to run photos or mention names here. The reason: part of the assessment of the gene therapy’s efficacy is for the subject to maneuver through a mobility course, a task impossible for a person with LCA2. The evaluators don’t know which participants had gene therapy and which didn’t. And while the evaluators know to stay away from Facebook, they could stumble upon this blog and see a face that could a year from now bias their observations. The lack of information about the clinical trial protocol I’d encountered was intentional.

But I still want to run the father’s blog, so I’ll call the boy Cliff. The events happened before the family returned home after the gene therapy. I’ve tweaked it enough so it can’t just be plopped into google. I hope. I can’t blame the parents for wanting to shout this news from the rooftops, but I do want to protect the clinical trial. So the photos are of other kids.

Double HelixGUEST POST FROM A GRATEFUL FATHER

“It’s been 16 days since Cliff had his surgery on his left eye, and 9 days since his surgery on his right eye. The first 24 hours after each surgery, he had to keep his eye patched. Then for 14 days, he had to patch his eye while he slept. For 7 days, both eyes were patched at night. These patches are not soft, but rather perforated metal held in place with tape. Needless to say, they can be a bit uncomfortable.

The effects can take anywhere from 7 to 14 days after the surgery of the second eye. At Cliff’s age, it can be difficult to verbalize what changes, if any, he is experiencing. As his parents, we’ve been hypersensitive in the hopes of noticing something. And so far, we have noticed things, some more significant than others.

Four days after his left eye surgery, we were in a sunny parking lot. Cliff looked at his mother and said, “your hair looks different.” Obviously, this could mean a number of things, and it was too soon to tell. But I made mental note of the comment.

Discovery of Gavin Stevens' LCA gene is the first step towards gene therapy. (Jennifer Stevens)

Discovery of Gavin Stevens’ LCA gene is the first step towards gene therapy. Gavin’s Groupies announced funding gene therapy research just days ago. Go Gavin! (Jennifer Stevens)

 

About 3 or 4 days after the second surgery, he asked for noodles. I stepped out to pick them up and he came along. It was already dark. We usually have to tell him to beware of an upcoming step or change in the road, otherwise he’d trip. On this day I forgot to tell him, and noticed that he just stepped up and down the curb while crossing the street. To test if it was just a fluke, I started to walk off and on the sidewalk. We were holding hands … was he following me, or could he see the curb? Again, too soon to tell… but definitely promising.

My aha moment came at dinner in a dimly lit restaurant. Usually, we would point out to Cliff what food was where on his plate, and we’d watch him touch his food as he ate. He would never look down at his plate, because he simply couldn’t see it in restaurants such as these. Most nights, he would get frustrated, and we’d end up helping him eat or feeding him.

But this night was different. They brought out his favorite meal: chicken strips, fries, mac & cheese, and ranch dressing. I was tucking a napkin into his shirt, and before I could help him start eating, he started on his own. I watched for a bit, as he picked up his fork and dove right in. I wanted to be sure that he was actually seeing his food, so as his mom distracted him, I rotated his plate 180 degrees and moved his fork. Now all the food was in different places. He took a drink, reached down, picked up his fork and started eating.

Finally, today, at dinner, Cliff said ” Daddy – you were sleeping. I had to use the potty… and my patch was on and the lights weren’t on, but I could see the potty with my left eye.”

I got so excited, I turned a few lights off, and started asking him to tell me how many fingers I was holding up. I left enough light on so that I could see… and started asking. He was getting them right… prior to the procedure, in that amount of light, there’s no way he would have been able to do it.

(NHGRI)

(NHGRI)

It’s amazing to experience this with him. Watching these baby steps, which may seem insignificant to some, brings tears to my eyes. Tasks that are so simple to the sighted are often times very difficult to those with visual impairment, especially while young. It makes me so happy to see him overcome these challenges, even if they are slight.”

Funding and plans are already well under way to bring gene therapy for LCA2 to the ophthalmological community, once FDA approval is granted. I look forward to the time when the gene therapy that seems so miraculous today becomes a routine intervention so early in a child’s life that he or she never has to navigate in a darkening world.

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NextCODE Health Mines deCODE’s Data, and More, to Catalyze Clinical Diagnosis

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imgresLike the mythical Phoenix bird reborn from its own ashes, deCODE Genetics, or at least its data, resurfaced in October in the form of a private company, NextCODE Health. The metaphor isn’t perfect, for deCODE still exists as a wholly owned subsidiary of Amgen, which paid $415 million for it at the end of 2012.

deCODE Genetics flew into the headlines in 1996 with its Icelandic Health Sector Database, an ambitious project to meld genealogical, genetic, and health records of the entire population of Iceland, with an “opt-out” model of presumed consent. deCODE kept the bioethics journals busy for years. And as  people all over the world debated informed versus presumed consent, deCODE published a series of discoveries, in top journals, about genes that increase risk for kidney disease, cancer, lupus, vascular disease, schizophrenia, osteoporosis, and found a protective gene variant against Alzheimer’s disease.

TONS OF DATA
IcelandWith genealogical records dating back to 874 AD and abundant genetic markers, deCODE developed a robust way to discover genes by comparing symptoms to the proportion of the genome that people related in a certain way share. A person shares on average half his or her genome with full siblings, parents, and children, but one-eighth with a first cousin, and lot less with his or her 5,000 or so fourth cousins, and so on.

Take 100,000 or so people, figure out the degree to which they’re related, and search for patterns in the genome that only the people with a specific diagnosis have in common. Or look at the problem the other way. For example, one study found that 750 women with endometriosis shared significantly more genome regions than did 750 matched controls without endometriosis. Either approach highlights places in the genome to look for a causative or risk gene. The more specific the diagnosis and the more people and markers, the stronger the associations.

NextCODE invited me to a luncheon towards the end of the American Society of Human Genetics meeting a few weeks ago in Boston. I didn’t expect to learn much, after four days of being bludgeoned with tales of annotating genomes and comparing exomes to solve diagnostic mysteries, but I was impressed.

NextCODE, operating independently of deCODE, has a five year exclusive license for the use of the largest proprietary database of sequence diversity, along with sequence analysis tools developed by deCODE, for use in clinical sequencing. They’ve got whole genome sequencing information on more than 300,000 individuals, 3,000 deeply, and 40 million variants. The company already has service agreements with Boston Children’s Hospital, Newcastle University, Saitama University, and Queensland University. CEO Hannes Smarason blogs about the coming projects here.

“We know what percentage of the genome any 2 people share, down to .01% allele frequencies for rare diseases and greater than 1% for more common conditions,” Jeff Gulcher, MD, PhD, co-founder of deCODE and president and CSO of the new company told the crowd. Their clinical sequencing services tap into an annotation pipeline that uses public domain databases plus the voluminous Icelandic information, all forming the Genomic Ordered Relational (GOR) database. Common sense conclusions emerge from all that data along with nailing down specific gene locations, such as the impact of a gene variant on lifespan. “We catalog age-specific allele frequencies. If a gene variant is in old Icelanders, it is unlikely to kill kids,” Dr. Gulcher said.

A CASE STUDY
The numbers were intriguing, but it was the case study that got my attention: sisters, ages 3 and 5, who had progressive blindness and deafness. The GOR database, fed the right information (complete genome sequences), nailed the diagnosis in 5 minutes.

The parents had spent years going from doctor to doctor, with no answers. Tests for single-gene retinal disorders, of which there are many, were negative, and they also didn’t have known conditions that impair hearing as well as sight, such as Usher syndrome. The next step: whole genome sequencing for parents and daughters.

