Abstract
Calendar age is the major risk factor for common disease. It is therefore expected that understanding the aging process will eventually lead to promotion of better health conditions in elderly populations. Such insight may be obtained by identifying the genetic determinants of familial and exceptional longevity and age-related disease. Research of these determinants has been performed in candidate gene, genome-wide association and linkage studies. Because exploration of the common variation in the genome did not explain much of the variation in the rate of aging and longevity, researchers in the field have only recently started to investigate the contribution of rare genetic variants to these traits. The increased throughput and decreased costs of next generation sequencing (NGS) have resulted in a great deal of novel applications for sequencing sets of candidate genes, whole exomes, and whole genomes of individuals. Most of the successful NGS applications are as yet those focused on genetic syndromes and cancers for which causal mutations are readily being identified. In this chapter, we discuss the genetic and phenomic aspects of human aging research and the use of NGS data to identify genes relevant for age-related diseases and lifespan regulation, and to investigate the accumulation of somatic genetic variation during the course of life.
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Abbreviations
- NGS:
-
next generation sequencing
- GWAS:
-
genome-wide association studies
- LOAD:
-
late-onset Alzheimer’s disease
- FOA:
-
familial generalised osteoarthritis
- SKAT:
-
sequence kernel association test
- BBMRI-NL:
-
Biobanking and Biomolecular Resources Research Infrastructure of the Netherlands
References
Oeppen J, Vaupel JW (2002) Demography. Broken limits to life expectancy. Science 296(5570):1029–1031 (PubMed PMID: 12004104)
Hitt R, Young-Xu Y, Silver M, Perls T (1999) Centenarians: the older you get, the healthier you have been. Lancet 354(9179):652 (PubMed PMID: 10466675)
Kirkwood TB, Austad SN (2000) Why do we age? Nature 408(6809):233–238 (PubMed PMID: 11089980)
Kirkwood TB (1977) Evolution of ageing. Nature 270(5635):301–304 (PubMed PMID: 593350)
Lopez-Otin C, Blasco MA, Partridge L, Serrano M, Kroemer G (2013) The hallmarks of aging. Cell 153(6):1194–1217 (PubMed PMID: 23746838. Pubmed Central PMCID: 3836174)
Jones OR, Scheuerlein A, Salguero-Gomez R, Camarda CG, Schaible R, Casper BB et al (2014) Diversity of ageing across the tree of life. Nature 505(7482):169–173 (PubMed PMID: 24317695)
Navarro CL, Cau P, Levy N (2006) Molecular bases of progeroid syndromes. Hum Mol Genet 15(Spec No 2):R151–161 (PubMed PMID: 16987878)
Perls TT, Wilmoth J, Levenson R, Drinkwater M, Cohen M, Bogan H et al (2002) Life-long sustained mortality advantage of siblings of centenarians. Proc Natl Acad Sci U S A 99(12):8442–8447 (PubMed PMID: 12060785. Pubmed Central PMCID: 123086)
Terry DF, Wilcox MA, McCormick MA, Pennington JY, Schoenhofen EA, Andersen SL et al (2004) Lower all-cause, cardiovascular, and cancer mortality in centenarians’ offspring. J Am Geriatr Soc 52(12):2074–2076 (PubMed PMID: 15571545)
Westendorp RG, van Heemst D, Rozing MP, Frolich M, Mooijaart SP, Blauw GJ et al (2009) Nonagenarian siblings and their offspring display lower risk of mortality and morbidity than sporadic nonagenarians: the leiden longevity study. J Am Geriatr Soc 57(9):1634–1637 (PubMed PMID: 19682117)
Schoenmaker M, de Craen AJ, de Meijer PH, Beekman M, Blauw GJ, Slagboom PE et al (2006) Evidence of genetic enrichment for exceptional survival using a family approach: the Leiden longevity study. Eur J Hum Genet 14(1):79–84 (PubMed PMID: 16251894)
Skytthe A, Pedersen NL, Kaprio J, Stazi MA, Hjelmborg JV, Iachine I et al (2003) Longevity studies in GenomEUtwin. Twin Res 6(5):448–454 (PubMed PMID: 14624729)
Herskind AM, McGue M, Holm NV, Sorensen TI, Harvald B, Vaupel JW (1996) The heritability of human longevity: a population-based study of 2872 Danish twin pairs born 1870–1900. Hum Genet 97(3):319–323 (PubMed PMID: 8786073)
