Index

Affymetrix, 117, 257
African American Diversity Project, 308–9
African American Heart Failure Trial (AHeFT), 304, 309
African Americans: as HGP donors, 110; as PDR donors, 111; pharmacogenomics and, xxix, 304, 309; precision medicine and, 309; rejection from genetic research, 298; sickle cell disease among, 299
Ahitav, Nadav, 87
AI (artificial intelligence). See Artificial intelligence
Albayrak, Gulsah, 191n6
Alberts, B., 481
Algorithms, xxx, 24, 267, 283–87, 451, 456, 461, 465
All of Us program (Precision Medicine Initiative), 218, 273–74
Alta Conference (1984), 124–25
American College of Medical Genetics, 234, 243
American College of Obstetrics and Gynecology, 234
American Indians. See Native Americans
American Recovery and Reinvestment Act of 2009 (ARRA), 81, 445
American Society for Human Genetics (ASHG), 64, 330
Amsterdamska, Olga, 343
Ancestry testing, 120–21, 237, 324
Animal modeling, 353, 356–62, 365–66
Ansorge, Wilhelm, 175
Anthropomorphism, 371n12
ARRA (American Recovery and Reinvestment Act of 2009), 81, 445
Artificial intelligence (AI), 284–85
Asbury, K., 388–89
ASHG (American Society for Human Genetics), 64, 330
Austin, Robert, 136–37

Bacterial Artificial Chromosomes (BACs): definition of, xlivn2; homologous clones from DNA libraries, 74; libraries used for sequencing, xxxvi–xxxviii, xliv, xlivn2, 233, 269; sequencing cost curve and, 53, 55, 59
Bailey, M. H., 487
BAP (Biotechnology Action Programme), 164
Barbujani, G., 303
Barker, A. D., 447
Barker hypothesis, 354
Barsh, G. S., 387
Baylor College of Medicine Human Genome Sequencing Center, 119, 161, 187, 444
Behavioral epigenetics, 362–64
Behavioral genetics, xliii, 5, 318–19, 323, 331, 388–89
Behavioral genomics, xliii, 240, 322, 331
Beijing Genomics Institute (BGI), xxix, 119
Bell Curve, The (Murray & Herrnstein), xxviii
Bellenson, Joel, 330
Bermuda Principles, 9, 11, 187, 253–54
Beta-thalassemia, 92–93
BiDil (heart failure drug), 309
Big data: biobanks and, 276; in biomedicine, 286; cancer genomics and, xxiii, 441, 461; as data-centric research, 462; letting the data lead, 442, 461; scientific publishing and, 146, 147
Big science, xviii, xix, xxxv–xxxvi, 264, 471, 479–81
Binet, Alfred, 391–92
Biobanks: big data and, 276; electronic health records and, 274–76, 278; emergence of, 270–71; pharmacogenomics and, 284; population-scale, 273, 275–76; precision medicine and, 271, 273, 274; private health systems and, 272–73; research clinics and, 271–72, 274, 286–87; sequencing costs and growth of, 218
Biochemical proxy strategy, 407, 414–15, 417–23, 426, 428–29, 432n11, 433n22
Bioethics, xxviii, 5–6, 14, 229, 231–33, 242, 298
Bioinformatics: for aggregation of data, xli; Department of Energy and, 6; functional genomics and, 416–17; in HGP research effort, 16, 35; polymorphisms distinguished from errors using, 259; resource centers and, 175; sequencing cost curve and, 54, 55; TCGA Project and, 487
Biological embedding, 348, 349, 354, 361
Biologism, 366–68
Biomedical and Health Research program (BIOMED), 174, 175, 193n15
Biomedicine: big data in, 286; Eurocentrism in, 308; nanotechnologies useful to, 137; race in, 294, 298, 303, 307, 308, 310–11. See also Epigenetics
Bionano Genomics, 66, 137
Biopolitics, 340–41
Biotechnology Action Programme (BAP), 164
Birney, Ewan, 95, 149, 153–54
Black-box paradigm, 344–49, 368
Blair, Tony, 160
Blumenbach, Johann Friedrich, xxx
Blumenthal, David, 231
Bobrow, Martin, 195n27
Bodmer, Walter, 177, 187–89, 296
Boem, F., 475
Bogaert, A. F., 321
Bohr effect, 380
Botstein, David, 166–67
Boyer, Herbert, 166
Boyle, A. P., 424
Branton, Daniel, 138–39
Brenner, Sydney, 183
Broad heritability, 393
Broad Institute (MIT/Harvard), 119, 323–25, 329, 444
Brooks, A. N., 433–34n22

Caenorhabditis elegans: cell identification, 195n25; genome sequencing of, 22–23, 165, 183–84, 188, 195n27; modENCODE and, 80–81, 419–20, 424, 432–33n15; modERN Project and, 433n20; physical mapping of, 183, 184
Campbell, Eric, 231
Campbell, Phillip, 149
Cancer and cancer genomics: algorithms and, 285; big data and, xxiii, 441, 461; chromosomal abnormalities and, 464n4; clinical sequencing for, 218; as common-complex disease, 196; as “discovery” science, 449–50; driver genes and mutations in, 442–43, 447–48, 450–51, 455–63, 464n2, 465nn7–8, 484; epidemiology and, 344, 370n7; epigenetics and, 448; epistemic structure of, 473; extra-genomic factors in, 448, 463; genetic testing for, 234; heterogeneity of genomes, 449, 454, 458–60, 462–63, 465n6; research types in, 464n1; sequencing process in, 450–51; structural variants and, 137, 223n9, 451; targeted therapies for, 445–47, 449, 464n3
Cancer Genome Atlas (TCGA) Project, The, 441–63; ARRA funding and, 445; challenges of, 452–55, 462, 463; contextual considerations, 442; cost point per genome for, 212–13; as data-driven vs. hypothesis-driven science, 441–43, 460–62; data production in, 59, 213, 223nn9–10; as epistemically centralizing project, 478, 483, 494; goals and objectives of, 445–49, 483, 484, 492; insights gained from, 213–14; Karenina paradox and, 454–60; as large-scale facilitator project, 492, 494; precision medicine and, 443; publications from, 153, 443, 445, 449, 487; research on new genes discovered by, 473, 487–93; research questions associated with, 214, 486, 487; sample considerations, 448–53, 464–65n5, 484–85, 496n18; as scaffolding future research, 442–43, 460; scientific background of, 450–54; team science approach of, 446; tumor sequencing project as origins of, 443–45
Candidate cis-regulatory elements (cCREs), 80, 83
Cantor, Charles, 138
Cao, Han, 137
Carugati, F., 390
Catalogue of Somatic Mutations in Cancer (COSMIC), 446
Causal narratives, 475, 495n7
Causal role (CR) account of function, 407–11, 413, 431n9
Cavalli-Sforza, Luigi Luca, 297, 298, 312n9
CCDGs (Centers for Common Disease Genomics), 46, 60–61, 63, 216
cCREs (candidate cis-regulatory elements), 80, 83
CDC (Centers for Disease Control and Prevention), 236, 312n6
CDCV (common disease, common variant) hypothesis, xxix, 114
cDNA. See Complementary DNA
CEER (Centers of Excellence) Program, 231, 240–41, 308
CEGS (Centers of Excellence in Genomic Science), 135–36
Celera Genomics: BAC libraries used by, xlivn2; draft sequence and, 158, 160, 190n2, 300, 479; establishment of, 257, 479; IHGSC rivalry with, xviii, 163; public contest with, xviii, xxv, xxxix, 29; racial diversity initiatives, 300–301; Science publication of human genome paper, 151; user-inclusive networks and, 193n17; Venter as CEO of, 160, 190n2, 300–301, 479
Cell (journal), 443, 445, 458
Centers for Common Disease Genomics (CCDGs), 46, 60–61, 63, 216
Centers for Disease Control and Prevention (CDC), 236, 312n6
Centers of Excellence in Genomic Science (CEGS), 135–36
Centers of Excellence (CEER) Program, 231, 240–41, 308
Centre for the Study of Human Polymorphism (CEPH), 115, 176–77
Chakravarti, Aravinda, 295, 300, 302
Chen, Z. X., 423
Cho, Mildred, 231
Chromatin-Immuno-Precipitation coupled to high-throughput sequencing (ChIP-seq), 417–18, 433n18
Chromatin-Immuno-Precipitation coupled to microarray analysis (ChIP-chip), 420, 433n18
Chromosome workshops, 168–73, 177, 185–87, 192–93n13, 196n30
Chronic diseases, 343, 345, 346, 354, 486
Clinical Genome Resource (ClinGen), 282
Clinical Sequencing Exploratory Research (CSER) Consortium, 242–43, 281–82
Clinton, Bill, 159–60, 187, 302
Cloud computing, 89, 283
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), 378, 385, 388, 397
Cohen, Daniel, 176
Cohen, Stanley, 166
Cold Spring Harbor Laboratory (CSHL), 42, 165, 168, 172, 313n18, 478
Collins, Francis: ENCODE Project and, 73, 95–96; Genetic Variation Program and, 111; as NCHGR/NHGRI director, xvii–xviii, 11, 29, 159–60, 300, 444–45, 479; as NIH director, xxiii, 186; Polymorphism Discovery Resource and, 300; TCGA Project and, 444–45, 447
Common-complex diseases, 196n31, 216–17, 223n13, 269
Common disease, common variant (CDCV) hypothesis, xxix, 114
Comparative genomics, 74, 209–12, 220, 222nn4–5, 415
Complementary DNA (cDNA), xvii, 14, 55, 59, 71, 163, 180–82, 194nn21–22
Confidentiality. See Privacy issues
Consent: for data sharing, 90–91, 112, 116; failure to obtain, xxxvii, 24; informed, xxviii, xliv, 236–37, 239
Constitutive skin color, 386
Contextual developmental construction, 382–83, 399
Conversion therapies, 328
Cook-Deegan, Robert, xxv
Cooperative agreements, 26, 31–32, 36, 45, 73, 85, 95
Coriell Institute for Medical Research, 111, 116
Corsaro, Cheryl, 128
COSMIC (Catalogue of Somatic Mutations in Cancer), 446
Cost curve. See Sequencing cost curve
Cox, Edward (Ted), 136–37
CR (causal role) account of function, 407–11, 413, 431n9
Craighead, Harold, 136–37
Crick, Francis, 183
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), 378, 385, 388, 397
CRISPR-Cas9 technologies, 88, 232
CSER (Clinical Sequencing Exploratory Research) Consortium, 242–43, 281–82
CSHL. See Cold Spring Harbor Laboratory
Cummings, Dominic, 388
Curd, M., 473
Cystic fibrosis, xxvii, 168, 223n11, 234, 299

