Regulation of photoreceptor phosphodiesterase by prenyl binding protein and by other interacting proteins in photoreceptor cells

Photoreceptor phosphodiesterase (PDE6) is a central component of the visual pathway. While initial PDE6 activation following light stimulation of photoreceptors is well understood, regulation of PDE6 during recovery and light adaptation may require additional components that interact with PDE6. Two approaches were taken to characterize these potential interactions. The first explored the interaction of PDE6 with prenyl binding protein (PrBP/delta) and demonstrated that changes in membrane localization of PDE6 may occur during light adaptation as a result of association with PrBP/delta. The second approach characterized the PDE6 interactome by a mass spectrometric identification of 75 proteins that co-purify with PDE6 upon release from photoreceptor membranes. This work advances our understanding of the role of PrBP/delta in photoreceptors and provides an initial characterization of the entire complement of PDE6 binding partners in photoreceptors

Genetic analysis of haemophilia A in Bulgaria

BACKGROUND: Haemophilias are the most common hereditary severe disorders of blood clotting. In families afflicted with heamophilia, genetic analysis provides opportunities to prevent recurrence of the disease. This study establishes a diagnostical strategy for carriership determination and prenatal diagnostics of haemophilia A in Bulgarian haemophilic population. METHODS: A diagnostical strategy consisting of screening for most common mutations in the factor VIII gene and analysis of a panel of eight linked to the factor VIII gene locus polymorphisms was established. RESULTS: Polymorphic analysis for carrier status determination of haemophilia A was successful in 30 families out of 32 (94%). Carrier status was determined in 25 of a total of 28 women at risk (89%). Fourteen prenatal diagnoses in women at high risk of having a haemophilia A – affected child were performed, resulting in 6 healthy boys and 5 girls. CONCLUSION: The compound approach proves to be a highly informative and cost-effective strategy for prevention of recurrence of haemophilia A in Bulgaria. DNA analysis facilitates carriership determination and subsequent prenatal diagnosis in the majority of Bulgarian families affected by haemophilia A

Caught you: threats to confidentiality due to the public release of large-scale genetic data sets

<p>Abstract</p> <p>Background</p> <p>Large-scale genetic data sets are frequently shared with other research groups and even released on the Internet to allow for secondary analysis. Study participants are usually not informed about such data sharing because data sets are assumed to be anonymous after stripping off personal identifiers.</p> <p>Discussion</p> <p>The assumption of anonymity of genetic data sets, however, is tenuous because genetic data are intrinsically self-identifying. Two types of re-identification are possible: the "Netflix" type and the "profiling" type. The "Netflix" type needs another small genetic data set, usually with less than 100 SNPs but including a personal identifier. This second data set might originate from another clinical examination, a study of leftover samples or forensic testing. When merged to the primary, unidentified set it will re-identify all samples of that individual.</p> <p>Even with no second data set at hand, a "profiling" strategy can be developed to extract as much information as possible from a sample collection. Starting with the identification of ethnic subgroups along with predictions of body characteristics and diseases, the asthma kids case as a real-life example is used to illustrate that approach.</p> <p>Summary</p> <p>Depending on the degree of supplemental information, there is a good chance that at least a few individuals can be identified from an anonymized data set. Any re-identification, however, may potentially harm study participants because it will release individual genetic disease risks to the public.</p

Factor VIII gene inversions causing severe hemophilia A originate almost exclusively in male germ cells

The factor VIII gene, which is defective In hemophilia A, is located in the last megabase of the long arm of the X chromosome. Inversions due to intrachromosomal homologous recombination between mispaired copies of gene A located within intron 22 of the gene and about 500 kb telomeric to it account for nearly half of all cases of severe hemophilia A. We hypothesized that pairing of Xq with its homolog inhibits the Inversion process, and that, therefore, the event originates predominantly in male germ cells. In all 20 informative cases In which the inversion originated in a maternal grandparent, DNA polymorphism analysis determined that it occurred in the male germline. In addition, all but one of 50 mothers of sporadic cases due to an Inversion were carriers. Thus, these data support the hypothesis and Indicate that factor VIII gene inversions leading to severe hemophilia A occur almost exclusively In male germ cell

Factor VIII haplotypes frequencies in Tunisian hemophiliacs A

<p>Abstract</p> <p>Background</p> <p>The development of inhibitors against factor 8 (F8) is the most serious complication of replacement therapy with F8 in children with severe hemophilia. It was suggested that mismatched F8 replacement therapy may be a risk factor for the development of anti-factor F8 alloantibodies. Recently four single nucleotide polymorphisms (SNPs) encoding six distinct haplotypes, designated H1 through H6, were studied in different populations. Two SNPs are components of the A2 and C2 immunodominant-inhibitor epitopes.</p> <p>The aim of this study is to determine the different types of haplotypes in relation with inhibitors developments and their frequencies in our Tunisian hemophiliac population.</p> <p>Materials and methods</p> <p>95/116 Tunisian patients with hemophilia A undergoing treatment at Hemophilia Treatment Center, Aziza Othmana hospital, participate in this study. Among them only six patients develop inhibitors. The four SNPs were amplified and sequenced.</p> <p>Results and Discussion</p> <p>In a total of 77 patients, we identified the H1, H2, H3 and the infrequent H5 haplotypes. The H1 and H2 haplotypes, which have the same amino acid sequence in the recombinant F8 molecules used clinically, are the most represented with the frequency of 0.763 and 0.157 respectively. This distribution is almost similar to that of Caucasians in which the frequencies are respectively 0.926 and 0.074, whereas it is 0.354 and 0.374 among Subsaharians. Four patients with inhibitors studied here have the H1 haplotype. For one patient who has a large deletion including the exon 10 we can't identify his haplotype. Theses frequencies may explain partially the low level of inhibitors in our patients.</p

