Copy number variants and common disorders: filling the gaps and exploring complexity in genome-wide association studies

Genetic epidemiology in aging research

Over the last two decades, aging research has expanded to include not only age-related disease models, and conversely, longevity and disease-free models, but also focuses on biological mechanisms related to the aging process. By viewing aging on multiple research frontiers, we are rapidly expanding knowledge as a whole and mapping connections between biological processes and particular age-related diseases that emerge. This is perhaps most true in the field of genetics, where variation across individuals has improved our understanding of aging mechanisms, etiology of age-related disease, and prediction of therapeutic responses. A close partnership between gerontologists, epidemiologists, and geneticists is needed to take full advantage of emerging genome information and technology and bring about a new age for biological aging research. Here we review current genetic findings for aging across both disease-specific and aging process domains. We then highlight the limitations of most work to date in terms of study design, genomic information, and trait modeling and focus on emerging technology and future directions that can partner genetic epidemiology and aging research fields to best take advantage of the rapid discoveries in each.

Is there still a need for candidate gene approaches in the era of genome-wide association studies?

Most genetic variants associated with complex diseases in humans are believed to have a small impact on risk. With traditional candidate gene/pathway approaches several associations with disease risk could be identified. However, now that genome-wide association studies are feasible, the question arises if there is still a need for these approaches. By using HapMap data, we evaluated to which extent commercially available microarrays cover, through linkage disequilibrium, all currently known genes and biological processes in different populations. Furthermore, we estimated the power to detect an association with any specific SNP. Our study shows that coverage of individual genes and pathways by current commercial genotyping platforms is satisfactory for the vast majority of RefSeq gene regions. However, depending on the gene or the population, there may still be a need for candidate gene approaches, especially when looking at polymorphisms with low allele frequencies.

Contemplating effects of genomic structural variation

Two developments have sparked new directions in the genetics-to-genomics transition for research and medical applications: the advance of whole-genome assays by array or DNA sequencing technologies, and the discovery among human genomes of extensive submicroscopic genomic structural variation, including copy number variation. For health care to benefit from interpretation of genomic data, we need to know how these variants contribute to the phenotype of the individual. Research is revealing the spectrum, both in size and complexity, of structural genotypic variation, and its association with a broad range of human phenotypes. Genomic disorders associated with relatively large, recurrent contiguous variants have been recognized for some time, as have certain Mendelian traits associated with functional disruption of single genes by structural variation. More recent examples from phenotype- and genotype-driven studies demonstrate a greater level of complexity, with evidence of incremental dosage effects, gene interaction networks, buffering and modifiers, and position effects. Mechanisms underlying such variation are emerging to provide a handle on the bulk of human variation, which is associated with complex traits and adaptive potential. Interpreting genotypes for personalized health care and communicating knowledge to the individual will be significant challenges for genomics professionals.

Copy number variation in the CCL4L gene is associated with susceptibility to acute rejection in lung transplantation

Lung transplantation (LT) has become an accepted therapy for selected patients with advanced lung disease. One of the main limitations to successful LT is rejection of the transplanted organ where chemokines are pivotal mediators. Here, we test the relationship between copy number variation (CNV) in the CCL4L chemokine gene and rejection risk in LT patients (n=161). Patients with no acute rejection showed a significantly lower mean number of CCL4L copies than patients that showed acute rejection (1.66 vs 1.96, P=0.014), with an even greater number of gene copies seen in patients with more than one episode of acute rejection (1.66 vs 2.30, P=0.001). Additionally, patients with > or =2 CCL4L copies had a significantly higher risk of acute rejection compared with patients that had 0-1 CCL4L copies (odds ratio 2.65; 95% confidence interval, 1.33-5.28; P=0.0046). A combined analysis of CCL4L CNV and the rs4796195 CCL4L single nucleotide polymorphism demonstrated that the effect of CCL4L copy number in acute rejection is mainly because of the number of copies of the CCL4L1 allelic variant. This finding constitutes the first report of CNV as a correlate factor in allograft rejection.