Davenport, C. B., 385
Davenport, G. C., 385
Davis, B. D., 480
Davis, Ronald, 166–67
Deamer, David, 138–39
deCODE genetics, 73, 97n1, 271
DeLisi, Charles, 478
Demographic Rule (FDA), 303
Deoxyribonucleic acid. See DNA
Department of Energy (DOE): Alta Conference convened by, 124–25; on cost estimate for genome projects, 42; ELSI Program for, 228, 229, 231; Health and Environmental Advisory Committee, 17, 229; Human Genome Diversity Project and, 296; Joint Genome Institute of, 161, 187; NIH collaboration with, 6–7, 14, 17, 30, 35, 126; research participant guidance from, xxxvii; technology development and, 6, 479; on women in genetic research, 299. See also Human Genome Project
Department of Health and Human Services, 37n2, 42, 295, 298, 313n20
Ding, Li, 443–45, 453–54
Direct-to-consumer (DTC) genetic testing, 273, 284
Discovery strategies, 473–78, 495nn4–5
Discrimination: ELSI Program priorities on, 296; in employment, xxviii, 232; Eurocentrism, 297, 300, 308; genetic information as basis for, xxviii, 232, 235; sexual orientation and, 324–25, 330. See also Racism
Diseases: chronic, 343, 345, 346, 354, 486; common-complex, 196n31, 216–17, 223n13, 269; Mendelian, 215, 218, 223n11, 273, 286; noncommunicable, 348, 370n6
DNA (deoxyribonucleic acid): biochemical features of, 86; cDNA, xvii, 14, 55, 59, 71, 163, 180–82, 194nn21–22; discovery of structure of, 161, 183, 188, 191nn4–5; junk, 196n31, 381, 430n3; methylation of, 87, 354, 363, 417; recombinant, 164, 166; transcription into RNA, 71, 76, 417, 418. See also Biobanks; Genetics; Genome sequencing
DOE. See Department of Energy
Donors: for BAC libraries, xxxvii; for biobanks, 271–74; for ENCODE, 90; for HapMap Project, 115–16; for HGP sequencing phase, 24, 110, 233, 270, 299; for Polymorphism Discovery Resource, 112, 300; privacy issues and, 116, 118, 299, 300; for sexual orientation study, 324
Draft sequence: Celera and, 158, 160, 190n2, 300, 479; completion of, xvii, xxxii, 26–27, 286, 302, 479; definition of, xlivn1, 52; estimated vs. actual cost of, 62; IHGSC and, 158, 160, 162, 177, 187, 264; publication in Nature, xxxix, xl, 145, 150–51, 160–63, 177, 187, 191n3, 264; sequencing centers in generation of, 25, 27, 160, 161, 191n3; White House ceremony for celebration of, xxxii, 27, 159–60, 302
Drell, Dan, 254–55
Drosophila melanogaster: genome sequencing of, 22, 165; Mendelian patterns of inheritance in traits of, 381; modENCODE and, 80–81, 419–24, 432–33n15, 433–34n22
DTC (direct-to-consumer) genetic testing, 273, 284
Duchenne muscular dystrophy, 223n11
Dulbecco, Renato, 447, 478
Dunham, Ian, 153–54
Dunston, Georgia, 308–9
Duster, Troy, 238

