An epidemiological perspective on the future of direct-to-consumer personal genome testing

Personal genome testing is offered via the internet directly to consumers. Most tests that are currently offered use data from genome-wide scans to predict risks for multiple common diseases and traits. The utility of these tests is limited, predominantly because they lack predictive ability and clear benefits for disease prevention that are specific for genetic risk groups. In the near future, personal genome tests will likely be based on whole genome sequencing, but will these technological advances increase the utility of personal genome testing? Whole genome sequencing theoretically provides information about the risks of both monogenic and complex diseases, but the practical utility remains to be demonstrated. The utility of testing depends on the predictive ability of the test, the likelihood of actionable test results, and the options available for the reduction of risks. For monogenic diseases, the likelihood of known mutations will be extremely low in the general population and it will be a challenge to recognize new causal variants among all rare variants that are found using sequencing. For complex diseases, the predictive ability of genetic tests will be mainly restricted by the heritability of the disease, but also by the genetic complexity of the disease etiology, which determines the extent to which the heritability can be understood. Given that numerous genetic and non-genetic risk factors interact in the causation of complex diseases, the predictive ability of genetic models will likely remain modest. Personal genome testing will have minimal benefits for individual consumers unless major breakthroughs are made in the near future

Runs of homozygosity do not influence survival to old age

Runs of homozygosity (ROH) are extended tracts of adjacent homozygous single nucleotide polymorphisms (SNPs) that are more common in unrelated individuals than previously thought. It has been proposed that estimating ROH on a genome-wide level, by making use of the genome-wide single nucleotide polymorphism (SNP) data, will enable to indentify recessive variants underlying complex traits. Here, we examined ROH larger than 1.5 Mb individually and in combination for association with survival in 5974 participants of the Rotterdam Study. In addition, we assessed the role of overall homozygosity, expressed as a percentage of the autosomal genome that is in ROH longer than 1.5 Mb, on survival during a mean follow-up period of 12 years. None of these measures of homozygosity was associated with survival to old age

Insulin VNTR and IGF-1 promoter region polymorphisms are not associated with body composition in early childhood: The generation R study

Objective: The objective of this study was to examine the associations between insulin gene variable number of tandem repeats (INS VNTR) and insulin-like growth factor 1 (IGF1) gene promoter region polymorphisms with body composition in early childhood. Methods: This study was embedded in an ongoing prospective cohort study. Growth in early childhood (body mass index, total subcutaneous fat mass and waist-hip ratio) was assessed at birth and at the ages of 6 weeks and 24 months. DNA for genotyping was available in 738 children. Results: The genotype distribution of the INS VNTR gene was I/I 50.4%, I/III 40.4%, and III/III 9.2%. IGF1 genotypes were categorized in the following categories based on their 192-bp allele: homozygous (wild-type) 43.1%, heterozygous 45.8%, and noncarrier 11.2%. No differences were found in body mass index, total subcutaneous fat mass and waist-hip ratio in early childhood between the three groups for both the INS VNTR and IGF1 genotypes. We also did not find interactions between these genotypes and gender or birth weight on the effects of body composition measures. Conclusions: Our results do not support previous studies showing associations between INS VNTR and IGF1 promoter region polymorphisms with body composition in early childhood. Copyrigh

Determinants of DNA yield and purity collected with buccal cell samples

Buccal cells are an important source of DNA in epidemiological studies, but little is known about factors that influence amount and purity of DNA. We assessed these factors in a self-administered buccal cell collection procedure, obtained with three cotton swabs. In 2,451 patients DNA yield and in 1,033 patients DNA purity was assessed. Total DNA yield ranged from 0.08 to 1078.0 μg (median 54.3 μg; mean 82.2 μg ± SD 92.6). The median UV 260:280 ratio, was 1.95. Samples from men yielded significantly more DNA (median 58.7 μg) than those from women (median 44.2 μg). Diuretic drug users had significantly lower purity (median 1.92) compared to other antihypertensive drug users (1.95). One technician obtained significantly lower DNA yields. Older age was associated with lower DNA purity. In conclusion, DNA yield from buccal swabs was higher in men and DNA purity was associated with age and the use of diuretics

