12. J. A. Lincoln and S. D. Cook, “An overview of gene-epigenetic-environmental contributions to MScausation,” Journal of the Neurological Sciences, 2009, 286(1–2): 54–7; L. Fugger, M. A. Friese, and J. I. Bell, “From genes to function: The next challenge to understanding multiple sclerosis,” Nature Reviews Immunology, 2009, 9(6): 408–17.
13. D. B. Goldstein, “Common genetic variation and human traits,” New England Journal of Medicine, 2009, 360(17): 1696–98.
14. S. P. Dickson, K. Wang, I. Krantz, H. Hakonarson, and D. B. Goldstein, “Rare variants create synthetic genome-wide associations,” PLoS Biology, 2010, 8(1): e1000294.
15. E. T. Cirulli and D. B. Goldstein, “Uncovering the roles of rare variants in common disease through whole-genome sequencing,” Nature Reviews Genetics, 2010, 11: 415–425.
16. Interview with Kevin Shianna, December 29, 2008.
17. Email from David Goldstein, August 14, 2009.
18. Email from Kristen Linney, September 8, 2009.
19. J. Karow, “Defective sequencing reagents to cost Illumina up to $23M in 2009; company says problem is solved,” In Sequence, November 3, 2009.
20. Interview with Esther Dyson, September 28, 2009.
21. D. E. Jonas and H. L. McLeod, “Genetic and clinical factors relating to warfarin dosing,” Trends in Pharmacological Sciences, 2009, 30(7): 375–86.
22. Z. E. Sauna, I. W. Kim, and S. V. Ambudkar, “Genomics and the mechanism of P-glycoprotein (ABCBL),” Journal of Bioenergetics & Biomembranes, 2007, 39(5–6): 481–87.
23. M. Uhr, A. Tontsch, C. Namendorf, et al., “Polymorphisms in the drug transporter gene ABCB1 predict antidepressant treatment response in depression,” Neuron, 2008, 57(2): 203–9.
24. Q. Liu, J. Yu, Q. L. Mao-Ying, et al., “Repeated clomipramine treatment reversed the inhibition of cell proliferation in adult hippocampus induced by chronic unpredictable stress,” Pharmacogenomics Journal, 2008, 8(6): 375–83.
25. M. L. Wong, C. Dong, J. Maestre-Mesa, and J. Licinio, “Polymorphisms in inflammation-related genes are associated with susceptibility to major depression and antidepressant response,” Molecular Psychiatry, 2008, 13(8): 800–12.
26. G. Laje, S. Paddock, H. Manji, et al., “Genetic markers of suicidal ideation emerging during citalopram treatment of major depression,” American Journal of Psychiatry, 2007, 164(10): 1530–38.
27. http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI: 88145.
28. R. H. Lipsky and A. M. Marini, “Brain-derived neurotrophic factor in neuronal survival and behavior-related plasticity,” Annals of the New York Academy of Sciences, 2007, 1122: 130–43; P. Bekinschtein, M. Cammarota, I. Izquierdo, and J. H. Medina, “BDNF and memory formation and storage,” Neuroscientist, 2008, 14(2): 147–56.
29. J. Fan and P. Sklar, “Genetics of bipolar disorder: Focus on BDNF Val66Met polymorphism,” Novartis Foundation Symposium, 2008, 289: 60–72; discussion 72–73, 87–93.
30. J. O. Groves, “Is it time to reassess the BDNF hypothesis of depression?” Molecular Psychiatry, 2007, 12(12): 1079–88.
31. J. K. Rybakowski, “BDNF gene: Functional Val66Met polymorphism in mood disorders and schizophrenia,” Pharmacogenomics, 2008, 9(11): 1589–93.
32. A. R. Brunoni, M. Lopes, and F. Fregni, “A systematic review and meta-analysis of clinical studies on major depression and BDNF levels: Implications for the role of neuroplasticity in depression,” International Journal of Neuropsychopharmacology, 2008, 11(8): 1169–80; H. Y. Lee and Y. K. Kim, “Plasma brain-derived neurotrophic factor as a peripheral marker for the action mechanism of antidepressants,” Neuropsychobiology, 2008, 57(4): 194–99.
