: Un numéro spécial de la revue Nature
- The human genome at ten
- Life is complicated (Erika Check Hayden)
- The human race (Alison Abbott)
- The sequence explosion
Opinion
- Has the revolution arrived? (Francis Collins)
- Multiple personal genomes await (J Craig Venter)
- Point: Hypotheses first (Robert Weinberg)
- Counterpoint: Data first (Todd Golub)
Books & Arts
- A reality check for personalized medicine (Muin J Khoury, James Evans & Wylie Burke)
samedi 10 avril 2010
mardi 6 avril 2010
Le livre de Moi. Par Richard Powers
The Book of Me, GQ, october 2008
http://www.gq.com/news-politics/big-issues/200810/richard-powers-genome-sequence
Richard powers is a professor at the University of Illinois at Urbana-Champaign. His most recent novel, The Echo Maker, was a National Book Award winner and a Pulitzer Prize finalist. This is his first story for gq.
If you could see into your future, would you want to? If you could know whether you're going to contract Alzheimer's, or if you're likely to battle cancer or die of heart disease, would you want to? Last summer Richard Powers decided he did and became one of nine people on earth to have his entire genome sequenced. Here, a glimpse into his—and your—future.
I come from a long line of folks, on my mother’s side, with congenital difficulty making choices. My father’s family, on the other hand, are born snap deciders. This time the paternal genes won out, and half an hour after reading the invitation, I was on board.
So I went shopping. A day online gave me my first taste of the bewildering range of consumer genetic products. There was Family Tree DNA, specializing in tracing genetic genealogies. There was DNA Direct, whose Web site asked, “Do you have a chronic, undiagnosed condition? It could be genetic.” For $260, I could get tested for cystic fibrosis; for $370, I could learn whether I’m at elevated risk of developing type 2 diabetes. Then there was Iceland-based deCODEme (“This is myCODE”), which could calculate my risks for twenty-five genetic maladies in one $985 package.
But why stop with just a few disease tests? As I always say, in for a few plot complications, in for the whole story.
Among the most visible of new genotyping services was 23andMe, with their slogan “Genetics just got personal.” Their attractive pastel home page wondered, “What do your genes say about you? Who were your ancient ancestors? Do you have your mother’s sense of taste?” For $999, a signed consent with legal waiver, and a cupful of spit, 23andMe would look at 600,000 SNPs—single-nucleotide polymorphisms, or individual points of possible variance—within the 6 billion base pairs of my diploid genome. I could then use the site’s interactive tools to browse the data and learn what my mutations mean.
Upping the ante a little was Navigenics (“My genes. My health. My life”). For $2,500 they would scan more than a million of my SNPs (pronounced “snips”) and supply me with genetic counseling to help me interpret the results. For a $250 subscription, I could get annual updates that would keep me current with the flood of new discoveries.
But these companies were selling genotyping, not full sequencing. They could identify some alleles—variations of particular genes—and tell me a little bit about the risks, predispositions, and susceptibilities I had inherited. They would look at something on the order of .02 percent of my 6 billion data points, with less than perfect accuracy. They were at best marketing a thumbnail synopsis, or better, an index of a book no one really knows how to read. I was after the unabridged version itself.
How big a number is 6 billion? The diploid genome has nearly as many independent data points as there are individual humans. If a standard 250-page book comprises about 500,000 letters, you would need 12,000 such books to publish an individual genome. Laid out in a line the diameter of a penny, the base pairs of the genome would circle the earth about three times. If the genome were a tune played at a nice bright allegro tempo of 120 beats per minute, it would take just short of a century to play.
Knome, Inc., another brand-new venture, was offering the whole 6-billion-base-pair sequence. Their bare, Zen-like Web site—“Know thyself”—announced that they were looking for twenty individuals who were ready to shed the unexamined life for whatever happens next. By being among the first individuals in history to have their whole genome sequenced, these participants will help pioneer the emerging field of personal genomics.