The Molecular Genetic Architecture of Self-Employment

Economic variables such as income, education, and occupation are known to affect mortality and morbidity, such as cardiovascular disease, and have also been shown to be partly heritable. However, very little is known about which genes influence economic variables, although these genes may have both a direct and an indirect effect on health. We report results from the first large-scale collaboration that studies the molecular genetic architecture of an economic variable-entrepreneurship-that was operationalized using self-employment, a widely-available proxy. Our results suggest that common SNPs when considered jointly explain about half of the narrow-sense heritability of self-employment estimated in twin data (σg2/σP2= 25%, h2= 55%). However, a meta-analysis of genome-wide association studies across sixteen studies comprising 50,627 participants did not identify genome-wide significant SNPs. 58 SNPs with p<10-5were tested in a replication sample (n = 3,271), but none replicated. Furthermore, a gene-based test shows that none of the genes that were previously suggested in the literature to influence entrepreneurship reveal significant associations. Finally, SNP-based genetic scores that use results from the meta-analysis capture less than 0.2% of the variance in self-employment in an independent sample (p≥0.039). Our results are consistent with a highly polygenic molecular genetic architecture of self-employment, with many genetic variants of small effect. Although self-employment is a multi-faceted, heavily environmentally influenced, and biologically distal trait, our results are similar to those for other genetically complex and biologically more proximate outcomes, such as height, intelligence, personality, and several diseases

Physical activity attenuates the influence of FTO variants on obesity risk: A meta-analysis of 218,166 adults and 19,268 children

Background: The FTO gene harbors the strongest known susceptibility locus for obesity. While many individual studies have suggested that physical activity (PA) may attenuate the effect of FTO on obesity risk, other studies have not been able to confirm this interaction. To confirm or refute unambiguously whether PA attenuates the association of FTO with obesity risk, we meta-analyzed data from 45 studies of adults (n = 218,166) and nine studies of children and adolescents (n = 19,268). Methods and Findings: All studies identified to have data on the FTO rs9939609 variant (or any proxy [r2>0.8]) and PA were invited to participate, regardless of ethnicity or age of the participants. PA was standardized by categorizing it into a dichotomous variable (physically inactive versus active) in each study. Overall, 25% of adults and 13% of children were categorized as inactive. Interaction analyses were performed within each study by including the FTO×PA interaction term in an additive model, adjusting for age and sex. Subsequently, random effects meta-analysis was used to pool the interaction terms. In adults, the minor (A-) allele of rs9939609 increased the odds of obesity by 1.23-fold/allele (95% CI 1.20-1.26), but PA attenuated this effect (pinteraction= 0.001). More specifically, the minor allele of rs9939609 increased the odds of obesity less in the physically active group (odds ratio = 1.22/allele, 95% CI 1.19-1.25) than in the inactive group (odds ratio = 1.30/allele, 95% CI 1.24-1.36). No such interaction was found in children and adolescents. Concl

A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes

dentification of sequence variants robustly associated with predisposition to diabetic kidney disease (DKD) has the potential to provide insights into the pathophysiological mechanisms responsible. We conducted a genome-wide association study (GWAS) of DKD in type 2 diabetes (T2D) using eight complementary dichotomous and quantitative DKD phenotypes: the principal dichotomous analysis involved 5,717 T2D subjects, 3,345 with DKD. Promising association signals were evaluated in up to 26,827 subjects with T2D (12,710 with DKD). A combined T1D+T2D GWAS was performed using complementary data available for subjects with T1D, which, with replication samples, involved up to 40,340 subjects with diabetes (18,582 with DKD). Analysis of specific DKD phenotypes identified a novel signal near GABRR1 (rs9942471, P = 4.5 x 10(-8)) associated with microalbuminuria in European T2D case subjects. However, no replication of this signal was observed in Asian subjects with T2D or in the equivalent T1D analysis. There was only limited support, in this substantially enlarged analysis, for association at previously reported DKD signals, except for those at UMOD and PRKAG2, both associated with estimated glomerular filtration rate. We conclude that, despite challenges in addressing phenotypic heterogeneity, access to increased sample sizes will continue to provide more robust inference regarding risk variant discovery for DKD.Peer reviewe

