Category Archives: Genome

Researchers at the University of B.C. have decoded the genome of the mountain pine beetle, an insect that has ravaged millions of hectares of the province's lodgepole pine forests.

It is the first time the pine beetle's genome has been sequenced, and scientists from UBC and the Michael Smith Genome Sciences Centre say the new information will help to manage the infestation in the future, according to a report published Tuesday in the Journal Genome Biology.

"We know a lot about what the beetles do," said Christopher Keeling, a research associate at the centre. "But without the genome, we don't know exactly how they do it."

The research revealed wide variation among individuals of the species, about four times greater than the variation among humans, the report said.

The researchers isolated genes that help detoxify defence compounds found under the bark of the tree, where the beetles live. They also found genes that degrade plant cell walls, which allow the beetles to get nutrients from the tree.

The study also involved researchers from the University of Northern British Columbia and the University of Alberta.

(c) CanWest MediaWorks Publications Inc.

View post:
Researchers map genome of insect

One of the world's most prestigious laboratories is frantically trying to resolve a row over its decision to publish the genome of one of the world's most studied human cell lines a set of cervical cancer cells.

The cells were taken in 1951 from a woman called Henrietta Lacks, without her consent. Her descendants argue that the published genome may reveal genetic traits of family members.

The HeLa cells, as they are dubbed, are exceptionally easy to grow in the lab and have become the cellular equivalent of lab rats. For decades, scientists have worked with these cells to unravel the secrets of cancer and develop new vaccines and treatments.

After publishing the HeLa genome in the online journal G3: Genes, Genomes and Genetics, researchers led by Lars Steinmetz at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, withdrew the data following a barrage of objections.

"It shouldn't have been published without our consent That is private family information," said Lacks' granddaughter Jeri Lacks-Whye, quoted in The New York Times in a commentary on the dispute by Rebecca Skloot, whose biography of Lacks, The Immortal Life of Henrietta Lacks, appeared in 2011.

EMBL has apologised to the family and is in talks with them to try to resolve the situation.

"As soon as we learned of this we removed our data from the internet out of respect for the family," says EMBL spokeswoman Raeka Aiyar. "We take their concerns very seriously and have reached out to them with our apologies, and to express our determination to work with them towards an appropriate course of action for handling the availability of this data. We are currently awaiting their response."

EMBL also gave the G3 journal a statement on why the researchers withdrew the data.

The paper revealed that the genome of HeLa cells is chaotic. That is as might be expected in cancer cells, which undergo abnormal genetic reorganisation.

Steinmetz found numerous regions where chromosomes are arranged in the wrong order, for example, as well as missing genes and surplus copies of others.

View post:
Storm erupts over publishing of HeLa genome

A micrograph of HeLa cells, derived from cervical cancer cells taken from Henrietta Lacks.

A micrograph of HeLa cells, derived from cervical cancer cells taken from Henrietta Lacks.

Last week, scientists announced they had sequenced the full genome of the most widely used human cell line in biology, the "HeLa" cells, and published the results on the web. But the descendents of the woman from whom the cells originated were never consulted before the genetic information was made public, and thus never gave their consent to its release.

Morning Edition's Renee Montagne spoke to Rebecca Skloot, author of the best-selling book The Immortal Life of Henrietta Lacks, which chronicles the cells and the family tied to them. Skloot also wrote an op-ed in Sunday's New York Times about the need for international standards to protect the privacy of genetic data.

Henrietta Lacks was a poor black tobacco farmer in southern Virginia. In 1951, she was diagnosed with cervical cancer. Her doctor, without telling her, took a little piece of her tumor to study it.

Lacks died soon afterward, but her cells kept growing and reproducing in the doctor's Johns Hopkins lab. As scientists recognized their surprising ability to grow indefinitely, the cells become hugely important to medical research. For the past 60 years, the HeLa cells have been used in experiments on topics as diverse as cloning, the effects of radiation, and the polio vaccine.

Lacks' family didn't find out about the immortal cells until the 1970s.

"It has been a long legacy within the family of 'research without consent,' and they've [experienced] quite a few privacy violations along the way," says Skloot.

Some of the HeLa genome has been available for years. The European researchers who sequenced the full genome initially claimed last week that no private medical information about Lacks or her descendents could come from the data they published online.

But right away other researchers began to refute that. They noted that although the cells have mutated, they still contain Henrietta's genes.