Exome sequencing was needed to diagnose Gavin Stevens' LCA, a form of hereditary blindness. (Jennifer Stevens)

Exome sequencing finally led to a diagnosis for Gavin Stevens’ rare form of  hereditary blindness. (Jennifer Stevens)

The many-years-to-a-diagnosis story is one I know well, for it was a recurring theme in my book about gene therapy and I’ve blogged about diagnostic journeys, such as that of five-year-old Gavin Stevens. It took years to diagnose his Leber congenital amaurosis because he had a mutation in a gene that hadn’t yet been discovered.

Dr. Gulcher took us quickly through the narrowing down to reach the diagnosis for the two little girls. Like my husband choosing seat warmers, XM radio, and a kayak rack for his new metallic blue Honda, Dr. Gulcher entered into the “Clinical Sequence Analyzer” the probable mode of inheritance (autosomal recessive), the symptoms, and frequency cut-off for candidate gene variants. The search included known syndromes and different types of mutations, such as single base substitutions, truncations, or repeats. “We looked at 423 exonic variants at <1% frequency, screening for autosomal recessives, and got 6 hits,” Dr. Gulcher explained.

We all watched shifting color bars on the image on the screen, which soon spit back “retinal dystrophy.” Not surprising, but it also identified a mutation in a gene called SLC52A2. It is a tweaked copy (duplication) of SLC52A3, known to cause Brown Vialetto Van Laere syndrome. Only a few dozen cases have ever been reported. The gene, on chromosome 20, encodes a protein that transports riboflavin into cells, where the vitamin is used to produce key molecules in energy metabolism.

The known form of the condition typically begins with deafness and does not include blindness, but sadly it is like amyotrophic lateral sclerosis, impairing neurons until death comes in adolescence. The NextCODE researchers identified two other families with SLC52A2 mutations, diagnosing teenage children posthumously from parental DNA.

NextCode’s “sequence-based clinical diagnosis” is “extremely affordable,” but company reps wouldn’t be specific. And they’ll have competition from institutions diagnosing patients with familial exome sequencing. But I don’t know if anyone else can match the power of the deeply-rooted Icelandic database. Which brings up the looming matter of participation of the public in sequencing projects.

PRIVACY vs THE NEED FOR MEGADATA

(NHGRI)

(NHGRI)

The question of informed consent still echoes around uses of population level databases to refine family level diagnoses, especially since the clever outing of identities of research participants using Google and a genealogy database led by grad student Melissa Gymrek earlier this year. And a comment on the most recent DNA Science post about tracing African-American roots through DNA testing questioned ancestry.com’s use of a database of DNA sequences from samples originally taken from indigenous peoples by a not-for-profit organization. Did those people give permission for future use of their personal information? Even if it’s de-identified?

Apparently the ruckus over use of deCODE’s data hasn’t died down. On May 28, 2013 Iceland’s Data Protection Authority denied the company’s request  to impute genotypes of 280,000 people using data from relatives who had consented to use of their genetic information. Unfortunately, genetics can complicate informed consent because relatives share genes in predictable patterns and proportions.

Did the Icelanders or the indigenous peoples give permission for their DNA information to be used to help diagnose two little girls years later, or to help African-Americans deduce where their ancestors came from? Use of DNA data from past collections is certainly a contentious area. I learned that this summer when my two blog posts challenging the classic case of DNA misuse of the Havasupai Indians  led to personal threats that grew so vicious that the blog was shut down.

I think that, with time, proprietary feelings surrounding personal genome information are going to fade away, for two reasons: The novelty of genome sequencing will diminish, and people will realize that those huge databases of A, T, C and G sequences are essential to interpreting personal genomes. Eventually, use of DNA sequences in a database, tied to symptoms but not personal identities, will become an accepted, if not expected, act of kindness.

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Tracing African-American Roots Through DNA

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ancestry.comAncestryDNA.com recently expanded its coverage of western Africa, enabling African-Americans to trace back to these areas, and to find cousins anywhere in the world. I had the pleasure of sitting down with three of their eight scientists at the American Society of Human Genetics meeting last week in Boston. The eight are among 1200+ employees of ancestry.com, where the DNA division debuted in May 2012.

FROM ACADEMIA TO PRACTICALITY
I wish genetic ancestry had been around when I was in grad school. We had to choose among molecular, developmental, or population genetics, and I elected to avoid the dreaded math of population genetics, which at the time seemed to lead only to careers sorting out groups of fruit flies. Today, it means connecting people. I get e-mails every week or so of mitochondrial DNA matches from Family Tree DNA and nearly daily about distant cousins from AncestryDNA.com, for whom I spit into a tube a few months ago.

Ancestry.com is well known for helping people trace their roots through documents, and the website is mesmerizing. Adding DNA was a natural extension.

African-Americans of course face a huge challenge in finding their origins due to the slave trade. I have a small taste of that, being 98% Ashkenazi.

My grandfather, Sam Aaronson, lived in 3 centuries. He was born in the U.S.

My grandfather, Sam Aaronson, was born here and lived to 103.

I know very little about my grandparents, because when you’re a kid, you don’t realize you should be peppering them with questions about where they came from – at least I didn’t. I know the most about my maternal grandmother, who came here as a small child at the turn of the twentieth century to escape pogroms in Russia. Just as African-Americans often bore the names of slaveholders, Jewish people and other immigrants with hard-to-pronounce or foreign-sounding names often were renamed at Ellis Island or Castle Garden, in New York.

FROM KUNTA KINTE TO DNA

Interest in African origins surged in 1976 with publication of Alex Haley’s historical fiction “Roots: The Saga of an American Family  and the TV series a year later. Decades after the Roots phenomenon I devoured President Obama’s Dreams from My Father: A Story of Race and Inheritance, still wondering why he isn’t considered half-Irish as often as he’s considered half-African-American.

hapmapUsing DNA to trace origins and find cousins grew out of the HapMap project, which identified single nucleotide polymorphisms. SNPs are single base sites in the genome that differ among a certain percentage of a population, set to reflect how deep into variation a researcher wants to delve. 1% and 5% variability are commonly used cut-offs.

We know of so many SNPs today – millions – that we can pretty much define our genomes by them, like signs posted in aisles of a supermarket to ease navigation. SNPs clustered in blocks, called haplotypes (or haplogroups if they’re really extensive) on their chromosome tend to be transmitted together to the next generation, a phenomenon called linkage disequilibrium.

Family lore is also important in tracing ancestry. These horse-drawn fire wagons were used to fight the Triangle Shirtwaist Factory fire in 1911.

Family lore is also important in tracing ancestry. These horse-drawn fire wagons were used to fight the Triangle Shirtwaist Factory fire in 1911.

I love how classical genetics impacts the latest biotechnologies: genetic linkage was discovered in 1911. That was the year that my grandmother stayed home one fateful day from her job at the Triangle Shirtwaist Factory in Manhattan, due to a cold. That was the March day when the factory burned, sending workers jumping out windows. Had she gone in, I might not be here.

Although SNPs travel in linked blocks, cross-overs do happen, when matching chromosomes exchange parts, and that can mix up the SNP sequences – which we can detect. If we know how often crossing over occurs, we can deduce when linkage blocks swapped, which in turn reflects when parents from different ancestries presumably met and mixed their DNA.

A few years ago, ancestry.com acquired a huge DNA collection, along with pedigrees, from the non-profit  Sorenson Molecular Genealogy Foundation, thanks to philanthropist James LeVoy Sorenson. The key was to document that the people providing the samples had lived in a particular geographic area for hundreds of years, because DNA tracks with geography, not skin color or other physical trait.

