THE FAILURE OF THE GENOME

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The Great DNA Data Deficit: AreGenes for Disease a Mirage?

December 8, 2010 Commentaries, Health, ScienceMedia 4 Comments

Jonathan Latham and Allison Wilson

Just before his appointment as head of the US NationalInstitutes of Health (NIH), Francis Collins, the most prominentmedical geneticist of our time, had his own genome scannedfor disease susceptibility genes. He had decided, so he said,that the technology of personalised genomics was finallymature enough to yield meaningful results. Indeed, theoutcome of his scan inspired The Language of Life, his recentbook which urges every individual to do the same and securetheir place on the personalised genomics bandwagon.

So, what knowledge did Collinss scan produce? His resultscan be summarised very briefly. For North American malesthe probability of developing type 2 diabetes is 23%. Collinssown risk was estimated at 29% and he highlighted this as theoutstanding finding. For all other common diseases, however,including stroke, cancer, heart disease, and dementia,Collinss likelihood of contracting them was average.

Predicting disease probability to within a percentage pointmight seem like a major scientific achievement. From theperspective of a professional geneticist, however, there is anobvious problem with these results. The hoped-for outcome isto detect genes that cause personal risk to deviate from theaverage. Otherwise, a genetic scan or even a whole genomesequence is showing nothing that wasnt already known. Thereal story, therefore, of Collinss personal genome scan is notits success, but rather its failure to reveal meaningfulinformation about his long-term medical prospects. Moreover,Collinss genome is unlikely to be an aberration. Contrary toexpectations, the latest genetic research indicates thatalmost everyones genome will be similarly unrevealing.

We must assume that, as a geneticist as well as head ofNIH, Francis Collins is more aware of this than anyone, but ifso, he wrote The Language of Life not out of raw enthusiasmbut because the genetics revolution (and not just personalisedgenomics) is in big trouble. He knows it is going to need allthe boosters it can get.

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the boosters it can get.

What has changed scientifically in the last three years is theaccumulating inability of a new whole-genome scanningtechnique (called Genome-Wide Association studies; GWAs)to find important genes for disease in human populations1. Instudy after study, applying GWAs to every common (non-infectious) physical disease and mental disorder, the resultshave been remarkably consistent: only genes with very minoreffects have been uncovered (summarised in Manolio et al2009; Dermitzakis and Clark 2009). In other words, thegenetic variation confidently expected by medical geneticiststo explain common diseases, cannot be found.

There are, nevertheless, certain exceptions to this blanketstatement. One group are the single gene, mostly rare,genetic disorders whose discovery predated GWA studies2.These include cystic fibrosis, sickle cell anaemia andHuntingtons disease. A second class of exceptions are ahandful of genetic contributors to common diseases andwhose discovery also predated GWAs. They are few enoughto list individually: a fairly common single gene variant forAlzheimers disease, and the two breast cancer genes BRCA1 and 2 (Miki et al. 1994; Reiman et al. 1996). Lastly, GWAstudies themselves have identified five genes each with asignificant role in the common degenerative eye diseasecalled age-related macular degeneration (AMD). With theseexceptions duly noted, however, we can reiterate thataccording to the best available data, genetic predispositions(i.e. causes) have a negligible role in heart disease, cancer3,stroke, autoimmune diseases, obesity, autism, Parkinsonsdisease, depression, schizophrenia and many other commonmental and physical illnesses that are the major killers inWestern countries4.

For anyone who has read about genes for nearly everydisease and the deluge of medical advances predicted tofollow these discoveries, the negative results of the GWAstudies will likely come as a surprise. They may even appearto contradict everything we know about the role of genes indisease. This disbelief is in fact the prevailing view of medicalgeneticists. They do not dispute the GWA results themselvesbut are now assuming that genes predisposing to commondiseases must somehow have been missed by the GWAmethodology. There is a big problem, however, in thatgeneticists have been unable to agree on where this darkmatter of DNA might be hiding.

If, instead of invoking missing genes, we take the GWAstudies at face value, then apart from the exceptions notedabove, genetic predispositions as significant factors in theprevalence of common diseases are refuted. If true, this wouldbe a discovery of truly enormous significance. Medicalprogress will have to do without genetics providing acomplete transformation in therapeutic medicine (FrancisCollins, White House Press Release, June 26, 2000 ).Secondly, as Francis Collins found, genetic testing will neverpredict an individuals personal risk of common diseases. Andof course, if the enormous death toll from common Westerndiseases cannot be attributed to genetic predispositions itmust predominantly originate in our wider environment. Inother words, diet, lifestyle and chemical exposures, to namea few of the possibilities.

