In the news

Combine genetic variants with prostate-specific antigen (PSA) testing to improve the performance of prostate cancer screening

A genome-wide association study was performed to locate genetic variants associated with PSA levels, based on data from 15,757 Icelandic and 454 British men not diagnosed with prostate cancer. This was followed by an assessment of the improvement in predictive accuracy of PSA testing when combined with either these genetic variants or all prostate cancer susceptibility variants in 415 Icelandic and 1,291 British men with information on biopsy-outcome (i.e. biopsy positive or negative). 

Variants at six loci were found to be associated with PSA levels, two of which were not also associated with prostate cancer risk. By applying the combined genetic effect of all 23 known PSA and prostate cancer susceptibility variants on the commonly used PSA threshold for biopsy, the test was slightly better able to discriminate between outcomes: the area under the ROC curve (AUC, which varies from 0.5-1.0, where a value of 1.0 indicates a perfect performance) improved from 0.704 to 0.732 in Icelandic men and 0.571 to 0.636 in British men. Applying this genetic correction, 6-7% of Icelandic men would be reclassified with respect to whether they should undergo biopsy.

The authors propose that a personalised PSA cut-off value, based on genotype, should be used when deciding to perform a prostate biopsy.

Although there is substantial international variation, PSA screening for prostate cancer is currently not offered systematically in the UK because it is unclear whether the benefits outweigh the harms due to the large number of false positive results (see previous news). This study is an important step towards trying to improve the balance, by using genetic factors in addition to PSA testing to determine whether a man is likely to have prostate cancer and should go on to have further testing. Although the addition of genetic variants associated with prostate cancer did improve the predictive accuracy of PSA testing, the improvement was marginal and the advice for the vast majority of men would be unchanged. As the accompanying perspective points out, “although this study presents an auspicious beginning, on the basis of the AUCs and reclassification analysis, it does not appear that SNP-adjusted PSA values are primed for translation into clinical practice without additional follow-up studies”. Further large population studies are needed to investigate whether using individual genetic factors, in combination with age and other risk factors, to modulate the PSA threshold for biopsy would substantially improve outcomes.  

To identify genetic loci associated with susceptibility to endometriosis.

The researchers performed a genome-wide association study (GWAS) comparing more than 500,000 SNPs in 3,194 patients with endometriosis and 7,060 healthy male and female controls from Australia and the UK. Initial findings were followed up in a replication sample of 2,392 patients and 2,271 controls from the US. The two cohorts were combined in a meta-analysis.

This study reports an association on chromosome 7p15.2 (rs12700667) located close to genes (NFE2L3, HOXA10, HOXA11) involved in placental and uterine development. The researchers were also able to replicate an association on chromosome 1p36, located near a gene (WNT4) involved in ovarian follicle and reproductive tract development, when combining their data with that of a Japanese GWAS.

The authors conclude that this new locus on chromosome 7p15.2 is significantly associated with endometriosis risk in European women as well as replicating a previous finding on chromosome 1p36. Both associations were stronger when patients were sub-catergorised into those with moderate to severe disease and both regions contain interesting biologically-plausible candidate genes. 

This study not only identified a novel association in women of European ancestry but also replicated an association previously identified in a smaller Japanese population study. Both regions contain biologically interesting candidate genes and so further work is needed to try to identify whether these candidate genes are causally involved in the development of endometriosis. The principal association from this study was estimated to account for less than 1% of the 51% heritability attributed to genetic factors and so much work remains to identify additional genetic risk loci as well as how these loci interplay with each other as well as with the environment.

To test the theory that the milder muscular dystrophy phenotype in mice with dystrophin gene mutations compared with humans (for example, with Duchenne muscular dystrophy, DMD) is due to longer telomeres and larger reserves of muscle stem cells. 

Mice with dystrophin mutations (mdx mice) were genetically modified to remove normal telomerase activity and assessed for symptoms of muscular dystrophy. 

The mice showed a severe phenotype similar to that of human DMD, with serious and progressive loss of muscle function and shortened life-spans. Transplantation of muscle stem cells into these mice alleviated some of these symptoms

The muscle defect caused by mutations in the dystophin gene in combination with gradual depletion of muscle stem cells over time produces the dystrophic phenotype. The much milder phenotype in mdx mice may be because mice have significantly longer telomeres than humans, giving their muscle stem cells greater ability to regenerate. DMD is not purely a genetic disease, but rather a multi-factorial condition. 

This study would be of great value merely in creating an improved mouse model to further ongoing research into the devastating disease DMD. However, it also opens a new line of scientific enquiry with respect to the underlying pathogenesis of the disease in humans, and raises the prospect of potential new therapeutic interventions – whether using stem cell treatments, or new approaches to enhance the telomere function or regenerative capacity of patients’ muscle stem cells.

To examine the genetic basis of disorders of sex determination (DSDs) and in particular to determine whether the disruption of MAP3K1 could be responsible for the DSDs in some patients.  

