Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults

Proceedings of the National Academy of Sciences of the United States of America

Volumn 115, Issue 14, 2018, Pages 3686-3691

  Perkins, Bradley A ^a   Caskey, C Thomas ^a,b   Brar, Pamila ^a   Dec, Eric ^a   Karow, David S ^a,c   Kahn, Andrew M ^a,d   Hou, Ying Chen Claire ^a   Shah, Naisha ^a   Boeldt, Debbie ^a,e   Coughlin, Erin ^a   Hands, Gabby ^a   Lavrenko, Victor ^a   Yu, James ^a   Procko, Andrea ^a   Appis, Julia ^a   Dale, Anders M ^c,f   Guo, Lining ^g   Jönsson, Thomas J ^g   Wittmann, Bryan M ^g   Bartha, Istvan ^a   Ramakrishnan, Smriti ^a   Bernal, Axel ^a   Brewer, James B ^a,f   Brewerton, Suzanne ^a   Biggs, William H ^a   Turpaz, Yaron ^a   Venter, J Craig ^a,h   more..

^a Human Longevity Inc   (United States)

^b BAYLOR COLLEGE OF MEDICINE   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e UNIVERSITY OF COLORADO   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g METABOLON INC   (United States)

^h J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Genome; Genomics; magnetic resonance imaging; Precision medicine; Screening

Indexed keywords

ADULT; AGED; AGING; ARTICLE; CHRONIC DISEASE; COHORT ANALYSIS; DIAGNOSTIC IMAGING; DISEASE ASSOCIATION; DUAL ENERGY X RAY ABSORPTIOMETRY; EARLY DIAGNOSIS; ECHOCARDIOGRAPHY; FEMALE; GENE MAPPING; GENETIC VARIABILITY; GENOMICS; HEART RHYTHM; HUMAN; MAJOR CLINICAL STUDY; MALE; METABOLOMICS; PERSONALIZED MEDICINE; PREMATURE MORTALITY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RISK ASSESSMENT; SCREENING; WHOLE BODY MRI; WHOLE GENOME SEQUENCING; CARDIOVASCULAR DISEASE; CLASSIFICATION; DISEASES; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; IMAGE PROCESSING; MIDDLE AGED; MUTATION; NEOPLASM; NEUROLOGIC DISEASE; PATHOLOGY; PROCEDURES; SEQUENCE ANALYSIS; VERY ELDERLY; YOUNG ADULT;

ADULT; AGED; AGED, 80 AND OVER; CARDIOVASCULAR DISEASES; DISEASE; FEMALE; GENETIC PREDISPOSITION TO DISEASE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MALE; MIDDLE AGED; MUTATION; NEOPLASMS; NERVOUS SYSTEM DISEASES; PRECISION MEDICINE; RISK ASSESSMENT; SEQUENCE ANALYSIS, RNA; WHOLE GENOME SEQUENCING; YOUNG ADULT;

EID: 85044862700     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1706096114     Document Type: Article

References (63)