Physiologically based toxicokinetic models and their application in human exposure and internal dose assessment

Human populations may exhibit large interindividual variation in toxicokinetic response to chemical exposures. Rapid developments in dosimetry research have brought medicine and public health closer to understanding the biological basis of this heterogeneity. The toxicokinetic behavior of chemicals is, in part, controlled by the properties of the epithelium surrounding organs, some of which are effective barriers to penetration into the systemic circulation. Physiologically based toxicokinetic (PBTK) models have been developed and used to simulate the mechanism of uptake into the systemic circulation, to extrapolate between doses and exposure routes, and to estimate internal dosimetry and sources of heterogeneity in animals and humans. Recent improvements to PBTK models include descriptions of active transport across biological membranes, carrier-mediated clearance, and fractal kinetics. The expanding area of toxicogenetics has provided valuable insight for delineating toxicokinetic differences between individuals; genetic differences include inherited single nucleotide polymorphisms, copy number variants, and dynamic changes in the methylation pattern of imprinted genes. This chapter discusses the structure of PBTK models and how toxicogenetic information and newer biological descriptions have improved our understanding of variability in response to toxicant exposures.

Glutamate Neurotransmission in Psychotic Disorders and Substance Abuse

Psychotropic substance abuse and addiction are very prevalent among individuals with major psychiatric disorders world wide. However, this significant association is poorly explained. The dopaminergic circuits have been implemented in addiction as well as in schizophrenia. Recently the important role of glutamatergic neurotransmission has gained attention and current theoretical models of psychosis and substance abuse support the role of interactions between glutamate and other neurotransmitters in the patho-physiology of both disorders. However, the identification of the underlying genetic risk factors remains challenging and not a single genomic variant has been identified with certainty, possibly due to important limitations of the methods used. Clinical trials with glutamatergic neurotransmission modulators, even though still controversial, support the role of glutamate in psychosis and justify further research.

The future of genetics in psychology and psychiatry: microarrays, genome-wide association, and non-coding RNA

BACKGROUND

Much of what we thought we knew about genetics needs to be modified in light of recent discoveries. What are the implications of these advances for identifying genes responsible for the high heritability of many behavioural disorders and dimensions in childhood?

METHODS

Although quantitative genetics such as twin studies will continue to yield important findings, nothing will advance the field as much as identifying the specific genes responsible for heritability. Advances in molecular genetics have been driven by technology, especially DNA microarrays the size of a postage stamp that can genotype a million DNA markers simultaneously. DNA microarrays have led to a dramatic shift in research towards genome-wide association (GWA) studies. The ultimate goal of GWA is to sequence each individual's entire genome, which has begun to happen.

RESULTS

GWA studies suggest that for most complex traits and common disorders genetic effects are much smaller than previously considered: The largest effects account for only 1% of the variance of quantitative traits. This finding implies that hundreds of genes are responsible for the heritability of behavioural problems in childhood, and that it will be difficult to identify reliably these genes of small effect. Another discovery with far-reaching implications for future genetic research is the importance of non-coding RNA (DNA transcribed into RNA but not translated into amino acid sequences), which redefines what the word gene means. Non-coding RNA underlines the need for a genome-wide approach that is not limited to the 2% of DNA responsible for specifying the amino acid sequences of proteins.

CONCLUSIONS

The only safe prediction is that the fast pace of genetic discoveries will continue and will increasingly affect research in child psychology and psychiatry. DNA microarrays will make it possible to use hundreds of genes to predict genetic risk and to use these sets of genes in top-down behavioural genomic research that explores developmental change and continuity, multivariate heterogeneity and co-morbidity, and gene-environment interaction and correlation. A crucial question is whether the prediction of genetic risk will be sufficiently robust to translate into genetically based diagnoses, personalized treatments, and prevention programmes.

