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Genetics of common complex diseases: a view from Iceland

  • David O. Arnar
    Correspondence
    Corresponding author at: Division of Cardiology, Internal Medicine Services, Landspitali – The National University Hospital of Iceland, Reykjavik, Iceland.
    Affiliations
    Division of Cardiology, Internal Medicine Services, Landspitali – The National University Hospital of Iceland, Reykjavik, Iceland

    Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
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  • Runolfur Palsson
    Affiliations
    Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland

    Division of Nephrology, Internal Medicine Services, Landspitali – The National University Hospital of Iceland, Reykjavik, Iceland
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Published:April 20, 2017DOI:https://doi.org/10.1016/j.ejim.2017.03.018

      Highlights

      • Genetic risk variants have been discovered for >100 common complex diseases.
      • High-throughput sequencing has revolutionized the study of genomic variation in humans.
      • The availability of genotype data for the majority of Icelanders provides unique opportunities.
      • Precision medicine proposes to tailor therapy based on genetic, lifestyle and environmental data.

      Abstract

      In the past decade, large scale genotyping has led to discoveries of numerous sequence variants that confer increased risk of many common complex diseases. Interestingly, a substantial proportion of pioneering genetic work has originated from the small nation of Iceland and has been facilitated by an extensive genealogy database. We provide examples of relevant observations made so far in several major disease categories central to internal medicine practice. Some of these findings offer new mechanistic clues into the pathophysiology of common disorders and may suggest novel approaches in diagnosis and drug therapy. However, a number of unresolved issues remain that will be subject of future research, driven by recent advances in high-throughput sequencing of the genome. At the same time, we are ready to begin transforming the abundant existing genetic data into practical clinical knowledge with the aim of improving the delivery of medical care. The era of precision medicine has arrived.

      Keywords

      1. Introduction

      Common complex diseases are caused by the interaction between multiple genetic factors and environmental exposures. Over the past decade, major advances in human genetics have led to discoveries of a large number of sequence variants in DNA that associate with increased risk of more than a hundred common complex diseases. This exciting era was heralded by the completion of the Human Genome Project in 2003 [
      • International Human Genome Sequencing Consortium
      Finishing the euchromatic sequence of the human genome.
      ] and the International HapMap Project in 2005 [
      • International HapMap Consortium
      A haplotype map of the human genome.
      ], which provided effective instruments for study of genetic contributions to common diseases. These tools include public databases containing the reference human genome sequence, a map of human genetic variation and new technologies that allow quick and accurate analysis of whole-genome samples. It was the deciphering of the haplotypic structure of the human genome that made it possible to survey for common genetic variants by genotyping hundreds of thousands of single nucleotide polymorphisms (SNPs) simultaneously in large groups of individuals. The development of microarray methods for rapid genotyping greatly facilitated studies of associations of common sequence variants with complex diseases. However, these techniques are less effective for genotyping structural variants, such as insertions, deletions, inversions, and copy number variants (CNVs), which are abundant in the human genome, though not as common as SNPs.
      Genome-wide association studies (GWAS) have yielded >10,000 published associations between DNA sequence variants and human diseases and traits [
      • MacArthur J.
      • Bowler E.
      • Cerezo M.
      • Gil L.
      • Hall P.
      • Hastings E.
      • et al.
      The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).
      ]. In recent years, the advent of high-throughput sequencing of the genome has enabled identification of low-frequency and rare variants in the DNA sequence, thereby further advancing our ability to study the role of genetic factors in the pathogenesis of common complex diseases [
      • Zhang J.
      • Chiodini R.
      • Badr A.
      • Zhang G.
      The impact of next-generation sequencing on genomics.
      ]. The transition from GWAS based on common SNPs on microarrays to studies analyzing a vast number of rare variants detected by whole-genome sequencing (WGS) and whole-exome sequencing (WES) presents new opportunities and challenges alike. At the beginning of the genetic revolution, it was widely believed that rapid changes in medical practice would soon occur as enhanced understanding of the pathogenesis of many chronic diseases would lead to more effective and focused therapies which could be tailored to each individual. We are still far away from achieving this goal, although genetic research has nevertheless led to accumulation of knowledge and better understanding of the role of the human genome in health and disease.