Read more:
Sequencing Of HeLa Genome Revives Genetic Privacy Concerns

Mar. 26, 2013 The genome of the mountain pine beetle -- the insect that has devastated British Columbia's lodgepole pine forests -- has been decoded by researchers at the University of British Columbia and Canada's Michael Smith Genome Sciences Centre.

This is a first for the mountain pine beetle and only the second beetle genome ever sequenced. The first was the red flour beetle, a pest of stored grains. The genome is described in a study published Tuesday in the journal Genome Biology.

"We know a lot about what the beetles do," says Christopher Keeling, a research associate in Prof. Joerg Bohlmann's lab at the Michael Smith Laboratories. "But without the genome, we don't know exactly how they do it."

"Sequencing the mountain pine beetle genome provides new information that can be used to help manage the epidemic in the future."

The genome revealed large variation among individuals of the species -- about four times greater than the variation among humans.

"As the beetles' range expands and as they head into jack pine forests where the defensive compounds may be different, this variation could allow them to be more successful in new environments," says Keeling.

Researchers isolated genes that help detoxify defence compounds found under the bark of the tree -- where the beetles live. They also found genes that degrade plant cell walls, which allow the beetles to get nutrients from the tree.

Keeling, Bohlmann and their colleagues also uncovered a bacterial gene that has jumped into the mountain pine beetle genome. This gene codes for an enzyme that digests sugars.

"It might be used to digest woody tissue and/or the microorganisms that grow in the beetle's tunnels underneath the bark of the tree," said Keeling. "Gene transfers sometimes make organisms more successful in their environments."

This study involved researchers from the University of Northern British Columbia and the University of Alberta.

More here:
Mountain pine beetle genome decoded

Public release date: 27-Mar-2013 [ | E-mail | Share ]

Contact: Dr. Hilary Glover hilary.glover@biomedcentral.com 44-020-319-22370 BioMed Central

The genome of the western painted turtle (Chrysemys picta bellii) one of the most widespread, abundant and well-studied turtles in the world, is published this week in Genome Biology. The data show that, like turtles themselves, the rate of genome evolution is extremely slow; turtle genomes evolve at a rate that is about a third that of the human genome and a fifth that of the python, the fastest lineage analyzed.

As a group, turtles are long-lived, can withstand low temperatures including freezing solid, can survive for long periods with no oxygen, and their sex is usually determined by the temperature at which their eggs develop rather than genetically. The painted turtle is most anoxia-tolerant vertebrate and can survive up to four months under water depending on the temperature. Turtles and tortoises are also the most endangered major vertebrate group on earth, with half of all species listed as endangered. This is the first turtle, and only the second non-avian reptile genome to be sequenced, and the analysis reveals some interesting insights about these bizarre features and adaptations, many of which are only known in turtles.

The western painted turtle is a freshwater species, and the most widespread turtle native to North America. Bradley Shaffer and colleagues place the western painted turtle genome into a comparative evolutionary context, showing that turtles are more closely related to birds and crocodilians than to any other vertebrates. They also find 19 genes in the brain and 23 in the heart whose expression is increased in low oxygen conditions including one whose expression changes nearly 130 fold. Further experiments on turtle hatchlings indicated that common microRNA was involved in freeze tolerance adaptation.

This work consistently indicates that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle achieving its extraordinary physiological capacities. The authors argue that the painted turtle may offer important insights into the management of a number of human health disorders, particularly those involved with anoxia and hypothermia.

###

Media contact

Dr Hilary Glover Scientific Press Officer, BioMed Central Tel: +44 (0) 20 3192 2370 Mob: +44 (0) 778 698 1967 Email: hilary.glover@biomedcentral.com

Notes

Read this article:
Getting under the shell of the turtle genome

Putting genome data into the public domain advances science, but nearly all of it can be linked to someone.

a.k.a. HeLa: Henrietta Lackss cells became a staple of biomedical research.

Last week European scientists were shamed into cutting off public access to a genome sequence. As far as I know, its the first instance of a genome pulled from the public record.

Its also a bad precedent.

The case involves a line of cervical cancer cells, known as HeLa. As told in the book The Immortal Life of Henrietta Lacks, a bestseller by reporter Rebecca Skloot, the HeLa cell line came from the body of Henrietta Lacks, a poor African-American tobacco farmer. The cells were collected without Lackss knowledge, and later researchers did even more dodgy research involving her children.

Lacks died of her cancer in 1951, but HeLa went on to become a big deal in science. In fact, it is the most widely used model cell line for studying human biology. Thats according to some German researchers who, on March 11, decided to expand that knowledge by publishing the HeLa genome.

