Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer

We conducted imputation to the 1000 Genomes Project of four genome-wide association studies of lung cancer in populations of European ancestry (11,348 cases and 15,861 controls) and genotyped an additional 10,246 cases and 38,295 controls for follow-up. We identified large-effect genome-wide associations for squamous lung cancer with the rare variants BRCA2 p.Lys3326X (rs11571833, odds ratio (OR) = 2.47, P = 4.74 × 10(-20)) and CHEK2 p.Ile157Thr (rs17879961, OR = 0.38, P = 1.27 × 10(-13)). We also showed an association between common variation at 3q28 (TP63, rs13314271, OR = 1.13, P = 7.22 × 10(-10)) and lung adenocarcinoma that had been previously reported only in Asians. These findings provide further evidence for inherited genetic susceptibility to lung cancer and its biological basis. Additionally, our analysis demonstrates that imputation can identify rare disease-causing variants with substantive effects on cancer risk from preexisting genome-wide association study data.

A novel subclass of bovine β-defensins links reproduction and immunology

β-defensins are effector molecules of the innate immune system, found in many diverse species. Their presence in invertebrates as well as vertebrates suggests highly conserved functional roles. Most β-defensins are believed to act as antimicrobial agents at epithelial surfaces, although additional functions have also been described, including immune regulatory activity, wound repair and a role in coat-colour determination. High expression of β-defensins have been found in testis and epididymidal epithelium as well as in the seminal fluid of humans, macaque, rat, mouse and cow. Human and macaque β-defensins have recently been shown to affect sperm motility while a mutation in β-defensin 126 is associated with reduced fertility in men. Genetic variation in bovine defensin genes may explain the increased incidence of low fertility in cattle. Here, we present a summary of the known functions of β-defensins as well as their emerging role in reproduction and their potential to improve fertility in cattle.

Bovine β-defensin gene family: opportunities to improve animal health?

Recent analysis of the bovine genome revealed an expanded suite of β-defensin genes that encode what are referred to as antimicrobial or host defense peptides (HDPs). Whereas primate genomes also encode α- and θ-defensins, the bovine genome contains only the β-defensin subfamily of HDPs. β-Defensins perform diverse functions that are critical to protection against pathogens but also in regulation of the immune response and reproduction. As the most comprehensively studied subclass of HDPs, β-defensins possess the widest taxonomic distribution, found in invertebrates as well as plants, indicating an ancient point of origin. Cross-species comparison of the genomic arrangement of β-defensin gene repertoire revealed them to vary in number among species presumably due to differences in pathogenic selective pressures but also genetic drift. β-Defensin genes exist in a single cluster in birds, but four gene clusters exist in dog, rat, mouse, and cow. In humans and chimpanzees, one of these clusters is split in two as a result of a primate-specific pericentric inversion producing five gene clusters. A cluster of β-defensin genes on bovine chromosome 13 has been recently characterized, and full genome sequencing has identified extensive gene copy number variation on chromosome 27. As a result, cattle have the most diverse repertoire of β-defensin genes so far identified, where four clusters contain at least 57 genes. This expansion of β-defensin HDPs may hold significant potential for combating infectious diseases and provides opportunities to harness their immunological and reproductive functions in commercial cattle populations.

Patchy 'coherence': using normalization process theory to evaluate a multi-faceted shared decision making implementation program (MAGIC)

BACKGROUND

Implementing shared decision making into routine practice is proving difficult, despite considerable interest from policy-makers, and is far more complex than merely making decision support interventions available to patients. Few have reported successful implementation beyond research studies. MAking Good Decisions In Collaboration (MAGIC) is a multi-faceted implementation program, commissioned by The Health Foundation (UK), to examine how best to put shared decision making into routine practice. In this paper, we investigate healthcare professionals' perspectives on implementing shared decision making during the MAGIC program, to examine the work required to implement shared decision making and to inform future efforts.