Auralliselle migreenille altistavien geneettisten alueiden tunnistaminen

Common migraine, i.e. migraine with (MA) or without aura (MO), is a chronic neurological disorder affecting about 10% of the Caucasian population. In MA, migraine headache is preceded by visual, sensoric and/or dysphasic reversible aura symptoms. Twin and family studies have suggested a multifactorial mode of inheritance for common migraine, and a stronger genetic component for MA than for MO. Since there is no biological or genetic marker to identify common migraine, aura symptoms provide a distinctive character to identify those suspected of suffering from migraine. The aim of this study was to identify MA susceptibility loci in well-phenotyped migraine samples with familial predisposition using different gene mapping methods. Genes coding for endothelin1 and its receptors EDNRA and ENDRB are potential candidate genes for cortical spreading depression (CSD), which is considered to be the underlying mechanism of migraine aura. The role of these genes in MA was studied in 850 Finnish migraine cases and 890 control individuals. Rare homozygous EDNRA SNPs showed nominal association with MA and with the age of onset trait (20 years). This result was also detected in the pooled analysis on 648 German MA cases and 651 control individuals when the test was adjusted for gender and sample origin. Evaluation of SNP genotyping reactions with two different DNA polymerase enzymes ensured that the genotype quality was high, and thus the discovered associations are considered reliable. The role of the 19p13 region was studied in a linkage analysis of 72 Finnish MA families. This region contains two migraine-associated genes: CACNA1A, which is associated with a predisposition to a rare Mendelian form of MA, familial hemiplegic migraine (FHM), and the insulin receptor gene (INSR) that is associated with common migraine. No evidence of linkage between the 19p13 and MA was detected. A novel visual aura locus was mapped to chromosome 9q21-q22 with significant evidence of linkage using a genome-wide linkage approach in 36 Finnish MA families. Five additional, potential loci were also detected. The 9q21-q22 region has previously been linked to occipitotemporal lobe epilepsy and MA, both of which involve prominent visual symptoms. Our result further supports a shared background for these episodic disorders.Migreeni on kohtauksellinen neurologinen sairaus, jonka esiintyvyys on 10-15% väestössä. Migreenipäänsärky on tavallisesti toispuoleista ja sykkivää ja pahentuu liikunnan yhteydessä. Päänsärkyä edeltää lyhytkestoinen näkö-, tunto- ja/tai puhehäiriö noin kolmanneksessa migreenikohtauksia. Tällöin kyseessä on aurallinen migreeni (MA). Migreeniauran ja päänsäryn perimmäisiä perinnöllisiä tai biologisia syitä ei tunneta. Tutkimusryhmämme on kerännyt yli 1400 migreeniperhettä ympäri Suomea vuodesta 1996 lähtien. Keräämiemme henkilöiden diagnosointi perustuu potilaan huolelliseen haastatteluun, koska migreenin tunnistamiseksi ei ole vielä olemassa biologista tai geneettistä testiä. Käyttämällä koko genomin kattavia kartoitusmenetelmiä tutkimusryhmämme on pystynyt tunnistamaan useita migreenille tai sen oireille altistavia alueita. Tässä tutkimustyössä selvitettiin erityisesti aurallisen migreenin perinnöllistä taustaa. Endoteliini1 ja sen reseptorit EDNRA ja EDNRB osallistuvat verisuonten seinämien liikkeisiin, jolla voi olla merkitystä migreeniaurassa. Näiden geenien liittymistä migreeniin tutkittiin vertaamalla 850 yksittäistä MA-potilasta 890 terveeseen verrokkihenkilöön. Sekä isältä että äidiltä periytyvän EDNRA-geenin harvinaisen emäsmuutoksen todettiin osoittavan viitteellistä MA-alttiutta suomalaisissa potilaissa. Väitöskirjatyössä tutkittiin myös kromosomi 19p13-alueen kytkeytymistä auralliseen migreeniin 72 suomalaisessa migreeniperheessä. Alueella sijaitsee kaksi migreeniin aikaisemmin liitettyä geeniä: kalsiumionikanavaa koodaava geeni CACNA1A ja insuliinireseptoria koodaava geeni INSR. Näistä CACNA1A-geenin emäsmuutosten tiedetään altistavan aurallisen migreenin harvinaiselle alamuodolle familiaaliselle hemiplegiselle migreenille, jossa päänsärkyä edeltävät toispuoleiset halvauskohtaukset. Tutkimuksemme osoitti, että 19p13-alue ei kytkeydy auralliseen migreeniin ainakaan tutkimissamme suomalaisperheissä. Väitöskirjan merkittävin löydös on kromosomiin 9 kytkeytyvä näköaura-alue, joka tunnistettiin 36 tarkoin diagnosoidusta suomalaisesta MA-perheestä käyttämällä koko genomin kattavaa kartoitusmenetelmää. Löytämämme alue, 9q21-q22, on äskettäin yhdistetty harvinaiseen takaraivo-ohimolohkoepilepsiaan yhdessä belgialaisessa perheessä, jossa oli myös useita MA-potilaita. Tutkimuksemme vahvistaa aikaisempia löydöksiä, joiden mukaan nämä kaksi kohtauksellista sairautta, MA ja epilepsia, voivat jakaa yhteisiä perinnöllisiä tekijöitä