A bird's-eye view of sex chromosome dosage compensation

Intensive study of a few genetically tractable species with XX/XY sex chromosomes has produced generalizations about the process of sex chromosome dosage compensation that do not fare well when applied to ZZ/ZW sex chromosome systems, such as those in birds. The inherent sexual imbalance in dose of sex chromosome genes has led to the evolution of sex-chromosome-wide mechanisms for balancing gene dosage between the sexes and relative to autosomal genes. Recent advances in our knowledge of avian genomes have led to a reexamination of sex-specific dosage compensation (SSDC) in birds, which is less effective than in known XX/XY systems. Insights about the mechanisms of SSDC in birds also suggest similarities to and differences from those in XX/XY species. Birds are thus offering new opportunities for studying dosage compensation in a ZZ/ZW system, which should shed light on the evolution of SSDC more broadly.

A novel custom high density-comparative genomic hybridization array detects common rearrangements as well as deep intronic mutations in dystrophinopathies

Background

The commonest pathogenic DMD changes are intragenic deletions/duplications which make up to 78% of all cases and point mutations (roughly 20%) detectable through direct sequencing. The remaining mutations (about 2%) are thought to be pure intronic rearrangements/mutations or 5'-3' UTR changes. In order to screen the huge DMD gene for all types of copy number variation mutations we designed a novel custom high density comparative genomic hybridisation array which contains the full genomic region of the DMD gene and spans from 100 kb upstream to 100 kb downstream of the 2.2 Mb DMD gene.

Results

We studied 12 DMD/BMD patients who either had no detectable mutations or carried previously identified quantitative pathogenic changes in the DMD gene. We validated the array on patients with previously known mutations as well as unaffected controls, we identified three novel pure intronic rearrangements and we defined all the mutation breakpoints both in the introns and in the 3' UTR region. We also detected a novel polymorphic intron 2 deletion/duplication variation. Despite the high resolution of this approach, RNA studies were required to confirm the functional significance of the intronic mutations identified by CGH. In addition, RNA analysis identified three intronic pathogenic variations affecting splicing which had not been detected by the CGH analysis.

Conclusion

This novel technology represents an effective high throughput tool to identify both common and rarer DMD rearrangements. RNA studies are required in order to validate the significance of the CGH array findings. The combination of these tools will fully cover the identification of causative DMD rearrangements in both coding and non-coding regions, particularly in patients in whom standard although extensive techniques are unable to detect a mutation.

Adaptive copy number evolution in malaria parasites

Copy number polymorphism (CNP) is ubiquitous in eukaryotic genomes, but the degree to which this reflects the action of positive selection is poorly understood. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive CNP. We provide compelling evidence that gch1 CNP is an adaptive consequence of selection by antifolate drugs, which target enzymes downstream in this pathway. (1) We compared gch1 CNP in parasites from Thailand (strong historical antifolate selection) with those from neighboring Laos (weak antifolate selection). Two percent of chromosomes had amplified copy number in Laos, while 72% carried multiple (2–11) copies in Thailand, and differentiation exceeded that observed at 73 synonymous SNPs. (2) We found five amplicon types containing one to greater than six genes and spanning 1 to >11 kb, consistent with parallel evolution and strong selection for this gene amplification. gch1 was the only gene occurring in all amplicons suggesting that this locus is the target of selection. (3) We observed reduced microsatellite variation and increased linkage disequilibrium (LD) in a 900-kb region flanking gch1 in parasites from Thailand, consistent with rapid recent spread of chromosomes carrying multiple copies of gch1. (4) We found that parasites bearing dhfr-164L, which causes high-level resistance to antifolate drugs, carry significantly (p = 0.00003) higher copy numbers of gch1 than parasites bearing 164I, indicating functional association between genes located on different chromosomes but linked in the same biochemical pathway. These results demonstrate that CNP at gch1 is adaptive and the associations with dhfr-164L strongly suggest a compensatory function. More generally, these data demonstrate how selection affects multiple enzymes in a single biochemical pathway, and suggest that investigation of structural variation may provide a fast-track to locating genes underlying adaptation.