Skytthe A, Valensin S, Jeune B, Cevenini E, Balard F, Beekman M et al (2011) Design, recruitment, logistics, and data management of the GEHA (Genetics of Healthy Ageing) project. Exp Gerontol 46(11):934–945 (PubMed PMID: 21871552. Pubmed Central PMCID: 3622890)
Gatz M, Reynolds CA, Fratiglioni L, Johansson B, Mortimer JA, Berg S et al (2006) Role of genes and environments for explaining Alzheimer disease. Arch Gen Psychiatry 63(2):168–174 (PubMed PMID: 16461860)
Fischer M, Broeckel U, Holmer S, Baessler A, Hengstenberg C, Mayer B et al (2005) Distinct heritable patterns of angiographic coronary artery disease in families with myocardial infarction. Circulation 111(7):855–862 (PubMed PMID: 15710764)
Newman AB, Glynn NW, Taylor CA, Sebastiani P, Perls TT, Mayeux R et al (2011) Health and function of participants in the long life family study: a comparison with other cohorts. Aging 3(1):63–76 (PubMed PMID: 21258136. Pubmed Central PMCID: 3047140)
Lai JY, Atzmon G, Melamed ML, Hostetter TH, Crandall JP, Barzilai N et al (2012) Family history of exceptional longevity is associated with lower serum uric acid levels in Ashkenazi Jews. J Am Geriatr Soc 60(4):745–750 (PubMed PMID: 22429185. Pubmed Central PMCID: 3325371)
De Rango F, Dato S, Bellizzi D, Rose G, Marzi E, Cavallone L et al (2008) A novel sampling design to explore gene-longevity associations: the ECHA study. Eur J Hum Genet 16(2):236–242 (PubMed PMID: 17989723)
Perls TT, Bochen K, Freeman M, Alpert L, Silver MH (1999) Validity of reported age and centenarian prevalence in New England. Age Ageing 28(2):193–197 (PubMed PMID: 10350418)
Styrkarsdottir U, Thorleifsson G, Helgadottir HT, Bomer N, Metrustry S, Bierma-Zeinstra S et al (2014) Severe osteoarthritis of the hand associates with common variants within the ALDH1A2 gene and with rare variants at 1p31. Nat Genet 46(5):498–502 (PubMed PMID: 24728293)
Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, Lango H et al (2007) Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 316(5829):1336–1341 (PubMed PMID: 17463249. Pubmed Central PMCID: 3772310)
Willcox BJ, Donlon TA, He Q, Chen R, Grove JS, Yano K et al (2008) FOXO3A genotype is strongly associated with human longevity. Proc Natl Acad Sci U S A 105(37):13987–13992 (PubMed PMID: 18765803. Pubmed Central PMCID: 2544566)
Flachsbart F, Caliebe A, Kleindorp R, Blanche H, von Eller-Eberstein H, Nikolaus S et al (2009) Association of FOXO3A variation with human longevity confirmed in German centenarians. Proc Natl Acad Sci U S A 106(8):2700–2705 (PubMed PMID: 19196970. Pubmed Central PMCID: 2650329)
Pawlikowska L, Hu D, Huntsman S, Sung A, Chu C, Chen J et al (2009) Association of common genetic variation in the insulin/IGF1 signaling pathway with human longevity. Aging Cell 8(4):460–472 (PubMed PMID: 19489743. Pubmed Central PMCID: 3652804)
Soerensen M, Dato S, Christensen K, McGue M, Stevnsner T, Bohr VA et al (2010) Replication of an association of variation in the FOXO3A gene with human longevity using both case-control and longitudinal data. Aging Cell 9(6):1010–1017 (PubMed PMID: 20849522. Pubmed Central PMCID: 2992870)
Schachter F, Faure-Delanef L, Guenot F, Rouger H, Froguel P, Lesueur-Ginot L et al (1994) Genetic associations with human longevity at the APOE and ACE loci. Nat Genet 6(1):29–32 (PubMed PMID: 8136829)
Christensen K, Johnson TE, Vaupel JW (2006) The quest for genetic determinants of human longevity: challenges and insights. Nat Rev Genet 7(6):436–448 (PubMed PMID: 16708071. Pubmed Central PMCID: 2726954)
Deelen J, Beekman M, Uh HW, Helmer Q, Kuningas M, Christiansen L et al (2011) Genome-wide association study identifies a single major locus contributing to survival into old age; the APOE locus revisited. Aging Cell 10(4):686–898 (PubMed PMID: 21418511. Pubmed Central PMCID: 3193372)