The question, therefore, of whether medical geneticists areacting reasonably in proposing some hitherto unexpectedgenetic hiding place, or are simply grasping at straws, is ahugely significant one. And there is more than one problemwith the medical geneticists position. Firstly, as lack ofagreement implies, they have been unable to hypothesise agenetic hiding place that is both plausible and large enough toconceal the necessary human genetic variation for disease.Furthermore, for most common diseases there exists plentifulevidence that environment, and not genes, can satisfactorilyexplain their existence. Finally, the oddity of denying thesignificance of results they have spent many billions of dollarsgenerating can be explained by realising that a shortage ofgenes for disease means an impending oversupply of medicalgeneticists.

You will not, however, gather this from the popular or evenscientific media, or even the science journals themselves. No-

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one so far has been prepared to point out the weaknesses inthe medical geneticists position. The closest up to now isfrom science journalist Nicholas Wade in the New York Timeswho has suggested that genetic researchers have goneback to square one. Even this is a massiveunderstatement, however. Human genetic research is notmerely at an impasse, it would seem to have excludedinherited DNA, its central subject, as a major explanation ofmost diseases.

The failure to find major disease genes

Advances in medical genetics have historically centered onthe search for genetic variants conferring susceptibility to rarediseases. Such genes are most easily detected when theireffects are very strong (in genetics this is called highlypenetrant), or a gene variant is present in unusually inbredhuman populations such as Icelanders or Ashkenazi Jews.This strategy, based on traditional genetics, has uncoveredgenes for cystic fibrosis, Huntingtons disease, the breastcancer susceptibility genes BRCA 1 and 2, and many others.Important though these discoveries have been, these defectivegenetic variants are relatively rare, meaning they do notaccount for disease in most people2. To find the genesexpected to perform analogous roles in more commondiseases, different genetic tools were needed, ones that weremore statistical in nature.

The technique of genome wide association (GWA) was notmerely the latest hot thing in genetics. It was in many waysthe logical extension of the human genome sequencingproject. The original project sequenced just one genome but,genetically speaking, we are all different. These differencesare, for many geneticists, the real interest of human DNA.Many thousands of minor genetic differences betweenindividuals have now been catalogued and medical geneticistswanted to use this seemingly random variation to tag diseasegenes. Using these minor DNA differences to screen largehuman populations, GWA studies were going to identify theprecise location of the gene variants associated withsusceptibility to common disorders and diseases.

To date, more than 700 separate GWA studies have beencompleted, covering about 80 different diseases. Everycommon disease, including dozens of cancers, heart disease,stroke, diabetes, mental illnesses, autism, and others, hashad one or more GWA study associated with it (Hindorff et al.2009). At a combined cost of billions of dollars, it wasexpected at last to reveal the genes behind human illness.And, once identified, these gene variants would become thelaunchpad for the personalised genomic revolution.

But it didnt work out that way. Only for one disease, AMD,have geneticists found any of the major-effect genes theyexpected and, of the remaining diseases, only for type 2diabetes does the genetic contribution of the genes with minoreffects come anywhere close to being of any public healthsignificance (Dermitzakis and Clark 2009; Manolio et al.2009). In the case of AMD, the five genes determineapproximately half the predicted genetic risk (Maller et al.2006). Apart from these, GWA studies have found littlegenetic variation for disease. The few conclusive examples inwhich genes have a significant predisposing influence on acommon disease remain the gene variant associated withAlzheimers disease and the breast cancer genes BRCA1 and2, all of which were discovered well before the GWA era (Mikiet al. 1994 and Reiman et al. 1996).

Though they have not found what their designers hoped theywould, the results of the GWA studies of common diseasesdo support two distinct conclusions, both with far-reachingimplications. First, apart from the exceptions noted, thegenetic contribution to major diseases is small, accounting atmost for around 5 or 10% of all disease cases (Manolio et al.2009). Secondly, and equally important, this geneticcontribution is distributed among large numbers of genes,each with only a minute effect (Hindorff et al. 2009). Forexample, the human population contains at least 40 distinctgenes associated with type I diabetes (Barrett et al. 2009).Prostate cancer is associated with 27 genes (Ioannidis et al.2010); and Crohns disease with 32 (Barrett et al. 2008).