      2. Genome-wide association studies

      The first successful GWAS, published in Science in 2005, reported two SNPs with significantly altered allele frequency in patients with age-related macular degeneration [
      • Klein R.J.
      • Zeiss C.
      • Chew E.Y.
      • Tsai J.Y.
      • Sackler R.S.
      • Haynes C.
      • et al.
      Complement factor H polymorphism in age-related macular degeneration.
      ]. Since then, GWAS have revealed numerous common sequence variants associated with a wide range of disorders frequently cared for by internists, such as coronary artery disease (CAD), atrial fibrillation (AF), type 2 diabetes (T2D), chronic kidney disease, dementia and cancer. The principle behind GWAS was to test hundreds of thousands or even more than one million common SNPs in individuals with a particular disease or trait and compare the allele distribution with control subjects. Approximately 500,000 carefully selected SNP's cover >80% of common variation in populations of European ancestry [
      • Barrett J.C.
      • Cardon L.R.
      Evaluating coverage of genome-wide association studies.
      ]. The common disease-common variant hypothesis assumes that the genetic impact on common complex diseases is attributable to a limited number of common allelic variants present in >5% of the population. Minor allele frequency (MAF) refers to the frequency at which the second most common allele occurs in a given population. It is widely used in genetic studies because it is useful for distinguishing common and rare variants in the population.
      Stringent methodology is essential for correct interpretation of GWAS data. Robust significance cut-off (P < 5 × 10−8) is necessary to avoid false positive results, due to multiple hypothesis testing (Bonferoni method) [
      • Manolio T.A.
      • Collins F.S.
      The HapMap and genome-wide association studies in diagnosis and therapy.
      ]. However, one must bear in mind that important SNP's not reaching this level of significance could potentially be missed. Very large sample sizes are frequently required to identify a SNP association with genome-wide significance. Moreover, replication of the initial discovery cohort in a separate sample of cases and controls is generally considered mandatory.
      Most of the common sequence variants detected by GWAS in various complex diseases are associated with very modest increase in risk, usually in the range of 10–40%. Age-related macular degeneration is the best example of a common complex disease, in which the heritability is largely explained by a small number of common variants with large effect sizes [
      • Black J.R.
      • Clark S.J.
      Age-related macular degeneration: genome-wide association studies to translation.
      ]. By contrast, a large fraction of the heritability remains unaccounted for in most complex diseases. Nonetheless, even small to modest genetic effects can provide insight into the pathophysiology of complex diseases. In fact, the pathobiological significance of common disease alleles appears to result from multiple sequence variants with small effects and their interactions. Thus, GWAS have led to substantial advances in understanding the variation in the genomic susceptibility to disease states. However, it should be noted that GWAS are associated with important limitations. In addition to the small or modest effect sizes, the elucidation of disease mechanisms has been hampered by many associated sequence variants falling outside of the coding regions, possibly suggesting a role in gene regulation [
      • Hindorff L.A.
      • Sethupathy P.
      • Junkins H.A.
      • Ramos E.M.
      • Mehta J.P.
      • Collins F.S.
      • et al.
      Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.
      ]. Indeed, causal variants have rarely been identified but rather susceptibility loci or genomic regions that contain one or more variants affecting disease risk. Finally, phenotypic diversity has also proved greater than initially thought.

      3. Whole-genome and whole-exome sequencing

      The GWAS era has taught us that studies of the human genome are much more complex than initially thought. Common variants with large effect sizes are very rare and rare variants with large effects are usually associated with Mendelian disorders (Fig. 1). Therefore, it is unlikely that rare variants with large effects contribute significantly to the heritability of most complex traits. On the other hand, it appears likely that a number of rare (MAF <0.5%) or low-frequency (MAF 0.55%) variants with low to modest effects contribute substantially to the heritability of complex diseases, although this may be hard to detect because of power issues. The recent transition to studies based on WGS and WES provides exciting opportunities to further explore the relationship between rare sequence variants and common diseases. Whole-genome sequencing is the most comprehensive method for analyzing the genome and reveals the complete DNA architecture [
      • Petersen B.S.
      • Fredrich B.
      • Hoeppner M.P.
      • Ellinghaus D.
      • Franke A.
      Opportunities and challenges of whole-genome and -exome sequencing.
      ]. The cost has rapidly decreased since this method first became available and is now only a fraction of the original price. Whole-genome sequencing is expected to yield rare variants with moderate effects and CNVs which GWAS may have missed. High-throughput sequencing is extremely efficient in Mendelian disorders, while results in complex diseases may be more variable.
      Fig. 1
      Fig. 1Feasibility of identifying genetic risk variants by risk allele frequency and strengths of the genetic effects (odds ratio). From Manolio T, et al., Nature 2009;461:747–753, with permission.
      Several studies based on WGS and WES have already uncovered rare variants associated with common complex diseases, including AF and sick sinus syndrome [
      • Gudbjartsson D.F.
      • Helgason H.
      • Gudjonsson S.A.
      • Zink F.
      • Oddson A.
      • Gylfason A.
      • et al.
      Large-scale whole-genome sequencing of the Icelandic population.
      ,
      • Holm H.
      • Gudbjartsson D.F.
      • Sulem P.
      • Masson G.
      • Helgadottir H.T.
      • Zanon C.
      • et al.
      A rare variant in MYH6 is associated with high risk of sick sinus syndrome.
      ]. These studies also provide unprecedented information about human sequence diversity and insights into the ancestry of human populations.

