Human Genomics: Difference between revisions

No edit summary
No edit summary
Line 9: Line 9:
== '''Introduction''':   ==
== '''Introduction''':   ==


== '''New Genetics: Scientific Pictures and Ordinary Heroes''' ==
== '''New Genetics: Scientific Pictures and Ordinary Heroes''' ==


<br> The genetics of the 1950s helped to signal a break from the associations that had been made between human genetics and forms of social eugenics in the late 19th century and first half of the 20th century. This period of ‘discovery’ science also lead the way in providing narratives of scientific heroes as ordinary guys (McNeil, 2011). A version of scientific discovery that still resonates today as genetic heroics were reproduced by Craig Venter and John Sulston during the Human Genome Project, in biographies, autobiographies, popular science writing, news media and documentary. In July 25, 1953 Rosalind Franklin and Gosling detail the distinctions between the A and B structures of the double helix in DNA and Watson and Crick publish their article on the structure of DNA. <br><br> Rosalind E. Franklin and R. G. Gosling<br> [http://www.nature.com/nature/dna50/franklingosling2.pdf Evidence for 2-Chain Helix in Crystalline Structure of Sodium Deoxyribonucleate] <br><br> J. D. Watson and F. H. C. Crick<br> [http://www.nature.com/nature/dna50/watsoncrick.pdf A Structure for Deoxyribose Nucleic Acid] <br><br>  
<br> The genetics of the 1950s helped to signal a break from the associations that had been made between human genetics and forms of social eugenics in the late 19th century and first half of the 20th century. This period of ‘discovery’ science also lead the way in providing narratives of scientific heroes as ordinary guys (McNeil, 2011). A version of scientific discovery that still resonates today as genetic heroics were reproduced by Craig Venter and John Sulston during the Human Genome Project, in biographies, autobiographies, popular science writing, news media and documentary. In July 25, 1953 Rosalind Franklin and Gosling detail the distinctions between the A and B structures of the double helix in DNA and Watson and Crick publish their article on the structure of DNA. <br><br> Rosalind E. Franklin and R. G. Gosling<br> [http://www.nature.com/nature/dna50/franklingosling2.pdf Evidence for 2-Chain Helix in Crystalline Structure of Sodium Deoxyribonucleate] <br><br> J. D. Watson and F. H. C. Crick<br> [http://www.nature.com/nature/dna50/watsoncrick.pdf A Structure for Deoxyribose Nucleic Acid] <br><br>  
Line 27: Line 27:
In the early 1980s the technique called PCR – Polymerase Chain Reaction was developed (see Rabinow 1996 for an anthropological account). Kary Mullis won the Nobel Prize for his work in this area but his key article ‘An unusual origin of PCR’ is not freely available and only accessible via subscription. However, a far more detailed and accessible article in the Journal of Biomedical Discovery and Collaboration (Fore, Weichers and Cook-Deegan 2006) is more useful at this point and is included here. &nbsp;This article examines the effect that the patent on PCR had on its use in the sciences. This is a useful piece because it provides a review of PCR in the genome sciences but also because it considers two key issues in genomics with particular relevance for the humanities. These are the related issues of commercial science and patenting.&nbsp;The two issues are linked but not inseparable. Commercial companies and publicly funded research institutions both take out patents on inventions or discoveries. PCR is a technique for reproducing large amounts of DNA and this facilitates sequencing. Kary Mullis’s work on this area was developed in a commercial setting. Patenting and other commercial imperatives in the life sciences are part of the everyday reality of working in this area. Genomics is a 20th century science and has been developed within a highly commercialised system.&nbsp;The most controversial dimensions of commercial practice in this area is not the patent on PCR per se, but is around the question of the patenting of genes and of genetic tests. This area is discussed further in relation to DNA in general in [http://www.nuffieldbioethics.org/patenting-dna The Ethics of Patenting DNA: A Discussion Paper] (2002, Nuffield Council on Bioethics). <br><br> Joe Fore Jr, Ilse R Wiechers, Robert Cook-Deegan<br> [http://www.j-biomed-discovery.com/content/1/1/7 The Effects of Business Practices, Licensing, and Intellectual Property on Development and Dissemination of the Polymerase Chain Reaction: Case Study] <br><br>  
In the early 1980s the technique called PCR – Polymerase Chain Reaction was developed (see Rabinow 1996 for an anthropological account). Kary Mullis won the Nobel Prize for his work in this area but his key article ‘An unusual origin of PCR’ is not freely available and only accessible via subscription. However, a far more detailed and accessible article in the Journal of Biomedical Discovery and Collaboration (Fore, Weichers and Cook-Deegan 2006) is more useful at this point and is included here. &nbsp;This article examines the effect that the patent on PCR had on its use in the sciences. This is a useful piece because it provides a review of PCR in the genome sciences but also because it considers two key issues in genomics with particular relevance for the humanities. These are the related issues of commercial science and patenting.&nbsp;The two issues are linked but not inseparable. Commercial companies and publicly funded research institutions both take out patents on inventions or discoveries. PCR is a technique for reproducing large amounts of DNA and this facilitates sequencing. Kary Mullis’s work on this area was developed in a commercial setting. Patenting and other commercial imperatives in the life sciences are part of the everyday reality of working in this area. Genomics is a 20th century science and has been developed within a highly commercialised system.&nbsp;The most controversial dimensions of commercial practice in this area is not the patent on PCR per se, but is around the question of the patenting of genes and of genetic tests. This area is discussed further in relation to DNA in general in [http://www.nuffieldbioethics.org/patenting-dna The Ethics of Patenting DNA: A Discussion Paper] (2002, Nuffield Council on Bioethics). <br><br> Joe Fore Jr, Ilse R Wiechers, Robert Cook-Deegan<br> [http://www.j-biomed-discovery.com/content/1/1/7 The Effects of Business Practices, Licensing, and Intellectual Property on Development and Dissemination of the Polymerase Chain Reaction: Case Study] <br><br>  