“The mission was not only to give good samples of genetic variants from human populations but to get out the message that we are a lot more alike than we are dissimilar,” Cathy Ball, PhD, vice president of genomics and bioinformatics at AncestryDNA, told me last week. “So ancestry.com got panels from all over the world. Some of the people are mixed up American mutts like me, but some are from expeditions to Nigeria, Mongolia, small villages in rural Mexico.” The DNA is from saliva samples, which was sometimes a problem to collect when people wouldn’t use the mouthwash for fear of alcohol, she added.

Slave routes (ancestrydna.com)

Slave routes (ancestrydna.com)

FROM DEEP ANCESTRY TO CURRENT COUSINS
Results from AncestryDNA.com are two-tiered: deep ancestry and cousins.

The SNP roster now exceeds 700,000, and African communities have been sampled, so deep ancestry testing can tell whether one’s family came, for example, from Ghana, Mali, Senegal, Cameroon, Nigeria, or other sources of slaves.

Africans have by far the most variable genomes, because we all, ultimately, came from there, but sampling is important. “Capturing genetic structure of a human population requires care in how you get the samples, from before people traveled. We have all this wonderful genealogical information that goes along with each sample,” Jake Byrnes, PhD, a bioinformaticist at the company, told me last week.

“People didn’t come just from the ports. People were enslaved from far inland and marched to the coast and put on ships. It’s complicated because populations moved around a lot. But we can see a stable genetic structure and that can give a sense of who a customer is most related to in a modern population in the area,” Dr. Byrnes said.

But once African slaves came here, their identities were obscured, if not erased. “It’s very challenging for African-American families to trace their family history back before 1860. If you had an ancestor who was enslaved they were enumerated on documents but not named. So paper records are phenomenally difficult to find. Almost anybody of African heritage will bump into a bunch of brick walls. It’s as if the ancestor just appeared in the world when emancipated. Our hope is that through DNA testing they can get a little bit of interesting information about where their ancestors came from. The truth is all over the entire coasts of western Africa,” said Dr. Ball, who is white but whose own DNA revealed an African-American first cousin of her mother’s. She smiled. “You can find living relatives rather than than dead ancestors.”

This 1930 U.S. census includes my mother and her parents and siblings. They came from Russia, likely Minsk. (ancestry.com)

This 1930 U.S. census includes my mother and her parents and siblings. They came from Russia, likely Minsk. (ancestry.com)

The ancestry.com website offers help in trying to fill in more recent blanks with a treasure trove of documents. Just a few minutes of searching turned up a cemetery index, World War 1 pension records, census data, the St. Croix US Virgin Islands Slave and Free People Records 1733-1930, and the Marion County Indiana public library death index. The site also includes emancipation records, slave ship manifests, military records, property and probate records, and wills that mention slaves. The US census didn’t begin to include African-Americans until 1870, although 175,000 blacks fought for the Union.

When you sign up with ancestry.com, you’re encouraged to figure out and post a family tree, listing as many surnames and birthplaces as possible. “That’s where to start digging. Our algorithm plots shared birth locations, perhaps finding a town where you and your matches both have ancestors. The algorithm combs through both trees and finds common ancestors,” Dr. Byrnes explained. By “matches” he means pairs of people who share a certain percentage of their haplotype blocks.

family tree“The way we do it differently is that we have a lot of customers that have large pedigrees. Once we do a genetic analysis we have something to compare to. We go back and use the pedigrees and DNA and fine tune our algorithms in a way that no one else does,” Ken Chahine, PhD, JD, senior vice president and general manager at ancestrydna.com told me several months ago when I had my DNA tested.

It seemed, though, that I’ve been hearing from quite a few fifth cousins. But that’s because we each, assuming no inbreeding, have 4,688 of them. So ironically, in the face of the complex algorithms and SNP maps, finding a cousin often comes down to knowing a small fact about a particular place and time.

People seek ancestry testing for many reasons, Dr. Ball said. “Every customer has her or his own personal story. People who are adopted are looking for birth parents, or trying to nail down whether a particular person is Jewish or Italian. Some people want to confirm a single relation to a distant cousin.” Said Dr. Chahine “We have stories of adoptees that find their first or second cousins after 20 to 30 years of trying to figure out who their biological parents are. With 700,000 markers, that’s a slam dunk.”

One of the newest members of the AncestryDNA.com team is Julie Granka, whose mother came to the U.S. from Italy in the 1950s. As an undergrad she liked biology in general and evolution in particular, and ended up getting her PhD working with dog DNA. “It’s exciting and scary to have real people see the results of your work and talk about it. Population genetics is no longer an abstract exercise.”

(Jane Ades, NHGRI)

(Jane Ades, NHGRI)

I can only imagine the giant leap forward understanding our ancestries will take once the databases embrace complete genome sequences. Just as efforts such as the Personal Genomes Project are getting people to place their genome sequences in the public domain for the general good — solving health problems — more widespread ancestry testing will uncover and strengthen the genetic links that bind us all. DNA will ultimately tell us how we are all connected.

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From Gene Therapy to Chromosome Therapy: The New Gets Old as The Old Becomes New

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FFB posterBOSTON     This week is the highlight of my year – the American Society of Human Genetics meeting. I headed straight to the gene therapy symposium yesterday, especially since Corey Haas, star of my book on the topic, was just crowned poster boy for the  Foundation Fighting Blindness. October isn’t only breast cancer awareness month – it’s also Blindness Awareness Month.

Corey was one of the first to be successfully treated for Leber congenital amaurosis type 2 with gene therapy, in 2008 when he was 8. He’s doing great. He recently got his turkey hunting license, and just entered an essay contest about “Our World, Our Future.” Go Corey!

Alas Corey’s clinical trial team had a greater presence at last year’s meeting, but the celebration of gene therapy’s renaissance continues. The number of people with newfound vision is growing, but it’s much slower going for applications other than the easy-to-reach eye, such as the brain. The reports at the symposium were for preclinical work, early stage clinical trials, and reboots of older trials. Even so, gene therapy seems to have recovered from the setbacks that began in the late 1990s, and is finally moving forward. But perhaps in a few years, it will share the therapeutic space with chromosome-based interventions.

The publication August 13 in Nature of a way to silence the extra chromosome 21 that causes Down syndrome exploded in the media, deservedly. Normally I wouldn’t cover research so thoroughly discussed already, but here at the meeting, immersed in all the large-scale sequencing studies, chromosome silencing stood out. We don’t think so much about chromosomes anymore.

“Gene therapy for single gene defects is gaining ground, but that approach was out of reach for chromosomal disorders. Trisomies involve hundreds of genes, making complex effects difficult to study,” began Jeanne Lawrence, MS, PhD, professor of cell and developmental biology & pediatrics at the University of Massachusetts Medical School, at the plenary lecture session Tuesday night.

TACKLING TRISOMY 21
Dr. Lawrence’s talk was spellbinding, and her idea to silence the third chromosome 21 of Down syndrome is perhaps the most brilliant idea I’ve heard in my many years of writing about genetics.

(MHGRI)

(NHGRI)

French pediatrician and geneticist Jérôme Lejeune discovered the extra chromosome of Down syndrome in 1958. This most common form of the syndrome is genetic but it’s not inherited – the extra chromosome 21 comes from off-kilter chromosome distribution (nondisjunction) that fails to part a pair of chromosome 21s as sperm or egg form.