Ecker, Joseph, 87
Eddy, S. R., 491
EEC (European Economic Community), 163–66, 172
Eichler, Evan, 250, 260, 261
Eisenberg, Rebecca, 231
Electronic health records (EHRs), 242, 266–67, 274–79, 283, 284
Electronic Medical Records and Genomics (eMERGE) network, 218, 277–81, 283, 284
ELSI Program. See Ethical, Legal, and Social Implications Program
EMBL (European Molecular Biology Laboratory), 159, 175, 177, 193–94n18
Encyclopedia of DNA Elements (ENCODE) Project, 70–96; ARRA funding and, 81–82; background of, 70–73, 121, 431n10; biological assays and data types for, 74, 75; communication strategies and, 75, 85; community publications, 78, 79, 92; Consortium organization and membership, 84–92; Consortium publications and community outreach, 75–83, 91–92, 430–31n3; controversy involving, 406–8, 421, 430–31n3, 431n7; cooperative agreements and, 73, 85, 95; criticisms of, 78–80, 406, 421, 431nn4–5; Data Analysis Center for, 77, 81–83, 95; Data Coordination Center for, 76–77, 81, 83, 88; data management and, 76–77, 88–89; data release and accessibility issues, 89–91; data standards development and, 89; ENCODE 1 (pilot phase), 71–76, 84–87, 89–91, 94, 131, 419, 432n12, 433n17; ENCODE 2, 76–82, 86, 87, 90, 95–96, 153, 419–21; ENCODE 3, 82–83, 86, 87, 90, 405; ENCODE 4, 83–84, 87, 88, 90–91, 94, 96, 405, 432n11; ENCODE Portal, 86, 88–89; end goal of creating “complete” catalog, xxi, 94–95; External Consultants Panel for, 85; future outlook for, 96; hallmark features of, 84–96; impact on research, 92–94; importance of common targets, samples, or reagents, 88; interactions with other genomics projects, 86, 90; lessons learned from, 95–96; mouse ENCODE, 82, 89, 92, 433n16; naming considerations, 73, 97n2; Nature publications related to, 77–78, 153–54; open-source software sharing and, 91; proxy strategies and, 414–19, 429; target sequences selected for analysis, 74–75; technology development and, 73, 77, 82, 85–88, 131; transparency and, 76, 80, 89. See also Model Organism Encyclopedia of DNA Elements (modENCODE) Project
Energy Department. See Department of Energy
Environmental epigenetics, 350, 353, 362, 363
Epidemiology: biobanks and, 273; biological evidence in, 342–49; biopolitics and, 340, 341; black-box paradigm and, 344–49, 368; cancer and, 344, 370n7; “from cells to society” approach and, 340–43, 347; integration of epigenetics into, 347–50, 366–68; pragmatic argument for, 346–47; in simulation of low SES via stress induction, 356–58; in simulation of parental care via pup licking, 358, 360; in simulation of war or childhood poverty via starvation, 354–56; “the social” in, 349–53, 358, 362; statistical nature of, 355–56; strategic argument for, 346, 347. See also Social epidemiology
Epigenetics: behavioral, 362–64; biological embedding and, 348, 349, 354, 361; biologism and, 366–68; cancer progression and, 448; emergence of, 347, 382, 400; environmental, 350, 353, 362, 363; integration into epidemiology, 347–50, 366–68; maternal immune mechanism and, 321; nutritional, 354–55; origins of term, 370n9; phenotypic plasticity and, 367; physiological stress response and, 356; sexual orientation and, 321; social, 340–42, 353–54; “the social” in, 353–54, 362, 363; style of reasoning specific to, 365–66
Escherichia coli, 22, 165, 206, 380
ESF (European Science Foundation), 193–94n18
ESTs (expressed sequence tags), xvii, 10, 182, 185
Ethical, Legal, and Social Implications (ELSI) Program, 227–44; Centers of Excellence Program, 231, 240–41, 308; clinically focused studies by, 234–35, 241–43; conceptual foundation for, 231–32; controversy involving, xviii, 227, 229; donor-related issues addressed by, 233; eMERGE network and, 278; establishment of, 227–29, 231; future outlook for, 243–44; genetic testing and, xxviii, 234, 296; Genetic Variation Program and, 109, 111; HapMap Project and, xxviii, 114, 116, 238–40; history of projects supported by, xxvii–xxviii, 294, 296; interdisciplinary collaboration and, 235, 238; Juengst as head of, 5–6, 231, 232; 1000 Genomes Project and, 240; policy-research debate within, 229–31; productive tensions and, 228, 231, 235, 243–44; race studies funded by, 299, 301–2, 312–13n13; SER Consortium and, 282; on stored tissue samples, 235–37; Watson’s proposal for creation of, xxvii, 5, 228
Eugenics: Galton as founder of, 391; genetic enhancement and, 379, 384, 385, 399, 400; genomic medicine and, xxix; intelligence and, 388, 389, 397; legacy of, xliii, xliv, 232; liberal, 389, 392, 401nn2–4; moderate, 401n2; persistence in genetics and genomics, xliii, 5; positive, 379, 400; predictive techniques of genetic medicine and, 173; stigma associated with, 167
Eumelanin, 384, 386–87
Eureka consortium, 191–92n8, 194n20
Eurocentrism, 297, 300, 308
European Bioinformatics Institute, 95, 116, 153
European Commission: BIOMED program and, 174, 175, 193n15; Biotechnology Action Programme of, 164; Eureka consortium and, 191–92n8; on genome mapping and sequencing, 159, 174, 189; NIH communication with, 28; research and development policies of, 164, 165, 167; yeast genome sequencing and, 163–65, 172–74. See also Human Genome Analysis Programme
European Economic Community (EEC), 163–66, 172
European Gene Mapping Project (EUROGEM), 175–76, 178–80
European Molecular Biology Laboratory (EMBL), 159, 175, 177, 193–94n18
European Science Foundation (ESF), 193–94n18
Evolutionary proxy strategy, 407, 414–17, 420, 423, 426, 428–29, 432n11
Expressed sequence tags (ESTs), xvii, 10, 182, 185
Eye color, genetics of, 384–86, 388

Facultative skin color, 386
FCCs (Functional Characterization Centers), 83, 87, 88
FDA (Food and Drug Administration), 303, 304, 446
Federal Grants and Cooperative Agreements Act of 1977, 45
Females. See Women
Ferguson-Smith, Malcolm, 173, 192–93n13
Fetal Origins Hypothesis, 354
FICV problem. See Functional Identification, Characterization, and Validation (FICV) problem
Flynn effect, 392
Food and Drug Administration (FDA), 303, 304, 446
Ford, E. B., 249
Fortun, Michael, 172, 192n11
Foster, Morris, 238
Fraternal birth order effect, 321, 322
“From cells to society” approach, 340–43, 347, 362, 364, 369, 369n2, 370n5
Fruit fly. See Drosophila melanogaster
Functional absence, 412, 413
Functional ambiguity, 411–13
Functional Characterization Centers (FCCs), 83, 87, 88
Functional genomics, 405–30; bioinformatics and, 416–17; challenges of, 405–6; CR account of function, 407–11, 413, 431n9; definition of, 405, 430n1; from-theory-to-practice assumption in, 407, 408, 410, 435n31; power and limitations of, 408; practical issues in, 408; proxy strategies in, 406–7, 412–23, 426, 428–30, 432n11, 433–34n22; SE account of function, 407, 409–14, 416, 431nn6–8; theoretical problems in, 408. See also Encyclopedia of DNA Elements (ENCODE) Project; Model Organism Encyclopedia of DNA Elements (modENCODE) Project
Functional Identification, Characterization, and Validation (FICV) problem, 405–15, 417–19, 421–23, 427–30
Functional parasitism, 412, 413, 417
Funding opportunity announcements (FOAs), 126–28, 132–35, 137, 139, 209–10, 215
Futuyma, Douglas, 249