Only three human beings—James Watson, J. Craig Venter, and an anonymous Chinese scientist—had had their essentially complete diploid genomes sequenced. A few more were in the works. Already the race was under way to make the process ordinary. Here was my real story: the infancy of direct-to-consumer complete genetic blueprints.
There was just one catch. Knome’s whole-genome sequence cost more than a third of a million dollars. However deep GQ’s pockets might be, they weren’t shelling out that kind of cash for a glimpse at anyone’s future.
I went back to shopping. That’s when I came across the Personal Genome Project (PGP), a remarkable nonprofit test bed under the auspices of Harvard. Ten volunteers had already signed up to sequence most of the regions of the genome known to have especially high medical or functional significance. This came to about 1 percent of the total 6 billion base pairs—midway between 23andMe’s .02 percent sampling and Knome’s 98 percent whole genome. Most impressive of all, the sequencing would be free, provided the volunteers made their information publicly available. I e-mailed the project’s director, George Church, to see if I might become the eleventh PGP volunteer. He wrote back saying that as long as I could pass an exam demonstrating a master’s-degree level of understanding about genetics, they could use me. I commenced to cram.
Among an exhausting list of other responsibilities, George Church directs the Lipper Center for Computational Genetics at Harvard Medical School. More than twenty years ago, for his Ph.D. under Nobelist Walter Gilbert, Church developed the first direct genomic-sequencing method. As a postdoc at Biogen and UCSF, he helped initiate the Human Genome Project (which would ultimately produce the first full sequence of human DNA). A decade later, he was still pioneering, helping to refine second-generation genome sequencing into something several orders of magnitude faster and cheaper than its predecessors. A few years ago, Church decided that it was time to bring the world reliable, effective, and responsible genomes for all.
Trade in a whole new kind of consumer good was about to explode, and society was as yet unprepared. A race to discover and market genetic associations could result in the privatization of vast amounts of genetic information. Unrealistic promises of data security by large biobanks could result in chaotic or hampered research, exploitative business practices, and ultimate public backlash. Church hoped to preempt all that with a collaborative public project—the PGP. As he told the journal Nature in a piece about the project, “We have to get this in place before everything just goes crazy.”
http://www.gq.com/news-politics/big-issues/200810/richard-powers-genome-sequence
Richard powers is a professor at the University of Illinois at Urbana-Champaign. His most recent novel, The Echo Maker, was a National Book Award winner and a Pulitzer Prize finalist. This is his first story for gq.
If you could see into your future, would you want to? If you could know whether you're going to contract Alzheimer's, or if you're likely to battle cancer or die of heart disease, would you want to? Last summer Richard Powers decided he did and became one of nine people on earth to have his entire genome sequenced. Here, a glimpse into his—and your—future.
I come from a long line of folks, on my mother’s side, with congenital difficulty making choices. My father’s family, on the other hand, are born snap deciders. This time the paternal genes won out, and half an hour after reading the invitation, I was on board.
So I went shopping. A day online gave me my first taste of the bewildering range of consumer genetic products. There was Family Tree DNA, specializing in tracing genetic genealogies. There was DNA Direct, whose Web site asked, “Do you have a chronic, undiagnosed condition? It could be genetic.” For $260, I could get tested for cystic fibrosis; for $370, I could learn whether I’m at elevated risk of developing type 2 diabetes. Then there was Iceland-based deCODEme (“This is myCODE”), which could calculate my risks for twenty-five genetic maladies in one $985 package.
But why stop with just a few disease tests? As I always say, in for a few plot complications, in for the whole story.
Among the most visible of new genotyping services was 23andMe, with their slogan “Genetics just got personal.” Their attractive pastel home page wondered, “What do your genes say about you? Who were your ancient ancestors? Do you have your mother’s sense of taste?” For $999, a signed consent with legal waiver, and a cupful of spit, 23andMe would look at 600,000 SNPs—single-nucleotide polymorphisms, or individual points of possible variance—within the 6 billion base pairs of my diploid genome. I could then use the site’s interactive tools to browse the data and learn what my mutations mean.