The implications for understanding how each persons health

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is affected by their genetic inheritance are remarkable. Foreach disease, even if a person was born with every knownbad (or good) genetic variant, which is statistically highlyunlikely, their probability of contracting the disease would stillonly be minimally altered from the average.

DNA is not the language of life or death

This dearth of disease-causing genes is without question ascientific discovery of tremendous significance. It iscomparable in stature to the discovery of vaccination, ofantibiotics, or of the nature of infectious diseases, because ittells us that most disease, most of the time, is essentiallyenvironmental in origin.

But such significance leaves a puzzle. Huge quantities ofnewspaper space has been devoted to genes, or even to hintsof genes for various diseases5. By rights then, reports of theGWA results should have filled the front pages of every worldnewspaper for a week. So, why has this coverage notoccurred?

It is possible to conceive of excuses for lack of coverage:refutation is inherently less interesting, and the GWA resultshave been reported piecemeal, but the more likely reason isthe disturbing implications for medical geneticists who are itsdiscoverers. The GWA studies were not envisaged as a testof the hypothesis: do genes cause common diseases?Rather, they were expected merely to straightaway identifythe guilty genes that everyone knew were there. Byapparently refuting the entire concept of genes for commondiseases, the GWA studies raise fundamental questionsabout money spent, hopes raised, and judgments made bymedical researchers.

In the first place, the GWA results raise what are probablyinsurmountable questions for the prospective geneticrevolution in healthcare. What use will personalised DNAtesting (or sequencing) be if genes cannot predict disease forthe vast majority of people? Are genes with only extremelyminor effects going to be of value as drug targets? How hardis it going to be to untangle their roles in disease when theyhave hardly any measurable effect? Should we still supposethat pouring more resources into human genetic research isgoing to rescue industrys faltering drug developmentpipelines? All of a sudden, the future of medicine, especiallyin the specialities dealing with degenerative diseases andmental illness, looks very different and a lot less promising.We no longer have a complete transformation to look forwardto, only a continuation of the incremental improvements andsetbacks that have characterised medicine for the last fiftyyears.

Shoring up the good ship medical genetics

In a rare public sign of the struggle to come to terms with thisgenetically impoverished world-view, the authors of a briefreview in Science magazine, Andrew Clark of CornellUniversity and Emmanouil Dermitzakis of the University ofGeneva Medical School, Switzerland have been alone instating the case even partly straightforwardly. According tothem, the GWA studies tell us that the magnitude of geneticeffects is uniformly very small and therefore commonvariants provide little help in predicting risk (Dermitzakis andClark 2009). Consequently, the likelihood that personalisedgenomics will ever predict the occurrence of commondiseases is bleak. This aim, they believe, will have to beabandoned altogether.

The first conclusion to be drawn from these quotes is thatsuch directness implies that if the GWA findings are notfinding their way to the front page the reason is not ambiguityin the results themselves. From a scientific perspective theGWA results, though negative, are robust and clear.

Most human geneticists view the GWA results somewhatdifferently, however. An invited workshop, convened by Collinsand others, discussed the then-accumulating results inFebruary 2009. The most visible outcome of this workshopwas a lengthy review published in Nature and titled: Findingthe Missing Heritability of Complex Diseases. (Manolio et al.2009).

For a review paper that does not lay out any new concepts or

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directions, 27 senior scientists as coauthors might beconsidered overkill. Finding the Missing Heritability, however,should be understood not so much as a scientific contributionbut as an effort to conceal the gaping hole in the science ofmedical genetics.

In their Science article, which was published almostsimultaneously, Dermitzakis and Clark paused only briefly toconsider whether so many genes could have been overlooked.Apparently, they thought it an unlikely possibility. Manolio etal., however, frame this as the central issue. According tothem, since heritability measurements suggest that genes fordisease must exist, they must be hiding under some as-yet-unturned genetic rock. They list several possible hidingplaces: there may be very many genes with exceedinglysmall effects; genes for disease may be highly represented byrare variants with large effects; disease genes may havecomplex genetic architectures; or they may exist as geneCopy Number Variants (CNVs). Since Manolio et al.presented their list, the scientific literature has seen furthersuggestions for where disease genes might be hiding. Theseinclude in mitochondrial DNA, epigenetics and in statisticalanomalies (e.g. Eichler et al. 2010; Petronis 2010).