Gadney, Max, 154
Galton, Francis, 391
Ganna, A., 319, 321–25, 328–32
Gannett, Lisa, 250, 261
Garvey, Clare, 154
Gefitinib, 445–47
GenBank, 24, 250–51, 253, 270
Gender: confusion regarding, 328; hair color and, 386; IQ tests and, 392; public health disparities and, 294; reflexive dimension of, 352. See also Women
Gene editing: CRISPR-based, 378, 385, 388, 397; germline editing, 232, 378–79, 384, 385; specificity and, 379, 384. See also Genetic enhancement
Genentech, 166
Gene specificity, 379, 384, 385, 397, 401n1
Gene therapies, 92–93
Généthon, 19, 176, 180, 187, 189, 194nn19–22
Genetic counseling, xxvii, 267–68
Genetic determinism, 327, 333, 388
Genetic engineering, 164, 167, 183
Genetic enhancement: of complex behavioral traits, 388–97, 399; ELSI Program and, 232; ethical issues of, 379, 384; eugenics and, 379, 384, 385, 399, 400; of physical traits, 384–88
Genetic exceptionalism, 227, 229, 235, 236, 243
Genetic information: as clinical tool, 281; discrimination based on, xxviii, 232, 235; ELSI Program and, xxvii, 227, 232, 234; equal access to benefits of, 232; functional genomics and, 405; genetic exceptionalism and, 235, 236; integration into clinical practice, 234; selling back to consumers, 273. See also Privacy issues
Genetic Information Nondiscrimination Act of 2008 (GINA), xxvii–xxviii, 232
Geneticization, defined, 333
Genetic mapping: chromosome workshops and, 168, 170, 173; circumscription of datasets for, xxxiv; EUROGEM and, 175, 176; GESTEC funding for, 18–19; lessons learned during, 20; NRC on desirability of, 13; team science approach to, 20; technology development and, 126, 128
Genetic proxy strategy, 407, 414, 415, 419, 433–34n22
Genetic reductionism, xxxi, 191, 318, 379, 381–82
Genetics: behavioral, xliii, 5, 318–19, 323, 331, 388–89; of eye color, 384–86, 388; of hair color, 386; of intelligence, 388–89, 392–93, 395–97; Mendel’s patterns of inheritance, 381, 384, 400; persistence of racism and eugenics in, xliii, 5; population, 109, 208–9, 249, 319; of sexual orientation, 318, 320–25, 328–33; of skin color, 386–88; social life of, 333; statistical, 109. See also Epigenetics; Medical genetics
Genetic testing: ancestry testing, 120–21, 237, 324; clinical guidelines for use of, 234; for cystic fibrosis, xxvii, 234, 299; direct-to-consumer, 273, 284; ELSI Program and, xxviii, 234, 296; for sickle cell anemia, 299
Genetic Variation Program, 109–21; background of, 109–10; ELSI Program and, 109, 111; HapMap Project and, 113–18; motivations for establishment of, 110; 1000 Genomes Project and, 118–20; Polymorphism Discovery Resource and, 110–12; uses of variation data, 120–21; on variants across the genome, 112–13
Genome mapping: European Commission support for, 159, 174; technology development and, 126, 128, 131, 138; Wellcome Trust and, 159, 172. See also Genetic mapping; Physical mapping
Genome Science and Technology Centers (GESTECs), 18–19, 127–30
Genome sequencing: Advisory Committee for, 23–24, 26, 36; BAC libraries used for, xxxvi–xxxviii, xliv, xlivn2, 233; budget for, 34–35, 46, 47; cDNA strategy for, 180–82; of C. elegans, 22–23, 165, 183–84, 188, 195–96n27; completion of high-quality sequence, 14, 27, 191n5; cost tracking for, 34, 43–51, 65–66, 203–20, 222n3, 224n16; cottage industry approach to, 166, 174, 188; data release policies, 9–10, 23, 25, 26, 37; of D. melanogaster, 22, 165; error rate in, xxxiv, 251–56, 260; GESTEC funding for, 19; nanopore, 134, 138–39; pilot project period, 23–25, 33, 206, 252–53; production metrics for, 44–46, 55–60; public sector effort, xviii, xxv, xxxix, 22–29; quality control measures for, 22–24, 33–34; resequencing, 34, 49, 53, 120, 205, 253, 256; single-molecule approach, 138; structure of discovery in, 221, 224n19; technology development and, xxii, xxiv, 41, 125–29, 134, 138–39; of yeast, xviii, 53, 163–67, 172–74, 184, 188, 191n7, 192n9. See also Draft sequence; Next-generation sequencing (NGS) platforms; Sequencing centers; Sequencing cost curve
Genome Sequencing Program (GSP), 46, 51–52, 60–61, 220
Genome-Wide Association Studies (GWAS): common disease studies, 216, 223n12; development of robustness in, xxx; genomic medicine and, 268–69, 277, 278; HapMap Project and, xxix, 113, 114, 118, 120, 209; on intelligence, 393, 395–97; linkage disequilibrium and, 121; on loci associated with skin color, 386; 1000 Genomes Project and, 118, 120; on sexual orientation, 318, 320–32; single nucleotide polymorphisms and, 93, 257, 321–22
Genome-wide polygenic scores (GPSs), 396–99
Genomic 5 (G5) sequencing centers, xxxviii, 161–63, 174, 177, 182, 187, 191n3, 195n24
Genomic information: access to data, 149; algorithms as translators of, 284; as clinical tool, 266, 279–81, 286, 287; division between producers and users of, 174; in electronic health records, 242, 279; ELSI Program and, 227, 234; genetic exceptionalism and, 227, 236; growth in volume of, 154; integration into clinical practice, 234
Genomic literacy, 419, 432n14
Genomic medicine, 264–88; algorithms and, 267, 283–87; building blocks of, 266–67; cancer therapies and, 445–46, 464n3; diagnostic and therapeutic decision-making in, 276–82; Genome-Wide Association Studies and, 268–69, 277, 278; medical promises of HGP and, 264–70, 282, 378; NHGRI division of, 241, 267, 276–77, 280–82; personalized, xxix, 268, 271, 274, 276, 382; pharmacogenomics and, xxix, 269, 279, 284–85, 303–5, 309, 313n17; racist and eugenicist concerns in, xxix; socioeconomic disparities in access to, 281. See also Biobanks; Precision medicine
Genomics: acceleration of, 162, 218; behavioral, xliii, 240, 322, 331; comparative, 74, 209–12, 220, 222nn4–5, 415; complete vs. comprehensive project aims, xxxviii–xlii; as discovery science vs. hypothesis-driven science, xxii, 220–21, 224n20; distributed approach to, 163, 188; FICV problem in, 405–15, 417–19, 421–23, 427–30; improvement of human health through, 84; medical genetics, relationship with, 158; Nature’s relationship with, 145, 151, 155; origins of term, 169; persistence of racism and eugenics in, xliii; pharmacogenomics, xxix, 269, 279, 284–85, 303–5, 309, 313n17; postgenomics, xxvi, xxxi–xlii, 163, 189, 340–41; scientific advancements in, 41, 45; social, xliii, 319, 322, 331; structural, 405, 430n1; systems biology and, 495n8. See also Cancer and cancer genomics; Epigenetics; Functional genomics
Genomics (journal), 169, 172
Genoscope, 176–77, 194n19
Genotype-Tissue Expression (GTEx) project, 86, 90
Genzentrum, 194nn21–22
Germline editing, 232, 378–79, 384, 385
Gerstein, M. B., 424
Gert, Bernard, 232
GESTECs (Genome Science and Technology Centers), 18–19, 127–30
Gilbert, Walter, 478, 482–83
Gillborn, D., 391
GINA (Genetic Information Nondiscrimination Act of 2008), xxvii–xxviii, 232
Goffeau, André, 165, 167, 172
Goldstein, A., 303
Gottesman, Michael, xvii, 10
Gould, S. J., 390–91
Govindan, R., 452, 456
GPSs (genome-wide polygenic scores), 396–99
Greeley, Henry, 298
Green, Eric, xliv, 72, 74, 430–31n3
Green, Phil, xviii, 33, 251, 253, 255–56, 260–62
GSP (Genome Sequencing Program), 46, 51–52, 60–61, 220
GTEx (Genotype-Tissue Expression) project, 86, 90
Gunter, Chris, 150
Guyer, Mark, xxxvii, 4, 72, 95–96
GWAS. See Genome-Wide Association Studies