Nebel A, Kleindorp R, Caliebe A, Nothnagel M, Blanche H, Junge O et al (2011) A genome-wide association study confirms APOE as the major gene influencing survival in long-lived individuals. Mech Ageing Dev 132(6–7):324–330 (PubMed PMID: 21740922)
Sebastiani P, Solovieff N, Dewan AT, Walsh KM, Puca A, Hartley SW et al (2012) Genetic signatures of exceptional longevity in humans. PloS One 7(1):e29848 (PubMed PMID: 22279548. Pubmed Central PMCID: 3261167)
Deelen J, Beekman M, Uh HW, Broer L, Ayers KL, Tan Q et al (2014) Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age. Hum Mol Genet 23(16):4420–4432 (PubMed PMID: 24688116)
Walter S, Atzmon G, Demerath EW, Garcia ME, Kaplan RC, Kumari M et al (2011) A genome-wide association study of aging. Neurobiol Aging 32(11):2109 e15–28 (PubMed PMID: 21782286. Pubmed Central PMCID: 3193030)
Lambert JC, Ibrahim-Verbaas CA, Harold D, Naj AC, Sims R, Bellenguez C et al (2013) Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease. Nat Genet 45(12):1452–1458 (PubMed PMID: 24162737. Pubmed Central PMCID: 3896259)
Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H et al (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337(6099):1190–1195 (PubMed PMID: 22955828. Pubmed Central PMCID: 3771521)
Beekman M, Nederstigt C, Suchiman HE, Kremer D, van der Breggen R, Lakenberg N et al (2010) Genome-wide association study (GWAS)-identified disease risk alleles do not compromise human longevity. Proc Natl Acad Sci U S A 107(42):18046–18049 (PubMed PMID: 20921414. Pubmed Central PMCID: 2964208)
Puca AA, Daly MJ, Brewster SJ, Matise TC, Barrett J, Shea-Drinkwater M et al (2001) A genome-wide scan for linkage to human exceptional longevity identifies a locus on chromosome 4. Proc Natl Acad Sci U S A 98(18):10505–10508 (PubMed PMID: 11526246. Pubmed Central PMCID: 56990)
Boyden SE, Kunkel LM (2010) High-density genomewide linkage analysis of exceptional human longevity identifies multiple novel loci. PloS One 5(8):e12432 (PubMed PMID: 20824210. Pubmed Central PMCID: 29308490
Edwards DR, Gilbert JR, Jiang L, Gallins PJ, Caywood L, Creason M et al (2011) Successful aging shows linkage to chromosomes 6, 7, and 14 in the Amish. Ann Hum Genet 75(4):516–528 (PubMed PMID: 21668908. Pubmed Central PMCID: 3756593)
Beekman M, Blanche H, Perola M, Hervonen A, Bezrukov V, Sikora E et al (2013) Genome-wide linkage analysis for human longevity: genetics of healthy aging study. Aging Cell 12(2):184–193 (PubMed PMID: 23286790. Pubmed Central PMCID: 3725963)
Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A et al (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature 452(7189):872–876 (PubMed PMID: 18421352)
Ng PC, Henikoff S (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res 31(13):3812–3814 (PubMed PMID: 12824425. Pubmed Central PMCID: 168916)
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P et al (2010) A method and server for predicting damaging missense mutations. Nat Methods 7(4):248–249 (PubMed PMID: 20354512. Pubmed Central PMCID: 2855889)
Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S (2010) Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol 6(12):e1001025 (PubMed PMID: 21152010. Pubmed Central PMCID: 2996323)
Kircher M, Witten DM, Jain P, O’Roak BJ, Cooper GM, Shendure J (2014) A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet 46(3):310–315 (PubMed PMID: 24487276. Pubmed Central PMCID: 3992975)
Maher B (2008) Personal genomes: the case of the missing heritability. Nature 456(7218):18–21 (PubMed PMID: 18987709)
MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K et al (2012) A systematic survey of loss-of-function variants in human protein-coding genes. Science 335(6070):823–828 (PubMed PMID: 22344438. Pubmed Central PMCID: 3299548)
Clancy DJ, Gems D, Harshman LG, Oldham S, Stocker H, Hafen E et al (2001) Extension of life-span by loss of CHICO, a Drosophila insulin receptor substrate protein. Science 292(5514):104–106 (PubMed PMID: 11292874)