Upping the ante a little was Navigenics (“My genes. My health. My life”). For $2,500 they would scan more than a million of my SNPs (pronounced “snips”) and supply me with genetic counseling to help me interpret the results. For a $250 subscription, I could get annual updates that would keep me current with the flood of new discoveries.
But these companies were selling genotyping, not full sequencing. They could identify some alleles—variations of particular genes—and tell me a little bit about the risks, predispositions, and susceptibilities I had inherited. They would look at something on the order of .02 percent of my 6 billion data points, with less than perfect accuracy. They were at best marketing a thumbnail synopsis, or better, an index of a book no one really knows how to read. I was after the unabridged version itself.
How big a number is 6 billion? The diploid genome has nearly as many independent data points as there are individual humans. If a standard 250-page book comprises about 500,000 letters, you would need 12,000 such books to publish an individual genome. Laid out in a line the diameter of a penny, the base pairs of the genome would circle the earth about three times. If the genome were a tune played at a nice bright allegro tempo of 120 beats per minute, it would take just short of a century to play.
Knome, Inc., another brand-new venture, was offering the whole 6-billion-base-pair sequence. Their bare, Zen-like Web site—“Know thyself”—announced that they were looking for twenty individuals who were ready to shed the unexamined life for whatever happens next. By being among the first individuals in history to have their whole genome sequenced, these participants will help pioneer the emerging field of personal genomics.
Only three human beings—James Watson, J. Craig Venter, and an anonymous Chinese scientist—had had their essentially complete diploid genomes sequenced. A few more were in the works. Already the race was under way to make the process ordinary. Here was my real story: the infancy of direct-to-consumer complete genetic blueprints.
There was just one catch. Knome’s whole-genome sequence cost more than a third of a million dollars. However deep GQ’s pockets might be, they weren’t shelling out that kind of cash for a glimpse at anyone’s future.
I went back to shopping. That’s when I came across the Personal Genome Project (PGP), a remarkable nonprofit test bed under the auspices of Harvard. Ten volunteers had already signed up to sequence most of the regions of the genome known to have especially high medical or functional significance. This came to about 1 percent of the total 6 billion base pairs—midway between 23andMe’s .02 percent sampling and Knome’s 98 percent whole genome. Most impressive of all, the sequencing would be free, provided the volunteers made their information publicly available. I e-mailed the project’s director, George Church, to see if I might become the eleventh PGP volunteer. He wrote back saying that as long as I could pass an exam demonstrating a master’s-degree level of understanding about genetics, they could use me. I commenced to cram.
Among an exhausting list of other responsibilities, George Church directs the Lipper Center for Computational Genetics at Harvard Medical School. More than twenty years ago, for his Ph.D. under Nobelist Walter Gilbert, Church developed the first direct genomic-sequencing method. As a postdoc at Biogen and UCSF, he helped initiate the Human Genome Project (which would ultimately produce the first full sequence of human DNA). A decade later, he was still pioneering, helping to refine second-generation genome sequencing into something several orders of magnitude faster and cheaper than its predecessors. A few years ago, Church decided that it was time to bring the world reliable, effective, and responsible genomes for all.
Trade in a whole new kind of consumer good was about to explode, and society was as yet unprepared. A race to discover and market genetic associations could result in the privatization of vast amounts of genetic information. Unrealistic promises of data security by large biobanks could result in chaotic or hampered research, exploitative business practices, and ultimate public backlash. Church hoped to preempt all that with a collaborative public project—the PGP. As he told the journal Nature in a piece about the project, “We have to get this in place before everything just goes crazy.”
Séquençage et apprentissage du chant chez les oiseaux
Mots clés: FOXP2, génome, oiseaux, Zebra finch, diamant mandarin
Les diamants mandarins (Zebra finch) constituent un modèle d'étude des capacités d'interprétation des sons par le cerveau, grâce à leur capacité à reconnaitre et réagir aux chants de leurs congénères.