METHODS

The MAGIC program approached implementation of shared decision making by initiating a range of interventions including: providing workshops; facilitating development of brief decision support tools (Option Grids); initiating a patient activation campaign ('Ask 3 Questions'); gathering feedback using Decision Quality Measures; providing clinical leads meetings, learning events, and feedback sessions; and obtaining executive board level support. At 9 and 15 months (May and November 2011), two rounds of semi-structured interviews were conducted with healthcare professionals in three secondary care teams to explore views on the impact of these interventions. Interview data were coded by two reviewers using a framework derived from the Normalization Process Theory.

RESULTS

A total of 54 interviews were completed with 31 healthcare professionals. Partial implementation of shared decision making could be explained using the four components of the Normalization Process Theory: 'coherence,' 'cognitive participation,' 'collective action,' and 'reflexive monitoring.' Shared decision making was integrated into routine practice when clinical teams shared coherent views of role and purpose ('coherence'). Shared decision making was facilitated when teams engaged in developing and delivering interventions ('cognitive participation'), and when those interventions fit with existing skill sets and organizational priorities ('collective action') resulting in demonstrable improvements to practice ('reflexive monitoring'). The implementation process uncovered diverse and conflicting attitudes toward shared decision making; 'coherence' was often missing.

CONCLUSIONS

The study showed that implementation of shared decision making is more complex than the delivery of patient decision support interventions to patients, a portrayal that often goes unquestioned. Normalizing shared decision making requires intensive work to ensure teams have a shared understanding of the purpose of involving patients in decisions, and undergo the attitudinal shifts that many health professionals feel are required when comprehension goes beyond initial interpretations. Divergent views on the value of engaging patients in decisions remain a significant barrier to implementation.

The silent mutational landscape of infant MLL-AF4 pro-B acute lymphoblastic leukemia

Over 90% of infants (< 1-year-old) diagnosed with leukemia have pro-B acute lymphoblastic leukemia (ALL) containing the MLL-AF4 fusion. When compared with other forms of paediatric ALL affecting later B-cell differentiation, MLL-AF4 pro-B is associated with a dismal prognosis with a typical 5-year disease-free survival of <20%. MLL-AF4 may be sufficient on its own for leukemogenesis or the gene-fusion product may alternatively predispose transformed cells to global genetic instability, enhancing the acquisition of additional key mutations. To gain insight into the genomic landscape of infant MLL-AF4 pro-B ALL we performed whole genome sequencing of diagnostic leukemic blasts and matched germline samples from three MLL-AF4 pro-B ALL infants. Our analysis revealed few somatic changes (copy number abnormalities, loss of heterozygosity, or single nucleotide variants), demonstrating that only a very small number of mutations are necessary to generate infant MLL-leukemia.

Meiosis and its deviations in polyploid plants

Meiosis is a fundamental process in all sexual organisms that ensures fertility and genome stability and creates genetic diversity. For each of these outcomes, the exclusive formation of crossovers between homologous chromosomes is needed. This is more difficult to achieve in polyploid species which have more than 2 sets of chromosomes able to recombine. In this review, we describe how meiosis and meiotic recombination 'deviate' in polyploid plants compared to diploids, and give an overview of current knowledge on how they are regulated. See also the sister article focusing on animals by Stenberg and Saura in this themed issue.

Correlates and characteristics of hepatitis C virus-specific T-cell immunity in exposed uninfected high-risk prison inmates