Recent comparative genomic hybridization studies have revealed extensive copy number variation in eukaryotic genomes. The first gene in the Plasmodium folate biosynthesis pathway, GTP-cyclohydrolase I (gch1), shows extensive copy number polymorphism (CNP). We provide compelling evidence that gch1 CNP is adaptive and most likely results from selection by antifolate drugs, which target enzymes downstream in this pathway. Gch1 CNP shows extreme geographical differentiation; hitchhiking reduces diversity and increases LD in flanking sequence, indicating recent rapid spread within Thailand, while amplicon structure reveals multiple origins and parallel evolution. Furthermore, strong association between elevated copy number and a critical mutation dhfr-I164L that underlies high-level antifolate resistance indicates functional linkage and fitness epistasis between genes on different chromosomes. These data reveal hidden complexity in the evolutionary response to antifolate treatment and demonstrate that analysis of structural variation can provide a fast-track to locating genes that underlie adaptation.

Modeling genetic inheritance of copy number variations

Copy number variations (CNVs) are being used as genetic markers or functional candidates in gene-mapping studies. However, unlike single nucleotide polymorphism or microsatellite genotyping techniques, most CNV detection methods are limited to detecting total copy numbers, rather than copy number in each of the two homologous chromosomes. To address this issue, we developed a statistical framework for intensity-based CNV detection platforms using family data. Our algorithm identifies CNVs for a family simultaneously, thus avoiding the generation of calls with Mendelian inconsistency while maintaining the ability to detect de novo CNVs. Applications to simulated data and real data indicate that our method significantly improves both call rates and accuracy of boundary inference, compared to existing approaches. We further illustrate the use of Mendelian inheritance to infer SNP allele compositions in each of the two homologous chromosomes in CNV regions using real data. Finally, we applied our method to a set of families genotyped using both the Illumina HumanHap550 and Affymetrix genome-wide 5.0 arrays to demonstrate its performance on both inherited and de novo CNVs. In conclusion, our method produces accurate CNV calls, gives probabilistic estimates of CNV transmission and builds a solid foundation for the development of linkage and association tests utilizing CNVs.

Recurrent CNVs disrupt three candidate genes in schizophrenia patients

Schizophrenia is a severe psychiatric disease with complex etiology, affecting approximately 1% of the general population. Most genetics studies so far have focused on disease association with common genetic variation, such as single-nucleotide polymorphisms (SNPs), but it has recently become apparent that large-scale genomic copy-number variants (CNVs) are involved in disease development as well. To assess the role of rare CNVs in schizophrenia, we screened 54 patients with deficit schizophrenia using Affymetrix's GeneChip 250K SNP arrays. We identified 90 CNVs in total, 77 of which have been reported previously in unaffected control cohorts. Among the genes disrupted by the remaining rare CNVs are MYT1L, CTNND2, NRXN1, and ASTN2, genes that play an important role in neuronal functioning but--except for NRXN1--have not been associated with schizophrenia before. We studied the occurrence of CNVs at these four loci in an additional cohort of 752 patients and 706 normal controls from The Netherlands. We identified eight additional CNVs, of which the four that affect coding sequences were found only in the patient cohort. Our study supports a role for rare CNVs in schizophrenia susceptibility and identifies at least three candidate genes for this complex disorder.

The biological effects of simple tandem repeats: lessons from the repeat expansion diseases

Tandem repeats are common features of both prokaryote and eukaryote genomes, where they can be found not only in intergenic regions but also in both the noncoding and coding regions of a variety of different genes. The repeat expansion diseases are a group of human genetic disorders caused by long and highly polymorphic tandem repeats. These disorders provide many examples of the effects that such repeats can have on many biological processes. While repeats in the coding sequence can result in the generation of toxic or malfunctioning proteins, noncoding repeats can also have significant effects including the generation of chromosome fragility, the silencing of the genes in which they are located, the modulation of transcription and translation, and the sequestering of proteins involved in processes such as splicing and cell architecture.