Tuesday night’s talk began with statistics on the prevalence of trisomy 21, which exceeds that of some dozen familiar single-gene disorders combined. “Chromosome disorders account for half of all miscarriages and 1/140 live births. Down syndrome occurs in 1 in 700 births, and 1 in 120 pregnancies in women over age 38, with 400,000 cases in the US. Fifty percent have heart defects, and there’s leukemia, immune and endocrine problems,” Dr. Lawrence told the crowd.

Dr. Lawrence and her team took an approach they call “translational epigenetics.”

REDIRECTING X INACTIVATION
In female mammals, silencing one X chromosome in each cell, early in prenatal development, evens out the chromosomal inequality of the sexes. Another pioneering female geneticist, Mary Lyon, described X inactivation in 1961, also in Nature.

Butterball Lewis, a diluted calico. (credit: Carly Lewis)

Butterball Lewis, a diluted calico. (credit: Carly Lewis)

In X-inactivation, a long DNA sequence called XIST encodes a non-protein-encoding RNA that coats the doomed X chromosome, altering the chromatin, methylating the DNA, and blocking transcription. This phenomenon, called dosage compensation, makes up for the fact that a male’s second sex chromosome isn’t a robust, gene-packed X, but the incredibly puny Y, which does little more than make him a he. X inactivation is commonly seen in calico and tortoiseshell cats, who are almost always female. (One in ten thousand calicos is a rare XXY male. I know my cats.)

Many years ago, Dr. Lawrence, who is also a genetic counselor, wondered if XIST could be harnessed to shut off an extra third chromosome. “We took a lesson from nature, silencing the X chromosome.” She was co-author on the 1992 publication, from the group of Carolyn Brown, that showed that XIST RNA coats the X chromosome.

Intentionally silencing a chromosome seemed possible, because translocations that place X chromosome material on an autosome (a non-sex chromosome) also shut off the autosome. If so, redirecting X inactivation to one copy of chromosome 21 would overcome what Dr. Lawrence described as the first obstacle in finding a treatment for Down syndrome: correcting the defect in cells. “We used dosage compensation to lessen the problem of a couple of hundred overexpressed genes,” she said.

Jeanne Lawrence

Jeanne Lawrence

The researchers delivered XIST RNA to two sites on chromosome 21 in induced pluripotent stem cells from a boy with trisomy 21. “We thought it wouldn’t work. XIST was too big. The cells might not respond.” But it did work, and the chromosome paint indicating the third copy of the chromosome dimmed and vanished within five days. Eight different techniques confirmed that what seemed to be happening actually was.

Fifteen days after turning off the extra chromosome, 20 to 30% more cells appeared in the cell cultures, including many neural progenitors, providing a very early picture of what goes wrong in Down syndrome.

NEW POSSIBILITIES

(National Down Syndrome Society)

(National Down Syndrome Society)

Silencing the extra chromosome 21 is a long way from therapy – it would need to affect all relevant cells, which means a very early intervention. But before that happens, the technique will still tell us a lot.

“The big picture is putting chromosome regulation and pathology together as a research tool. You get two samples, silence one, and compare them, using stem cells so we can study differentiation and development. Then we can figure out the pathways and look for drugs,” Dr. Lawrence summed up. The technique will also reveal which genes on chromosome 21 cause the syndrome, and which control expression of genes on other chromosomes.

The idea of treating Down syndrome other than symptomatically isn’t something people have really thought much about, Diana Bianchi, MD, professor of pediatrics at Tufts University told me as we rehashed the talk the next day. “That’s achievable now,” she said. Dr. Bianchi is exploring an exciting new way to intervene during pregnancy to lessen the effects of Down syndrome, which I’ll save for another post.

So move over gene therapy, there may soon be a new kid on the block. In this age of sequencing everything we can, chromosomes have made a comeback.

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Keeping Up With the Hominins

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Artist's rendition of newly unveiled human ancestor, Homo. (J. H. Matternes)

Artist’s rendition of newly unveiled human ancestor, Homo. (J. H. Matternes)

Late Sunday night I had just finished revising chapter 16, Human Origins, in my genetics textbook when the news releases for the upcoming issue of Science came in and turned much of what I’d just written upside down.

Homo, traditionally described as a cluster of rather narrowly-defined branches on our family tree — distinct species — might be just one sort of animal. Should I delete H. habilis, H. erectus, and the other more ancient H.’s, before plunging into the various archaic humans (H.’s idaltu, neanderthalensus, and denisova)?

What the cat dragged in. A small and large chipmunk, or different species?

What the cat dragged in. A small and large chipmunk, or different species?

I’ve often wondered how paleontologists distinguish species of australopithecines, who were ancestral to and contemporary with Homo, based on a few fossils – like the famed Lucy and Dikika from Ethiopia, separated in time by 300,000 years, and the trio of footprints, presumably parents and a child, left millions of years ago in Tanzania. Isn’t paleontology a little like declaring that my backyard is home to different species of rodent for each diverse collection of Tamius striatus that my cats drag in each day? Last week they brought me one with a huge head – was it a macrocephalic chipmunk, or a different species?

SKULL 5 REWRITES THE TEXTBOOKS

I almost never change anything in a textbook based on a single report, but skull 5, and the four others near it, reported in Science this week may be an exception. The journal nicely put together a phone press conference so three of the researchers could describe what they’d found.

I’ve learned from past hominin discoveries (hominid and hominin are not interchangeable, but I’ll leave that to the textbook) that describing a skull that makes headlines actually represents many years of work. The jaw that fits skull 5 was unearthed in 2000, five years before its cranium, in Dmanisi, Georgia, a location that one of the researchers, Marcia Ponce de León, from the Anthropological Institute at the University of Zürich, called “a wonderful place that every paleoanthropologist dreams of.”

And what a specimen! “The preservation is exceptional. Many previously unknown aspects of the skeleton can be studied, and in more than one individual,” said David Lordkipanidze, director of the Georgian National Museum. The site also held remains of plants and other animals that lived in the forests or on the steppes of the temperate and humid area. Stone tools found near the skulls and animal bones bearing cutmarks indicate that these forebears knew how to prepare meat. The fossils provide “a real snapshot at one point in time of an ecosystem from 1.8 million years ago,” Lordkipanidze added.

The discovery that will lead to rewriting the textbooks stems from the finding of a mini paleopopulation – fossils from more than one individual – providing an unprecedented peek at physical variation. The first task was to show that the fossils were indeed from the same time and place, like girls at a Justin Bieber show. Next came comparisons of the skulls to each other, using classical as well as newer computer-aided methods to evaluate and quantify three-dimensional features. Finally, the anthropologists stepped back and eyeballed the variability.

Mick_Jaegger“The amount of variation within the 5 individuals is equal to the amount we see in any 5 human individuals picked out at random, or 5 randomly picked chimps or bonobos,” said Christoph Zollikofer, a neurobiologist at the University of  Zurich’s Anthropological Institute. That is, if the five Homo at the site in Georgia were considered separate species, so might the members of the Rolling Stones.

Ancestral Homo erectus

Ancestral Homo erectus (Smithsonian National Museum of Natural History, Human Origins Program)

That variability implies that rather than several Homo species, a single lineage with diverse features emerged. “We’re pretty sure that the variation we see in Dmanisi is within a paleospecies. We infer that the variation in the fossil sample is no more than variation in Homo erectus,” the best-studied type, said Zollikofer.

But the ancestor who left behind Skull 5 didn’t look much like traditional views of early Homo, said Ponce de León. “The combination of features is puzzling. The braincase is very small, around a third of that of a modern human at 546 cc – that was unexpected. But the face is quite large, with massive jaws and teeth that are big and large.”