      4. Contribution of Iceland to genetic research

      While many countries have contributed extensively to the recent advances in human genetics and genomics, it is intriguing that a considerable proportion of the pioneering work has originated from the small nation of Iceland. This can largely be attributed to research carried out at deCODE genetics, a human genetic research institute founded in 1996 by Dr. Kari Stefansson. From the outset, the principal goal of deCODE genetics was to find genetic variation in humans that associates with common complex diseases and traits and apply this knowledge to uncover pathogenic mechanisms to guide the development of diagnostic tests and drug therapies. To date, deCODE in collaboration with the University Hospital in Reykjavik and several other Icelandic institutions, as well as investigators worldwide, has discovered numerous genes believed to be involved in a host of complex diseases, including cardiovascular disease, diabetes, chronic kidney disease, kidney stones, cancer, Alzheimer's disease (AD) and schizophrenia (http://www.decode.is).
      Despite a population of only 330.000, which largely remained isolated for many centuries, inbreeding has been shown to be modest, a finding that is also reflected by a low incidence of autosomal recessive disorders [
      • Helgason A.
      • Palsson S.
      • Gudbjartsson D.F.
      • Kristjansson T.
      • Stefansson K.
      An association between the kinship and fertility of human couples.
      ]. The population is relatively homogenous and the genetic makeup is a Northern European mix, with approximately 75% of the males of Scandinavian origin and 66% of the women of Celtic origin [
      • Helgason A.
      • Sigurdardottir S.
      • Gulcher J.R.
      • Ward R.
      • Stefansson K.
      mtDNA and the origin of the Icelanders: deciphering signals of recent population history.
      ]. In addition, an extensive genealogy database in Iceland has greatly facilitated research in this field. This database, which is derived from church books, contains information about almost all ancestors of contemporary Icelanders dating back to the year 1650.
      The majority of Icelanders have participated in the research projects at deCODE. Until now, about 150.000 Icelanders have been genotyped using DNA microarray platforms and close to 40.000 of those individuals have also had their entire genome sequenced (Stefansson K, personal communication). The large fraction of the Icelandic population that has been genotyped, allows for precise long-range phasing of the genome, thereby enabling accurate imputation of variants obtained by whole-genome sequencing into the chip-typed individuals [
      • Gudbjartsson D.F.
      • Helgason H.
      • Gudjonsson S.A.
      • Zink F.
      • Oddson A.
      • Gylfason A.
      • et al.
      Large-scale whole-genome sequencing of the Icelandic population.
      ]. Imputation denotes prediction of unobserved sequence variants, which can be accurately carried out to an allelic frequency of 0.01%. Furthermore, the extensive knowledge of the Icelandic genealogy permits reliable imputation of genotypes into close relatives of chip-typed individuals, creating in silico genotypes for virtually all Icelanders. The large set of imputed genomes can then be tested for association with an extensive range of phenotypes. The availability of genetic information for the vast majority of the Icelandic nation provides unique opportunities for both research and clinical practice.

      5. Examples of genetic influence on common complex diseases managed by internists

      To facilitate a deeper understanding of the influence of genetic variation on common complex diseases, several examples of disorders that are frequently encountered by the internist are provided.

      5.1 Coronary artery disease

      Family studies of acute myocardial infarction (AMI) suggest a strong contribution of genetic factors to the pathogenesis of this leading cause of morbidity and mortality. Coronary artery disease is one of the archetypal complex diseases, believed to involve a number of genes (Fig. 2), environmental factors and complex gene-gene and gene-environmental interactions [
      • Bjorkegren J.L.
      • Kovacic J.C.
      • Dudley J.T.
      • Schadt E.E.
      Genome-wide significant loci: how important are they? Systems genetics to understand heritability of coronary artery disease and other common complex disorders.
      ]. Dyslipidemia, hypertension and diabetes are examples of classical risk factors that are too some extent genetically determined [
      • Levy D.
      • Ehret G.B.
      • Rice K.
      • Verwoert G.C.
      • Launer L.J.
      • Dehghan A.
      • et al.
      Genome-wide association study of blood pressure and hypertension.
      ,
      • Willer C.J.
      • Sanna S.
      • Jackson A.U.
      • Scuteri A.
      • Bonnycastle L.L.
      • Clarke R.
      • et al.
      Newly identified loci that influence lipid concentrations and risk of coronary artery disease.
      ]. A large international consortium had by the end of 2013 identified 46 sequence variants with genome-wide significant association with CAD and AMI [
      • CARDIoGRAMplusC4D Consortium
      • Deloukas P.
      • Kanoni S.
      • Willenborg C.
      • Farrall M.
      • Assimes T.L.
      • et al.
      Large-scale association analysis identifies new risk loci for coronary artery disease.
      ]. Of these, 40% overlapped with dyslipidemia (24%), hypertension (10%), diabetes (2%), or a combination of these risk factors (4%). However, 35 loci were in genomic regions not associated with known risk factors, raising the possibility of elucidating previously unknown mechanisms contributing to atherosclerosis. To date, numerous associations of sequence variants with classical risk factors of CAD have been uncovered, including >200 variants associated with blood lipids, >10 with blood pressure and >50 associated with diabetes (http://www.ebi.ac.uk/gwas). Many variants that affect serum levels of LDL or non-HDL cholesterol also affect the risk of CAD, suggesting a causal relationship. In 2016, a rare loss-of-function mutation in ASGR1, encoding a subunit of the asialoglycoprotein receptor, was found to lower non-HDL cholesterol and protect against CAD [
      • Nioi P.
      • Sigurdsson A.
      • Thorleifsson G.
      • Helgason H.
      • Agustsdottir A.B.
      • Norddahl G.L.
      • et al.
      Variant ASGR1 associated with a reduced risk of coronary artery disease.
      ]. On average, the ASGR1 mutation associated with a 0.40 mmol/L decrease in non-HDL cholesterol and a 34% reduction in the risk of CAD. Interestingly, this reduction in coronary risk is considerably larger than would be expected from the lowering of non-HDL cholesterol alone.
      Fig. 2
      Fig. 2Manhattan plot summarizing results of genome-wide association meta-analysis of coronary artery disease. The −log10 (P value) is plotted against the physical position of each SNP on each chromosome. The threshold for genome-wide significance, P < 5 × 10−8, is indicated by the horizontal line. From Nikpay M, et al., Nat Genet 2015;47:1121–1130, with permission.
      The relationship between sequence variants and clinical phenotypes in CAD has been thoroughly studied. The first variant identified in relation to CAD was located on chromosome 9p21 and has since been confirmed in multiple cohorts [
      • Samani N.J.
      • Erdmann J.
      • Hall A.S.
      • Hengstenberg C.
      • Mangino M.
      • Mayer B.
      • et al.
      Genomewide association analysis of coronary artery disease.
      ,
      • McPherson R.
      • Pertsemlidis A.
      • Kavaslar N.
      • Stewart A.
      • Roberts R.
      • Cox D.R.
      • et al.
      A common allele on chromosome 9 associated with coronary heart disease.
      ,
      • Helgadottir A.
      • Thorleifsson G.
      • Manolescu A.
      • Gretarsdottir S.
      • Blondal T.
      • Jonasdottir A.
      • et al.
      A common variant on chromosome 9p21 affects the risk of myocardial infarction.
      ]. This common variant, is present in homozygous form in 21% of the population, and was shown to carry a 1.64 fold risk of developing AMI compared with non-carriers. Interestingly, all variants that have been discovered on chromosome 9p21 are located in an area containing the tumor suppressor genes CDKN2A and CDKN2B which encode proteins that regulate cellular proliferation, senescence and apoptosis [
      • McPherson R.
      Chromosome 9p21.3 locus for coronary artery disease: how little we know.
      ].
      Recently, an Icelandic study used a large dataset to search for rare and low-frequency variants that affect lipid fractions and CAD, resulting in the discovery of 13 variants with large effects and confirming 14 previously reported variants [
      • Helgadottir A.
      • Gretarsdottir S.
      • Thorleifsson G.
      • Hjartarson E.
      • Sigurdsson A.
      • Magnusdottir A.
      • et al.
      Variants with large effects on blood lipids and the role of cholesterol and triglycerides in coronary disease.
      ]. Five variants, located in PCSK9, APOA1, ANGPLL4 and LDLR, were found to associate with CAD. The strongest association with CAD was observed for the non-HDL genetic risk score. Collectively, all the susceptibility loci that have been detected in CAD only explain around 10% of the heritability of the disease.