Habitus, defined, 363
Hacking, I., 365
Hair color, genetics of, 386
Hamers, Dean, 318, 322, 329
Haplotypes: definition and description of, 112; linkage disequilibrium and, 112–14, 119, 208; 1000 Genomes Project and, 119, 120; SNP Consortium and, 305–6. See also International HapMap Project
HapMap. See International HapMap Project
HD (hypothetico-deductive) system, 475
Health and Environmental Advisory Committee (HERAC), 17, 229
Health and Human Services Department. See Department of Health and Human Services
Healy, Bernadine, xvii, xxvii, 10–11
Herceptin (trastuzumab), 284, 446
Heritability, 249, 320, 393–96, 398, 399
HGAP. See Human Genome Analysis Programme
HGDP. See Human Genome Diversity Project
HGP. See Human Genome Project
Hilgartner, Stephen, 160, 161, 166, 177, 478
Hogben, L., 399
Homosexuality. See Same-sex sexual behavior
Howard Hughes Medical Institute, 7, 28, 172
HUGO. See Human Genome Organization
Human Gene Mapping Workshops, 159
Human genome: block structure of, 113, 114; complexity of, 479, 496n12; euchromatic portion of, xxxix–xl, xlivn1, 14, 258, 260; heterochromatic portion of, xxxix, 110; near invariance from cell to cell, 94; number of base pairs in, 33, 47–48, 253; protein-coding genes encoded in, 71, 192n10; viewed as property of all mankind, 9
Human Genome Analysis Programme (HGAP): cDNA sequencing strategy and, 180–82; chromosome workshops organized by, 173, 185, 187, 192–93n13; distributed approach of, 163, 188; establishment of, 158, 162, 172–73; European Data Resource and, 176; funding for, 173, 174, 193n15; goals and objectives of, 158, 162, 173, 174, 189; HGP and IHGSC compared to, 159–63; overshadowed by draft sequence, 158, 162, 191n6; on patenting practices, 195n24; Reference Library System and, 177; resource centers and, 175–76, 180–83, 189; user-inclusive networks and, 174–77, 180
Human Genome Diversity Project (HGDP), xxix–xxxi, 114, 116, 239, 296–99
Human Genome Organization (HUGO), 7, 28, 172, 187, 192n11, 192–93n13, 196n29, 296
Human Genome Project (HGP): accomplishments of, 14–15, 19–20; Advisory Committee for, 7–8; ancillary activities in, 16, 35; beginnings of, xxiii, 3–4, 13–14, 17, 124–25, 161, 294, 478–79; Bermuda Principles on, 9, 11, 187, 253–54; challenges related to, xxi, 4–11, 15–16; completeness in description of goals for, xxxviii, xxxix–xl; complex features of, xviii–xix, xxxiv–xxxv, xlii, 16; contingent nature of, xvii–xix, xxxiii, xxxv, xlii; controversies involving, xviii–xix, xxv–xxvi, xxxv–xxxviii, xlii; criticisms of, 4–5, 15–16, 30, 78, 250, 265, 297, 381, 479–81; error standard for, 250, 253–55, 260–61; Eurocentrism in, 297, 300; finished sequence produced by, 52, 62, 250–51; five-year plans for, 9, 17, 25, 30, 35–36, 70, 126, 230, 295–96, 301, 479; funding committed to, 174, 295; input from outside experts, 15, 17, 36; international collaboration on, 7, 20, 22, 28, 160, 479; as large-scale facilitator project, 478, 482–83, 494; leadership considerations, 28–29; lessons learned during, 20, 27–37; medical promises of, 264–70, 282, 378; Nature publications related to, xxxix, xl, 160–62, 191n3; plurality of perspectives regarding, xix–xxi, xxv–xxxi, xlii; racial diversity initiatives, 299–301, 305; reductionism and, xxvi, xxviii–xxxi, xxxiii–xxxv, 381; sequencing cost curve and, 51–53, 62; technology development and, 8, 16, 29, 32, 35, 124–35, 139. See also Ethical, Legal, and Social Implications Research (ELSI) Program; Genome mapping; Genome sequencing
Human Genome Sciences, 182
Human Heredity and Health in Africa Project, 309
Huntington’s Disease, 7, 168
Hurst, C. C., 385
Hutter, Carolyn, 448–51, 464n4
Hygienist movement, 346, 370n8
Hypothesis generation, 473–77, 485–86, 494
Hypothetico-deductive (HD) system, 475

IHEC (International Human Epigenome Consortium), 86, 89
IHGSC. See International Human Genome Sequencing Consortium
Illumina, 48–50, 55–59, 61, 65–66, 87, 117, 119, 275
Illuminating the Druggable Genome Consortium (IDG), 493
Imperial Cancer Research Fund (ICRF), 176, 177, 180, 187, 189
Implementing Genomics in Practice (IGNITE) Network consortium, 280–81, 283, 284
Informed consent, xxviii, xliv, 236–37, 239
Institute for Genome Research, The (TIGR), 181–82
Institutional facts, 352–53
Intellectual property, xxviii, 117, 231, 241. See also Patents
Intelligence, xxvii, 384, 388–93, 395–97, 399
International Cancer Genomics Consortium, 446
International HapMap Project (HapMap): CDCV hypothesis and, xxix, 114; community consultation in, 116, 239; complete vs. comprehensive aims of, xl, xli; complex features of, xxxiv–xxxv; continental grouping of races by, xxix; cost point per genome for, 207–8; Data Coordination Center for, 116; data release policies for, 117; deterministic nature of, xxxiii; ELSI Program and, xxviii, 114, 116, 238–40; Genetic Variation Program and, 113–18; Genome-Wide Association Studies and, xxix, 113, 114, 118, 120, 209; insights gained from, 208–9; interactions with other genomics projects, 86; proxy strategies and, 434n30; race and, xxxi, 293, 306–7; research questions associated with, 208, 209; selection of populations for inclusion in, 114–16; single nucleotide polymorphisms and, 113–14, 117, 118, 257; working groups for, 116–17
International Human Epigenome Consortium (IHEC), 86, 89
International Human Genome Sequencing Consortium (IHGSC): Celera rivalry with, xviii, 163; charitable funding within, 195n24; completeness as defined by, xxxix–xl; on completion of high-quality genome sequence, 14, 191n5; draft sequence completed by, 158, 160, 162, 177, 187, 264; Hilgartner on emergence of, 160; on protein-coding genes encoded in human genome, 71
International Mouse Phenotyping Consortium, 493
IQ tests, 390–92

Jacob, F., 380
Janssens, Cecile, 329
Johnson, Boris, 388
Johnston, Mark, 167, 184
Joint Genome Institute (DOE), 161, 187
Jordan, Elke, xvii, 127–28
Juengst, Eric, 5–6, 231, 232

Kell, D. B., 220
Kendler, Kenneth, 329
Kertbeny, Karl-Maria, 320
Kitcher, Philip, xxvi
Knorr-Cetina, K., 471, 476, 481, 483
Korlach, Jonas, 137
Krieger, Nancy, 352
Kwok, Pui Yan, 307

Laboratory of Molecular Biology of Cambridge (LMB), 183, 184
Lander, Eric, xxiii, xxxvi, 222n3, 294, 302, 306
Large-scale biology projects: as big science, 471, 480, 481; as epistemically centralizing, 470, 473, 478, 481, 483, 494; as facilitators, 470, 472, 477, 478, 482–83, 492, 494; impact on molecular biology, 470–73, 477–78, 481–82, 494
Large-Scale Sequencing and Analysis Centers (LSACs): annual review of, 35; funding for, 25, 46, 161, 166, 186; progress reports from, 53–55, 59; sequencing cost curve and, 47, 51, 53–60, 62; top down approach of, 187–88; yeast genome sequencing and, 166–67. See also specific sequencing centers
Lawrence, M. S., 459–60
LD. See Linkage disequilibrium
Lee, E. S., 422
Legal implications of research. See Ethical, Legal, and Social Implications (ELSI) Program
Lehrach, Hans, 177, 180
Leng, G., 495n7
Leng, R. I., 495n7
Leonelli, S., 462
Ley, Tim, 452, 453, 457–58, 465nn8–9
Liberal eugenics, 389, 392, 401nn2–4
Link, Daniel, 458
Linkage disequilibrium (LD), 112–14, 117–19, 121, 208, 258
Linkage mapping. See Genetic mapping
Linnaeus, Carl, 383, 441
Lipman, David, 10
LMB (Laboratory of Molecular Biology of Cambridge), 183, 184
LSACs. See Large-Scale Sequencing and Analysis Centers