Two families were recruited with several members affected by DSDs, and additional sporadic cases were also examined. Some of the people participating in the study were women with apparently male karyotypes, and others were males who had abnormal sex development. The MAP3K1 gene from all participants was sequenced; this gene is a member of the MAP kinase signalling pathway and of interest because the mouse equivalent shows strong expression throughout the sex-determining stage of gonad development.

Affected members of the two families and two of the sporadic cases were found to have an alteration in their MAP3K1 gene. Several variants were identified but none previously reported as a known SNP. The mutations were shown to alter the regulation of the MAP3K1 gene in cultured lymphoblastoid cell lines.

Mutations in the MAP3K1 gene result in specific human DSDs with abnormal gonadal development. The results of the study suggest that the MAP kinase pathway may be involved in the balance of expression between the various genes involved in directing the undifferentiated gonad to become a testis or an ovary. 

These findings shed new light on the genetic causes of DSDs, which are often associated with fertility problems and emotional and social stress, and identify a potentially important biological switch in the process of sex determination during development. They could also improve the clinical management of DSDs patients as alterations in MAP3K1 can lead to the development of life-threatening tumors. Removal of the gonads early in life could therefore be an important preventative intervention.  

Determine the genetic profile of a fetus at risk of inheriting beta-thalassaemia, using cell-free DNA circulating in the maternal blood. 

The mother and father were genotyped using a SNP-array, and deep sequencing was performed on cell-free DNA fragments extracted from maternal plasma using next generation sequencing technology. Following alignment of the plasma DNA against a reference human genome, comparison with parental SNPs was used to determine the proportion and size of fetal DNA in the maternal plasma, to infer maternal and paternal inheritance patterns, and to create a genome-wide profile of the fetus.

The entire fetal genome was represented in maternal plasma, comprising just over 11% of cell-free DNA (at 12 weeks gestation). The fetus was found to have inherited the paternal beta-thalassaemia mutation but not the maternal one. 

This proof-of-principle study suggests the feasibility of using genome-wide scanning to construct a fetal genetic map and determine the mutational status of the fetus from maternal plasma. The method could be applied to non-invasive diagnosis of numerous fetal genetic disorders including autosomal recessive conditions that are not currently possible using standard techniques.

Non-invasive prenatal diagnosis would allow couples at risk of passing on an inherited condition to their child to avoid a 1% risk of miscarriage associated with invasive diagnostic tests such as amniocentesis. This pioneering study is the first to produce a genome-wide profile for the fetus from a maternal blood sample, and describes a methodology that is potentially applicable to non-invasive diagnosis of almost any genetic condition, rather than being limited to specific traits (such as the sex of the fetus) like most previous methods. However, before such a test could be offered in the clinic, a much larger study is required to determine the robustness of the technique, and numerous logistical, economic and ethical issues need to be addressed, including how to deal with unexpected or incidental findings.

To create recommendations and guidelines that encourage and allow greater participation of developing countries in documenting the human genetic variation observed worldwide.

Building on the Human Variome Project (see previous news), two planning and implementation workshops in 2008 and 2010 allowed participants from both developing and developed countries to discuss the importance of developing world participation. They also documented current work on National/Ethnic Mutation Databases (NEMDBs), and considered how to harmonise and extend data collection in order to maximise utility.

The following seven guidelines and recommendations were made.

Documenting these population and ethnic specific genetic variation data in developing countries can produce real and tangible benefits not only in improving disease understanding and improving health but also in economic benefit (such as increased human capital).

Whilst inclusion of data from populations in developing countries is important, the value of genomics for such countries is not merely via large-scale research projects, but also in using existing and emerging genomic technologies for immediate public health needs (see recent report on global public health in the genomic era). Several of these recommendations are also implicitly included in the PHG Foundation Framework for action on birth defects project.

Identify genetic variants associated with risk of the common birth defect hypospadias, malformation of the male urethral opening on the penis. 

 A genome-wise association study (GWAS) using SNP microarrays was performed on 436 cases and 494 controls (European descent), and replicated in two additional groups – a Dutch sample of 133 cases and their parents, and a Swedish sample of 266 cases and 402 controls.

Ten genetic variants were identified as potentially associated with hyposapdias in the first GWAS analysis, and statistically significant association of two of these ten SNPs with risk of hyposapdias was confirmed in the replication analyses. These two SNPs were both located in the DGKK gene on the X- chromosome and appear to more than double the risk of the condition.

The authors calculated that around one third of hypospadias cases were associated with a single SNP in the DGKK gene; although careful to note that ‘independent population-based studies should be performed to verify the validity of the estimate’, they point out that, if verified, it would be a relatively strong genetic association for a multifactorial disorder, comparable to the APOE4 variant and Alzheimer’s disease risk. 

Hypospadias is often (though not always) a relatively minor birth defect, correctable by surgery , but it is also a very common abnormality, affecting around 1 in 750 births in Europe, and hence a not insignificant public health issue. Moreover, it can be associated with other birth defects, and so better understanding of the underlying genetics could also shed light on related malformations. Further studies would therefore be a good idea.