DNA EVIDENCE FROM ARCHAIC HUMANS ALSO BLURS SPECIES LINES

(credit: Chris Stringer)

The large branch on the right is Homo (credit: Chris Stringer)

Just as Skull 5 has spurred a rethinking of species boundaries back near our beginnings, genome sequencing has blurred lines more recently by revealing that modern Europeans have about 2 percent Neanderthal DNA, and various groups – Australian aborigines, Polynesians, Melanesians, and some others – have about 3.5% Denisovan DNA (a recent ancestor known from the DNA in a finger and two molars). I’d prefer to use the language that Bill Maher would use to describe the goings on that must have led to archaic DNA infusions into our genomes, but scientists politely call it “admixture.” The narrative that seems to be emerging is that whenever ancient human populations expanded or migrated enough to meet, sex happened.

The topics of “out of Africa” and “admixture” are where I appreciate my own antiquity, for I clearly remember the bickering that went on in the late 1980s and throughout the 1990s about whether modern humans originated solely in Africa and replaced later migrants (“the single origin” hypothesis), or that waves of early peoples left Africa and persisted in small populations outside Africa, an idea known as the “multiregional” or “regional continuity” hypothesis. Coverage went back and forth in my textbooks for several editions.

The single origin hypothesis grew out of the discovery of “mitochondrial Eve” in 1986. This was initially the work of post-doc Wesley Brown at the University of California, Berkeley, who  used the revved up mutation rate of mitochondrial DNA (mtDNA) as a molecular clock. Brown compared mtDNA from 21 people of diverse ethnic background, and soon after, because Brown didn’t have sufficient information on the geographic origins of the 21, the late Allan Wilson (the father of molecular clocks), grad student Rebecca Cann, and Mark Stoneking expanded the mtDNA sample to 147. They tallied the sequence differences, applied the mutation rate, and traced back the last common ancestor of us all to a female from about 200,000 years ago, whom the media immediately named mitochondrial Eve. (Mitochondria are inherited only from mothers because the sperm’s unfortunate mitochondria are left outside the egg after the head burrows in and the tail is discarded.)

The trunk of the deduced evolutionary tree that bore mitochondrial Eve was firmly rooted in Africa. We are all her children. But Africans have the most varied genomes, and given rates of mutation, that means their ancestors go back the farthest. Jane Gitschier’s 2010 interview with Rebecca Cann in PLOS Genetics discusses the hate mail and threats she got following the media frenzy over the metaphorical Eve.

(The debate resurfaced in 2011 when Michael Hammer from the University of Arizona and his team discovered DNA sequences from archaic humans in isolated groups in sub-Saharan Africa. This finding added the twist of yet another archaic group, but one that stayed in Africa. And I haven’t even touched on the resetting of evolutionary clocks fueled by discovery of de novo mutations from sequencing genomes of parents and their children – data that are sometimes at odds with results from direct analysis of ancient DNA from preserved bones.)

photo

My kids loved this cover because my name is next to a photo of an angry gorilla.

I duly covered both views of the origin of modern humanity – single origin vs multiregional — in the six incarnations of my intro bio textbook “Life.” I leaned towards the “single origin” Eve camp, which had more of a consensus, although always aware that some fossil evidence pointed to an Asian origin. Then in the later ‘90s things got too nasty for a textbook, so I shortened the coverage, but wrote about the controversy in a cover story for The Scientist in 2004. I seem to recall a scientific meeting where attendees nearly came to blows over the dueling hypotheses.

Throughout the debate, people did try to bridge the gap, to explain all the data. I wrote in the second edition of Life, in 1995, “Possibly, some combination of the single origin and regional continuity models is closest to the truth. Perhaps African peoples migrated to Asia and Europe, where they met and mixed with other early humans, forming the gene pools we ultimately arose from.”

The story of our origins, whatever it may be, beautifully illustrates how we do science, how we think up and then set about disproving hypotheses. The phrase “scientific proof” always makes me cringe, for science doesn’t work that way. New results force us to re-evaluate what we thought we knew, and we can’t predict what technologies not yet invented will enable us to see. To say we’ve proven anything about the natural world is arrogance. Instead, science is built on evidence and interpretation. Both change, evolve.

The scattered skulls of fossil evidence for many years suggested a scenario of different species of Homo. Now discovery of Skull 5 counters that view, that instead, Homo was one type of animal. Similarly, mitochondrial Eve told us one tale, and the genome sequences of Neanderthals, Denisovans, and ourselves are now telling us another. The evidence doesn’t really contradict or even disprove – it provides glimpses that talented anthropologists and geneticists are assembling into an increasingly detailed portrait of our past.

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How Craig Venter Created Life

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venter bookLast week’s DNA Science post caused an uproar because I suggested that some people might think life begins at a period other than conception. This week’s post continues that theme with how a researcher created life. But not just any researcher – J. Craig Venter, now head of Synthetic Genomics Inc (SGI).

A Great Read
I usually don’t read books about DNA, because I write books about DNA. But when offered a copy of Dr. Venter’s new book, Life at the Speed of Light(Viking; publishing October 17), I couldn’t resist. Not just another tale of genome sequencing, Dr. Venter’s latest effort tackles synthetic biology – chemically creating a simple genome, then transferring it into a receptive cell minus its own genome. Creating life, plus sampling bits of various environments and trolling for genomes – metagenomics – are what he’s been up to since the human genome project days.

Captain Kirk, Starship Enterprise

Captain Kirk, Starship Enterprise

I raced through the book, flashing back to grad school with every historical anecdote or recounted experiment that built to the ability to recapitulate the genetic headquarters of a living cell. Venter’s excitement is palpable, if a little reminiscent of Captain Kirk: “We were now ready to attempt to go where no one had gone before, to create a whole bacterial synthetic genome and try to produce the first synthetic cell.

The tiny genome of Mycoplasma genitalium, the smallest of a free-living organism at a mere 582,970 bases, inspired the first synthetic genome. The story of creating the first synthetic genome-driven cell isn’t a gee-whiz, aren’t-we-brilliant narrative, because Venter intersperses the blind alleys and failures with the hard-won successes.

A case in point: using Deinococcus radiodurans as a model for stitching together a genome, for this bacterium does just that after radiation shreds its genome to smithereens. It uses a superb repair system and conveniently has extra copies of its genome. Helpfully, Venter and his team at the Institute for Genomic Research (TIGR) had sequenced the organism’s genome in 1999 “Brilliant!” I thought. But then Venter wrote, “After a tremendous effort, we were forced to give up. We had hit a dead end and needed a new strategy.” The team eventually harnessed the yeast  Saccharomyces cerevisiae to test the synthetic genome.

Mycoplasma genitalium genome (DOE)

Mycoplasma genitalium genome (DOE)

First came a synthetic chromosome, dubbed Mycoplasma genitalium JCVI-1.0. The final experiments sent the synthetic genome into different Mycoplasma, changing one species into another. Another glitch happened right near the end: a one-base deletion, which threw off the three-base reading frame, creating gibberish genomes. But correcting that glitch worked. The researchers even stitched their names into the recreated genome using a lexicon of DNA triplets corresponding to letters of the alphabet, used as “watermarks” to distinguish synthetic life from the old kind.

The birth announcement for the first synthetic genome-driven cell came in the May 20, 2010 online edition of Science: Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. It’s name: Mycoplasma mycoides JCVI-syn1.0.