A problem for all these hypotheses, however, is that anyonewishing to take them seriously needs to consider oneimportant question. How likely is it that a quantity of geneticvariation that could only be called enormous (i.e. more than90-95% of that for 80 human diseases) is all hiding in whatuntil now had been considered genetically unlikely places? Inother words, they all require the science of genetics to beturned on its head. For epigenetics, for example, there isscant evidence that important traits can be inherited throughacquired modifications of DNA. Similarly, if rare variants withstrong effects keep appearing in the population and causingmajor illnesses, why is there no evidence for thisphenomenon, since it must have been occurring in the past?With unanswered questions such as these, it is unsurprisingthat none of the mooted explanations has attracted any kindof consensus among geneticists and in fact the CNVexplanation is already looking highly unlikely (Conrad et al.2010; The Wellcome Trust Case Control Consortium 2010).As the first of these two papers summarised we concludethat, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by CNVs(Conrad et al. 2010).

Now, it is not impossible that human diseases follow uniquegenetic rules, but the apparently overlooked possibility is thatthe GWA studies are indicating a simple truth: that genes arenot important causes of major diseases.

As stated so far, the case against the importance of genes fordisease seems strong. However, the missing heritabilityargument is based on numerous predictions of a large geneticcontribution to human diseases that are derived fromheritability measurements. These heritability estimates areobtained from the study of identical and non-identical twins. Acrucial question becomes, therefore, are these estimates trulyreliable?

How robust is the historical evidence for geneticcausation?

A perennial feature of research into human health has alwaysbeen the mountain of evidence that environment isoverwhelmingly important in disease. People who migrateacquire the spectrum of diseases of their adopted country.Populations who take up Western habits, or move to citieswith Western lifestyles, acquire Western diseases, and so on(e.g. Campbell and Campbell 2008 ). These data are hardto refute, not least because they are so simple, butgeneticists, when discussing them, invariably wheel out theirown version of incontrovertible evidence: twin studies of theheritability of complex diseases. When Francis Collins talksabout missing heritability it is to studies such as these thathe is referring. They provide the basic evidence for geneticinfluences on human disease.

A classic example of this contradiction is myopia. A largebody of evidence suggests that myopia is an environment-induced disorder caused by some combination of nightlighting, close reading, lack of distance viewing and diet (e.g.

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Quinn et al. 1999). Moreover, under the influence ofWesternisation, genetically unchanged populations, forexample, are known to have switched in a single generationfrom close to 0% to a prevalence of myopia of over 80%(Morgan 2003). And myopia is only one of many examples ofdiseases with very strong evidence for its environmental origin.In 2009, for example, researchers demonstrated that verymoderate improvements in lifestyle could reduce anindividuals probability of contracting type 2 diabetes by 89%(Mozzafarian et al. 2009). The subjects of this study just hadto smoke less than the average, keep trim, exercisemoderately and not eat too much fat.

In stark contrast, twin studies (which compare the extent ofsimilarity exhibited by identical and non-identical twins)estimate that myopia is a disease with a heritability (calledh2) of about 0.8 (out of a possible 1.0), indicating that formyopia genetic causes dominate environmental ones. Thesefindings are clearly incompatible with the availableepidemiological data on myopia and no satisfactory resolutionto them has ever been proposed (e.g. Rose et al. 2002;Morgan 2003). This contradiction, between the results of twinstudies and the results of epidemiological and clinicalresearch, is repeated for almost every human disease.

A meaningful resolution to these contradictions is,nevertheless, necessary. Since it is unlikely that the manyobservations identifying environment as a dominant disease-causing factor are all incorrect, the parsimonious solution tothe conundrum, even before the GWA studies were reported,was to propose that heritability studies of twins are inherentlymistaken or misinterpreted.