The publication set off a tizzy of criticism online, tracked here by researcher Jonathan Eisen. Although no law required the Germans to ask permission from Lackss family, it seemed in very poor taste not to have done so, especially given the notoriety of the case. Eventually Skloot, whose book is being made into a movie by Oprah Winfrey and HBO, got involved. She briefed the Lacks family and conveyed their concerns to the scientists, who then agreed to put a block on the data.

In her write-up of the episode for the New York Times, Skloot quotes one of Lackss granddaughters, Jeri Lacks-Whye, as telling her: That is private family information It shouldnt have been published without our consent.

Private information? Whatever the past injustices the Lackses have suffered, thats just entirely wrong. There is no law here or in Germany (that I know of) that lets anyone put a claim on the DNA information of another person.

Even what right you have to your own DNA information isnt settled. Some states have sought to pass laws that attempt to define DNA as personal property. That way, no one could surreptitiously collect yours and publish it. Eric Topol, a doctor at the Scripps Institute, tweeted at me to say, Individuals should own their own DNA data!

See more here:
The Dawn of Genome Trolling

Genome - Cancer Subtype Relationships - Strata Ignite 2013
Tom Plunkett #39;s #39; Ignite talk, "Genome - Cancer Subtype Relationships", at the 2013 Strata Conference in Santa Clara, California.

By: OreillyMedia

See the original post:
Genome - Cancer Subtype Relationships - Strata Ignite 2013 - Video

Scientists Release Full Neandertal Genome
Scientists in Germany were able to map a Neanderthal #39;s entire genome from DNA found in a toe bone.