33. Emails from David Goldstein and Anna Need, January 3, 2010.
34. Interview with Kevin Shianna, December 29, 2008, October 13, 2009.
35. Ibid.
36. Ibid.
37. Ibid.
38. Ibid.
39. Interview with Jason Smith, October 21, 2009.
40. Ibid.
41. Ibid.
42. Ibid.
43. Interview with Kevin Shianna, December 29, 2008, October 13, 2009.
44. http://people.genome.duke.edu/~dg48/index.php
45. D. Ge, K. Zhang, A. C. Need et al., “WGAViewer: Software for genomic annotation of whole genome association studies,” Genome Research, 2008, 18(4): 640–43.
46. J. Karow, “Duke to sequence 50 human genomes on Illumina GA; plans more large sequencing studies,” In Sequence, January 20, 2009.
47. Interviews with Dongliang Ge, October 2009.
48. Ibid.
49. Ibid.
50. Ibid.
51. Ibid.
52. J. J. Michiels, A. Gadisseur, U. Budde, et al., “Characterization, classification, and treatment of von Willebrand diseases: A critical appraisal of the literature and personal experiences,” Seminars in Thrombosis & Hemostasis, 2005, 31(5): 577–601.
53. Interviews with Dongliang Ge, October 2009.
54. Ibid.
55. Ibid.
56. Interview with Hugh Rienhoff, December 7, 2008.
57. http://www.snpedia.com/index.php/SNPedia:FAQ#How_many_SNPs_are_in_SNPedia.3F.
58. http://www.ncbi.nlm.nih.gov/projects/SNP/snp_summary.cgi.
59. Interview with Greg Lennon, December 17, 2008.
60. http://wiki.github.com/xwu/trait-o-matic.
61. http://www.pharmgkb.org/.
62. Email from Sasha Zaranek, December 1, 2009.
63. P. D. Stenson, M. Mort, E. V. Ball, et al., “The Human Gene Mutation Database: 2008 update,” Genome Medicine, 2009, 1(1): 13.
64. Email from Mike Cariaso, October 22, 2009.
65. http://www.ncbi.nlm.nih.gov/omim/
66. http://www.genetests.org.
67. M. Angrist, “We are the genes we’ve been waiting for: Rational responses to the gathering storm of personal genomics,” American Journal of Bioethics, 2009, 9(6): 30–31.
68. A. Barton and J. Worthington, “Genetic susceptibility to rheumatoid arthritis: An emerging picture,” Arthritis & Rheumatism, 2009, 61(10): 1441–46.
69. T. A. Cooper, L. Wan, and G. Dreyfuss, “RNA and disease,” Cell, 2009, 136(4): 777–93; G. S. Wang and T. A. Cooper, “Splicing in disease: Disruption of the splicing code and the decoding machinery,” Nature Reviews Genetics, 2007, 8(10): 749–61.
70. R. Alcalai, J. G. Seidman, and C. E. Seidman, “Genetic basis of hypertrophic cardiomyopathy: From bench to the clinics,” Journal of Cardiovascular Electro-physiology, 2008, 19(1): 104–10.
71. Email from Steven Pinker, September 29, 2009.
CHAPTER 13: ANTARCTICA
1. Email from Abraham Rosenbaum, August 25, 2009.
2. Interview with Abraham Rosenbaum, June 11, 2009.
3. http://wiki.github.com/xwu/trait-o-matic.
4. K. Gronskov, J. Ek, and K. Brondum-Nielsen, “Oculocutaneous albinism,” Orphanet Journal of Rare Diseases, 2007, 2: 43; T. Suzuki and Y. Tomita, “Recent advances in genetic analyses of oculocutaneous albinism types 2 and 4,” Journal of Dermatological Science, 2008, 51(1): 1–9.