Translational mini-review series on the immunogenetics of gut disease: immunogenetics of coeliac disease

Recent advances in immunological and genetic research in coeliac disease provide new and complementary insights into the immune response driving this chronic intestinal inflammatory disorder. Both approaches confirm the central importance of T cell-mediated immune responses to disease pathogenesis and have further begun to highlight other relevant components of the mucosal immune system, including innate immunity and the control of lymphocyte trafficking to the mucosa. In the last year, the first genome wide association study in celiac disease led to the identification of multiple new risk variants. These risk regions implicate genes involved in the immune system. Overlap with autoimmune diseases is striking with several of these regions being shown to confer susceptibility to other chronic immune-mediated diseases, particularly type 1 diabetes.

How segmental duplications shape our genome: recent evolution of ABCC6 and PKD1 Mendelian disease genes

The completion of the Human Genome Project has brought the understanding that our genome contains an unexpectedly large proportion of segmental duplications. This poses the challenge of elucidating the consequences of recent duplications on physiology. We have conducted an in-depth study of a subset of segmental duplications on chromosome 16. We focused on PKD1 and ABCC6 duplications because mutations affecting these genes are responsible for the Mendelian disorders autosomal dominant polycystic kidney disease and pseudoxanthoma elasticum, respectively. We establish that duplications of PKD1 and ABCC6 are associated to low-copy repeat 16a and show that such duplications have occurred several times independently in different primate species. We demonstrate that partial duplication of PKD1 and ABCC6 has numerous consequences: the pseudogenes give rise to new transcripts and mediate gene conversion, which not only results in disease-causing mutations but also serves as a reservoir for sequence variation. The duplicated segments are also involved in submicroscopic and microscopic genomic rearrangements, contributing to structural variation in human and chromosomal break points in the gibbon. In conclusion, our data shed light on the recent and ongoing evolution of chromosome 16 mediated by segmental duplication and deepen our understanding of the history of two Mendelian disorder genes.

Systematic assessment of copy number variant detection via genome-wide SNP genotyping

SNP genotyping has emerged as a technology to incorporate copy number variants (CNVs) into genetic analyses of human traits. However, the extent to which SNP platforms accurately capture CNVs remains unclear. Using independent, sequence-based CNV maps, we find that commonly used SNP platforms have limited or no probe coverage for a large fraction of CNVs. Despite this, in 9 samples we inferred 368 CNVs using Illumina SNP genotyping data and experimentally validated over two-thirds of these. We also developed a method (SNP-Conditional Mixture Modeling, SCIMM) to robustly genotype deletions using as few as two SNP probes. We find that HapMap SNPs are strongly correlated with 82% of common deletions, but the newest SNP platforms effectively tag about 50%. We conclude that currently available genome-wide SNP assays can capture CNVs accurately, but improvements in array designs, particularly in duplicated sequences, are necessary to facilitate more comprehensive analyses of genomic variation.

Beyond the HapMap Genotypic Data: Prospects of Deep Resequencing Projects

The International HapMap Project provides a key resource of genotypic data on human samples including lymphoblastoid cell lines derived from individuals of four major world populations of African, European, Japanese and Chinese ancestry. Researchers have utilized this resource to identify genetic elements that correlate with various phenotypes such as risks of common diseases, individual drug response and gene expression variation. However, recent comparative studies have suggested that the currently available HapMap genotypic data may not capture a substantial proportion of rare or untyped SNPs in these populations, implying that the HapMap SNPs may not be sufficient for comprehensive association studies. In this paper, three large-scale deep resequencing projects covering the HapMap samples: ENCODE (Encyclopedia of DNA Elements), SeattleSNPs and NIEHS (National Institute of Environmental Health Sciences) Environmental Genome Project are discussed. Prospectively, once integrated with the HapMap resource, these efforts will greatly benefit the next wave of association studies and data mining using these cell lines.