By: NewsyScience

More:
Scientists Release Full Neandertal Genome - Video

PMWC13: Yaniv Erlich - Genome Hacking

By: Yaniv Erlich

Read more:
PMWC13: Yaniv Erlich - Genome Hacking - Video

You have your genome or exome (the protein-encoding part) sequenced to help diagnose a puzzling set of symptoms, and something totally unrelated, and unexpected, turns up - a so-called "incidental finding."Surprises, of course, aren't new in medicine. The term "incidental finding" comes from "incidentaloma," coined in 1995 to describe an adrenal tumor found on a scan looking for something else. I had one -- a CT scan of my appendix revealed a polycystic liver. A friend had it much worse. She volunteered to be a control in an Alzheimer's imaging trial, and her scan revealed two brain aneurysms!Geneticists have long expected an avalanche of incidental findings from clinical (exome or genome) sequencing. Researchers from Baylor College of Medicine and NHGRI and elsewhere described several cases at the American Society of Human Genetics annual meeting last fall. My favorites:- A boy had his genome sequenced as part of a project to better diagnose syndromes of developmental delay, intellectual disability, and seizures. Researchers found the aorta weakening of Marfan syndrome, gave the boy a repurposed drug in clinical trials, and he's ok.- A family with several members having their genomes sequenced to evaluate heart disease discovered that their "writer's cramp" is myoclonus dystonia, a neuromuscular disease.- A man had his genome sequenced in a study to investigate atherosclerosis and learned he had a deafness mutation. Although he claimed he had normal hearing, further testing showed he didn't - he'd adapted so well for so long that he hadn't known he was missing a sense.To provide guidelines for clinicians having to disclose a medical surprise, the American College of Medical Genetics and Genomics released much-anticipated recommendations on March 21, to kick off the annual meeting.The most important points come near the end of the 27-page document, especially the table of conditions to be tested for. And while the report is very clear, the accompanying news release uses some fuzzy definitions that often crop up when genetics is simplified. I know from genetic counseling and writing textbooks that misuse of certain terms can confuse. ("Genetic code" for "DNA sequence," and "carrier" in for "pre-symptomatic," when it more traditionally refers to someone who has one recessive allele, and no corresponding illness or trait.) News aggregators that boil down news releases may miss such nuances.So here are 12 major points I've distilled from the report.1. Labs doing clinical sequencing should test for well-studied mutations in 57 genes that cause or can theoretically cause disease. The mutations are fairly common, albeit among the rare - I've seen 3 in patients just this week. Most are "actionable," some even life-saving. Certain heart conditions and malignant hyperthermia, for example, can cause a first (and last) symptom of sudden death when a person takes a certain drug. A good thing to know.2. The list of 57 doesn't really mean 57 illnesses, from a patient's point of view. Tumor/cancer syndromes account for 25 of the 57, cardiovascular problems 23, and mutations in seven genes cause Marfan and related syndromes. Add the two lone conditions (a type of Ehlers-Danlos syndrome and malignant hyperthermia) and the list collapses to 5 to a patient.3. Of people having clinical sequencing, 1-2% are expected to have one of the 57 mutations. Technically, these aren't incidental findings, because they aren't found by accident, like my cystic liver - labs are looking for them. But that's ok. Just semantics.4. We don't know if the 57 variants that may cause disease in families who are having clinical sequencing to evaluate symptoms may do so in others. Due to effects of other genes and the environment, a mutation that causes a disease in one person may not in another.5. Clinical sequencing is not the sort of testing that some direct-to-consumer (DTC) companies offer. At the present time, for example, 23andMe's $99 test for 247 illnesses and traits include carrier tests that would already be part of a diagnostic work-up based on symptoms, family history, or newborn screening; and risks based on genetic marker (SNP) patterns that may or may not predict anything about the person sending in spit, due to population differences between the spitter and the study on which the test is based. DTC tests in their current incarnation are informational, not diagnostic.6. Patients and their families won't be able to "opt-out" of knowing about the big 57, unless they refuse clinical sequencing. "Duty to warn" trumps patient autonomy.7. Kids count, contrary to precedent. Huntington disease set the pattern here - people under age 18 with an affected parent are generally not tested to see if they will develop HD 20 years later, because there's no treatment. But for the clinical sequencing guidelines, informing parents and even children is okay, because so many of the conditions can be prevented, treated, or risk reduced with lifestyle choices, even if an illness such as cancer won't start for many years.8. A negative result doesn't assure health. I'm thinking of Bruce Springsteen's "57 Channels (And Nothin' On)." Finding nothing on the 57 tests doesn't mean you're healthy or will stay that way. A person who has normal BRCA genes, for example, can still develop breast cancer from other genes going haywire. And sequencing won't spot missing, extra, or moved DNA; unusual mutations; or those lurking in genome regions with light sequencing coverage. (See "The Battle of the Prenatal Tests")9. Genetic counseling. Clinicians should provide it or refer for it - before and after testing. To help, ACMG will soon release informed consent guidelines for clinical sequencing. But physicians-in-training still get woefully little training in genetics and genomics.10. Genetic testing and sequencing are on a collision course, with mutation databases from patients edging toward the rapidly-growing databases from healthy people sending samples to DTC companies. (23andMe expects a million submissions by year's end.) But this convergence will be to everyone's benefit, I think. With all of these data, in a few years we'll know what the variations in the human genome, point by point, actually mean.11. Price is driving clinical sequencing. It's already cheaper to do a whole exome than to sequence a "big chunky" gene and all of its known mutations.If Amazon offered you a dozen books for the price of one, wouldn't you take it?12. Finally, at the end of the recommendations come some interesting terms that capture the disconnect I've long noticed between those of us who are more hesitant about sequencing and its enthusiasts: the "genetic empiricist" versus the "genetic libertarian".I've been an empiricist, against genetic testing when the info may be ambiguous because we don't yet know enough. A report in this week's Proceedings of the National Academy of Sciences from Yuval Itan and colleagues at Rockefeller University takes a major step in providing this needed context. They introduce the human gene connectome, a computational way to sort out gene-gene interactions that will be vital for making sense of genome information. Does a mutation in one gene protect against another? Imagine finding out you have a 3-fold increased risk of Alzheimer's, before researchers discover a protective variant that you also have?I still fear that too casual an approach to testing - like urging people to give spit kits for Christmas -- could create a population of Woody Allen-like hypochondriacs who overtax the health care system and take too many not-without-risk tests. Others will be falsely reassured.We genetic empiricists want evidence that a testing outcome is beneficial, that it "does no harm." That's still not known for all genetic tests.In contrast, "genetic libertarians" believe that everyone has the right to know everything. From responses to my blog posts, testimonials at the 23andMe website, and the streams of popular articles and books by people having their exomes/genomes "done," the genetic libertarians seem to far outnumber the genetic empiricists. Or at least they're more vocal.The new guidelines on clinical DNA sequencing present a starting point for handling what our genomes are telling us, focusing first on revelations that we can do something with, under the care of trained medical professionals. So by the time that devices the size of a dorm fridge are sequencing patients' DNA and spitting out risks, diagnoses, and suggested courses of action in the average internist's office, we'll be able to make the most of the information in our genomes. Follow Scientific American on Twitter @SciAm and @SciamBlogs.Visit ScientificAmerican.com for the latest in science, health and technology news. 2013 ScientificAmerican.com. All rights reserved.

Visit link:
Incidental Findings from Genome Sequencing Nuances and Caveats