== '''Bioinformatics &nbsp;<!--StartFragment--><span style="font-size: 11pt; font-family: Arial; color: black;">&nbsp;</span>'''<span style="font-size:11.0pt; font-family:Arial;color:black" /> ==
== '''Bioinformatics'''  ==


=== a) Bioinformatic Approaches <br> ===
=== a) Bioinformatic Approaches <br> ===


Bioinformatics has become the dominant paradigm for working with genomics in many areas. This does raise the question of who can make sense of genomics – biologists or computer scientists. The exome paper below can been seen as one of the ways in which a debate about who is qualified to make sense of genomics is playing out. Jenny Reardon’s (2011)&nbsp;paper available via subscription to ''Personalised'' Medicine(also available via Medscape) examines these tensions in the field explicitly and gives a clear picture of some of the stakes. <br><br> Pauline C. Ng, Samuel Levy, Jiaqi Huang, Timothy B. Stockwell, Brian P. Walenz, Kelvin Li, Nelson Axelrod, Dana A. Busam, Robert L. Strausberg, J. Craig Venter<br> [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000160 Genetic Variation in an Individual Human Exome] <br><br>  
Bioinformatics has become the dominant paradigm for working with genomics in many areas. This does raise the question of who can make sense of genomics – biologists or computer scientists. The exome paper below can been seen as one of the ways in which a debate about who is qualified to make sense of genomics is playing out. Jenny Reardon’s (2011)&nbsp;paper available via subscription to ''Personalised'' Medicine(also available via Medscape) examines these tensions in the field explicitly and gives a clear picture of some of the stakes. <br><br> Pauline C. Ng, Samuel Levy, Jiaqi Huang, Timothy B. Stockwell, Brian P. Walenz, Kelvin Li, Nelson Axelrod, Dana A. Busam, Robert L. Strausberg, J. Craig Venter<br> [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000160 Genetic Variation in an Individual Human Exome] <br><br>  


=== b) Genome Wide Association Studies (GWAS): From Universal Human Genome to Population Variation<br> ===
=== b) Genome Wide Association Studies (GWAS): From Universal Human Genome to Population Variation<br> ===