Prediction of individual genetic risk of complex disease

Most common diseases are caused by multiple genetic and environmental factors. In the last 2 years, genome-wide association studies (GWAS) have identified polymorphisms that are associated with risk to common disease, but the effect of any one risk allele is typically small. By combining information from many risk variants, will it be possible to predict accurately each individual person's genetic risk for a disease? In this review we consider the lessons from GWAS and the implications for genetic risk prediction to common disease. We conclude that with larger GWAS sample sizes or by combining studies, accurate prediction of genetic risk will be possible, even if the causal mutations or the mechanisms by which they affect susceptibility are unknown.

A HapMap harvest of insights into the genetics of common disease

The International HapMap Project was designed to create a genome-wide database of patterns of human genetic variation, with the expectation that these patterns would be useful for genetic association studies of common diseases. This expectation has been amply fulfilled with just the initial output of genome-wide association studies, identifying nearly 100 loci for nearly 40 common diseases and traits. These associations provided new insights into pathophysiology, suggesting previously unsuspected etiologic pathways for common diseases that will be of use in identifying new therapeutic targets and developing targeted interventions based on genetically defined risk. In addition, HapMap-based discoveries have shed new light on the impact of evolutionary pressures on the human genome, suggesting multiple loci important for adapting to disease-causing pathogens and new environments. In this review we examine the origin, development, and current status of the HapMap; its prospects for continued evolution; and its current and potential future impact on biomedical science.

Detection, imputation, and association analysis of small deletions and null alleles on oligonucleotide arrays

Copy-number variation (CNV) is a major contributor to human genetic variation. Recently, CNV associations with human disease have been reported. Many genome-wide association (GWA) studies in complex diseases have been performed with sets of biallelic single-nucleotide polymorphisms (SNPs), but the available CNV methods are still limited. We present a new method (TriTyper) that can infer genotypes in case-control data sets for deletion CNVs, or SNPs with an extra, untyped allele at a high-resolution single SNP level. By accounting for linkage disequilibrium (LD), as well as intensity data, calling accuracy is improved. Analysis of 3102 unrelated individuals with European descent, genotyped with Illumina Infinium BeadChips, resulted in the identification of 1880 SNPs with a common untyped allele, and these SNPs are in strong LD with neighboring biallelic SNPs. Simulations indicate our method has superior power to detect associations compared to biallelic SNPs that are in LD with these SNPs, yet without increasing type I errors, as shown in a GWA analysis in celiac disease. Genotypes for 1204 triallelic SNPs could be fully imputed, with only biallelic-genotype calls, permitting association analysis of these SNPs in many published data sets. We estimate that 682 of the 1655 unique loci reflect deletions; this is on average 99 deletions per individual, four times greater than those detected by other methods. Whereas the identified loci are strongly enriched for known deletions, 61% have not been reported before. Genes overlapping with these loci more often have paralogs (p = 0.006) and biologically interact with fewer genes than expected (p = 0.004).

Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p<0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.

Hereditary pancreatitis caused by a double gain-of-function trypsinogen mutation

Hereditary pancreatitis, an autosomal dominant disease with approximately 80% penetrance, can be caused by both 'gain-of-function' missense and copy number mutations in the cationic trypsinogen gene (PRSS1). Here we demonstrate a heterozygous hybrid PRSS2 (encoding anionic trypsinogen)/PRSS1 gene in a French white family with hereditary pancreatitis, by means of quantitative fluorescent multiplex PCR and RT-PCR analyses. The hybrid gene, in which exons 1 and 2 are derived from PRSS2 and exons 3-5 from PRSS1, apparently resulted from a non-allelic homologous recombination (NAHR) event between the chromosome 7 homologs or sister chromatids during meiosis. Interestingly, this hybrid gene causes the disease through a combination of its inherent 'double gain-of-function' effect, acting simultaneously as a 'quantitative' copy number mutation and a 'qualitative' missense mutation (i.e. the known disease-causing p.N29I mutation). Our finding reveals a previously unknown mechanism causing human inherited disease, enriches the lexicon of human genetic variation and goes beyond the known interaction between copy number variations (CNVs) and single nucleotide substitutions in health and disease. Our finding should also stimulate more interest in analyzing both types of genetic variation whenever one tries to determine the contribution of a specific locus to a given disease phenotype.