Studies of human twins estimate heritability (h2) bycalculating disease incidence in monozygotic (geneticallyidentical) twins versus dizygotic (fraternal) twins (who share50% of their DNA). If monozygotic twin pairs share disordersmore frequently than do dizygotic twins, it is presumed that agenetic factor must be involved. A problem arises, however,when the number resulting from this calculation is consideredto be an estimate of the relative contribution of genes andenvironment over the whole population (and environment) fromwhich the twins were selected. This is because themeasurements are done in a series of pairwise comparisons,meaning that only the variation within each twin pair isactually being measured. Consequently, the method implicitlydefines as environment only the difference within each twinpair. Since each twin pair normally shares location, parentingstyles, food, schooling, etc., much of the environmentalvariability that exists between individuals in the widerpopulation is de facto excluded from the analysis. In otherwords, heritability (h2), when calculated this way, fails toadequately incorporate environmental variation and inflates therelative importance of genes.

Heritability studies of humans are classic experiments thathave been conducted many times and they have strongdefenders among modern geneticists (e.g. Visscher et al.2008). Nevertheless, criticisms such as those above are notnovel. They are a specific example of the general problem,formulated by Richard Lewontin (of Harvard University), thatthe contributions of genes to a trait normally depend on theparticular environment. And further, that susceptibility toenvironment depends on genes. In consequence, there can beno universal constant (such as h2) that defines theirrelationship to one another (Lewontin, Rose and Kamin 1984;Lewontin 1993). Lewontin is not alone among geneticists inhis dismissal of heritability as it is used in human genetics.Martin Bobrow of Cambridge University, for example, hascalled human heritability a poisonous concept and almostuninterpretable6.

If one accepts either that h2 is consistently inflated, or that itis essentially meaningless, even poisonous, then the onlycurrent evidence supporting genetic susceptibility as a majorcause of disease disappears. The Missing Heritability ofComplex Diseases, DNAs so-called dark matter, becomessimply an artefact arising from overinterpretation of twinstudies.

A mutually convenient untruth

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Genetic determinist ideas, especially in the form ofexplanations for health and disease, are powerful forces in oursociety (Lewontin 1993). Their pervasive influence, however,requires some explanation because the purely scientificevidence for genetic causation has always been weak, sinceit depended heavily on disputed heritability studies. Tounderstand the significance a repudiation of inherited DNA asa disease explanation has, it is first necessary to understandthe role genetic determinism plays in consolidating the socialorder.

Politicians like genetic determinism as a theory of diseasebecause it substantially reduces their responsibility forpeoples ill-health. By shifting blame towards individuals andtheir genetic predispositions it greatly dilutes the pressurethey may feel to regulate, ban, or tax harmful products andcontaminants, courses of action that typically offend theirbusiness constituents. For a politician, therefore, spendingtax dollars on medical genetics is an easy and even populardecision.

Corporations like genetic determinism, again because it shiftsblame. The Salt Institute website, for example, currentlymaintains that diseases linked to salt reflect the existence ofa small number of highly predisposed individuals. Thisassertion, sandwiched (on the website ) between otherquestions about salt and health, is clearly intended toundermine efforts to restrict salt in the diet. For the samereason, the tobacco industry has for many years encouragedresearch into the genetics of nicotine addiction (Gundle et al.2010). This same reasoning, that disease is the fault of thevictims genes, also protects corporate defendants from after-the-fact liability. If lung cancer patients, for example, sufferfrom even the possibility of a genetic predisposition, suingtobacco companies is very much harder than it would beotherwise (Tokuhata and Lilienfeld, 1963). There is evidence,too, that genetic determinism influences decisions well beforethe full facts are known. At least sometimes, it can evenencourage the vendor knowingly to place on the marketproducts with harmful effects (Gundle et al. 2010).

Medical researchers are also partial to genetic determinism.They have noticed that whenever they focus on geneticcausation, they can raise research dollars with relative ease.The last fifteen years, coinciding with the rise of medicalgenetics, have seen unprecedented sums of money directedat medical research. At the same time, research on pollution,nutrition and epidemiology has not benefited in anycomparable way. It is hard not to conclude that this fundingdisparity is strongly influenced by the fit of genetics to theneeds of businesses and politicians. In the words of HomerSimpson, It takes two to lie, Marge. One to lie and one tolisten.

Recognising their value, these groups have tended to elevategenetic explanations for disease to the status of unquestionedscientific facts, thus making their dominance of officialdiscussions of health and disease seem natural and logical.This same mindset is accurately reflected in the media whereeven strong environmental links to disease often receive littleattention, while speculative genetic associations can be frontpage news . It is astonishing to think that all this hasoccurred in spite of the reality that genes for commondiseases were essentially hypothetical entities.