Machine learning, 284–85
Markel, Howard, 232
Marker papers, 84, 88, 90, 94, 149, 449, 451, 453
Maroñas, O., 386
Massively parallel reporter assays (MPRAs), 87, 432n11
Maternal immune mechanism, 321
Max Planck Institute for Human Genetics, 119, 303
McGill University (Canada), 191n7, 192n9
McKusick, Victor, 169, 172
Medical genetics: chromosome workshops and, 168–69, 172–73, 185, 192–93n13; common-complex diseases and, 196n31, 216–17, 223n13, 269; European community and, 162, 167–69, 172; expressed sequence tags and, 182; genomics, relationship with, 158; institutional base of, 167–68; integration into clinical practice, 234, 235; Mendelian diseases and, 215, 218, 223n11, 273, 286; predictive techniques of, 173
Melanin, 384–87
Mendelian diseases, 215, 218, 223n11, 273, 286
Merton, Robert, xxiv
Messenger RNA (mRNA), xvii, 482
Meyerson, Michael, 444, 454–55
Micklos, David, 232
Microarray data, 147–48
MicroRNA, 420, 448
Model Organism Encyclopedia of DNA Elements (modENCODE) Project, 419–29; ARRA funding and, 81–82; Consortium publications, 81; Data Analysis Center for, 81–82; data management and release policy, 89–90; establishment of, 76, 80, 407, 431–32n10; impact on research, 92, 432–33n15, 434nn28–29; investigative goals of, 419, 432–33n15; phase 1 (biochemical traces), 420–21, 429, 433n19; phase 2 (abstract principles of genomic function), 423–24, 427–29, 434nn25–26; proxy strategies and, 415, 419–23, 426, 428–30, 433–34n22; selection of organisms for, 80–81, 419, 434n23; theoretical tension and, 425–29, 434n27; timeline in relation to ENCODE phases, 419, 420; validation of elements, 421–23, 428, 433n21, 433–34n22
Model Organism Encyclopedia of Regulatory Networks (modERN) Project, 433n20
Moderate eugenics, 401n2
Molecular biology: biopolitics and, 340; causal narratives in, 475, 495n7; data production grants and, 130; discovery strategies in, 473–78, 495nn4–5; epistemic independence of labs, 473, 481, 483; ethos of, 185, 480; explanatory power of, 348; foundational moment within, 161; “from cells to society” approach and, 340–43, 347, 362; hypothesis generation phase in, 473–77, 485; impact of large-scale biology projects on, 470–73, 477–78, 481–82, 494; knowledge culture in, 470, 471, 481; paradigm of, 479, 496n11; reductionism and, 380–81; in simulation of low SES via stress induction, 356–58; in simulation of parental care via pup licking, 358–60; in simulation of war or childhood poverty via starvation, 354–56; as small science, 470–73, 480, 483, 485, 493; social epidemiology and, 341; of social position, 358, 362; uncertainty regarding large-scale biology projects, 471
Monod, J., 380
Morgan, Michael, 159, 186
Morgan, Thomas Hunt, 381
Mouse Encyclopedia of DNA Elements (mouse ENCODE) Project, 82, 89, 92, 433n16
MPRAs (massively parallel reporter assays), 87, 432n11
mRNA (messenger RNA), xvii, 482
Mueller-Wille, S., 480
Mugny, G., 390
Muscular dystrophy, 223n11
Mutation calling, 450–54
Myers, Richard, 130–31

Nagel, T., 362
Nakamura, Yusuke, 115
Nanopore sequencing, 134, 138–39
National Academy of Sciences (NAS), 22, 29, 42–43, 160
National Advisory Council for Human Genome Research (NACHGR), 17, 25, 72–74, 76, 83, 135–36, 229
National Cancer Institute (NCI), 212, 442, 452, 483. See also Cancer Genome Atlas (TCGA) Project, The
National Center for Advancing Translational Science, 493
National Center for Biotechnology Information (NCBI), 10, 111, 116, 488
National Center for Human Genome Research (NCHGR): Collins as director of, xvii, 11; evolution of OHGR into, 3, 37n2, 43, 139n1; Gottesman as acting director of, xvii, 10; Jordan as deputy director of, xvii; mapping phase of HGP and, 19; organizational structure of, 4; original branches of, xxvii; required input from NACHGR, 17; on women in genetic research, 299. See also Human Genome Project; National Human Genome Research Institute; Office for Human Genome Research
National Genographic Project, 309, 313n23
National Heart Lung and Blood Institutes TOPMed program, 216
National Human Genome Research Institute (NHGRI): close management of research activities, 31–33; Collins as director of, xvii–xviii, 11, 29, 159–60, 300, 444–45, 479; comparative genomics projects, 209–10, 222n4; complete vs. comprehensive project aims of, xxxix–xli; cooperative agreements and, 26, 31–32, 36, 45; evolution of NCHGR into, 3, 11, 37n2, 43, 139n1; flexibility of approach, 29–30, 45; FOAs issued by, 126–28, 132–35, 137, 139, 209–10, 215; Genetic Variation Program, 109–21; Genome Sequencing Program, 46, 51–52, 60–61, 220; genomic medicine division, 241, 267, 276–77, 280–82; Green as director of, xxiii; History of Genomics Program at, xviii, xx, xxiii–xxiv, xliii, xliv, 266; Jordan as deputy director of, xvii, 127; lessons learned during HGP, 27–37; mapping phase of HGP and, 19–20; Oral History Collection, 266; organizational complexity of, xviii, xix, 27; racial diversity initiatives, 299–300, 302, 308; required input from NACHGR, 17, 25; scope of collaborative network, 41–42; sequencing phase of HGP and, 22–27; tumor sequencing project sponsored by, 443–45. See also Cancer Genome Atlas (TCGA) Project, The; Encyclopedia of DNA Elements (ENCODE) Project; Human Genome Project; International HapMap Project; National Center for Human Genome Research; Office for Human Genome Research; Sequencing cost curve; Technology development grants
National Institute of General Medical Sciences (NIGMS), 3, 4, 37n2, 126, 127, 296
National Institutes of Health (NIH): All of Us program (Precision Medicine Initiative), 218, 273–74; ARRA funding received by, 81; calls for funding and data use from large-scale projects, 473; Collins as director of, xxiii, 186; Common Fund Programs, 86, 493; communication with international agencies, 28; Consensus Development Conference, 234; DOE collaboration with, 6–7, 14, 17, 30, 35, 126; GenBank, 24, 250–51, 253, 270, 471, 480; Genomic Data Sharing Policy, 236; grants awarded by, 6–7, 16–18, 29–30, 45; Healy as director of, xvii, xxvii, 10–11; political appointment of directors, 10; on public health disparities, 294–95, 307–8; racial issues deliberated by, 294–95, 311n4; research participant guidance from, xxxvii; restructuring under Trump administration, xliii; RoadMap Epigenomics Project, 80, 82, 86, 89, 154; Varmus as director of, 11, 444; Wyngaarden as director of, 4, 42. See also Human Genome Project
National Institutes of Health Revitalization Act of 1993, 297–98
National Research Council (NRC), 8, 13–15, 36, 125, 228, 252, 298
National Science Foundation (NSF), 109, 296
Native Americans, 111, 115, 298, 300, 306, 307
Nature (journal): data availability and release policies, 148–51; draft sequence published by, xxxix, xl, 145, 150–51, 160–63, 177, 187, 191n3, 264, 479; editors’ role in shaping publications, 146–47; ENCODE papers published in, 77–78, 153–54; genome papers freely available through, 151–52; at “International Data Release Meeting,” 149; microarray data standards and, 147–48; mission statement for, 145–46; relationship with genomics field, 145, 151, 155; supplementary data policy used by, 152–53; TCGA Project publications in, 153, 443, 445; “thread” innovation and, 78, 153–55
Nature Genetics (journal), 153, 302–3, 308, 311n3
NCBI (National Center for Biotechnology Information), 10, 111, 116, 488
NCDs (noncommunicable diseases), 348, 370n6
NCHGR. See National Center for Human Genome Research (NCHGR)
NCI. See National Cancer Institute
Nègre, N., 433–34n22
Next-generation sequencing (NGS) platforms: biobanks and, 275; cost point per genome and, 209; ENCODE and, 87–88; sequencing cost curve and, 46, 49, 54–59, 66; TCGA Project and, 445; technology development grants for, 134
NHGRI. See National Human Genome Research Institute
NIGMS. See National Institute of General Medical Sciences
NIH. See National Institutes of Health
Nitromed, 309, 313n22
Noncommunicable diseases (NCDs), 348, 370n6
NRC. See National Research Council
NSF (National Science Foundation), 109, 296
Nutritional epigenetics, 354–55