Haplotype mapping raises a whole set of debates and questions about race and human difference. This article sets out some of the later findings of the HapMap and demonstrates the kinds of typing that is going on in this area. For detailed accounts of the practices and challenges of this kind of human genomics see both Jenny Reardon’s ''Race to the Finish'' and Amade M’Charek’s ''The Human Genome Diversity Project''. <br><br> International HapMap Consortium<br> [http://hapmap.ncbi.nlm.nih.gov/downloads/presentations/nature_hapmap3.pdf A Second Generation Human Haplotype Map of Over 3.M million SNPs] <br><br>  
Haplotype mapping raises a whole set of debates and questions about race and human difference. This article sets out some of the later findings of the HapMap and demonstrates the kinds of typing that is going on in this area. For detailed accounts of the practices and challenges of this kind of human genomics see both Jenny Reardon’s ''Race to the Finish'' and Amade M’Charek’s ''The Human Genome Diversity Project''. <br><br> International HapMap Consortium<br> [http://hapmap.ncbi.nlm.nih.gov/downloads/presentations/nature_hapmap3.pdf A Second Generation Human Haplotype Map of Over 3.M million SNPs] <br><br>  
Line 41: Line 41:
<br> The Human Genome Project ran from the late 1980s to 2003 and produced the human reference genome. These two articles signal the completion of the so-called first draft, which was announced to the world by the leaders of the USA and UK governments in 2000. <br><br>  
<br> The Human Genome Project ran from the late 1980s to 2003 and produced the human reference genome. These two articles signal the completion of the so-called first draft, which was announced to the world by the leaders of the USA and UK governments in 2000. <br><br>  


== '''Individual Genomes: Biodigital Artefacts''' ==
== '''Individual Genomes: Biodigital Artefacts''' ==


=== a) Mobilizing Consumer Data<br> ===
=== a) Mobilizing Consumer Data<br> ===


In this article the direct-to-consumer genetics company,&nbsp;''23andMe'', publish their results from self-reporting or crowd sourced samples. These participant driven studies potentially open up consumer derived genetic databases and self reported phenotypical information to biomedical research. <br><br> Nicholas Eriksson, J. Michael Macpherson1, Joyce Y. Tung, Lawrence S. Hon, Brian Naughton, Serge Saxonov, Linda Avey, Anne Wojcicki, Itsik Pe'er, Joanna Mountain<br> [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993 Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits] <br><br>  
In this article the direct-to-consumer genetics company,&nbsp;''23andMe'', publish their results from self-reporting or crowd sourced samples. These participant driven studies potentially open up consumer derived genetic databases and self reported phenotypical information to biomedical research. <br><br> Nicholas Eriksson, J. Michael Macpherson1, Joyce Y. Tung, Lawrence S. Hon, Brian Naughton, Serge Saxonov, Linda Avey, Anne Wojcicki, Itsik Pe'er, Joanna Mountain<br> [http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000993 Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits] <br><br>  


=== b) Attempting Clinical Relevance<br> ===
=== b) Attempting Clinical Relevance<br> ===


So far personal genomics has not had much application in clinical contexts. The overwhelming amount of highly specialised data generated by whole genome sequencing, and the light touch probabilities of genome scanning present either too much, or too little information. This paper outlines an attempt to put personal genomics in a clinical context. <br><br> Euan A. Ashley, Atul J. Butte, Matthew T. Wheeler, Rong Chen, Teri E. Klein, Frederick E. Dewey, Joel T. Dudley, Kelly E. Ormond, Aleksandra Pavlovic, Louanne Hudgins, Li Gong, Laura M. Hodges, Dorit S. Berlin, Caroline F. Thorn, Katrin Sangkuhl, Joan M. Hebert, Mark Woon, Hersh Sagreiya, Ryan Whaley, Alexander A. Morgan, Dmitry Pushkarev, Norma F Neff, Joshua W. Knowles, Mike Chou, Joseph Thakuria, Abraham Rosenbaum, Alexander Wait Zaranek, George Church, Henry T. Greely, Stephen R. Quake, and Russ B. Altman<br> [http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical Assessment Incorporating a Personal Genome] <br><br> [http://www.livingbooksaboutlife.org/books/Human_genomics/Attributions Attributions]
So far personal genomics has not had much application in clinical contexts. The overwhelming amount of highly specialised data generated by whole genome sequencing, and the light touch probabilities of genome scanning present either too much, or too little information. This paper outlines an attempt to put personal genomics in a clinical context. <br><br> Euan A. Ashley, Atul J. Butte, Matthew T. Wheeler, Rong Chen, Teri E. Klein, Frederick E. Dewey, Joel T. Dudley, Kelly E. Ormond, Aleksandra Pavlovic, Louanne Hudgins, Li Gong, Laura M. Hodges, Dorit S. Berlin, Caroline F. Thorn, Katrin Sangkuhl, Joan M. Hebert, Mark Woon, Hersh Sagreiya, Ryan Whaley, Alexander A. Morgan, Dmitry Pushkarev, Norma F Neff, Joshua W. Knowles, Mike Chou, Joseph Thakuria, Abraham Rosenbaum, Alexander Wait Zaranek, George Church, Henry T. Greely, Stephen R. Quake, and Russ B. Altman<br> [http://www.ncbi.nlm.nih.gov/pubmed/20435227 Clinical Assessment Incorporating a Personal Genome] <br><br> [http://www.livingbooksaboutlife.org/books/Human_genomics/Attributions Attributions]