The first third of the book capture the discoveries and inventions leading up to creating synthetic life, while the middle third describes, sometimes in a bit too much detail for the average reader, the creation itself. The final third probes reactions and repercussions.

(NOAA)

(NOAA)

Venter readily acknowledges the skeptics – I was among them – who posit that creating life means allowing the genome to fashion the cell around it, not take over an existing one like a hermit crab taking up residence in an abandoned shell. But even renting a cell rather than building one’s own is scary, because it skirts the constraints of natural selection. “Synthetic biology frees the design of life from the shackles of evolution,” Venter writes.  The language veers towards the anthropomorphic, which tends to happen when trying to capture the wonder of evolution. But cells didn’t “cooperate” to build multicellular organisms. Evolution is an ebb and flow of surviving phenotypes based on selective pressure, perhaps tweaked by mutation and altered by genetic drift. It isn’t a willful striving.

Like good science, Life at the Speed of Light raises more questions than it answers. Do we know enough to use synthetic life technology to create cells that can improve the world? Might one inventor’s idea of improvement become another’s weapon? What are unforeseen consequences of creating combinations of genes not seen in nature? Can the synthetic life community police itself, warding off what my grad school mentor Thom Kaufman called “triple-headed purple monsters” circa 1978, a time when the pioneers of recombinant DNA technology were establishing the containment procedures that persist today.

Mad_scientist.svgVenter touches on the “dual use” threat, but focuses more on happier applications: vaccines that could head off a flu pandemic, alternatives to antibiotics, and new energy sources from unexplored parts of the planet and possibly beyond. If anyone could harness a Martian energy source, it would be he.

Meeting Craig Venter
I’ve had a few interesting encounters with Dr. Venter. The man has a Darth Vader-like reputation in some circles, but my fleeting contacts with him have been quite positive.

Early in my career, when I was writing mostly for The Scientist and Genetic Engineering News, CV was always available to provide a quote, easy to reach on the phone in those pre-Internet and pre-genome days.

J. Craig Venter (Brett Shipe)

J. Craig Venter (Brett Shipe)

In 1999 he interviewed me, for a short writing gig – he’d wanted to create an atlas of normal, non-disease traits, only the genome hadn’t been sequenced just yet. Meeting him, walking down a hallway at Celera Genomics, I felt a bit like Dorothy approaching the great and powerful Wizard of Oz, but he wasn’t like that at all. Within minutes we were finishing each other’s sentences.

A year later, mid-winter 2000, I faced a conundrum. The fourth edition of my human genetics textbook was due to be published in July, I could make no further edits after April, and I knew that the two teams sequencing the human genome were careening towards the finish line. Who would be first? When? And most importantly, would it be done by the fall, when my book would be in the hands of students?

The government folks wouldn’t return my calls. CV emailed that he couldn’t tell me. I knew something was up. So, being in textbook mode, I sent him a test question:

If I were to write, in a genetics book published in July 2000, that the human genome had been sequenced, would that be (a) True or (b) False. He answered.

Some years later, Dr. Venter gave the closing talk at the American Society of Human Genetics annual meeting. Not too many were in attendance. CV described his risk variants for Alzheimer’s and cardiovascular diseases, and also announced that he learned that he has blue eyes, a preference for evening activities and novelty seeking, and a tendency towards substance abuse. “I can have two double lattes and wash it down with a Red Bull and not be affected by it,” he also learned from his genome sequence. Comparing his genome to that of DNA-discoverer Jim Watson, Venter quipped, “You probably wouldn’t suspect this based on our appearance, but we are both bald, white scientists.”

dnaThrough it all, the expressed sequence tag saga from when he was at the NIH, through the human genome sequencing, what excited me the most about Craig Venter’s long research career was the sequencing of the Mycoplasma genome, an organism so stripped-down that it just might reveal the minimal gene set required for life. My textbook always included that idea. And being so small, Mycoplasma provided a goal should one want to try to create a living cell. And that’s what Dr. Venter and his many colleagues did. And again, it intersected my career.

On May 20, 2010, I was attending the Presidential Symposium of the American Society of Gene and Cell Therapy’s annual meeting, in Washington DC. In a room packed with 2,000 geneticists, many crying, a 9-year-old boy walked onstage – Corey Haas had become able to see thanks to gene therapy. His story is the subject of my book The Forever Fix: Gene Therapy and the Boy Who Saved It  (St. Martin’s Press, 2012).

I’d wondered why the gene therapy press conference had been so poorly attended, and no obvious media at the historic presentation. Because across town, Craig Venter was announcing that he had created life, inspiring my blog post Creating Life and Curing Blindness.

My most surprising recollection of a Venter talk was at the 4th International Meeting on Single Nucleotide Polymorphisms and Complex Genome Analysis, held in Stockholm on October 10-15, 2001. Attendance was down due to the recent attacks on September 11. The Scientist had sent me, back in the days when publications did that. CV not only showed up, but shocked the sparse crowd when, after he’d spoken for half an hour and predicted that human genome sequencing would one day take two hours, he grew suddenly silent.

(National Park Service)

(National Park Service)

Craig Venter lowered his head for an uncomfortably long time as photos of Ground Zero flashed behind him. Said he, finally looking up but still not back at the screen, in tears, “these are difficult slides for me to look at, and they should be for you, too. I was there last week. The forensics officials asked Celera to help with the sequencing, to use our high-throughput methods to help identify remains for the families. So I took these photos.” Another long silence. “I never, ever thought we would have to do DNA forensics at this level, and for this reason.”

I’m glad that today, he has a new reason – exploring what life can do.

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When Does a Human Life Begin? 17 Timepoints

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(Bonnie Gruenberg photography)

(Bonnie Gruenberg photography)

On September 24, the direct-to-consumer genetic testing company 23 and Me was granted patent no. 8543339, covering the selection of traits in offspring by genotyping eggs and sperm. (“Gamete donor selection based on genetic calculations.”) An analysis of the ethical issues the patent raises is published today in Genetics in Medicine. (Coincidentally, a co-author of the paper was so critical of a recent DNA Science blog post that comments had to be cut off. Small world.)

I’d started thinking about today’s post a few weeks ago, when a prominent science writer posted on a listserv “What was the CEO of AAAS thinking?” and then quoted Alan I. Leshner telling the New York Times: “K-12 students need to know the nature of science, how scientists work and the domains and limits of science. Science can’t tell you about God. Or when life begins.”

“Um…when life begins is a pretty basic idea in biology,” commented the originator of the compelling listserv thread that followed. Actually, no.

I’m the author of an intro college biology textbook called “Life,” my having nabbed that title before Keith Richards did.  Life science textbooks from traditional publishers (I’m with McGraw-Hill) don’t explicitly state when life begins, because that is a question not only of biology, but of philosophy, politics, psychology, religion, technology, and emotions. Rather, textbooks list the characteristics of life, leaving interpretation to the reader. But I can see where the idea comes from that textbooks define life as beginning at conception. Consider a report from the Association of Pro-life Physicians. After a 5-point list of life’s characteristics from “a scientific textbook,” this group’s analysis concludes with “According to this elementary definition of life, life begins at fertilization, when a sperm unites with an oocyte.” Sneaky.

Being a biologist, a textbook author, and a mother, I’ve thought a great deal about the question of when a human life begins. So here are my selections of times at which a biologist might argue a human organism is alive. I’ll save my preference for the end.