5. Interview with Hugh Rienhoff, May 20, 2008.
6. L. Stanchina, V. Baral, F. Robert, et al., “Interactions between Sox10, Edn3 and Ednrb during enteric nervous system and melanocyte development,” Developmental Biology, 2006, 295(1): 232–49; N. M. Le Douarin, S. Creuzet, G. Couly, and E. Dupin, “Neural crest cell plasticity and its limits,” Development, 2004, 131(19): 4637–50.
7. G. L. Moldovan and A. D. D’Andrea, “How the Fanconi anemia pathway guards the genome,” Annual Review of Genetics, 2009, 43: 223–49.
8. http://research.nhgri.nih.gov/projects/bic/Member/cgi-bin/bic_full_summary.cgi?table=brca1_exons.
9. http://research.nhgri.nih.gov/projects/bic/Member/cgi-bin/bic_full_summary.cgi?table=brca2_exons.
10. R. C. Panguluri, L. C. Brody, R. Modali, et al., “BRCA1 mutations in African Americans,” Human Genetics, 1999, 105(1–2): 28–31.
11. Email from Mary-Claire King, October 28, 2009.
12. B. Yngvadottir, Y. Xue, S. Searle, et al., “A genome-wide survey of the prevalence and evolutionary forces acting on human nonsense SNPs,” American Journal of Human Genetics, 2009, 84(2): 224–34.
13. Interview with Andrea Loehr, June 8, 2009.
14. Interview with Hugh Rienhoff, December 9, 2008.
15. K. Sanneh, “Discriminating tastes,” New Yorker, August 10, 2009.
16. http://www.fas.harvard.edu/~amciv/faculty/gates.shtml.
17. http://www.pbs.org/wnet/facesofamerica/.
18. Interview with Henry Louis Gates, Jr., January 7, 2010.
19. Interviews with Henry Louis Gates, Jr., January 7, 2010, and Rick Kittles, January 30, 2010.
20. Interview with Henry Louis Gates, Jr., January 7, 2010.
21. Ibid.
22. Interview with Rick Kittles, January 30, 2010.
23. Interview with Henry Louis Gates, Jr., January 7, 2010.
24. Ibid.
25. Interview with George Church, November 24, 2009.
26. J. H. Relethford, “Genetic evidence and the modern human origins debate,” Heredity, 2008, 100(6): 555–63.
27. M. Via, E. Ziv, and E. G. Burchard, “Recent advances of genetic ancestry testing in biomedical research and direct to consumer testing,” Clinical Genetics, 2009, 76(3): 225–35.
28. M. D. Shriver and R. A. Kittles, “Genetic ancestry and the search for personalized genetic histories,” Nature Reviews Genetics, 2004, 5(8): 611–18.
29. http://spittoon.23andme.com/2009/11/19/introducing-relative-finder-the-newest-feature-from-23andme/.
30. Interview with Henry Louis Gates, Jr., January 7, 2010.
31. E. Lott, “Criticism in the vineyard: Twenty years after ‘Race,’ Writing, and Difference,” PMLA, 2008, 123(5): 1522–27.
32. D. A. Bolnick, D. Fullwiley, T. Duster, et al., “Genetics. The science and business of genetic ancestry testing,” Science, 2007, 318(5849): 399–400; A. Nordgren and E. Juengst, “Can genomics tell me who I am? Essentialistic rhetoric in direct-to-consumer DNA testing,” New Genetics & Society, 2009, 28(2): 157–72.
33. Interview with Henry Louis Gates, Jr., January 7, 2010.
34. T. Ray, “Illumina delivers personal genome sequencing results to first consumer: Amadeus capital’s Hauser,” Pharmacogenomics Reporter, September 2, 2009.
35. Interview with Henry Louis Gates, Jr., January 7, 2010.
36. Interview with Rick Kittles, January 30, 2010.
37. Interview with Duana Fullwiley, March 10, 2008.
38. Interview with Henry Louis Gates, Jr., January 7, 2010.
39. Ibid.
40. N. Scola, “Crowdsourcing the genome,” SEED, February 27, 2009.
41. M. P. O’Donnell, “The genetic information nondiscrimination act—a wake-up call: Great intentions, but a setback for health impact and cost-effectiveness of workplace health promotion,” American Journal of Health Promotion, 2010, 24(3): iv–v.