      5.2 Atrial fibrillation

      In population-based studies, both from Iceland and the US, AF has been shown to segregate in families, indicating a genetic predisposition [
      • Arnar D.O.
      • Thorvaldsson S.
      • Manolio T.A.
      • Thorgeirsson G.
      • Kristjansson K.
      • Hakonarson H.
      • et al.
      Familial aggregation of atrial fibrillation in Iceland.
      ,
      • Fox C.S.
      • Parise H.
      • D'Agostino Sr., R.B.
      • Lloyd-Jones D.M.
      • Vasan R.S.
      • Wang T.J.
      • et al.
      Parental atrial fibrillation as a risk factor for atrial fibrillation in offspring.
      ]. A number of common sequence variants associating with AF have been demonstrated by GWAS [
      • Gudbjartsson D.F.
      • Arnar D.O.
      • Helgadottir A.
      • Gretarsdottir S.
      • Holm H.
      • Sigurdsson A.
      • et al.
      Variants conferring risk of atrial fibrillation on chromosome 4q25.
      ,
      • Tucker N.R.
      • Clauss S.
      • Ellinor P.T.
      Common variation in atrial fibrillation: navigating the path from genetic association to mechanism.
      ,
      • Gudbjartsson D.F.
      • Holm H.
      • Gretarsdottir S.
      • Thorleifsson G.
      • Walters G.B.
      • Thorgeirsson G.
      • et al.
      A sequence variant in ZFHX3 on 16q22 associates with atrial fibrillation and ischemic stroke.
      ]. The two strongest variants were identified on chromosome 4q25, yielding an OR of 1.72 and 1.39 per copy which is rather large for common variants. About 35% of Europeans have at least one of the variants. The sequence variants on 4q25 are located in a non-coding area of the chromosome, suggesting that the two variants might affect gene regulation [
      • Gudbjartsson D.F.
      • Arnar D.O.
      • Helgadottir A.
      • Gretarsdottir S.
      • Holm H.
      • Sigurdsson A.
      • et al.
      Variants conferring risk of atrial fibrillation on chromosome 4q25.
      ]. An interesting candidate is the most proximal gene, PITX2, a transcription factor that determines the presence of pulmonary myocardium, i.e. atrial tissue which can be found in the pulmonary veins [
      • Mommersteeg M.T.
      • Brown N.A.
      • Prall O.W.
      • de Gier-de Vries C.
      • Harvey R.P.
      • Moorman A.F.
      • et al.
      Pitx2c and Nkx2-5 are required for the formation and identity of the pulmonary myocardium.
      ]. This may be an important factor in the pathogenesis of AF, since ectopic beats from myocardial tissue in the pulmonary veins may be the trigger for AF [
      • Haissaguerre M.
      • Jais P.
      • Shah D.C.
      • Takahashi A.
      • Hocini M.
      • Quiniou G.
      • et al.
      Spontaneous initiation of atrial fibrillation by ectopic beats originating in the pulmonary veins.
      ]. A recent Icelandic study utilizing WGS data [
      • Gudbjartsson D.F.
      • Holm H.
      • Sulem P.
      • Masson G.
      • Oddsson A.
      • Magnusson O.T.
      • et al.
      A frameshift deletion in the sarcomere gene MYL4 causes early-onset familial atrial fibrillation.
      ], revealed a rare truncating frameshift deletion in the MYL4 gene that was noted to associate with early-onset AF under a recessive mode of inheritance. The MYL4 gene encodes the myosin alkali light chain, a sarcomeric protein that is specifically expressed in the cardiac atrium. Eight homozygous carriers of the mutation were discovered, all of whom had been diagnosed with AF at a very early age. In six of these individuals the diagnosis of AF had been made by the age of thirty and three had suffered an ischemic stroke at a young age, despite having a low-risk CHA2DS2-VASc score. A previous study, also performed in Iceland [
      • Holm H.
      • Gudbjartsson D.F.
      • Sulem P.
      • Masson G.
      • Helgadottir H.T.
      • Zanon C.
      • et al.
      A rare variant in MYH6 is associated with high risk of sick sinus syndrome.
      ], showed a rare variant in another sarcomere gene, MYH6, to be associated with AF and the sick sinus syndrome. The association of both MYH6 and MYL4 with AF strongly implies that variants encoding sarcomere genes may be involved in the pathogenesis of this common arrhythmia, causing a subclinical atrial cardiomyopathy and affecting cellular electrophysiology. These findings may offer a unique insight into the pathophysiology of AF and even point towards novel therapeutic approaches.

