Pharmacogenetics driving personalized medicine: Analysis of genetic polymorphisms related to breast cancer medications in Italian isolated populations

BACKGROUND: Breast cancer is the most common cancer in women characterized by a high variable clinical outcome among individuals treated with equivalent regimens and novel targeted therapies. In this study, we performed a population based approach intersecting high-throughput genotype data from Friuli Venezia Giulia (FVG) isolated populations with publically available pharmacogenomics information to estimate the frequency of genotypes correlated with responsiveness to breast cancer treatment thus improving the clinical management of this disease in an efficient and cost effective way. METHODS: A list of 80 variants reported to be related to the efficacy or toxicity of breast cancer drugs was obtained from PharmGKB database. Fourty-one were present in FVG, 1000G European (EUR) and ExAC (Non Finnish European) databases. Their frequency was extracted using PLINK software and the differences tested by Fisher's exact test. RESULTS: Statistical analyses revealed that 13 out of the 41 (32 %) variants were significantly different in frequency in our sample as compared to the EUR/ExAC cohorts. For nine variants the available level of evidence (LOE) included polymorphisms related to cyclophosphamide, tamoxifen, doxorubicin, fluorpyrimidine and paclitaxel. In particular, for trastuzumab two variants were detected: (1) rs1801274-G within FCGR2A and associated with decreased efficacy (LOE 2B); (2) rs1136201-G located within ERBB2 and associated with increased toxicity (LOE 3). Both these two variants were underrepresented in the FVG population compared to EUR/ExAC population thus suggesting a high therapeutic index of this drug in our population. Moreover, as regards fluoropyrimidines, the frequency of two polymorphisms within the DPYD gene associated with drug toxicity (e.g., rs2297595-C allele and rs3918290-T allele, LOE 2A and 1, respectively) was extremely low in FVG population thus suggesting that a larger number of FVG patients could benefit from full dosage of fluoropyrimidine therapy. CONCLUSIONS: All these findings increase the overall knowledge on the prevalence of specific variants related with breast cancer treatment responsiveness in FVG population and highlight the importance of assessing gene polymorphisms related with cancer medications in isolated communities

Genetic testing and genomic analysis: A debate on ethical, social and legal issues in the Arab world with a focus on Qatar

In 2013 both Saudi Arabia and Qatar launched genome projects with the aim of providing information for better diagnosis, treatment and prevention of diseases and, ultimately to realize personalized medicine by sequencing hundred thousands samples. These population based genome activities raise a series of relevant ethical, legal and social issues general, related to the specific population structure as well as to the Islamic perspective on genomic analysis and genetic testing. To contribute to the debate, the Authors after reviewing the existing literature and taking advantage of their professional experience in the field and in the geographic area, discuss and provide their opinions. In particular, the Authors focus on the impact of consanguinity on population structure and disease frequency in the Arab world, on genetic testing and genomic analysis (i.e. technical aspects, impact, etc.) and on their regulations. A comparison between the Islamic perspective and the ethical, social and legal issues raised in other population contexts is also carried. In conclusion, this opinion article with an up-to-date contribution to the discussion on the relevance and impact of genomic analysis and genetic testing in the Arab world, might help in producing specific national guidelines on genetic testing and genomic analysis and help accelerate the implementation and roll out of genome projects in Muslim countries and more specifically in Qatar, and other countries of the Gulf

HPV vaccination and allocative efficiency: regional analysis of the costs and benefits with the bivalent AS04-adjuvanted vaccine, from the perspective of public health, for the prevention of cervical cancer and its pre-cancerous lesions