42. M. Angrist, “Eyes wide open: The personal genome project, citizen science and veracity in informed consent,” Personalized Medicine, 2009, 6(6): 691–99.
43. http://investor.illumina.com/phoenix.zhtml?c=121127&p=IROL-news Article&ID=1298128.
44. http://venturebeat.com/2007/11/29/got-350000-knome-has-your-full-genome/.
45. C. Ayres, “Personal genome sequence is must-have accessory for billionaires, says Knome head,” Times of London, November 14, 2009.
46. R. Drmanac, A. B. Sparks, M. J. Callow, et al., “Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays,” Science, 2009.
47. "Complete Genomics nears commercial launch; eyes thousands of genomes in 2010,” GenomeWeb Daily News, January 14, 2010.
48. http://investor.illumina.com/phoenix.zhtml?c=121127&p=IROL-newsArticle&ID=1374339&highlight=.
49. K. Davies, “It’s ‘Watson meets Moore’ as ion torrent introduces semiconductor sequencing,” Bio-IT World, March 1, 2010.
50. arep.med.harvard.edu/gmc/ppt/09Jun9_CGC_Hynes.pdf.
51. Interview with Maynard Olson, May 2, 2008.
52. A. Kong, V. Steinthorsdottir, G. Masson, et al., “Parental origin of sequence variants associated with complex diseases,” Nature, 2009, 462(7275): 868–74.
53. http://www.youtube.com/watch?v=8qxMbP2gWpU.
EPILOGUE: HERE IS A HUMAN BEING
1. http://www.technologyreview.com/blog/editors/25125.
2. Email from Jason Bobe, January 5, 2010.
3. Interview with George Church, June 9, 2009.
4. Email from Jason Bobe, August 12, 2009.
5. M. J. Khoury, C. M. McBride, S. D. Schully, et al., “The Scientific Foundation for personal genomics: Recommendations from a National Institutes of Health–Centers for Disease Control and Prevention multidisciplinary workshop,” Genetics in Medicine, 2009, 11(8): 559–67.
6. http://kara.allthingsd.com/20090904/23andme-co-founder-linda-avey-leaves-start-up-to-focus-on-alzheimers-research/.
7. Interview with Dietrich Stephan, June 10, 2009.
8. Interview with Linda Avey, November 17, 2009.
9. http://www.ignitehealth.org/about/leadership.asp.
10. J. Karow, “Ignite Institute to install 100 ABIO SOLiD 4 systems by year end under life tech collaboration,” In Sequence, January 28, 2010.
11. Interview with Dietrich Stephan, June 10, 2009.
12. J. Kaiser, “Biotechnology. Bankruptcy won’t stop decode, says its founder, Stefansson,” Science, 2009, 326(5957): 1172.
13. M. Carmichael, “The world’s most successful failure,” Newsweek, February 12, 2010.
14. http://www.techcrunch.com/2009/10/29/layoffs-confirmed-at-23andme/.
15. B. Japsen and S. M. Jones, “Walgreens postpones carrying Pathway Genomics genetic test kit,” Los Angeles Times, May 13, 2010.
16. http://energycommerce.house.gov/index.php?option=com_content&view=article&id+2009:committee-investigates-personal-genetic-testing-kits&catid=12:media-advisories&Itemid=55.
17. http://www.techcrunch.com/2009/12/23/23andme-funding/.
18. Email from George Church, September 7, 2009.
19. G. M. Church, “Genomes for all,” Scientific American, 2006, 294(1): 46–54.
Index
The pagination of this electronic edition does not match the edition from which it was created. To locate a specific passage, please use the search feature of your e-book reader.