Mutually convenient or not, by the criteria normally applied inscience, the hypothesis that genes are significant causes ofcommon diseases stands refuted. The history of scientificrefutation, however, is that adherents of established theoriesconstruct ever more elaborate or unlikely explanations to fendoff their critics (Ziman 2000). The invocation of genetic darkmatter and the search for hiding genetic variation shows thatthe process of special pleading is already well underway (e.g.Manolio et al. 2009; Eichler et al. 2010). Implausible thoughthe suggested hiding places seem, it is nevertheless going tobe difficult to rule them all out in the near future.Consequently, those geneticists wishing to do so will have theopportunity to obfuscate for some while yet.

Needed: A declaration of dependence

In societies, including our own, much of the social fabric isarranged around our conception of the proper place of death

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and disease. Confidence in the genetic paradigm has led usto explain non-infectious disease as primarily a naturalmanifestation of genetic predispositions and thus a normaloutcome of aging. This normalisation of diseases hasobscured the contrary evidence that these same diseasescan be all but absent in other cultures and often were rare inhistorical times. With the GWA results confirming theepidemiological studies, however, we are confronted with thenecessity of constructing a new narrative. To be consistentwith the facts, this new narrative must incorporate Westerndiseases not as unavoidable, but as indicators of humanfragility in the face of industrialisation and modern life.

That we are so vulnerable to our social and physicalsurroundings, is an uncompromising message. But to the verybest of our scientific knowledge it is the truth. Fortunately, itis a truth that offers hope. If we can change our environmentfor the worse, we can also change it for the better. And if amagic medical cure-all pill is not going to materialise after all,it may be that it wasnt needed in the first place.

Change for better health can occur in part through individualeffort. The new understanding implies that we are not fated todevelop any of the common diseases and that the efforts wemake to eat well and live a healthy life will be amply rewarded.We should not be surprised if specific lifestyle changes canreverse decades of disease progression (Esselstyn et al.1995). Or that Seventh Day Adventists, who are non-smoking,non-drinking vegetarians, live on average to 88, eight yearsbeyond the average Americans life expectancy (Fraser andShavlik 2001). These examples suggest what can be achievedwith relatively modest lifestyle changes. By focusing moreexclusively on health-related lifestyle modifications than evenSeventh Day Adventists do, we could probably extend our lifeexpectancy still further. Exactly how much further is now amuch more interesting question than we previously thought.

For most people, life expectancy is only truly of value if it isaccompanied by life quality. We should expect, however, anyfuture diminution of the burden of degenerative diseases fromlifestyle modification to both extend life expectancy andenhance life quality7. If so, it might make the most commonend-of-life experience very different from the actual prospectfacing most Westerners for whom old age is commonly aprocess of ever more aggressive medical interventionculminating in a hospital room attached to drips andelectrodes.

While individual effort has a place, many positive lifestyle andsocial changes require the cooperation of the state.Nevertheless, most governments cooperate far more, forexample, with their food industries than with those who wishto eat a healthy diet. The laying to rest of genetic determinismfor disease, however, provides an opportunity to shift thiscynical political calculus. It raises the stakes by confrontingpolicy-makers as never before with the fact that they haveevery opportunity, through promoting food labeling, taxing junkfood, or funding unbiased research, to help their electoratesmake enormously positive lifestyle choices. And, when theirconstituents realise that current policies are robbing every oneof them of perhaps whole decades of healthy living, thesecitizens might start to apply the necessary political pressure.