      5.3 Type 2 diabetes

      Type 2 diabetes clusters in families and it is well established that the risk of developing this prevalent disorder depends on both genetic and environmental factors. Early studies of T2D identified several candidate genes, including TCF7L2 which was found through a linkage study carried out in the Icelandic population and mapped to chromosome 10 [
      • Grant S.F.
      • Thorleifsson G.
      • Reynisdottir I.
      • Benediktsson R.
      • Manolescu A.
      • Sainz J.
      • et al.
      Variant of transcription factor 7-like 2 (TCF7L2) gene confers risk of type 2 diabetes.
      ]. This observation was replicated in Danish, European, and US cohorts and is currently known to be associated across ethnic groups worldwide [
      • Ali O.
      Genetics of type 2 diabetes.
      ]. TCF7L2 encodes a transcription factor and is an important regulatory gene of glucose homeostasis in the pancreatic islets as determined through several in vitro experiments in mouse models. Until now, >120 variants have been convincingly replicated for association with T2D and many more with diabetes-related traits [
      • Prasad R.B.
      • Groop L.
      Genetics of type 2 diabetes-pitfalls and possibilities.
      ]. Still, these variants only explain a small proportion of the total heritability of T2D. In T2D, the majority of GWAS loci appear to act primarily through defects in insulin secretion and, therefore, implicate the beta cells [
      • Ali O.
      Genetics of type 2 diabetes.
      ]. These findings have unraveled unexpected pathways that appear to play a role in the pathogenesis of T2D, including cell cycle regulation and CREBBP-related transcription factor activity [
      • Morris A.P.
      • Voight B.F.
      • Teslovich T.M.
      • Ferreira T.
      • Segre A.V.
      • Steinthorsdottir V.
      • et al.
      Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.
      ].
      Several established T2D susceptibility loci contain genes known to harbor causal variants for rare Mendelian syndromes related to T2D, e.g. HNF1A, HNF1B, WFS1, PPARG, KCNJ11, HNF4A and GCK [
      • Tallapragada D.S.
      • Bhaskar S.
      • Chandak G.R.
      New insights from monogenic diabetes for "common" type 2 diabetes.
      ]. This may suggest that variants in these genes have a large effect on the phenotype.

      5.4 Alzheimer's disease

      Both early- and late-onset forms of AD are associated with significant genetic predisposition. The first discoveries of important genetic factors were made by linkage analysis about 20 years ago, uncovering rare variants in APP, PSEN1 and PSEN2, which associated with early-onset AD, and a variant in the ε4-allele of the APOE gene, encoding apolipoprotein E, that was implicated in familial late-onset AD [
      • Giri M.
      • Zhang M.
      • Lu Y.
      Genes associated with Alzheimer's disease: an overview and current status.
      ]. Genome-wide association studies have observed >20 genetic loci associated with late-onset AD [
      • Giri M.
      • Zhang M.
      • Lu Y.
      Genes associated with Alzheimer's disease: an overview and current status.
      ]. Recently, WGS and WES have enabled the identification of several rare sequence variants. In Iceland, WGS revealed rare variants in APP and TREM2 that affect susceptibility to the sporadic, late-onset form of AD [
      • Jonsson T.
      • Atwal J.K.
      • Steinberg S.
      • Snaedal J.
      • Jonsson P.V.
      • Bjornsson S.
      • et al.
      A mutation in APP protects against Alzheimer's disease and age-related cognitive decline.
      ,
      • Jonsson T.
      • Stefansson H.
      • Steinberg S.
      • Jonsdottir I.
      • Jonsson P.V.
      • Snaedal J.
      • et al.
      Variant of TREM2 associated with the risk of Alzheimer's disease.
      ]. Moreover, variants that are likely to affect protein function were discovered in both cases. In the TREM2 gene, which encodes the triggering receptor expressed on myeloid cells 2, a rare missense variant was found to confer a significant risk of AD (odds ratio, 2.92) and this finding was replicated in cohorts from the United States, Norway, the Netherlands, and Germany, implicating the TREM2 variant in the pathogenesis of AD [
      • Jonsson T.
      • Stefansson H.
      • Steinberg S.
      • Jonsdottir I.
      • Jonsson P.V.
      • Snaedal J.
      • et al.
      Variant of TREM2 associated with the risk of Alzheimer's disease.
      ]. The fact that TREM2 has been reported to have an anti-inflammatory role in the brain, suggests that the increased risk of AD is mediated through inflammatory pathways. By contrast, a missense mutation detected in the APP gene, encoding the amyloid precursor protein, associates with a decreased risk of AD [
      • Jonsson T.
      • Atwal J.K.
      • Steinberg S.
      • Snaedal J.
      • Jonsson P.V.
      • Bjornsson S.
      • et al.
      A mutation in APP protects against Alzheimer's disease and age-related cognitive decline.
      ]. The variant is located adjacent to the aspartyl protease b-site in the amyloid precursor protein and results in an approximately 40% reduction in the formation of amyloidogenic peptides in vitro. The strong protective effect of this variant against AD supports the hypothesis that reduction of the b-cleavage of the amyloid precursor protein may guard against the disease. Furthermore, the risk allele also protects against cognitive decline in the elderly without AD, suggesting that the effect may be mediated through the same or similar mechanisms. Finally, loss-of-function variants in ABCA7 that confer risk of AD were identified in Icelanders and replicated in samples from Europe and the United States [
      • Steinberg S.
      • Stefansson H.
      • Jonsson T.
      • Johannsdottir H.
      • Ingason A.
      • Helgason H.
      • et al.
      Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease.
      ]. The progress made in understanding the role of genetic factors in the pathogenesis of AD offers hope for the development of novel treatments for this devastating disease.