ABCB1 gene, 245–46
Advances in Genome Biology and
Technology meetings, Marco Island, Florida, 78–79, 84, 87, 98, 133–37, 192, 229
Afeyan, Noubar, 91
Affymetrix (firm), 57, 58, 59, 92, 113, 144, 150, 204
Agencourt Personal Genomics (firm), 94, 193, 194, 197
albinism, 262–63
alpha-1-antitrypsin deficiency, 237
Alpha-1 Association, 237
Altshuler, David, 269
Alzheimer’s disease, 4, 61–62, 138, 150–51, 155–57, 207. See also APOE gene
American Association of Tissue Banks, 106
American Civil Liberties Union, gene patenting lawsuit, 216–17
American College of Medical Genetics, 63
Amersham (firm), 82, 91
amyotropic lateral sclerosis (Lou Gehrig’s disease), 6, 27, 74–75
ancestry, genetic testing for, 268–74
Andrews, Lori, 35
Angrist, Misha (author), 1–2
M. Cariaso report on genomic data of, 146–49, 245, 257
genetic testing of, by DNA Direct and 23andMe, 211–14, 257, 264
genomic findings on disease risk and drug response of, 5–8, 32n, 141–42, 148–49, 150–54, 204–5, 211, 212–14, 221, 245–47, 254–55, 262–67
Health Compass Profile from Navigenics for, 150–54, 204
mother’s breast cancer, 32n, 190–92, 212, 213, 263–65
participation in Personal Genome Project by, 2–5, 29–33, 38–39, 20
4–5, 209–11, 239–40, 260–63, 274–78, 282–83
personal genome sequencing of, by D. Goldstein and K. Shianna lab, 239–59, 263–67
study of Hirschsprung’s disease by, and nephew Jesse, 5–8, 262–63
Angrist, Noam (author’s nephew), 199, 245
Annas, George, 25, 26
anonymity. See privacy and confidentiality issues, genomics and APOE gene, 4, 77, 155–57, 208.
See also Alzheimer’s disease author’s, 150–51
S. Pinker’s, 113, 157
J. Watson’s, 27n, 41, 47, 48, 52, 138–40, 157, 209
apolipoprotein E. See APOE gene Applied Biosystems (ABI), 79, 82–83, 87, 89, 92, 135, 193, 225
Archon X Prize, 83–84, 224, 229
Argonne National Laboratory, 226
Ashburner, Michael, 39
Augie’s Quest (foundation), 74
Aull, Kay, human genetic testing by, 169–75
automated imaging, 91
autosomal markers, 270
Avey, Linda, 56n, 57–60, 69, 70, 72, 73, 75, 113, 214, 216, 233, 281
Bard, Terry, 22–23, 160, 260–61
Batchelder, Keith, as Personal Genome Project subject, 113–16, 206
Bayesian probability, 212n
Beals, Rodney, 177
Beals-Hecht syndrome, 177
Beijing Genomics Institute, 277n
Biesecker, Les, 160–61
biohacking, 170–71, 173
biological measurement, 94
BioLogos Foundation, 44
Biology of Genomes meeting, Cold Spring Harbor Laboratory (CSHL), 40–41, 44–49, 70, 191, 232
BioWeatherMap, 174
Bobe, Jason, 53, 77, 163, 165, 174
Boston Biomedical Research Institute, 128–29
BRCA1 and BRCA2 gene mutations, 4–5, 32n, 65, 118, 118n, 120, 191, 213, 214, 216, 218, 263–65
gene patents on, 213, 214–18
brain-derived neurotrophic factor (BDNF), 246–47
Brand, Stewart, 71
Breast Cancer Information Core (BIC), 264–65
Brenner, Steve, 72–73
Brin, Sergey, 57, 59
breast cancer, 4–5, 32n, 190–92, 212, 213, 263–65. See also BRCA1 and BRCA2 gene mutations
Brugada syndrome, 201
Burke, Wylie, 208
Burlington Northern Santa Fe Railway, 3
Bush, George W., 4, 125
Here Is a Human Being Page 36