Addendum:Following publication of The Great DNA Data Deficit variousreaders have contacted us with relevant publications andbooks of which we were unaware. These importantcontributions to the issue of whether genes might causedisease extend or otherwise support the discussionconsiderably. They are listed below in chronological order. Oursincere thanks to readers for sending these in:

Clerget-Darpoux, F. and Cambon-Thomsen, A. (2010) Howseriously should we take risk predictions formultifactorial illnesses? Text endorsed by a communityof 11 French professional societies involved in genetic issues.Jay Joseph and Carl Ratner (2010) The Fruitless Search forGenes in Psychiatry and Psychology: Time to Re-examine a Paradigm?Claudia Chaufan (2007) How much can a large populationstudy on genes, environments, their interactions andcommon diseases contribute to the health of theAmerican people? Social Science & Medicine 65: 1730-

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1741.Helen M. Wallace (2006) A model for gene-gene andgene-environment interactions and its implications fortargeting environmental interventions by genotype.Theoretical Biology and Medical Modelling 3: 35-58.Jay Joseph The Missing Gene (2006)Buchanan, A; Weiss K and Fullerton S Dissecting complexdisease: the quest for the Philosophers Stone? (2005)Jay Joseph The Gene Illusion (2004)Jay Joseph (2002) Twin studies in psychiatry andpsychology: science or pseudoscience? PsychiatricQuarterly 73: 71-82.Joseph D Terwilliger and Kenneth M Weiss Linkagedisequilibrium mapping of complex disease: fantasy orreality? Current Opinion in Biotechnology 9: 578-594(1998)

Footnotes

(1) Genes for disease is shorthand for genetic variantspredisposing the carrier to disease.

(2) The definition of a genetically rare disease is usually that itaffects fewer than 1 in 1,000 people. Approximately 6,000 rarediseases have been identified in humans.

(3) The famous alleles BRCA 1 and 2 are important in somefamilies and populations but otherwise are fairly rare.

(4) According to the World Health Organisation, heart diseasecauses 17.1% of all deaths worldwide. Cancer causes 15% ofall deaths. Stroke causes 10% of all deaths. WHOfactsheet .

(5) The explanation of the contradiction between the GWAstudies and the newspaper reports is that much of thiscoverage was hype. Almost without exception thesenewspaper reports covered discoveries whose significancecould be questioned. Typically, they concernedunsubstantiated results, or the genes were for very minordiseases or the medical and genetic implications of thediscovery were substantially overplayed.

(6) Why geneticists disagree about heritability has a historicalcontext that usefully illuminates this issue. Once upon a timethe term heritability was used differently. When Sewall Wright,one of the founders of genetics, developed the concept ofheritability, he titled a key paper The Relative Importance ofHeredity and Environment in Determining the Piebald Patternof Guinea Pigs (Wright, 1920). He used this title even thoughall animals in the study were kept in identical conditions.Clearly, therefore, he wasnt defining environment as we nowdo. Instead, in that paper he explicitly defined environment asthe irregularities of development due to the intangible sorts ofcauses to which the word chance is applied. All of thesubsequent questions (like Lewontins) surrounding thevalidity of twin studies have arisen precisely because Wrightsmethod, which defined heritability in opposition to chancevariations in development, was extended to populations ofhumans living in variable and varying environments.

(7) In popular speech, aging and degeneration are oftenconflated, leading sometimes to a rejection of health adviceas simply life-span extension. However, aging, by definition, issimply the passage of time and research shows that typically,extended life expectancy is correlated with improved health,when age is taken into account (Fraser and Shavlik 2001). Incase one is tempted to confuse aging and disease, it may behelpful to think of children. For them, aging is a process ofbecoming stronger.

ReferencesBarrett J. et al. (2008) Genome-wide association defines morethan 30 different susceptibility loci for Crohns disease. NatureGenet. 40: 955-962.Barrett J. et al. (2009) Genome-wide association study andmeta-analysis find that over 40 different loci affect risk of type1 diabetes. Nature Genet. 41: 703-707.Campbell T.C. and Campbell T.M. (2008) The China Study.Benbella books, Inc. USACollins F.S. (2009) The Language of Life. Harper, NY, USA.Conrad D.F. et al. (2010) Origins and functional impact ofcopy number variation in the human genome. Nature 464:

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704-712.Dermitzakis E.T. and Clark A.G. (2009) Life after GWAstudies. Science 326: 239-240.Gundle K. et al. (2010) To prove this is industrys best hope:big tobaccos support of research on the genetics of nicotineaddiction. Addiction 105: 974-983.Eichler, E. et al. (2010) Missing heritability and strategies forfinding the underlying causes of complex disease. NatureGenetics 11: 446.Essselstyn C.S., Ellis S.G. Medendorp S.V., Crowe T.D.(1995) A strategy to arrest and reverse coronary arterydisease: a 5-year longitudinal study of a single physicianspractice. J. Family Practice 41: 560-568.Fraser G.S. and Shavlik D.J. (2001) Ten Years of Life: Is It aMatter of Choice? Arch. Int. Medicine 161: 1645-52.Hindorff L. et al. (2009) Potential etiologic and functionalimplications of genome-wide association loci for humandiseases and traits. Proc. Natl. Acad. Sci 106: 9362-67.Ioannidis, JPA, Castaldi P. and Evangelou E. (2010) ACompendium of Genome-Wide Associations for Cancer:Critical Synopsis and Reappraisal. J. of the National CancerInstitute 102: 846-858.Lewontin R.C., Rose S. and Kamin L.J. (1984) Not in ourgenes. Pantheon books New York, USA.Lewontin R.C. (1993) Biology as ideology Penguin books NewYork, USA.Maller J. et al. (2006) Common variation in three genes,including a non-coding variant in CFH, strongly influences riskof age-related macular degeneration. Nature Genet. 38: 1055-59.Manolio T. et al. (2009) Finding the missing heritability ofcomplex diseases. Nature 461: 747-753.Miki Y. et al. (1994) A strong candidate for the breast andovarian cancer susceptibility gene BRCA1. Science: 266 66-71.Mozaffarian D., Kamineni A., Carnethon M., Djouss L.,Mukamal K.J., and Siscovick D. (2009) Lifestyle Risk Factorsand New-Onset Diabetes Mellitus in Older Adults. Arch. Int.Med. 169: 798807.Morgan I. (2003) The biological basis of myopic refractiveerror. Clinical and Experimental Optometry 86: 276-288.Petronis A. (2010) Epigenetics as a unifying principle in theaetiology of complex traits and diseases. Nature 465: 721-727.Quinn G.E. et al. (1999) Myopia and ambient lighting at night.Nature 399: 113-14.Reiman E. et al. (1996) Preclinical Evidence of AlzheimersDisease in Persons Homozygous for the 4 Allele forApolipoprotein E. New England Journal of Medicine 334: 752-758.Rose K.A. Morgan I.G. Smith W. Mitchell P. (2002) Highheritability of myopia does not preclude rapid changes inprevalence. Clinical and Experimental Opthalmology 30: 168-172.Tokuhata G.K. and Lilienfeld A.M. (1963) Familial aggregationof lung cancer in humans. J. of the National Cancer Institute30: 289-312.Visscher P.M. et al. (2008) Heritability in the genomics era-concepts and misconceptions. Nature Rev. Genetics 9:255-266.The Wellcome Trust Consortium (2010) Genome-wideassociation study of CNV in 16,000 cases of eight commondiseases and 3,000 shared controls. Nature 464: 713-720.Wright S. (1920) The Relative Importance of Heredity andEnvironment in Determining the Piebald Pattern of GuineaPigs. Proc. Natl. Acad. Sci 6:320-332.Ziman J. (2000) Real Science: What It Is and What It Means.Cambridge University Press. UK

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CURRENTLY THERE ARE "4 COMMENTS" ON THIS ARTICLE:

Inge Lindseth says:January 21, 2012 at 7:43 pm

Hi,

Could the authors comment on this:

http://www.dailymail.co.uk/news/article-2088625/Blood-test-

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reveal-likely-live-100.html

Inge, Norway

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jrlatham says:January 23, 2012 at 1:09 am

Dear IngeDo you know where this was published? Idont see a reference. Can you send it to us/link to it in acomment?YoursJonathan

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Inge Lindseth says:January 23, 2012 at 4:25 pm

Here is the retracted version referred to in The DailyMail:http://www.sciencemag.org/content/early/2011/07/20/science.1190532.abstract?maxtoshow=&resourcetype=HWCIT&RESULTFORMAT=&FIRSTINDEX=0&searchid=1&minscore=5000&hits=10

Here is some more info on Perls: http://sph.bu.edu/index.php?Itemid=366&articleid=2941&id=623&option=com_insidernews&task=view

SincerelyInge

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jrlatham says:January 23, 2012 at 10:04 pm

IngePerhaps when there is a publication todiscuss we can go further with this discussion, but the(now retracted) Science paper was a very surprising resultin that no-one else has mapped such strong geneticinfluences. That it would end up attracting methodologicalcriticism and end up retracted is not a big surprise, in myopinion.Jonathan

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