      5.5 Cancer

      Cancer is caused by acquired alterations in the DNA sequence of the genome of somatic cells. A subset of the genetic changes, called driver mutations, promote the malignant transformation and tumor growth, while the remainder are passenger mutations [
      • Stratton M.R.
      • Campbell P.J.
      • Futreal P.A.
      The cancer genome.
      ]. Large-scale genome sequencing of all major cancer types has enabled characterization of driver and passenger mutations, thereby facilitating the molecular classification of cancer [
      • De S.
      • Ganesan S.
      Looking beyond drivers and passengers in cancer genome sequencing data.
      ]. Cancer genome projects such as the Cancer Genome Atlas Network, funded by the US National Institutes of Health [
      • Cancer Genome Atlas Research Network
      • Weinstein J.N.
      • Collisson E.A.
      • Mills G.B.
      • Shaw K.R.
      • Ozenberger B.A.
      • et al.
      The cancer genome atlas pan-cancer analysis project.
      ], were instrumental in the detection and characterization of genomic alterations that drive the carcinogenesis process across multiple types of malignancies. These findings have enhanced our understanding of cancer biology and have generated drug targets, resulting in novel therapeutic options. In fact, it is now possible in some cases to individualize cancer treatment according to the gene mutation profiles.
      An important example is breast cancer, the most common malignant disease and a leading cause of cancer-related deaths in women. The discovery of BRCA1 and BRCA2, the most important breast cancer genes, more than 20 years ago was a seminal event [
      • Narod S.A.
      • Foulkes W.D.
      BRCA1 and BRCA2: 1994 and beyond.
      ]. The lifetime risk of breast cancer among female carriers of mutations in BRCA1 or BRCA2 is 50–85% [
      • Shiovitz S.
      • Korde L.A.
      Genetics of breast cancer: a topic in evolution.
      ]. In addition, both genes are associated with increased risk of ovarian cancer. Loss-of-function mutations in the PALB2 gene have also been shown to be an important cause of hereditary breast cancer, with an estimated cumulative risk of 35% by age 70 years [
      • Antoniou A.C.
      • Casadei S.
      • Heikkinen T.
      • Barrowdale D.
      • Pylkas K.
      • Roberts J.
      • et al.
      Breast-cancer risk in families with mutations in PALB2.
      ]. Genome-wide association studies have unraveled >80 loci significantly associated with sporadic breast cancer [
      • Skol A.D.
      • Sasaki M.M.
      • Onel K.
      The genetics of breast cancer risk in the post-genome era: thoughts on study design to move past BRCA and towards clinical relevance.
      ]. In spite of this progress, the sequence variants identified thus far explain only 16% of the familial risk of breast cancer [
      • Michailidou K.
      • Beesley J.
      • Lindstrom S.
      • Canisius S.
      • Dennis J.
      • Lush M.J.
      • et al.
      Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer.
      ]. Hence, the majority of the genetic contribution to breast cancer etiology remains unknown.