Des études sur les diamants mandarin ont ainsi montré que le gène FoxP2 était davantage exprimé dans les régions du cerveau des mâles lors des phase d'apprentissage du chant. Ce résultat qui vient en appui de l'hypothèse en faveur d'un rôle important du gène humain homologue, FOXP2, dans l'acquisition du langage par l'enfant et donc dans l'évolution de la faculté de langage de l'espèce humaine.
En mars 2010, des chercheurs américains ont obtenu d'importants résultats en décodant le génome d’un oiseau, le zebra finch, dont les mâles apprennent de leurs pères un chant nuptial, appris de leurs pères et qu'ils répètent pendant toute leur vie.
Une équipe menée par Wesley C Warren et Richard K. Wilson à l’université Washington de Saint-Louis dans le Missouri a récemment décodé le génome de cet oiseau pour 1 000 000 de dollars. Cette somme est très éloignée des 10 millions de dollars requis il y a plusieurs années pour décoder le génome du poulet.
Environ 50 laboratoires dans le monde étudient les oiseaux les diamants mandarin. La plupart espère ainsi recueillir des informations sur la façon dont le langage humain est enseigné. Comme les humains et quelques autres espèces, le diamant mandarin peut imiter les sons qu'il entend.
Le mécanisme de l'apprentissage vocal semble être assez similaire chez les oiseaux et chez les humains. Il met en œuvre quelques gênes spécifiques. Les personnes ayant une mutation d'un gène FOXP2 peuvent avoir plusieurs types de troubles du langage. Les oiseaux qui ne peuvent pas chanter peuvent également avoir des anomalies de ce gênes.
Avec le génome du zebra finch décodé, les chercheurs ont appris qu'un certain nombre de gènes des oiseaux sont impliquées dans le chant et son apprentissage et dans l’écoute du chant des autres oiseaux.
Environ huit cent gênes sont actifs dans les neurones pendant le chant. Lorsque un oiseau écoute un chant, les gènes neuronaux produisent un grand nombre de transcrits, qui sont les produits de l’expression des gènes.
Ces gênes modulent l'activité d'autres gênes impliqués dans l’écoute du chant. Ces transcrit ne produisent pas de protéines et sont non-codant. Ils sont impliquées dans la régulation d'autres gênes et sont activés en temps réel.
Cette travail est une des premières études montrant une importante activité génétique et une importante régulation génique survenant lors d'un comportement naturel.
La base biologique de cet apprentissage est en général étudiée chez le rat ou la souris sur des modèles de comportement artificiel. Dans ce modèle d'oiseaux chanteur, les chercheurs ont trouvé une façon d'étudier un comportement naturel.
Il s'agit d'étudier la contribution génétique à l'apprentissage du chant. Il s'agit également d'identifier pourquoi cet oiseau apprend une chanson et n’en change jamais.
Les oiseaux ont un génome d'environ milliard d'unités ADN, environ un tiers de la taille du génome humain. Il possède cependant à peu près le même nombre de gênes car leur génome contient beaucoup moins dans de séquence d'ADN répétées.
A coté de l'apprentissage vocal, cette étude permettra de comprendre les bases génétique d'autres aspects du comportement des oiseaux, en particulier le soin parental, la territorialité et la sélection des partenaires sexuels.
Références
- From a Songbird, New Insights Into the Brain, New York Times, By NICHOLAS WADE ; April 5, 2010
- Taeniopygia guttata ou Zebra finch ou diamant mandarin sur oiseaux.net, wikipedia.fr, wikipedia.org
- Zebra Finch videos, photos & sounds on the Internet Bird Collection
Les diamants mandarins (Zebra finch) constituent un modèle d'étude des capacités d'interprétation des sons par le cerveau, grâce à leur capacité à reconnaitre et réagir aux chants de leurs congénères.