Genetic approach to pediatric septic shock

Septic shock is a complex and heterogeneous clinical syndrome, triggered by infection, and having significant morbidity and mortality in children. Emerging data indicate that the genetic make-up of the pediatric host may have a strong influence on the development and outcome of septic shock in children. Herein, we review this broad topic by focusing on pediatric-specific data (both recent and historical), as well as the broad topics of SNPs, genome-wide association studies and epigenetics. The historical and emerging data strongly suggest that a genetics-based perspective will need to be considered in future investigations and strategies aimed at improving the outcome of children with septic shock.

Identifying the susceptibility genes for coronary artery disease: from hyperbole through doubt to cautious optimism

The genetic basis of coronary artery disease (CAD) is complex, and the fact that an alarmingly high proportion of reported associations between genetic variants and CAD are not replicated has generated uncertainty as to whether molecular genetics is ever going to deliver on the promises delivered in the late 1990s. However, during 2007, the first generation of large-scale genome-wide association studies using high-density, single nucleotide polymorphism genotyping arrays have revealed genetic variants that are robustly associated with CAD and CAD-related traits such as type 2 diabetes and obesity. In particular, a robust susceptibility locus for CAD has been identified on chromosome 9p21. Also, evidence has been obtained that multiple rare alleles with fairly strong phenotypic effects may contribute to the genetic heritability of CAD, in addition to common variants with a modest impact on risk. Furthermore, new mechanistic connections have been discovered between different common complex diseases including CAD. This review focuses on the challenges and recent advances of molecular genetics in dissecting the molecular pathophysiology of atherothrombosis and defining novel targets for treatment.

Genetic determinants of phenotypic diversity in humans

New techniques are enabling the identification of genetic variants underlying complex diseases and phenotypic traits.

New technologies for rapidly assaying DNA sequences have revealed that the degree and nature of human genetic variation is far more complex then previously realized. These same technologies have also resulted in the identification of common genetic variants associated with more than 30 human diseases and traits.

Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum

Background

Duplications of stretches of the genome are an important source of individual genetic variation, but their unrecognized presence in laboratory organisms would be a confounding variable for genetic analysis.

Results

We report here that duplications of 15 kb or more are common in the genome of the social amoeba Dictyostelium discoideum. Most stocks of the axenic 'workhorse' strains Ax2 and Ax3/4 obtained from different laboratories can be expected to carry different duplications. The auxotrophic strains DH1 and JH10 also bear previously unreported duplications. Strain Ax3/4 is known to carry a large duplication on chromosome 2 and this structure shows evidence of continuing instability; we find a further variable duplication on chromosome 5. These duplications are lacking in Ax2, which has instead a small duplication on chromosome 1. Stocks of the type isolate NC4 are similarly variable, though we have identified some approximating the assumed ancestral genotype. More recent wild-type isolates are almost without large duplications, but we can identify small deletions or regions of high divergence, possibly reflecting responses to local selective pressures. Duplications are scattered through most of the genome, and can be stable enough to reconstruct genealogies spanning decades of the history of the NC4 lineage. The expression level of many duplicated genes is increased with dosage, but for others it appears that some form of dosage compensation occurs.

Conclusion

The genetic variation described here must underlie some of the phenotypic variation observed between strains from different laboratories. We suggest courses of action to alleviate the problem.