Introduction: by means of the decisions on whether to introduce the HPV vaccination, Public Health has already established the importance of associating the vaccination strategy to the policy of secondary prevention. The screening + vaccination strategy is more effective than the two methods taken individually. In support of this combined strategy and in order to make available per each region concrete elements for their regional planning, an assessment has been made, which also takes into account the effect of cross-protection regarding high-risk strains not contained in both vaccines, bivalent and quadrivalent, and more frequently responsible for pre-cancerous lesions and cervical cancer (CCU). This analysis evaluates the costs and benefits of screening + vaccination strategy in a 12-year-old female cohort. Furthermore, the paper provides results that may be useful to assess the opportunity to extend the vaccination to a second cohort of 24-25-year-old women. The analysis is preceded by a brief summary of CCU epidemiology available data, public health policies that give precise guidelines for vaccination strategies and analytical tools suitable to support public policy makers to efficiently allocate resources. Methods: two different models were used for two regional analyses.The vaccines may have different sustained- and cross-protection levels against non-vaccine oncogenic HPV-types. In the first analysis, a prevalence-based model estimated the potential net difference in HPV-related lesions (abnormal pap smear, cervical intraepithelial neoplasia (CIN), cervical cancer (CC) and genital warts (GW)) and associated costs generated by the two vaccines. Vaccine efficacy rates were based on published data for each vaccine. Lifetime vaccine efficacy was assumed. Results are reported over one year after reaching a steady state. Incidence and treatment costs were obtained from Italian and European sources. We also performed a cost-effectiveness analysis with a Markov model for each Italian region, previously described and successfully adapted to the national scenario. The analysis compares the HPV vaccination of a single cohort (12-year-old females) with a multiple cohort (12- + 25-year-old girls). Resource use was based on a standard therapeutic path applied to all regions. However we quantified the impact of the so-called "decentralization progress" by collecting regional data on: pap test coverage, tariffs for treatments, and cost of the vaccination course. Results: the results are set out in 21 regional reports. Conclusions: in the Italian scenario, characterized by decentralization and local autonomy, a further level of detail is essential in order to describe the specific local settings and implications of a new health intervention. The results show that the vaccination on a multiple cohort is more effective than a single cohort. Indeed, a major number of pre-cancerous lesions, cases of cancer, and related deaths are avoided. In a period of sharp decline in the health budget, investment in prevention seems to be the most reasonable choice in view of avoiding in the medium term pre-cancerous and cancerous lesions generating a significant expense. Our analysis places the extent of HPV vaccination among the measures that the regional decision-makers should put in place to maximize the efficiency of scarce resource

Detection and genotyping of human Papillomavirus in urine samples from unvaccinated male and female adolescents in Italy

The introduction of vaccination against Human Papillomavirus (HPV) in adolescent girls in 2006 has focused virological surveillance on this age group. As few studies have evaluated HPV infections in young populations, further data are needed in order to improve and extend prophylactic policy and to monitor epidemiological changes. The present study aimed at evaluating overall and type-specific HPV prevalence in both female and male adolescents in Italy. HPV DNA detection and genotyping was performed on urine samples collected from 870 unvaccinated adolescents (369 females, 501 males, 11-18 years of age) in five cities in Italy. Following DNA extraction by means of a commercial kit (NucliSENS®-miniMAG®, bioMérieux), the L1 gene fragment was PCR amplified and genotyped by restriction fragment length polymorphism analysis. HPV DNA was detected in 1.5% of all samples, and in 3% and 0.4% of samples from females and males, respectively. In approximately 70% of HPV DNA positive adolescents, the infection was due to a single genotype, with 88.9% of genotypes belonging to the HR-clade. The only two HPV-positive boys (14 and 18 years old) had HPV-70 genotype. Only one of the 11 HPV-infected girls was in the 11-14 age-group. HPV prevalence was 4.2% in girls aged 15-18 years and 60% of infections were due to vaccine types HPV-16 or HPV-6/-11. This is one of the few studies, the first conducted in Italy, on HPV infection in adolescents. Urine testing is the easier way of detecting HPV infection in younger populations. Our data revealed a very low HPV prevalence, and no infections were observed in the 12-year-old vaccine target population. The majority of infections were seen in females aged 15-18 years. Overall, more than 50% and 30% of the potentially persistent HPV infections detected in this group could have been prevented by the quadrivalent and the bivalent vaccines, respectively

62. Proteasome Activity Restricts Lentiviral Gene Transfer into Hematopoietic Stem Cells and Is Down-Regulated by Cytokines That Enhance Transduction

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Muscle differentiation in a colonial ascidian: organisation, gene expression and evolutionary considerations