1. Life is a continuum. Gametes (sperm and oocyte) link generations.

2. The germline. As oocytes and sperm form, their imprints – epigenetic changes from the parents’ genomes – are lifted.

A human fertilized ovum. (Spike Walker, Wellcome Images)

A human fertilized ovum. (Spike Walker, Wellcome Images)

3. The fertilized ovum. Of the hundreds of sperm surviving the swim upstream to the oocyte, one jettisons its tail and nuzzles inside the much larger cell, which obligingly becomes an ovum, completing its own meisosis. A fertilized ovum = conception.

4. Pronuclei merge, within 12 hours. After fertilization, the packets of DNA from male and female — the pronuclei — approach, merge, and the intermingling chromosomes pair and part, as the first mitotic division looms. A new human genome forms. Following that first division, some genes from the new genome are accessed to make proteins, but maternal transcripts still dominate development.

5. Cleavage. Divisions ensue. The cells of an 8-celled embryo (day 3) have not yet committed to becoming part of the embryo “proper” (one with layers) or the supportive membranes. Such a cell can still, on its own, develop. An 8-celled embryo whose cells are teased apart could lead to an octomom situation.

A day 5 human embryo, at upper left. (David Becher, Wellcome Images)

A day 5 human embryo, at upper left. (David Becher, Wellcome Images)

6. Day 5. The new genome takes over as maternal transcripts are depleted. The inner cell mass (icm) separates from the hollow ball of cells and takes up residence on the interior surface. It will become the embryo proper, distinguishing itself from the remaining part of the ball fated to become the extra-embryonic membranes. The icm is what all the fuss about human embryonic stem (hES) cells is about — the stem cells aren’t the icm cells, but are cultured from them.

7. End of the first week. The embryo implants in the uterine lining.

8. Day 16. The gastrula. Tissue layers form, first the ectoderm and endoderm, then the sandwich filling, the mesoderm. Each layer gives rise to specific body parts.

9. Day 14. The primitive streak forms, classically the first sign of a nervous system and when some nations set the deadline for no longer using human embryos in experiments.

10. Day 18. The heart beats.

11. Day 28. The neural tube closes, within which the notochord, preliminary to the spinal cord, will form, while the bulge at the top will come to house the brain. If the tube doesn’t close completely, a neural tube defect (anencephaly, spina bifida, and a few others) results.

A human embryo on the brink of becoming a fetus.

A human embryo on the brink of  becoming a fetus.

12. End of week 8. The embryo becomes a fetus, all structures present in rudimentary form.

13. Week 14 or thereabouts. “Quickening,” the flutter a woman feels in her abdomen that will progress to squirms and kicks from within.

14. Week 22.  A fetus has a chance of becoming a premature baby if delivered.

15. Birth.

puberty16. Puberty. The Darwinian definition of what matters on a population and species level, when reproduction becomes possible.

17. Acceptance into medical school. I don’t know where this came from, a joke about Jewish mothers, but in some circles it might now apply to acceptance into preschool. Or when one’s grown offspring leave home.

My answer? #14. The ability to survive outside the body of another sets a practical limit on defining when a sustainable human life begins.

Having a functional genome, tissue layers, a notochord, a beating heart … none of these matter if the organism cannot survive where humans survive. Technology has taken us to the ends of the prenatal spectrum, yet not provided too much for the middle, other than fetal surgeries for a handful of conditions. We can collect and select gametes, now thanks to patent no. 8543339. We collect and select very early embryos in pre-implantation genetic diagnosis, allowing those without a specific disease to continue development. And although the gestational age at which a premature infant can survive has crept younger, it hasn’t by much, not since I starting thinking about these things back when I was a stage #16.

Until an artificial uterus becomes a reality, technology defines, for me, when a human life begins, rather than biology. Alternative views are welcome!

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A BRCA Journey

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(Tom Ellenberger, Wash. U School of Medicine)

(Tom Ellenberger, Wash. U School of Medicine)

The day after PLOS Genetics asked me to blog in relation to Jane Gitschier’s interview with Mary-Claire King, my friend Lisa’s daughter Maya got her  BRCA1 test results. It had been a confusing eight months.

When Dr. King’s group published their 1990 paper identifying the chromosomal home of breast cancer susceptibility gene BRCA1, Maya was two years old. In each of her cells, one chromosome 17 bore a mutation in BRCA1, but she wouldn’t know that for 22 years.

In late 2012, Maya’s younger brother Justin sent a DNA sample to 23andMe “for fun.” Included in the company’s genotyping panel were the BRCA founder mutations seen mostly among eastern European Jews (the Ashkenazim). Justin had one, 5382insC: insertion of a cytosine, disrupting the gene’s reading frame. Presumably, so did his mother, because she’s Jewish, her husband Eric not.

Lisa came to me, panicked, for an unofficial genetic counseling session. She talked as I sketched the pedigree. Like most families, a few people on each side had cancers, mostly older folks. When I blogged about that conversation in February, we assumed Lisa had passed the mutation to her son and possibly her daughter.

A whirlwind of emotions engulfed the family. Lisa was petrified, Justin confused, Eric disbelieving and Maya enraged.

23andMe confirmed Justin’s result and offered to test the rest of the family, for free. Lisa’s nurse practitioner, unfamiliar with BRCA testing, sent a blood sample to Myriad Genetics on my suggestion. Eric didn’t get tested, assuming Lisa was the one transmitting the mutation. But then Lisa’s test came back from Myriad, and she didn’t have the mutation.

A breast cancer cell (NHGRI).

A breast cancer cell (NHGRI).

Had someone in Eric’s family tree converted from Judaism? Apparently not — 23andMe’s genotyping of Justin had included ancestry information, and he was half Ashkenazi, Lisa’s half. Had the son’s founder mutation arisen spontaneously? If so, then the father wouldn’t have a mutation and Maya needn’t worry. Eric finally took Myriad’s test, the family still thinking there’d been a lab error. But there hadn’t been. Eric indeed had the mutation typically found in Ashkenazi Jews.

What, exactly, is the cancer risk to Eric, Justin, or Maya (if she had the mutation), given that they have an Ashkenazi mutation resident on a non-Ashkenazi chromosome 17? Their pedigree didn’t look like those from the early-onset families that pepper Mary-Claire King’s 1990 paper, which was festooned with the solid symbols indicating mutations in every generation, with average age of onset under 45.

Since then, risk estimates for genotype becoming phenotype for the two BRCA genes have declined as studies included people of more diverse genetic backgrounds. A meta analysis from 2003 considered 22 studies involving 8,139 cases unselected for family history, and for BRCA1, gave a 65% lifetime risk of breast cancer and 39% of ovarian. The wide ranges — for breast 44%-78%, and for ovarian 18%-54% — suggested input from other genes. The highest lifetime risk published, 87% from 1994, reflects the early emphasis on high-risk families necessary to nail down the gene.

Might the Ashkenazi mutation in a non-Ashkenazi chromosome confer a lower risk, due to different surrounding gene variants? What might be the effect of those variants coming from Lisa’s chromosome 17? This was a cis/trans situation – would two genes that interact on the same chromosome do so if on different ones?

It seemed that Myriad and 23andMe wondered this too, because they requested more information. 23andMe’s algorithm came up with, for Justin’s 5382insC mutation, a ”lifetime risk of breast cancer for women is increased from 12% to about 60% and risk of ovarian cancer is increased from less than 2% to about 40%” and warns of elevated risk of breast cancer in men and prostate cancer.” I don’t know whether that was a boilerplate answer or whether it had factored in the unusual circumstances.

Before reading Angelina Jolie's story, Maya thought she'd opt for frequent scans if she had a mutation. She changed her mind.

Before reading Angelina Jolie’s story, Maya thought she’d opt for frequent scans if she had a mutation. She changed her mind.