Sebastiani P, Riva A, Montano M, Pham P, Torkamani A, Scherba E et al (2011) Whole genome sequences of a male and female supercentenarian, ages greater than 114 years. Front Genet 2:90 (PubMed PMID: 22303384. Pubmed Central PMCID: 3262222)
Ye K, Beekman M, Lameijer EW, Zhang Y, Moed MH, van den Akker EB et al (2013) Aging as accelerated accumulation of somatic variants: whole-genome sequencing of centenarian and middle-aged monozygotic twin pairs. Twin Res Hum Genet 16(6):1026–1032 (PubMed PMID: 24182360)
Han J, Ryu S, Moskowitz DM, Rothenberg D, Leahy DJ, Atzmon G et al (2013) Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing. Mech Ageing Dev 134(10):478–485 (PubMed PMID: 23376243. Pubmed Central PMCID: 3787996)
Ramos YF, Bos SD, van der Breggen R, Kloppenburg M, Ye K, Lameijer EW et al (2014) A gain of function mutation in TNFRSF11B encoding osteoprotegerin causes osteoarthritis with chondrocalcinosis. Ann Rheum Dis. doi:10.1136/annrheumdis-2013-205149 (PubMed PMID: 24743232)
Guerreiro R, Bilgic B, Guven G, Bras J, Rohrer J, Lohmann E et al (2013) Novel compound heterozygous mutation in TREM2 found in a Turkish frontotemporal dementia-like family. Neurobiol Aging 34(12):2890 e1–5 (PubMed PMID: 23870839. Pubmed Central PMCID: 3898264)
Lee S, Moore EW, Marohn JA (2012) A unified picture of cantilever frequency-shift measurements of magnetic resonance. Phys Rev B, Condens Matter Mater Phys 85(16):165447–165453 (PubMed PMID: 24523575. Pubmed Central PMCID: 3918878)
MacCluer JW, Stern MP, Almasy L, Atwood LA, Blangero J, Comuzzie AG et al (1999) Genetics of atherosclerosis risk factors in Mexican Americans. Nutr Rev 57(5 Pt 2):S59–65 (PubMed PMID: 10391028)
Tanaka D, Nagashima K, Sasaki M, Funakoshi S, Kondo Y, Yasuda K et al (2013) Exome sequencing identifies a new candidate mutation for susceptibility to diabetes in a family with highly aggregated type 2 diabetes. Mol Genet Metab 109(1):112–117 (PubMed PMID: 23499280)
Jonsson T, Atwal JK, Steinberg S, Snaedal J, Jonsson PV, Bjornsson S et al (2012) A mutation in APP protects against Alzheimer’s disease and age-related cognitive decline. Nature 488(7409):96–99 (PubMed PMID: 22801501)
Jin SC, Benitez BA, Karch CM, Cooper B, Skorupa T, Carrell D et al (2014) Coding variants in TREM2 increase risk for Alzheimer’s disease. Hum Mol Genet 23(21):5838–5846 (PubMed PMID: 24899047)
Nho K, Corneveaux JJ, Kim S, Lin H, Risacher SL, Shen L et al (2013) Whole-exome sequencing and imaging genetics identify functional variants for rate of change in hippocampal volume in mild cognitive impairment. Mol Psychiatry 18(7):781–787 (PubMed PMID: 23608917. Pubmed Central PMCID: 3777294)
Boomsma DI, Wijmenga C, Slagboom EP, Swertz MA, Karssen LC, Abdellaoui A et al (2014) The genome of the Netherlands: design, and project goals. Eur J Hum Genet 22(2):221–227 (PubMed PMID: 23714750. Pubmed Central PMCID: 3895638)
The Genome of the Netherlands C (2014) Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat Genet 46(8):818–825 (PubMed PMID: 24974849)
Curtis HJ (1963) Biological mechanisms underlying the aging process. Science 141(3582):686–694 (PubMed PMID: 14024359)
Orgel LE (1973) Ageing of clones of mammalian cells. Nature 243(5408):441–445 (PubMed PMID: 4591306)
Baranzini SE, Mudge J, van Velkinburgh JC, Khankhanian P, Khrebtukova I, Miller NA et al (2010) Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 464(7293):1351–1356 (PubMed PMID: 20428171. Pubmed Central PMCID: 2862593)
Holstege H, Pfeiffer W, Sie D, Hulsman M, Nicholas TJ, Lee CC et al (2014) Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis. Genome Res 24(5):733–742 (PubMed PMID: 24760347. Pubmed Central PMCID: 4009603)
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van den Akker, E., Deelen, J., Slagboom, P., Beekman, M. (2015). Exome and Whole Genome Sequencing in Aging and Longevity. In: Atzmon, PhD, G. (eds) Longevity Genes. Advances in Experimental Medicine and Biology, vol 847. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2404-2_6
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