Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Hearing impairment in patients with myotonic dystrophy type 2

International audienceObjective To systematically assess auditory characteristics of a large cohort of patients with genetically confirmed myotonic dystrophy type 2 (DM2). Methods Patients with DM2 were included prospectively in an international cross-sectional study. A structured interview about hearing symptoms was held. Thereafter, standardized otologic examination, pure tone audiometry (PTA; 0.25, 0.5, 1, 2, 4, and 8 kHz), speech audiometry, tympanometry, acoustic middle ear muscle reflexes, and brainstem auditory evoked potentials (BAEP) were performed. The ISO 7029 standard was used to compare the PTA results with established hearing thresholds of the general population according to sex and age. Results Thirty-one Dutch and 25 French patients with DM2 (61% female) were included with a mean age of 57 years (range 31–78). The median hearing threshold of the DM2 cohort was higher for all measured frequencies, compared to the 50th percentile of normal ( p < 0.001). Hearing impairment was mild in 39%, moderate in 21%, and severe in 2% of patients with DM2. The absence of an air–bone gap with PTA, concordant results of speech audiometry with PTA, and normal findings of BAEP suggest that the sensorineural hearing impairment is located in the cochlea. A significant correlation was found between hearing impairment and age, even when corrected for presbycusis. Conclusions Cochlear sensorineural hearing impairment is a frequent symptom in patients with DM2, suggesting an early presbycusis. Therefore, we recommend informing about hearing impairment and readily performing audiometry when hearing impairment is suspected in order to propose early hearing rehabilitation with hearing aids when indicated