Office for Human Genome Research (OHGR): creation of, 37n2; evolution into NCHGR, 3, 37n2, 43, 139n1; Jordan as deputy director of, 127; Watson as director of, 165, 188. See also Human Genome Project; National Center for Human Genome Research (NCHGR); National Human Genome Research Institute
Office of Technology Assessment, 8, 42, 125, 228
Oliver, S. G., 220
Olson, Maynard, xviii–xix, 21, 166–67, 183, 251, 255–56, 260–62
1000 Genomes Project: community consultation in, 116, 119, 239–40; comprehensive aims of, xli–xlii; cost point per genome for, 212, 222–23n7; Data Coordination Center for, 119; ELSI Program and, 240; Genetic Variation Program and, 118–20; Genome-Wide Association Studies and, 118, 120; haplotypes and, 119, 120; objections to, 222–23n7; race and, xxxi, 293; research questions associated with, 212; selection of populations for inclusion in, 119; single nucleotide polymorphisms and, 119–20; supplementary information document from main paper on, 152; technology development and, 63; tracking of data production from, 59; working groups for, 119
Optical mapping, 137–38, 219
Oxford Nanopore Technologies (ONT), 49, 66, 139, 219

Pacific Biosciences, 49, 66, 137, 219
Palazzo, A. F., 422
Pan-Cancer Atlas project, 447, 448
Panofsky, Aaron, 310, 312n10, 323
Parolini, Giuditta, 165
Past-present ambiguity, 411, 413, 427
Patents: Bermuda Principles and, 9; cooperative agreements and, 45; ELSI Program and, 231; for expressed sequence tags, xvii, 10, 182, 185; HapMap Project and, 117; Venter on, 182, 185, 195n24; Watson on, xvii, 10, 479
PDR (Polymorphism Discovery Resource), 110–12, 299–300, 312n12
Pearson, Peter, 173
Personalized medicine, xxix, 268, 271, 274, 276, 382
Pharmacogenomics, xxix, 269, 279, 284–85, 303–5, 309, 313n17
Phenotypic plasticity, 367, 383–84
Pheomelanin, 384, 386
Phillippy, Adam, xl
Phred scores, 33, 253, 255, 258
Physical mapping: of C. elegans, 183, 184; chromosome workshops and, 168, 171, 173; circumscription of datasets for, xxxiv; clone libraries for use in, 131; EUROGEM and, 176; GESTEC funding for, 18–19; NRC on desirability of, 13; quality control measures for, 21–22; Sequence-Tagged Sites and, 21, 177; technology development and, 126, 128, 131, 138; of yeast, xviii, 166, 183
Plomin, Robert, 388–90, 392–93, 395–98
Polygenic scores, 322, 396–99
Polymer physics-based studies, 136–38
Polymorphism Discovery Resource (PDR), 110–12, 299–300, 312n12
Polymorphisms: absence in simple sequence repeats, 259; errors distinguished from, xxxiv, 250, 251, 254–61; population genetics and, 209, 249; restriction fragment length, 19, 209, 257. See also Single nucleotide polymorphisms
Population genetics, 109, 208–9, 249, 319
Postgenomics, xxvi, xxxi–xlii, 163, 189, 340–41
Precision medicine: African Americans and, 309; biobanks and, 271, 273, 274; continuous medicine and, 275; CSER and ClinGen for, 282; as public health priority, 273–74; research clinics as key sites for, 271, 287; as scientific paradigm, 268, 287–88; TCGA Project and, 443
Precision Medicine Initiative (All of Us program), 218, 273–74
Privacy issues: donors and, 116, 118, 299, 300; electronic health records and, 278; genetic records and, xxvii; stored tissue samples and, 236

Quake, Stephen, 138

Rabago-Smith, M., 385
Race, 293–311; in biomedicine, 294, 298, 303, 307, 308, 310–11; conflation of ancestral geography with, 115; continental groupings of, xxix, xxx, 297–99, 306, 310, 312nn7–10; ELSI Program studies on, 299, 301–2, 312–13n13; folk beliefs and categories of, xxx, 238, 239; HapMap Project and, xxxi, 293, 306–7; inclusion in genetic research, 295–302, 305–11, 311n1; intelligence and hierarchy of, 390; 1000 Genomes Project and, xxxi, 293; pharmacogenomics and, 303–5, 309, 313n17; as proxy for human variation, 293, 294, 303; public health disparities and, 294–95, 305, 308, 313n20; reductionistic accounts of, xxviii–xxxii, xliii; US federal taxonomy for, 294–95, 297–99, 305–7, 310, 311n4, 312nn10–11. See also specific racial groups
Racism: biological effects of, 294, 311, 313n25; genomic medicine and, xxix; HGDP data interpretations and, 298; institutionalized, 384; intelligence and, xxvii, 384, 391; legacy of, xliii, xliv; persistence in genetics and genomics, xliii; scientific, xxviii, xxix, xliii; skin color and, 384, 387
Reardon, J., xxxi–xxxii
Rechsteiner, M. C., 480, 481
Reductionism: causal, 367; definition of, 380; genetic, xxxi, 191, 318, 379, 381–82; HGP and, xxvi, xxviii–xxxi, xxxiii–xxxv, 381; molecular biology and, 380–81; postgenomics as break from, xxxii; race and, xxviii–xxxii, xliii; scientific, 349, 370n10
Reference Library System, 177, 180
Reilly, Steven, 329
Responsible Research and Innovation framework, 331–32
Restriction fragment length polymorphisms (RFLPs), 19, 209, 257
Reynolds number, 426
Rheinberger, H.-J., 359, 475, 480
Ribonucleic acid. See RNA
Rice, W. R., 320
Richardson, K., 390
Richardson, S. S., xxxii
Riken Institute (Japan), xxix, 191n7
Risch, Neil, 330
RNA (ribonucleic acid): isoforms and, 71, 88; messenger, xvii, 482; micro, 420, 448; non-coding, 79, 363, 417, 418; transcription of DNA into, 71, 76, 417, 418
RoadMap Epigenomics Project, 80, 82, 86, 89, 154
Rose, N., 361
Rosenberg, N. A., 397
Rotimi, Charles, 115, 308, 309
Roundworm. See Caenorhabditis elegans
Ruddle, Frank, 168, 169, 172
Russell, Camisha, xliii
Rutherford, Ernest, 220, 224n18