Revision as of 10:54, 17 September 2011

 

HumanGenomicsCover1.jpg
HumanGenomicsCover1.jpg

Human Genomics: From Hypothetical Genes to Biodigital Materializations

Edited by Kate O'Riordan


Introduction

New Genetics: Scientific Pictures and Ordinary Heroes


The genetics of the 1950s helped to signal a break from the associations that had been made between human genetics and forms of social eugenics in the late 19th century and first half of the 20th century. This period of ‘discovery’ science also lead the way in providing narratives of scientific heroes as ordinary guys (McNeil, 2011). A version of scientific discovery that still resonates today as genetic heroics were reproduced by Craig Venter and John Sulston during the Human Genome Project, in biographies, autobiographies, popular science writing, news media and documentary. In July 25, 1953 Rosalind Franklin and Gosling detail the distinctions between the A and B structures of the double helix in DNA and Watson and Crick publish their article on the structure of DNA.

Rosalind E. Franklin and R. G. Gosling
Evidence for 2-Chain Helix in Crystalline Structure of Sodium Deoxyribonucleate

J. D. Watson and F. H. C. Crick
A Structure for Deoxyribose Nucleic Acid

Maps of Life: Catalogues, Mapping and Sequencing

a) Maps


D. Botstein, R. L. White, M. Skolnick, R. W. Davis
Construction of a Genetic Linkage Map in Man Using Restriction Fragment Length Polymorphisms[1]

Subcommittee of the 
Health and Environmental Research Advisory Committee (HERAC)
Report on the Human Genome Initiative for the Office of Health and Environmental Research, 1987

U.S. Congress, Office of Technology Assessment
Mapping Our Genes:The Genome Projects. How Big, How Fast?

b) Catalogues

In 1966 a medical field comes together through a catalogue and Dr Victor McKusick publishes the first print edition of Mendelian Inheritance in Man (MIM). This was an attempt to catalogue what was known about Mendelian phenotypes – or the physical expression of genetic material - as medically relevant characteristics. It later became Online Mendelian Inheritance in Man (OMIM).

Joanna Amberger, Carol A. Bocchini, Alan F. Scott, and Ada Hamosh McKusick
Online Mendelian Inheritance in Man (OMIM®)

c) Sequencing

In the early 1980s the technique called PCR – Polymerase Chain Reaction was developed (see Rabinow 1996 for an anthropological account). Kary Mullis won the Nobel Prize for his work in this area but his key article ‘An unusual origin of PCR’ is not freely available and only accessible via subscription. However, a far more detailed and accessible article in the Journal of Biomedical Discovery and Collaboration (Fore, Weichers and Cook-Deegan 2006) is more useful at this point and is included here.  This article examines the effect that the patent on PCR had on its use in the sciences. This is a useful piece because it provides a review of PCR in the genome sciences but also because it considers two key issues in genomics with particular relevance for the humanities. These are the related issues of commercial science and patenting. The two issues are linked but not inseparable. Commercial companies and publicly funded research institutions both take out patents on inventions or discoveries. PCR is a technique for reproducing large amounts of DNA and this facilitates sequencing. Kary Mullis’s work on this area was developed in a commercial setting. Patenting and other commercial imperatives in the life sciences are part of the everyday reality of working in this area. Genomics is a 20th century science and has been developed within a highly commercialised system. The most controversial dimensions of commercial practice in this area is not the patent on PCR per se, but is around the question of the patenting of genes and of genetic tests. This area is discussed further in relation to DNA in general in The Ethics of Patenting DNA: A Discussion Paper (2002, Nuffield Council on Bioethics).