The effect of pedigree structure on detection of deletions and other null alleles

Deletions and other null alleles for genetic markers can be detected as a special case of non-Mendelian inheritance, ie when a parent and a child appear to be homozygous for different alleles. The probability to detect a deletion for a fixed overall number of investigated individuals was calculated for biallelic and multiallelic markers with varying allele frequencies. To determine the effect of increasing the number of parents and grandparents, the probability for this event was derived for a parent and one child, a trio, a trio with one grandparent and a trio with two grandparents. The results for biallelic markers show that for a fixed total number of individuals, a sample of trios with two grandparents is always more efficient than the other family types, despite a lower total number of founder chromosomes in the sample. For multiallelic markers the outcome varies. The effect of adding additional children to a nuclear family was also investigated. For nuclear families, the optimal number of children is two or three, depending on the allele frequencies. It is shown that adding children is more efficient than adding grandparents.

Submicroscopic chromosome imbalance in patients with developmental delay and/or dysmorphism referred specifically for Fragile X testing and karyotype analysis

BACKGROUND

Microdeletion syndromes are generally identified because they usually give rise to specific phenotypic features; many of these deletions are mediated by duplicons or LCRs. The phenotypes associated with subtelomeric deletions are also becoming recognised. However, reciprocal duplication events at these loci are less easily recognised and identified, as they may give rise to milder phenotypic features, and the individuals carrying them may not therefore be referred for appropriate testing. 403 patients with developmental delay and/or dysmorphism, referred to our Genetics Centre for karyotyping and Fragile X expansion testing, were assessed for chromosome imbalance by Multiplex Ligation-dependent Probe Amplification (MLPA). Two MLPA kits were used, one containing probes for the subtelomere regions, and one containing probes for common microdeletion loci. 321 patients were tested with both kits, 75 with the subtelomere kit alone, and 7 with the microdeletion kit alone.

RESULTS

32 patients had abnormal results; the overall abnormality detection rate was 2.5% for karyotype analysis and 7.2% for MLPA testing; 5.5% of subtelomere tests and 2.1% of microdeletion tests gave abnormal results. Of the abnormal MLPA results, 5 were in cases with cytogenetically visible abnormalities; of the remaining, submicroscopic, changes, 3 results were established as de novo and 8 were inherited; parental samples were not available for the remaining cases. None of the patients was found to have a Fragile X expansion.

CONCLUSION

Karyotype analysis in combination with MLPA assays for subtelomeres and microdeletion loci may be recommended for this patient group.

Identification of new susceptibility markers for rheumatoid arthritis and systemic lupus erythematosus in the STAT4 gene

Evaluation of: Remmers EF, Plenge RM, Lee AT et al.: STAT4 and the risk of rheumatoid arthritis and systemic lupus erythematosus. N. Engl. J. Med. 6(10), 977–986 (2007). Rheumatoid arthritis is an autoimmune disease with a strong genetic component. The genetic component of rheumatoid arthritis is thought to be complex, with a wide number of predisposing alleles, each of them conferring a modest risk. The identification of the genetic component of complex diseases is of great interest, since a fuller understanding of disease etiology and pathogenesis is expected to lead to improved risk predictions for susceptibility, severity and outcome and, ultimately, may lead to the development of novel therapies. Until very recently, only two reproducible genetic associations were described. For 30 years, only HLA genes have been identified as sufficiently validated rheumatoid arthritis genetic risk factors. A second, more modest, association has been recently identified with the PTPN22 gene. In the study by Remmers et al., a new susceptibility marker for rheumatoid arthritis is identified, the STAT4 rs7574865 polymorphism. Interestingly, this SNP is also associated with systemic lupus erythematosus.

The road to genome-wide association studies

The recent crop of results from genome-wide association studies might seem like a sudden development. However, this blooming follows a long germination period during which the necessary concepts, resources and techniques were developed and assembled. Here, I look back at how the necessary pieces fell into place, focusing on the less well-chronicled days before the launch of the HapMap project, and speculate about future developments.