      6. The future of genomics research

      The tremendous progress made in recent years indicates that exciting times in genomics research are ahead. However, better understanding of the human genome is required to provide the necessary foundation for improvements in treatment and outcome of many common diseases. The possibility to assess the risk of disease in individuals and tailor interventions based on genomic information is a fundamental step. Linking public genetic databases to available clinical information in electronic medical records, may become a powerful tool for physicians when faced with complex clinical decisions.
      The application of high-throughput sequencing techniques will continue to focus the work on discovery of important rare and low-frequency genetic variants in common complex diseases. Whole-exome and whole-genome sequencing will also facilitate the diagnosis of monogenic disorders, which then can be separated from common diseases. In addition, high-throughput sequencing of mRNA is a promising method for analyzing gene expression. RNA-sequencing data, often referred to as the transcriptome, can provide information on differential gene expression, alternatively spliced transcripts, post-transcriptional modifications and the presence of gene fusion products. RNA sequencing also provides a better functional understanding of the genome than analysis of DNA sequence variants. However, the potential of this technology is balanced by several limitations, including fragility and instability of RNA derived from formalin-fixed, paraffin-embedded tissue samples.
      Future studies will also focus on epigenetic modifications, such as DNA methylation and chromatin assembly states, which contribute to altered gene expression and may account for some of the missing heritability in common diseases. Genealogy data will undoubtedly prove very useful as exemplified by the work carried out in Iceland. Finally, the value of robust phenotyping is becoming much more appreciated with electronic medical records emerging as an important source of data to define phenotype algorithms. Phenome-wide association studies (PheWas) offer an alternative and complementary strategy to GWAS by using a genotype-to-phenotype strategy where selected genetic variants are tested for associations with an extensive set of phenotypes and traits.
      Several areas warrant further consideration. The fact that multiple genes appear to be involved in most common diseases makes the investigation of gene-gene interaction, or epistasis, a priority. Another important phenomenon is termed pleiotropy, indicating that genetic variation at a single locus has an effect on more than one phenotype. Hitherto, genomics research has mostly relied on the paradigm of Mendelian or near-Mendelian rules of genetics in which a single gene affects a single phenotype. Common alleles which contribute to a given disease when interacting with other genes and environmental factors, may yield a different phenotypic expression in the setting of a variable genetic background and, hence, another disorder. A good example is the APOE4 allele which is associated with increased risk of both AD and CAD and has also been shown to exert a protective effect on the risk of age-related macular degeneration [
      • Solovieff N.
      • Cotsapas C.
      • Lee P.H.
      • Purcell S.M.
      • Smoller J.W.
      Pleiotropy in complex traits: challenges and strategies.
      ].
      A key limitation of GWAS is the inherent difficulty in interpreting the pathobiological relevance of susceptibility loci. As the ultimate goal is to enhance our understanding of the pathogenesis of common complex diseases, it would be desirable that the GWAS findings unravel functional variants and biologic pathways that can be experimentally validated. Thus, cell biologic studies will be needed to evaluate the functional role of genetic variants that have been identified.