Saccharomyces cerevisiae. See Yeast
Same-sex sexual behavior: conversion therapies for, 328; genetics of, 318, 320, 322, 328–30; “third sex” concept and, 320. See also Sexual orientation
Sanger Centre (United Kingdom): establishment of, 184, 479; as G5 sequencing center, 161, 187; HUGO’s divergent approach from, 196n29; research programs in cancer genomics at, 446; SNP Consortium and, 313n18; Wellcome Trust funding of, 7, 184, 195–96n27, 196n30; yeast genome sequencing by, 164, 191n7, 192n9
SCD (sickle cell disease), 92–93, 299
Schaffner, K. F., 353
Schneider, William, 232, 238
Schwartz, David C., 137–38
Schwartz, Y. B., 433–34n22
Science (journal), 75–76, 150–51, 190n2, 293, 300, 318, 330, 479
Scientific publications, 145–55; author contribution statements in, 147; big data and, 146, 147; consortia-authored papers and, 147, 153–55; data availability and release issues for, 148–51; editors’ role in, 145–47; future outlook for, 155; marker papers and, 84, 88, 90, 94, 149, 449, 451, 453; microarray data and, 147–48; peer review and, 146, 148–49. See also specific publications
Scientific racism, xxviii, xxix, xliii
Scientific reductionism, 349, 370n10
Second-generation sequencing platforms. See Next-generation sequencing (NGS) platforms
Selected-effects (SE) account of function, 407, 409–14, 416, 431nn6–8
Sequence-Tagged Sites (STSs), 21, 177, 180
Sequencing Advisory Committee, 23–24, 26, 36
Sequencing centers: administration of, 23–24, 26; draft sequence generated by, 25, 27, 160, 161, 191n3; funding for, 7, 25, 33, 46, 161, 166, 184–86, 195–96n27; future outlook for, 221–22; G5, xxxviii, 161–63, 174, 177, 182, 187, 191n3, 195n24; Phred score adopted by, 33; progress reports from, 23, 24, 26, 52–55, 59–61; quality control measures for, 23–24, 33–34; yeast genome sequencing and, 166–67, 192n9. See also Large-Scale Sequencing and Analysis Centers; specific sequencing centers
Sequencing cost curve, 41–66; actual project costs compared to, 62–63; changes in reporting over periods of large-scale sequencing, 51–61; in commercial vs. research and development setting, 63–64; definition and description of, 41; experience curve effects, 44; future of cost tracking, 65–66; graph components for, 46–51; history of cost estimates and tracking, 42–45; methodological considerations, 46–61; sequencing platforms and, 46, 49, 54–59, 61, 62, 66; success of genomics field represented by, 64–65; technology development and, 41, 50, 51, 53–55, 62
SES (socioeconomic status), 351, 354, 356–58, 371n11
Sexual orientation, 318–33; categorization of, 322; discrimination based on, 324–25, 330; fraternal birth order effect and, 321, 322; genetics of, 318, 320–25, 328–33; Genome-Wide Association Studies on, 318, 320–32; maternal immune mechanism and, 321; socially responsible research on, 319–20, 323–25, 328. See also Same-sex sexual behavior
Shendure, Jay, 87
Sickle cell disease (SCD), 92–93, 299
Single nucleotide polymorphisms (SNPs): definition and description of, 112; genetic contribution to disease and, xli; Genome-Wide Association Studies and, 93, 257, 321–22; HapMap Project and, 113–14, 117, 118, 257; linkage disequilibrium and, 113–14, 118, 258; occupational/educational attainment and, xliii; 1000 Genomes Project and, 119–20; variation in, xliii, 112, 254, 258, 260
Sinsheimer, Robert, 478
Skin color, genetics of, 386–88
Skorska, M. N., 321
Small science, xxxvi, 470–73, 480–81, 483–85, 487, 493
SNP Consortium, xxxi, 257–58, 293, 305–6, 313n18
SNPs. See Single nucleotide polymorphisms
Social epidemiology: definition of, 341, 349–50; historical rise of, 343–45, 348; integration of epigenetics into, 349, 350, 366–68; molecular biology and, 341; “the social” in, 349–53, 358; style of reasoning specific to, 366
Social epigenetics, 340–42, 353–54
Social genomics (sociogenomics), xliii, 319, 322, 331
Social implications of research. See Ethical, Legal, and Social Implications (ELSI) Program
Socially responsible research, 319–20, 323–25, 328, 331–32
Socioeconomic status (SES), 351, 354, 356–58, 371n11
Spencer, Quayshawn, xxx
Stanford–Binet IQ tests, 392
Stanford DNA Sequencing and Technology Center, 166, 191n7, 313n18
Statistical genetics, 109
Sternberg, Robert, 390
Stevens, H., xxxii
Stoddard, Charlotte, 154
Stored tissue samples, 235–37
Strasser, B. J., 441, 480, 481
Stratton, M. R., 455
Structural genomics, 405, 430n1
Structural variants (SVs): in cancer genome, 137, 223n9, 451; cost considerations and, 219, 220; in disease architecture, 259, 260; measurement challenges, 250, 251, 254–55, 259, 262; 1000 Genomes Project working group for, 119; single nucleotide polymorphisms and, 112
STSs (Sequence-Tagged Sites), 21, 177, 180
Styles of reasoning, 365–66
Sulston, John, 22–23, 182–87, 195n25, 196n29
Sussman, Hillary, 154
SVs. See Structural variants
Systems biology, 495n8
Szymanski, Erika, 167

TCGA Project. See Cancer Genome Atlas (TCGA) Project, The
Team science, 20, 446
Technology development: CEGS program and, 135–36; for counting applications, 222n2; data production and, 130, 139; Department of Energy and, 6, 479; ENCODE and, 73, 77, 82, 85–88, 131; genome mapping and, 126, 128, 131, 138; genome sequencing and, xxii, xxiv, 41, 125–29, 134, 138–39; HGP and, 8, 16, 29, 32, 35, 124–35, 139; multidisciplinary approach to, 125–27; 1000 Genomes Project and, 63; peer review and, 125, 127–28, 133; scientific advances in relation to, 203; sequencing cost curve and, 41, 50, 51, 53–55, 62. See also Next-generation sequencing (NGS) platforms
Technology development grants, 124–39; calls for proposals for, 126–27; career award program and, 129; criteria for, 128–29; ENCODE and, 87, 131; FOAs for, 126–28, 132–35, 137, 139; GESTECs and, 18–19, 127–30; HGP and, 124, 126–28; investigator-initiated, 132–33, 136, 138; for nanopore sequencing, 138–39; peer review and, 127–28, 133; for polymer physics-based studies, 136–38; for single-molecule sequencing, 138
Telomere-to-Telomere Consortium (T2T), xxxiii
Terman, Lewis, 391
Thalassemia, 92–93, 299
Thomson, Elizabeth, xxvii, xxxvii, 232, 234
TIGR (The Institute for Genome Research), 181–82
TOPMed program (National Heart Lung and Blood Institutes), 216
Trastuzumab (Herceptin), 284, 446
Turner, Stephen W., 137
23andMe, 273, 284, 324, 330, 332

United Kingdom: biobank launched in, 271; Human Genome Mapping Project, 177, 180–81, 184; Medical Research Council, 22, 28, 184; Resource Centre, 180–82, 194n22. See also Sanger Centre; Wellcome Trust
United Nations Educational, Science, and Culture Organization (UNESCO), 298
University of Tokyo, 192n9

Varmus, Harold, 11, 444
Venter, Craig: as CEO of Celera, 160, 190n2, 300–301, 479; expressed sequence tags and, 10, 182, 185; patenting efforts of, 182, 185, 195n24; on race, 301, 302; TIGR led by, 181–82
Vitti, Joe, 329–30
Von Stumm, S., 393, 396, 397

Washington University Genome Sequencing Center, 119, 161, 166–67, 183–84, 187, 191n7, 313n18, 444
Wasserman, David, 232
Waters, C. K., 496n11
Waterston, Robert, 22–23, 182–87
Watson, James: on C. elegans genome sequencing, 183, 184, 188; as co-discoverer of DNA structure, 183, 188, 191n5; as CSHL director, 165; Healy’s firing of, xvii; HUGO established by, 7; as OHGR director, 165, 188; paper on complete genome sequence of, 148; in patenting controversy, xvii, 10, 479; proposal for ELSI Program, xxvii, 5, 228; publicity campaign for HGP led by, xxi, 5, 6; recruitment for HGP, 8; on whole-genome sequencing, 159, 172; on yeast genome sequencing, 165–67, 188
Webb, Watt, 137
Wedow, Robbee, 324, 333–34n2
Weinberg, R., 480
Welch, John, 458, 465n9
Wellcome Trust (United Kingdom): chromosome workshops sponsored by, 186, 187, 196n30; genome mapping supported by, 159, 172; HapMap Project and, 114; “International Data Release Meeting” sponsored by, 149; NIH communication with, 28; racial diversity initiatives, 309; sequencing centers funded by, 7, 33, 161, 184–86, 195–96n27
Wexler, Nancy, 7
White, D., 385
Whitehead Institute, 161, 187, 313n18
Women: inclusion in genetic research, 294, 297, 299; maternal immune mechanism in, 321; task forces on health of, 295. See also Gender
World Health Organization, 370n6
Wyngaarden, James, 4, 10, 42

Yang, Henry, 115
Yeast: artificial chromosomes and, 21; genome sequencing of, xviii, 53, 163–67, 172–74, 184, 188, 191n7, 192n9; modENCODE and, 80; physical mapping of, xviii, 166, 183

Zinder, Norton, 8

Show the following:

Adjust appearance:

Notes

Index

Annotate