Background: Ascidians are tunicates, the taxon recently proposed as sister group to the vertebrates. They possess a chordate-like swimming larva, which metamorphoses into a sessile adult. Several ascidian species form colonies of clonal individuals by asexual reproduction. During their life cycle, ascidians present three muscle types: striated in larval tail, striated in the heart, and unstriated in the adult body-wall. Results: In the colonial ascidian Botryllus schlosseri, we investigated organisation, differentiation and gene expression of muscle beginning from early buds to adults and during zooid regression. We characterised transcripts for troponin T (BsTnT-c), adult muscle-type (BsMA2) and cytoplasmic-type (BsCA1) actins, followed by in situ hybridisation (ISH) on sections to establish the spatio-temporal expression of BsTnT-c and BsMA2 during asexual reproduction and in the larva. Moreover, we characterised actin genomic sequences, which by comparison with other metazoans revealed conserved intron patterns. Conclusion: Integration of data from ISH, phalloidin staining and TEM allowed us to follow the phases of differentiation of the three muscle kinds, which differ in expression pattern of the two transcripts. Moreover, phylogenetic analyses provided evidence for the close relationship between tunicate and vertebrate muscle genes. The characteristics and plasticity of muscles in tunicates are discussed. </p

Marche

In Marche region 68% of women (aged 24-64) are screened regularly, meaning every 3 years. The analysis on cross-protective activity exercised by bivalent and quadrivalent vaccines shows that the bivalent vaccine could prevent more pre-cancerous lesions and cases of cervicocarcinoma than quadrivalent, and that the latter could prevent genital warts that are not prevented by bivalent. The major number of cases avoided by the bivalent make it possible to fully offset the cost savings related to warts associated with the quadrivalent vaccine. Furthermore, a cost-effectiveness analysis shows that, considering regional tariffs, the multiple cohort (12-year-old + 25-year-old women) vaccination strategy with a 90% coverage could prevent 18 cases of cervicocarcinoma and 8 related deaths more than the vaccination of only 12-year-old girls, and thus proves to be cost-effective (10,700 €/QALY)

Genetic Landscape of Slovenians: Past Admixture and Natural Selection Pattern

The Slovenian territory played a crucial role in the past serving as gateway for several human migrations. Previous studies used Slovenians as a source population to interpret different demographic events happened in Europe but not much is known about the genetic background and the demographic history of this population. Here, we analyzed genome-wide data from 96 individuals to shed light on the genetic role and history of the Slovenian population. Y chromosome diversity splits into two major haplogroups R1b and R1a with the latter suggesting a genetic contribution from the steppe. Slovenian individuals are more closely related to Northern and Eastern European populations than Southern European populations even though they are geographically closer. This pattern is confirmed by an admixture and clustering analysis. We also identified a single stream of admixture events between the Slovenians with Sardinians and Russians around 3c2630 BCE (2149-3112). Using ancient samples, we found a significant admixture in Slovenians using Yamnaya and the early Neolithic Hungarians as sources, dated around 3c1762 BCE (1099-2426) suggesting a strong contribution from the steppe to the foundation of the observed modern genetic diversity. Finally, we looked for signals of selection in candidate variants and we found significant hits in HERC2 and FADS responsible for blue eye color and synthesis of long-chain unsaturated fatty acids, respectively, when Slovenians were compared to Southern Europeans. While the comparison was done with Eastern Europeans, we identified significant signals in PKD2L1 and IL6R which are genes associated with taste and coronary artery disease, respectively

TBC1D24 and non-syndromic autosomal dominant hearing loss: the identification of an additional Italo-American family carrying the p.(S178L) mutation

Hearing loss is the most common sensorineural disorder, affecting approximately 1:1000 new-borns. In developed countries, more than half of the cases of congenital hearing loss are due to genetic causes and both syndromic and non-syndromic forms may be recognized. Approximately 20% of the cases of nonsyndromic hearing loss are inherited according to an autosomal dominant pattern. Autosomal dominant hereditary hearing loss (ADHHL) is characterized by a wide genetic heterogeneity and by inter- and intrafamilial clinical variability, making genotype-phenotype correlations extremely complicated. Here we describe a large multi-generation Italo-American kindred affected by ADHHL. After a complete clinical evaluation and hearing function assessment through pure tone audiometry, the proband underwent a multiple-step genetic testing. Eventually, whole exome sequencing was performed on his and other selected family members’ DNA leading to the identification of a heterozygous missense variant in the TBC1D24 gene. Mutations in this gene have been associated with a variety of conditions that are inherited in an autosomal recessive pattern and that may or may not include hearing loss. Interestingly, the variant identified in our kindred is the only mutation in the TBC1D24 gene that has been associated with ADHHL in previous studies. Our case report confirms the role of the TBC1D24 gene and specifically of the p.(S178L) variant in the etiopathogenesis of ADHHL, underlining once again the clinical variability associated with variants in this gene