But Maya didn’t care whether her risk was 87%, 60% or 40%, she just cared that it was pretty high. Reading Angelina Jolie’s “My Medical Choice” in the New York Times in May pushed her off her couch of indecision and she took the test, from Myriad, in July.

Last week, Maya learned she had not inherited the mutation. At lunch soon after, she was like a different person. All smiles, chatty. But the cloud fleetingly returned when I asked if she regretted her brother’s taking the test, and would she take another type of genetic test?

Absolutely not!” She wishes the entire 8 months of stress had never happened. And while acknowledging that the test could have saved her life, she resents a view of genetic testing as what her brother once called “fun”. More extensive, in-person genetic counseling might have dampened the family’s angst and helped in decision-making.

 (NHGRI)

(NHGRI)

My friend’s family’s journey with BRCA testing illustrates many things: people’s reactions to genetic information are unpredictable; people have a right to choose not to know genetic information; and there’s a lot we still don’t know, such as specific gene-gene interactions. I hope that delivery of genetic test results can keep up with the coming demands from exome and genome sequencing.

 

 

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DNA Analysis of Chobani Yogurt: Guest Post by Nick Conley

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chobani 1Identification-by-DNA has had eclectic uses: outing fake sushi, detecting horsemeat in Ikea meatballs, and capturing a murderer thanks to a telltale hair from Snowball the cat, for example. Nick Conley decided to take on Chobani yogurt, a delicious product accused a few weeks ago of harboring a contaminant. I love Chobani yogurt and their company headquarters is in a tiny town about an hour from me in upstate New York.

Nick sent me his blog post from his company, Epibiome, and has graciously offered to share it. He’s joined at Epibiome by physicist Aaron Tynes Hammack and physical chemist Hsiao-lu Lee. Nick’s PhD is in chemistry and he did a post-doc in developmental biology, both at Stanford, generating an impressive publication record and a cosmetics company. But most important to me is that he has basset hounds, my favorite dog.

Many thanks Nick!

Sept 9      We had just extracted bacterial DNA from a set of facial microbiome samples when I decided to reward myself with a cup of lime-flavored Chobani Greek yogurt. Oddly, the foil on the cup was bulging, the yogurt was thin, and it was extremely carbonated. Note the comparison to a “normal” strawberry flavored cup in the photo.

A quick google search brought me to Chobani’s Facebook page, which showed that many people were reporting the same issue. Since lots of bacteria are capable of lactic acid fermentation, we decided to extract the bacterial DNA from this funky lime cup and a “normal” strawberry cup and do 16S rDNA sequencing to identify the bacteria present.
Since the time we commenced our study, Chobani announced a voluntary recall and has since reported that it believes the contamination is from a mold (Mucor circinelloides).

Our technique will only give us information about the bacteria present, not about molds, which are a type of fungus. Nevertheless, we are very excited to see if there are any unexpected bacteria in the culture and to understand how the mold contamination changes the composition of the original bacteria in the yogurt culture. We will report our results within a few days.

And yes, I ate the lime yogurt and I was fine. The carbonation was exciting, generating a kefir-like (mojito-like?) yogurt. While Greek yogurt purists might take issue (would they really be eating lime-flavored yogurt anyway?), I think Chobani should try to achieve the carbonation with a lactic acid fermenting bacterium and launch it as a new product.

Sept 10     We are happy to announce the bacterial 16S rDNA sequencing results from our two Chobani Greek yogurt samples: a strawberry-flavored cup of normal appearance, and a recalled lime cup.

We have determined unambiguously that the lime cup used in our study was involved in the recall because the IMS number matches exactly that posted on the FDA recall site (and the yogurt showed all of the characteristics). No such IMS number could be located on the strawberry cup, whose contents appeared normal, so we used it to compare with the recalled lime yogurt.

We do not contest anything Chobani has reported about the cause of the recall, including the mold contaminant and its non-hazardous nature. Although the FDA is investigating complaints of illness related to the recalled yogurt, no determination has been made whether or not such a link exists. Importantly, the data we present below do not in any way show that the recalled Chobani yogurt was capable of causing illness or caused illness of any kind.

Our study was conducted purely to satisfy curiosity, and our experiment has several shortcomings, including: (a) a very small samples size (n = 2), (b) the comparison of 0% fat strawberry and 2% fat lime flavors, (c) inhomogeneity in the yogurt cup, which could lead to an unrepresentative sample being collected, (d) PCR bias PCR bias, (e) the possibility of misidentification of organisms sharing a common 16S rDNA sequence, (f) sequencing errors resulting in mischaracterization of bacterial taxonomy, (g) incorrect alignment databases, and (h) possibility of DNA contamination. There may be other shortcomings of which we are not aware.

Below are pie charts showing the taxonomic order associated with the most abundant 16S rDNA reads from the normal-appearing strawberry cup and the recalled lime cup.

chobani 2Chobani indicates that they have three probiotic cultures in their yogurt: Lactobacillus acidophilus, Lactobacillus casei, and Bifidus. The first two belong to taxonomic orders Lactobacillales and the latter belongs to Bifidobacteriales, which is consistent with what we found by sequencing bacterial DNA in the normal strawberry cup.

chobani 3However, the recalled lime yogurt shows a considerably different distribution. Out of a total of 1,950,616 reads for this sample, 190,331 (9.8%) belonged to the order Oceanospirillales. Fortunately, the sequence data contain more information than the order; they also give insight into the taxonomic family of the bacterium (Oceanrickettsiaceae) and the genus (Oceanrickettsia). This is where things get extremely obscure, however, because aside from a couple of sequence entries in Genbank in Genbank  on an organism sharing the same genus (Oceanrickettsia ariakensis), we know almost nothing about these bacteria. So little, in fact, that the taxonomic family and genus have not been formally accepted and the organism has been relegated to a list of “unclassified Gammaproteobacteria.”

800px-Oyster_Ushimado03sFrom what little we can glean, two Chinese scientists affiliated with the South China Sea Institute of Oceanology, Drs. Xiangyun Wu and Yang Zhang, deposited the sequence data for Oceanrickettsia ariakensis into the database in 2005 and indicated that they isolated the bacteria from an oyster (Crassostrea ariakensis). They believed that the bacteria infected the oyster and contributed to its massive die-off.

It’s very important to note that there is no evidence that this bacterium would be pathogenic in humans. Furthermore, the work of Wu and Zhang doesn’t appear to have been independently verified or subjected to peer review (to the best of our knowledge).

Does this mean that the Chobani yogurt recall had anything to do with oyster contamination? Absolutely not! It’s possible that the bacteria whose DNA we detected may have already been present in tiny quantities in one of the yogurt’s ingredients, and when the mold took over the yogurt culture, it created conditions that allowed it to thrive. In support of this theory, we observed 198 reads out of 1,713,939 total that corresponded to order Oceanospirillales (0.012%) in the strawberry yogurt. Or perhaps our findings do provide some insight into the contamination source. It’s too early to say.

But what we can say is that we have a lot more to learn about bacteria. We can only culture (and therefore, thoroughly study) about 1% of the bacterial species on the planet. With the latest generation of sequencing technologies, we can sequence everything. Wonder what else is out there? So do we.

398px-Basset_hound_0003I haven’t stopped eating Chobani yogurt and am still a big fan! Many trusted brands have faced a recall at some point during their history. Microbial contamination is a constant concern among food manufacturers and is not uncommon. The overwhelming majority of the time, the extra passengers we call bacteria simply go along for the ride, completely unnoticed.

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