Some hepatitis C (HCV)-uninfected, high-risk individuals have HCV-specific cellular immunity without viraemia or seroconversion. The characteristics of these responses and the risk behavioural associations were studied in 94 subjects in a prospective cohort of recently seronegative prisoners reporting injecting drug use (IDU). Detailed behavioural data were collected. HCV antibody and PCR testing were performed. ELISpot assays for HCV-induced interferon (IFN)-γ and interleukin (IL)-2 production by T lymphocytes, as well as multiplex in vitro cytokine production assays, were performed. Seventy-eight subjects remained antibody and PCR negative and 16 seroconverted. Of the seronegative group, 22 (28%) had IFN-γ ELISpot responses in comparison with 13 of the 16 seroconverters (82%). This seronegative immune status was associated positively with injecting anabolic steroids and negatively with a recent break from IDU. The IFN-γ ELISpot responses involved both CD4 and CD8 T lymphocytes and were comparable in magnitude, but narrower in specificity, in uninfected subjects than in seroconverters. A subset of seronegative subjects had HCV-induced cytokine production patterns comparable with the seroconverters with increased production of IFN-γ, IL-2 and tumour necrosis factor (TNF)-α and reduced IL-10 in response to nonstructural peptides. In conclusion, comparable patterns of HCV-specific cellular immunity are found in recently infected subjects and in a minority of high-risk, uninfected subjects. Further characterization of these responses and their protective efficacy will inform HCV vaccine development.

Option Grids: shared decision making made easier

OBJECTIVE

To describe the exploratory use of short decision support tools for patients, called Option Grids. Option Grids are summary tables, using one side of paper to enable rapid comparisons of options, using questions that patients frequently ask (FAQs) and designed for face-to-face clinical encounters. To date, most evidence about 'patient decision aids' has been based on tools with high content levels, designed for patients to use independently, either before or after visits.

METHODS

We studied the use of Option Grids in a quality improvement project, collecting field notes and conducting interviews with clinical teams.

RESULTS

In the 'Making Good Decisions in Collaboration' (MAGIC) program, clinicians found that using Option Grids made it easier to explain the existence of options and reported a 'handover' effect, where patient involvement in decision making was enhanced.

CONCLUSION

Option Grids made options more visible and clinicians found it easier to undertake shared decision making when these tools were available. Used in a collaborative way, they enhance patients' confidence and voice, increasing their involvement in collaborative dialogs.

PRACTICE IMPLICATIONS

Further work to confirm these preliminary findings is required, to measure processes and to assess whether these tools have similar impact in other clinical settings.

Variation at 3p24.1 and 6q23.3 influences the risk of Hodgkin's lymphoma

In addition to HLA, recent genome-wide association studies (GWASs) of Hodgkin's lymphoma (HL) have identified susceptibility loci for HL at 2p16.1, 8q24.21 and 10p14. In this study, we perform a GWAS meta-analysis with published GWAS (totalling 1,465 cases and 6,417 controls of European background), and follow-up the most significant association signals in 2,024 cases and 1,853 controls. A combined analysis identifies new HL susceptibility loci mapping to 3p24.1 (rs3806624; P=1.14 × 10(-12), odds ratio (OR)=1.26) and 6q23.3 (rs7745098; P=3.42 × 10(-9), OR=1.21). rs3806624 localizes 5' to the EOMES (eomesodermin) gene within a p53 response element affecting p53 binding. rs7745098 maps intergenic to HBS1L and MYB, a region previously associated with haematopoiesis. These findings provide further insight into the genetic and biological basis of inherited susceptibility to HL.

Shared decision making: a model for clinical practice

The principles of shared decision making are well documented but there is a lack of guidance about how to accomplish the approach in routine clinical practice. Our aim here is to translate existing conceptual descriptions into a three-step model that is practical, easy to remember, and can act as a guide to skill development. Achieving shared decision making depends on building a good relationship in the clinical encounter so that information is shared and patients are supported to deliberate and express their preferences and views during the decision making process. To accomplish these tasks, we propose a model of how to do shared decision making that is based on choice, option and decision talk. The model has three steps: a) introducing choice, b) describing options, often by integrating the use of patient decision support, and c) helping patients explore preferences and make decisions. This model rests on supporting a process of deliberation, and on understanding that decisions should be influenced by exploring and respecting "what matters most" to patients as individuals, and that this exploration in turn depends on them developing informed preferences.

Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk

We performed a meta-analysis of five genome-wide association studies to identify common variants influencing colorectal cancer (CRC) risk comprising 8,682 cases and 9,649 controls. Replication analysis was performed in case-control sets totaling 21,096 cases and 19,555 controls. We identified three new CRC risk loci at 6p21 (rs1321311, near CDKN1A; P = 1.14 × 10(-10)), 11q13.4 (rs3824999, intronic to POLD3; P = 3.65 × 10(-10)) and Xp22.2 (rs5934683, near SHROOM2; P = 7.30 × 10(-10)) This brings the number of independent loci associated with CRC risk to 20 and provides further insight into the genetic architecture of inherited susceptibility to CRC.

Elicitation of health state utilities in neuroendocrine tumours

BACKGROUND

Neuroendocrine tumours (NETs) are a rare form of neoplasm that can arise in most organs of the body and which share many common pathologic features. Although curative surgery can be conducted for patients with localised disease, once progression occurs and the disease becomes metastatic or un-resectable, treatment aims to extend life and maintain quality-of-life for as long as possible. The aim of the study was to elicit utilities for health state vignettes describing the burdens associated with receiving therapy for advanced NETs.

METHODS

Health state vignettes were developed by reviewing published literature and conducting in-depth interviews with patients and clinical experts. These states described the burden associated with both stable and progressive disease, in addition to the experience of a number of serious toxicities commonly associated with treatments (grade III/IV diarrhoea, hand-foot syndrome, hyperglycaemia, nausea/vomiting, pneumonitis, rash, stomatitis, and thrombocytopenia). One hundred members of the UK general public valued the states using the time trade-off methodology to determine utility values.

RESULTS

Stable disease had a utility value of 0.77 whilst disease progression was associated with a significant decline in health-related quality-of-life (HRQoL) and a value of 0.61. Toxicities experienced in the context of stable disease exhibited varying degrees of impact, with several being deemed as debilitating as disease progression (such as hand-foot syndrome [0.58] and stomatitis [0.56]).

CONCLUSION

Although vignette studies have been criticised for the difficulty in establishing their validity, the collection of health utilities in rare populations is challenging. The findings from this study suggest that advanced NETs is associated with a considerable HRQoL burden, both as a direct result of the disease and the potential of experiencing a number of severe adverse events. These values could assist in future economic evaluation processes.

The 14q22.2 colorectal cancer variant rs4444235 shows cis-acting regulation of BMP4

Common genetic variation at human 14q22.2 tagged by rs4444235 is significantly associated with colorectal cancer (CRC) risk. Re-sequencing was used to comprehensively annotate the 17kb region of strong linkage disequilibrium encompassing rs4444235. Through bioinformatic analyses using H3K4Me1, H3K4Me3, and DNase-I hypersensitivity chromatin signatures and evolutionary conservation we identified seven candidate disease-causing single-nucleotide polymorphisms mapping to six regions within the 17-kb region predicted to have regulatory potential. Reporter gene studies of these regions demonstrated that the element to which rs4444235 maps acts as an allele-specific transcriptional enhancer. Allele-specific expression studies in CRC cell lines heterozygous for rs4444235 showed significantly increased expression of bone morphogenetic protein-4 (BMP4) associated with the risk allele (P<0.001). These data provide evidence for a functional basis for the non-coding risk variant rs4444235 at 14q22.2 and emphasizes the importance of genetic variation in the BMP pathway genes as determinants of CRC risk.

Common variation at 3p22.1 and 7p15.3 influences multiple myeloma risk

To identify risk variants for multiple myeloma, we conducted a genome-wide association study of 1,675 individuals with multiple myeloma and 5,903 control subjects. We identified risk loci for multiple myeloma at 3p22.1 (rs1052501 in ULK4; odds ratio (OR) = 1.32; P = 7.47 × 10(-9)) and 7p15.3 (rs4487645, OR = 1.38; P = 3.33 × 10(-15)). In addition, we observed a promising association at 2p23.3 (rs6746082, OR = 1.29; P = 1.22 × 10(-7)). Our study identifies new genomic regions associated with multiple myeloma risk that may lead to new etiological insights.