Routes for breaching and protecting genetic privacy

We are entering the era of ubiquitous genetic information for research, clinical care, and personal curiosity. Sharing these datasets is vital for rapid progress in understanding the genetic basis of human diseases. However, one growing concern is the ability to protect the genetic privacy of the data originators. Here, we technically map threats to genetic privacy and discuss potential mitigation strategies for privacy-preserving dissemination of genetic data.Comment: Draft for comment

Public Access to Genome-Wide Data: Five Views on Balancing Research with Privacy and Protection

Introductory paragraph: Just over twelve months ago, PLoS Genetics published a paper [1] demonstrating that, given genome-wide genotype data from an individual, it is, in principle, possible to ascertain whether that individual is a member of a larger group defined solely by aggregate genotype frequencies, such as a forensic sample or a cohort of participants in a genome-wide association study (GWAS). As a consequence, the National Institutes of Health (NIH) and Wellcome Trust agreed to shut down public access not just to individual genotype data but even to aggregate genotype frequency data from each study published using their funding. Reactions to this decision span the full breadth of opinion, from ‘‘too little, too late—the public trust has been breached’’ to ‘‘a heavy-handed bureaucratic response to a practically minimal risk that will unnecessarily inhibit scientific research.’’ Scientific concerns have also been raised over the conditions under which individual identity can truly be accurately determined from GWAS data. These concerns are addressed in two papers published in this month’s issue of PLoS Genetics [2,3]. We received several submissions on this topic and decided to assemble these viewpoints as a contribution to the debate and ask readers to contribute their thoughts through the PLoS online commentary features. Five viewpoints are included. The Public Population Project in Genomics (P3G) is calling for a universal researcher ID with an access permit mechanism for bona fide researchers. The contribution by Catherine Heeney, Naomi Hawkins, Jantina de Vries, Paula Boddington, and Jane Kaye of the University of Oxford Ethox Centre outlines some of the concerns over possible misuse of individual identification in conjunction with medical and family history data, and points out that if geneticists mishandle public trust, it will backfire on their ability to conduct further research. George Church posits that actions directed toward restricting data access are likely to exclude researchers who might provide the most novel insights into the data and instead makes the argument that full disclosure and consent to the release of genomic information should be sought from study participants, rather than making difficult-to-guarantee promises of anonymity. Martin Bobrow weighs the risks and benefits and proposes four steps that represent a middle ground: Retain restricted access for now, make malicious de-identification practices illegal, increase public awareness of the issues, and encourage recognition that scientists have a special professional relationship of trust with study participants. Finally, Bruce Weir provides a commentary on the contribution of the two research articles from Braun et al. [2] and Visscher and Hill [3]

Ethical implications of the use of whole genome methods in medical research

The use of genome-wide association studies (GWAS) in medical research and the increased ability to share data give a new twist to some of the perennial ethical issues associated with genomic research. GWAS create particular challenges because they produce fine, detailed, genotype information at high resolution, and the results of more focused studies can potentially be used to determine genetic variation for a wide range of conditions and traits. The information from a GWA scan is derived from DNA that is a powerful personal identifier, and can provide information not just on the individual, but also on the individual's relatives, related groups, and populations. Furthermore, it creates large amounts of individual-specific digital information that is easy to share across international borders. This paper provides an overview of some of the key ethical issues around GWAS: consent, feedback of results, privacy, and the governance of research. Many of the questions that lie ahead of us in terms of the next generation sequencing methods will have been foreshadowed by GWAS and the debates around ethical and policy issues that these have created

Mutation spectrum of 122 hemophilia A families from Taiwanese population by LD-PCR, DHPLC, multiplex PCR and evaluating the clinical application of HRM

<p>Abstract</p> <p>Background</p> <p>Hemophilia A represents the most common and severe inherited hemorrhagic disorder. It is caused by mutations in the F8 gene, which leads to a deficiency or dysfunctional factor VIII protein, an essential cofactor in the factor X activation complex.</p> <p>Methods</p> <p>We used long-distance polymerase chain reaction and denaturing high performance liquid chromatography for mutation scanning of the F8 gene. We designed the competitive multiplex PCR to identify the carrier with exonal deletions. In order to facilitate throughput and minimize the cost of mutation scanning, we also evaluated a new mutation scanning technique, high resolution melting analysis (HRM), as an alternative screening method.</p> <p>Results</p> <p>We presented the results of detailed screening of 122 Taiwanese families with hemophilia A and reported twenty-nine novel mutations. There was one family identified with whole exons deletion, and the carriers were successfully recognized by multiplex PCR. By HRM, the different melting curve patterns were easily identified in 25 out of 28 cases (89%) and 15 out of 15 (100%) carriers. The sensitivity was 93 % (40/43). The overall mutation detection rate of hemophilia A was 100% in this study.</p> <p>Conclusion</p> <p>We proposed a diagnostic strategy for hemophilia A genetic diagnosis. We consider HRM as a powerful screening tool that would provide us with a more cost-effective protocol for hemophilia A mutation identification.</p