Joe Fore Jr, Ilse R Wiechers, Robert Cook-Deegan
The Effects of Business Practices, Licensing, and Intellectual Property on Development and Dissemination of the Polymerase Chain Reaction: Case Study

Bioinformatics

a) Bioinformatic Approaches

Bioinformatics has become the dominant paradigm for working with genomics in many areas. This does raise the question of who can make sense of genomics – biologists or computer scientists. The exome paper below can been seen as one of the ways in which a debate about who is qualified to make sense of genomics is playing out. Jenny Reardon’s (2011) paper available via subscription to Personalised Medicine(also available via Medscape) examines these tensions in the field explicitly and gives a clear picture of some of the stakes.

Pauline C. Ng, Samuel Levy, Jiaqi Huang, Timothy B. Stockwell, Brian P. Walenz, Kelvin Li, Nelson Axelrod, Dana A. Busam, Robert L. Strausberg, J. Craig Venter
Genetic Variation in an Individual Human Exome

b) Genome Wide Association Studies (GWAS): From Universal Human Genome to Population Variation

Haplotype mapping raises a whole set of debates and questions about race and human difference. This article sets out some of the later findings of the HapMap and demonstrates the kinds of typing that is going on in this area. For detailed accounts of the practices and challenges of this kind of human genomics see both Jenny Reardon’s Race to the Finish and Amade M’Charek’s The Human Genome Diversity Project.

International HapMap Consortium
A Second Generation Human Haplotype Map of Over 3.M million SNPs

c) Publishing the Reference Genome


The Human Genome Project ran from the late 1980s to 2003 and produced the human reference genome. These two articles signal the completion of the so-called first draft, which was announced to the world by the leaders of the USA and UK governments in 2000.

Individual Genomes: Biodigital Artefacts

a) Mobilizing Consumer Data

In this article the direct-to-consumer genetics company, 23andMe, publish their results from self-reporting or crowd sourced samples. These participant driven studies potentially open up consumer derived genetic databases and self reported phenotypical information to biomedical research.

Nicholas Eriksson, J. Michael Macpherson1, Joyce Y. Tung, Lawrence S. Hon, Brian Naughton, Serge Saxonov, Linda Avey, Anne Wojcicki, Itsik Pe'er, Joanna Mountain
Web-Based, Participant-Driven Studies Yield Novel Genetic Associations for Common Traits

b) Attempting Clinical Relevance

So far personal genomics has not had much application in clinical contexts. The overwhelming amount of highly specialised data generated by whole genome sequencing, and the light touch probabilities of genome scanning present either too much, or too little information. This paper outlines an attempt to put personal genomics in a clinical context.

Euan A. Ashley, Atul J. Butte, Matthew T. Wheeler, Rong Chen, Teri E. Klein, Frederick E. Dewey, Joel T. Dudley, Kelly E. Ormond, Aleksandra Pavlovic, Louanne Hudgins, Li Gong, Laura M. Hodges, Dorit S. Berlin, Caroline F. Thorn, Katrin Sangkuhl, Joan M. Hebert, Mark Woon, Hersh Sagreiya, Ryan Whaley, Alexander A. Morgan, Dmitry Pushkarev, Norma F Neff, Joshua W. Knowles, Mike Chou, Joseph Thakuria, Abraham Rosenbaum, Alexander Wait Zaranek, George Church, Henry T. Greely, Stephen R. Quake, and Russ B. Altman
Clinical Assessment Incorporating a Personal Genome

Attributions