1. Olshansky SJ (2016) Articulating the case for the longevity dividend. Cold Spring Harb Perspect Med 6:a025940.
2. Bauer UE, Briss PA, Goodman RA, Bowman BA (2014) Prevention of chronic disease in the 21st century: Elimination of the leading preventable causes of premature death and disability in the USA. Lancet 384:45–52.
3. Cirulli ET, Goldstein DB (2010) Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11:415–425.
4. Manolio TA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461:747–753.
5. Vogelstein B, et al. (2013) Cancer genome landscapes. Science 339:1546–1558.
6. Murray CJ, et al.; US Burden of Disease Collaborators (2013) The state of US health, 1990-2010: Burden of diseases, injuries, and risk factors. JAMA 310:591–608.
7. Benziger CP, Roth GA, Moran AE (2016) The global burden of disease study and the preventable burden of NCD. Glob Heart 11:393–397.
8. Levy S, et al. (2007) The diploid genome sequence of an individual human. PLoS Biol 5: e254.
9. Telenti A, et al. (2016) Deep sequencing of 10,000 human genomes. Proc Natl Acad Sci USA 113:11901–11906.
10. Ashley EA, et al. (2010) Clinical assessment incorporating a personal genome. Lancet 375:1525–1535.
11. Gonzalez-Garay ML, McGuire AL, Pereira S, Caskey CT (2013) Personalized genomic disease risk of volunteers. Proc Natl Acad Sci USA 110:16957–16962.
12. Guo L, et al. (2015) Plasma metabolomic profiles enhance precision medicine for volunteers of normal health. Proc Natl Acad Sci USA 112:E4901–E4910.
13. Caskey CT, Gonzalez-Garay ML, Pereira S, McGuire AL (2014) Adult genetic risk screening. Annu Rev Med 65:1–17.
14. Ashley EA (2016) Towards precision medicine. Nat Rev Genet 17:507–522.
15. Green RC, et al.; CSER Consortium (2016) Clinical sequencing exploratory research consortium: Accelerating evidence-based practice of genomic medicine. Am J Hum Genet 99:246.
16. Patel CJ, et al. (2013) Whole genome sequencing in support of wellness and health maintenance. Genome Med 5:58.
17. Holland D, Brewer JB, Hagler DJ, Fennema-Notestine C, Dale AM; Alzheimer’s Disease Neuroimaging Initiative (2009) Subregional neuroanatomical change as a biomarker for Alzheimer’s disease. Proc Natl Acad Sci USA 106:20954–20959, and erratum (2010) 107:6551.
18. erratum (2010) 107:6551.
19. Brunsing RL, et al. (2017) Restriction spectrum imaging: An evolving imaging biomarker in prostate MRI. J Magn Reson Imaging 45:323–336.
20. West J, et al. (2016) Feasibility of MR-based body composition analysis in large scale population studies. PLoS One 11:e0163332.
21. Long T, et al. (2017) Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites. Nat Genet 49:568–578.
22. Evans AMBB, et al. (2014) High resolution mass spectrometry improves data quantity and quality as compared to unit mass resolution mass spectrometry in high-throughput profiling metabolomics. Metabolomics 4:132.
23. Cobb J, et al. (2013) A novel fasting blood test for insulin resistance and prediabetes. J Diabetes Sci Technol 7:100–110.
24. Evans JP, Berg JS, Olshan AF, Magnuson T, Rimer BK (2013) We screen newborns, don’t we?: Realizing the promise of public health genomics. Genet Med 15:332–334.
25. CDC (2008) Impact of expanded newborn screening—United States, 2006. Morb Mortal Wkly Rep 57:1012–1015.
26. Schork AJ, et al.; Tobacco and Genetics Consortium; Bipolar Disorder Psychiatric Genomics Consortium; Schizophrenia Psychiatric Genomics Consortium (2013) All SNPs are not created equal: Genome-wide association studies reveal a consistent pattern of enrichment among functionally annotated SNPs. PLoS Genet 9:e1003449.
27. Richards S, et al.; ACMG Laboratory Quality Assurance Committee (2015) Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 17:405–424.
28. Kalia SS, et al. (2017) Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): A policy statement of the American College of Medical Genetics and Genomics. Genet Med 19:249–255.
29. Jethva R, Bennett MJ, Vockley J (2008) Short-chain acyl-coenzyme A dehydrogenase deficiency. Mol Genet Metab 95:195–200.
30. Corydon MJ, et al. (1996) Ethylmalonic aciduria is associated with an amino acid variant of short chain acyl-coenzyme A dehydrogenase. Pediatr Res 39:1059–1066.
31. Gieger C, et al. (2008) Genetics meets metabolomics: A genome-wide association study of metabolite profiles in human serum. PLoS Genet 4:e1000282.
32. Suhre K, et al.; CARDIoGRAM (2011) Human metabolic individuality in biomedical and pharmaceutical research. Nature 477:54–60.
33. Shin SY, et al.; Multiple Tissue Human Expression Resource (MuTHER) Consortium (2014) An atlas of genetic influences on human blood metabolites. Nat Genet 46: 543–550.
34. Beardmore TD, Kelley WN (1971) Mechanism of allopurinol-mediated inhibition of pyrimidine biosynthesis. J Lab Clin Med 78:696–704.
35. Chamberlain JJ, Rhinehart AS, Shaefer CF, Jr, Neuman A (2016) Diagnosis and management of diabetes: Synopsis of the 2016 American Diabetes Association Standards of Medical Care in Diabetes. Ann Intern Med 164:542–552.
36. Grundy SM, et al.; American Heart Association; National Heart, Lung, and Blood Institute (2005) Diagnosis and management of the metabolic syndrome: An American Heart Association/National Heart, Lung, and Blood Institute scientific statement. Circulation 112:2735–2752.