Des études sur les diamants mandarin ont ainsi montré que le gène FoxP2 était davantage exprimé dans les régions du cerveau des mâles lors des phase d'apprentissage du chant. Ce résultat qui vient en appui de l'hypothèse en faveur d'un rôle important du gène humain homologue, FOXP2, dans l'acquisition du langage par l'enfant et donc dans l'évolution de la faculté de langage de l'espèce humaine.
En mars 2010, des chercheurs américains ont obtenu d'importants résultats en décodant le génome d’un oiseau, le zebra finch, dont les mâles apprennent de leurs pères un chant nuptial, appris de leurs pères et qu'ils répètent pendant toute leur vie.
Une équipe menée par Wesley C Warren et Richard K. Wilson à l’université Washington de Saint-Louis dans le Missouri a récemment décodé le génome de cet oiseau pour 1 000 000 de dollars. Cette somme est très éloignée des 10 millions de dollars requis il y a plusieurs années pour décoder le génome du poulet.
Environ 50 laboratoires dans le monde étudient les oiseaux les diamants mandarin. La plupart espère ainsi recueillir des informations sur la façon dont le langage humain est enseigné. Comme les humains et quelques autres espèces, le diamant mandarin peut imiter les sons qu'il entend.
Le mécanisme de l'apprentissage vocal semble être assez similaire chez les oiseaux et chez les humains. Il met en œuvre quelques gênes spécifiques. Les personnes ayant une mutation d'un gène FOXP2 peuvent avoir plusieurs types de troubles du langage. Les oiseaux qui ne peuvent pas chanter peuvent également avoir des anomalies de ce gênes.
Avec le génome du zebra finch décodé, les chercheurs ont appris qu'un certain nombre de gènes des oiseaux sont impliquées dans le chant et son apprentissage et dans l’écoute du chant des autres oiseaux.
Environ huit cent gênes sont actifs dans les neurones pendant le chant. Lorsque un oiseau écoute un chant, les gènes neuronaux produisent un grand nombre de transcrits, qui sont les produits de l’expression des gènes.
Ces gênes modulent l'activité d'autres gênes impliqués dans l’écoute du chant. Ces transcrit ne produisent pas de protéines et sont non-codant. Ils sont impliquées dans la régulation d'autres gênes et sont activés en temps réel.
Cette travail est une des premières études montrant une importante activité génétique et une importante régulation génique survenant lors d'un comportement naturel.
La base biologique de cet apprentissage est en général étudiée chez le rat ou la souris sur des modèles de comportement artificiel. Dans ce modèle d'oiseaux chanteur, les chercheurs ont trouvé une façon d'étudier un comportement naturel.
Il s'agit d'étudier la contribution génétique à l'apprentissage du chant. Il s'agit également d'identifier pourquoi cet oiseau apprend une chanson et n’en change jamais.
Les oiseaux ont un génome d'environ milliard d'unités ADN, environ un tiers de la taille du génome humain. Il possède cependant à peu près le même nombre de gênes car leur génome contient beaucoup moins dans de séquence d'ADN répétées.
A coté de l'apprentissage vocal, cette étude permettra de comprendre les bases génétique d'autres aspects du comportement des oiseaux, en particulier le soin parental, la territorialité et la sélection des partenaires sexuels.
Références
- From a Songbird, New Insights Into the Brain, New York Times, By NICHOLAS WADE ; April 5, 2010
- Taeniopygia guttata ou Zebra finch ou diamant mandarin sur oiseaux.net, wikipedia.fr, wikipedia.org
- Zebra Finch videos, photos & sounds on the Internet Bird Collection
mercredi 24 mars 2010
Séquençage du transcriptome des carcinomes buccaux
Mayo Scientists Sequence Transcriptome of Oral Cancer Tumor on SOLiD, Home in on Allelic Imbalance.