      7. Clinical use of genetic information: precision medicine

      The term precision medicine, also referred to as personalized medicine, has been introduced to highlight the ability to integrate genetic, clinical, and environmental markers of disease risk in order to tailor preventive strategies and treatments to individuals. There is a growing interest in this concept and as an example, former President Barack Obama launched a precision medicine initiative in the United States in 2015 [
      • Collins F.S.
      • Varmus H.
      A new initiative on precision medicine.
      ]. This ambitious plan involves genotyping up to one million individuals who are willing to participate in this program. Similar initiatives are underway in several other countries. Iceland may, however, be in a unique position in this regard as a wealth of genetic and computerized clinical information is already available for the whole nation. Nonetheless, a constructive utilization of these data requires an orchestrated effort that still awaits the required initiative.
      Precision medicine aims to individualize care based on differences in genetic makeup, lifestyle and the environment. This strategy challenges the “one size fits all” approach that defines much of current medical practice. Until recently, this concept has found its greatest application in oncology, but establishing specific prognostic biomarkers in other fields of internal medicine is also becoming feasible. Tests that identify people with an inherited cancer risk can guide preventive strategies and aid in early diagnosis. One well-known example of the potential impact of genomic medicine involves mutations in the BRCA1 and BRCA2 genes and the associated high risk of breast cancer and ovarian cancer in women and prostate cancer in men [
      • King M.C.
      • Levy-Lahad E.
      • Lahad A.
      Population-based screening for BRCA1 and BRCA2: 2014 Lasker Award.
      ]. The overall lifetime risk of developing any cancer is increased almost fivefold in the carriers of a five base deletion in exon 9 of BRCA2, the predominant mutation in Iceland [
      • Letters from Iceland
      ]. Moreover, the life expectancy of these BRCA2 mutation carriers is decreased by 11 years for women and 7 years for men. Although some of the BRCA2 mutation carriers in Iceland have been discovered through testing on clinical indications, the majority have been found through research efforts at deCODE genetics. As the study subjects have only consented for participation in research, contacting them to deliver information about their risk would be controversial. The use of available genetic data to screen for cancer-causing mutations has gained some support in recent years. Nevertheless, the right of the individual to choose not to receive any information about genetic test results, i.e. the right not to know, is undisputed. Indeed, it is well known that disclosing this type of information might have severe and long-lasting psychological consequences, counteracting the potential benefit associated with modifying the risk of developing breast cancer. For these reasons, it is of paramount importance that such disclosure is accompanied by appropriate counselling and medical care when appropriate. The possibility of influencing the risk and prognosis of large numbers of people by this approach poses a new challenge for the healthcare system, including the requirement of specialized multidisciplinary genetics clinics in order to provide optimal and appropriate care to mutation carriers. In our opinion, the available information on carriers of the BRCA2 mutation in Iceland provides a unique opportunity for early diagnosis of breast and ovarian cancer and even prevention of these life-threatening diseases.
      Similarly, exponential growth in the understanding of cancer genomics is already leading towards individualized cancer treatment. The discovery of driver mutations has accelerated strategies for cancer prevention and the development of new therapies. While the efficacy of such an approach is still very limited due to lack of effective treatments, genomic sequencing is already guiding the drug development process and will hopefully generate novel targeted therapeutics. An example is the recognition of the important role of the driver mutation BRAF V600E, present in approximately half of patients with metastatic melanoma, which provided the rationale for clinical trials evaluating the efficacy of the BRAF inhibitor, vemurafenib [
      • Holderfield M.
      • Deuker M.M.
      • McCormick F.
      • McMahon M.
      Targeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond.
      ]. A significant increase in progression-free survival among patients who received vemurafenib compared with dacarbazine was demonstrated. In addition, approximately 10-40% of non-small cell cancers of the lung harbor epidermal growth factor receptor aberrations, most frequently deletions within exon 19 or L858R mutation within exon 21 of the gene, and have been found to respond favorably to tyrosine kinase inhibitors [
      • Hirsch F.R.
      • Scagliotti G.V.
      • Mulshine J.L.
      • Kwon R.
      • Curran Jr., W.J.
      • Wu Y.L.
      • et al.
      Lung cancer: current therapies and new targeted treatments.
      ].
      In cardiovascular medicine, there are intriguing opportunities to use genetic information to evaluate risk and impact prognosis. Existing genotypic data in some countries, such as Iceland, could be used to create a genetic risk score for CAD for use in conjunction with other risk factors. Furthermore, genomic information could prove useful for identifying high-risk individuals for potential intervention aimed at improving their prognosis. A good example is sudden cardiac death (SCD), a major cause of mortality in Western societies. Although most cases of arrhythmic death occur in elderly individuals and are more often than not associated with CAD, the occurrence of SCD in persons under 40 years of age is not so rare. Sudden death of a young and apparently healthy person is clearly among the more challenging scenarios in clinical medicine, not the least because of the perceived risk of the same fate in surviving relatives.
      The majority of SCD events in the young occur as a consequence of inherited arrhythmogenic disorders, which can be divided into two distinct groups: cardiomyopathies and channelopathies [
      • Wilde A.A.
      • Behr E.R.
      Genetic testing for inherited cardiac disease.
      ]. Among these disorders are the long QT syndrome, Brugada syndrome, catecholaminergic polymorphic ventricular tachycardia, short QT syndrome, arrhythmogenic right ventricular cardiomyopathy and hypertrophic cardiomyopathy. Inherited arrhythmogenic disorders are relatively uncommon conditions with a large number of known causative genes [
      • Wilde A.A.
      • Behr E.R.
      Genetic testing for inherited cardiac disease.
      ]. However, the phenotype of inherited arrhythmogenic disorders can be highly variable, even within the same family, due to the influence of environmental and genetic modifiers. Many individuals are asymptomatic and the electrocardiogram may be normal. Hence, the diagnosis is frequently difficult and, therefore, often delayed. Consequently, the possibility of preventive therapy is missed in some cases.
      The extensive genetic database at deCODE genetics, together with availability of digitalized medical and health information for the entire nation and easy access to people through national identification numbers, offers a unique opportunity to study individuals who carry the most common known genetic risk variants for inherited arrhythmogenic disorders and SCD in the young. This work could yield unprecedented knowledge of genetic epidemiology, genotype-phenotype relationship and risk of serious adverse cardiac events, as well as the possibility of using genetic information for clinical risk stratification. Moreover, integrating clinical and molecular data could lead to interventions to prevent SCD. This strategy is the reverse of the classical paradigm in genetic research. Instead of searching for sequence variants that associate with existing phenotypic information, this approach involves precise phenotypic characterization of patients with a known at-risk genotype.
      Preventive initiatives may include lifestyle modification, detailed recommendations of drugs to avoid in disorders like the long QT syndrome, the use of prophylactic medications, for instance a beta blocker when indicated, or even use of devices such as an implantable cardioverter defibrillator in cases of extreme phenotypes. Of course, there are many practical and ethical concerns that need to be addressed. Nevertheless, this direction in medical care is certainly within the realm of possibility.
      The advent of precision medicine has several direct implications for drug development. The balance of efficacy and toxicity will likely be altered in a favorable direction. More importantly, a generalizable approach for drug development that can be applied to any disease in a cost-effective manner will be called for, as the current timeline and costs of developing new medicines will not be sustainable much longer. Finally, pharmacogenomic tests have the potential to guide drug prescribing according to individual variability in the genetic basis of response to numerous medications, thereby augmenting safety and effectiveness of pharmacologic therapies.
      In conclusion, a wealth of genetic data has been accumulated through genomics research over the past one or two decades, generating new insights into the pathobiological pathways of various common diseases. Identification of all human genes and their regulatory regions provides the essential framework for our understanding of the molecular basis of disease. Although a lot remains to be learned about the contribution of genetic factors to human disease, we are already taking the first steps into the age of precision medicine. Iceland has a unique opportunity to assume a leading role in this critical initiative which could reshape the practice of medicine.

      Disclosures

      Dr. Arnar is a consultant to deCODE genetics and Dr. Palsson is a research collaborator of deCODE genetics.

      Acknowledgements

      Funding: This work was supported in part by grants from Landspitali University Hospital Science Fund to Drs. Arnar and Palsson and by a grant from the Sigurlidi Kristjansson and Helga Jonsdottir Memorial Fund to Dr. Arnar.

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