37. Angulo P, et al. (2007) The NAFLD fibrosis score: A noninvasive system that identifies liver fibrosis in patients with NAFLD. Hepatology 45:846–854.
38. Weiner C (2014) Anticipate and communicate: Ethical management of incidental and secondary findings in the clinical, research, and direct-to-consumer contexts (December 2013 report of the Presidential Commission for the Study of Bioethical Issues). Am J Epidemiol 180:562–564.
39. Manrai AK, Bhatia G, Strymish J, Kohane IS, Jain SH (2014) Medicine’s uncomfortable relationship with math: Calculating positive predictive value. JAMA Intern Med 174: 991–993.
40. Konings IC, et al.; Dutch Research Group on Pancreatic Cancer Surveillance in High-Risk Individuals (2017) Prevalence and progression of pancreatic cystic precursor lesions differ between groups at high risk of developing pancreatic cancer. Pancreas 46: 28–34.
41. Etminan N, Rinkel GJ (2017) Unruptured intracranial aneurysms: Development, rupture and preventive management. Nat Rev Neurol 13:126.
42. Katsanis N (2016) The continuum of causality in human genetic disorders. Genome Biol 17:233.
43. Manrai AK, Ioannidis JP, Kohane IS (2016) Clinical genomics: From pathogenicity claims to quantitative risk estimates. JAMA 315:1233–1234.
44. Boyle EA, Li YI, Pritchard JK (2017) An expanded view of complex traits: From polygenic to omnigenic. Cell 169:1177–1186.
45. Marouli E, et al.; EPIC-InterAct Consortium; CHD Exome+ Consortium; ExomeBP Consortium; T2D-Genes Consortium; GoT2D Genes Consortium; Global Lipids Genetics Consortium; ReproGen Consortium; MAGIC Investigators (2017) Rare and low-frequency coding variants alter human adult height. Nature 542:186–190.
46. di Iulio J, et al. (2016) The human functional genome defined by genetic diversity, bioRxiv:10.1101/082362.
47. Telenti A, Perkins BA, Venter JC (2016) Dynamics of an aging genome. Cell Metab 23: 949–950.
48. Ference BA, et al. (2016) Variation in PCSK9 and HMGCR and risk of cardiovascular disease and diabetes. N Engl J Med 375:2144–2153.
49. Desikan RS, et al. (2016) Personalized genetic assessment of age associated Alz-heimers disease risk. bioRxiv:10.1101/074864.
50. Ellinghaus D, et al.; International IBD Genetics Consortium (IIBDGC); International Genetics of Ankylosing Spondylitis Consortium (IGAS); International PSC Study Group (IPSCSG); Genetic Analysis of Psoriasis Consortium (GAPC); Psoriasis Association Genetics Extension (PAGE) (2016) Analysis of five chronic inflammatory diseases identifies 27 new associations and highlights disease-specific patterns at shared loci. Nat Genet 48: 510–518.
51. Loscalzo J, Kohane I, Barabasi AL (2007) Human disease classification in the post-genomic era: A complex systems approach to human pathobiology. Mol Syst Biol 3:124.
52. Hibar DP, et al. (2017) Novel genetic loci associated with hippocampal volume. Nat Commun 8:13624.
53. Zhang Z, Huang H, Shen D; Alzheimer’s Disease Neuroimaging Initiative (2014) Integrative analysis of multi-dimensional imaging genomics data for Alzheimer’s disease prediction. Front Aging Neurosci 6:260.
54. CMS (2012) Chronic Conditions among Medicare Beneficiaries, Chartbook (Department of Health and Human Services, Baltimore).
55. Shieh Y, et al.; Athena Breast Health Network Investigators (2017) Breast cancer screening in the precision medicine era: Risk-based screening in a population-based trial. J Natl Cancer Inst 109:djw290.
56. Tripepi G, Jager KJ, Dekker FW, Zoccali C (2010) Stratification for confounding–part 2: Direct and indirect standardization. Nephron Clin Pract 116:c322–c325.
57. GBD 2015 Mortality and Causes of Death Collaborators (2016) Global, regional, and national life expectancy, all-cause mortality, and cause-specific mortality for 249 causes of death, 1980-2015: A systematic analysis for the Global Burden of Disease Study 2015. Lancet 388:1459–1544.
58. DeFronzo RA, Tobin JD, Andres R (1979) Glucose clamp technique: A method for quantifying insulin secretion and resistance. Am J Physiol 237:E214–E223.
59. Ferrannini E, et al. (2013) Early metabolic markers of the development of dysglycemia and type 2 diabetes and their physiological significance. Diabetes 62:1730–1737.
60. Gall WE, et al.; RISC Study Group (2010) Alpha-hydroxybutyrate is an early biomarker of insulin resistance and glucose intolerance in a nondiabetic population. PLoS One 5: e10883.
61. Tripathy D, et al. (2015) A novel insulin resistance index to monitor changes in insulin sensitivity and glucose tolerance: The ACT NOW study. J Clin Endocrinol Metab 100: 1855–1862.
62. Lloyd-Jones DM, et al. (2017) Estimating longitudinal risks and benefits from cardiovascular preventive therapies among medicare patients: The million hearts longitudinal ASCVD risk assessment tool: A special report from the American Heart Association and American College of Cardiology. J Am Coll Cardiol 69:1617–1636.
63. Landrum MJ, et al. (2016) ClinVar: Public archive of interpretations of clinically relevant variants. Nucleic Acids Res 44:D862–D868.