The technique, based on an RNA sequencing approach that identifies transcriptional direction, allowed the researchers to identify allelic imbalances, and show that these are associated with copy number changes. GenomeWeb
The technique, based on an RNA sequencing approach that identifies transcriptional direction, allowed the researchers to identify allelic imbalances, and show that these are associated with copy number changes. GenomeWeb
XGen 2010 :
Au congrés XGen de mars 2010, de nombreux chercheurs se sont interrogés sur l'intérêt des programmes de séquençage des génomes tumoraux.
Références
- Researchers Question Whether Sequencing Whole Cancer Genomes has Clinical Relevance
March 23, 2010 GenomeWeb
Références
- Researchers Question Whether Sequencing Whole Cancer Genomes has Clinical Relevance
March 23, 2010 GenomeWeb
Les meilleurs blogs recherche de l'année
Les meilleurs blogs recherche de l'année ont été décernés par les Research Blogging Awards 2010
En biomédecine:
- Science-Based medicine par Steven Novella (http://www.sciencebasedmedicine.org/)
Meilleur nouveau blog recherche: Hannah, étudiante en Master à Philadelphie.
Twitteur de l'année : Bora Zivkovic / BoraZ http://twitter.com/BoraZ
Références
- GenomeWeb http://www.genomeweb.com/blog/research-bloggers-honor-their-own
En biomédecine:
- Science-Based medicine par Steven Novella (http://www.sciencebasedmedicine.org/)
Meilleur nouveau blog recherche: Hannah, étudiante en Master à Philadelphie.
Twitteur de l'année : Bora Zivkovic / BoraZ http://twitter.com/BoraZ
Références
- GenomeWeb http://www.genomeweb.com/blog/research-bloggers-honor-their-own
mardi 23 février 2010
11e Congrès AGBT
11 Congrès AGBT (Advances in Genome Biology and Technology) à Marco Island en Floride, du 24 au 27 février 2010.
The 11th annual Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 24-27, 2010. The AGBT meeting is now widely regarded as the premier scientific forum for capturing information about the latest advances in new DNA sequencing technologies and their applications to diverse areas in biology and biomedical research. The meeting will have daytime plenary sessions that feature keynote speakers, additional invited speakers, and abstract-selected talks. These sessions will highlight cutting-edge research in areas such as next-generation DNA sequencing technologies, genome structure and function, cancer genomics, metagenomics, medical sequencing, complex genetic diseases, and population genomics. Technical approaches being developed and utilized in contemporary genomics research will be presented during evening concurrent sessions. Our annual pre-meeting 'training' workshop will feature talks on practical applications of various next-generation sequencing instruments from experienced practitioners. Please plan to join us in Marco Island, where the relaxed atmosphere and outstanding science at the 2010 AGBT meeting will again provide an exceptional opportunity to meet and interact with scientific leaders from the many disciplines being advanced by large-scale DNA sequencing and genomics.
The 11th annual Advances in Genome Biology and Technology (AGBT) meeting will be held in Marco Island, Florida, from February 24-27, 2010. The AGBT meeting is now widely regarded as the premier scientific forum for capturing information about the latest advances in new DNA sequencing technologies and their applications to diverse areas in biology and biomedical research. The meeting will have daytime plenary sessions that feature keynote speakers, additional invited speakers, and abstract-selected talks. These sessions will highlight cutting-edge research in areas such as next-generation DNA sequencing technologies, genome structure and function, cancer genomics, metagenomics, medical sequencing, complex genetic diseases, and population genomics. Technical approaches being developed and utilized in contemporary genomics research will be presented during evening concurrent sessions. Our annual pre-meeting 'training' workshop will feature talks on practical applications of various next-generation sequencing instruments from experienced practitioners. Please plan to join us in Marco Island, where the relaxed atmosphere and outstanding science at the 2010 AGBT meeting will again provide an exceptional opportunity to meet and interact with scientific leaders from the many disciplines being advanced by large-scale DNA sequencing and genomics.
jeudi 18 février 2010
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