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

Bi-allelic loss-of-function CACNA1B mutations in progressive epilepsy-dyskinesia

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment

The predictive ability of the 313 variant–based polygenic risk score for contralateral breast cancer risk prediction in women of European ancestry with a heterozygous BRCA1 or BRCA2 pathogenic variant

Abstract: Purpose: To evaluate the association between a previously published 313 variant–based breast cancer (BC) polygenic risk score (PRS313) and contralateral breast cancer (CBC) risk, in BRCA1 and BRCA2 pathogenic variant heterozygotes. Methods: We included women of European ancestry with a prevalent first primary invasive BC (BRCA1 = 6,591 with 1,402 prevalent CBC cases; BRCA2 = 4,208 with 647 prevalent CBC cases) from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), a large international retrospective series. Cox regression analysis was performed to assess the association between overall and ER-specific PRS313 and CBC risk. Results: For BRCA1 heterozygotes the estrogen receptor (ER)-negative PRS313 showed the largest association with CBC risk, hazard ratio (HR) per SD = 1.12, 95% confidence interval (CI) (1.06–1.18), C-index = 0.53; for BRCA2 heterozygotes, this was the ER-positive PRS313, HR = 1.15, 95% CI (1.07–1.25), C-index = 0.57. Adjusting for family history, age at diagnosis, treatment, or pathological characteristics for the first BC did not change association effect sizes. For women developing first BC < age 40 years, the cumulative PRS313 5th and 95th percentile 10-year CBC risks were 22% and 32% for BRCA1 and 13% and 23% for BRCA2 heterozygotes, respectively. Conclusion: The PRS313 can be used to refine individual CBC risks for BRCA1/2 heterozygotes of European ancestry, however the PRS313 needs to be considered in the context of a multifactorial risk model to evaluate whether it might influence clinical decision-making

A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers

Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10−8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers

Optimal control of a moving boundary by laser heating in a 2-phase Stefan problem

The 2-phase heat control problem by a single laser point input is studied and a method of overcoming the moving boundary problem is introduced. This is achieved by applying a sequence of linear time varying control problems which converge to the single nonlinear problem which can be obtained from the joint moving boundary problems

Polymer-coated compliant receivers for intact laser-induced forward transfer of thin films: experimental results and modelling

In this study, we investigate both experimentally and numerically laser-induced forward transfer (LIFT) of thin films to determine the role of a thin polymer layer coating the receiver with the aim of modifying the rate of deceleration and reduction of material stress preventing intact material transfer. A numerical model of the impact phase during LIFT shows that such a layer reduces the modelled stress. The evolution of stress within the transferred deposit and the substrate as a function of the thickness of the polymer layer, the transfer velocity and the elastic properties of the polymer are evaluated. The functionality of the polymer layer is verified experimentally by LIFT printing intact 1µm-thick bismuth telluride films and polymeric light-emitting diode pads onto a layer of 12µm-thick polydimethylsiloxane and 50-nm-thick poly(3,4-ethylenedioxythiophene) blended with poly(styrenesulfonate) (PEDOT:PSS), respectively. Furthermore, it is demonstrated experimentally that the introduction of such a compliant layer improves adhesion between the deposit and its substrate

Petrology and geochemistry of the 2014–2015 Holuhraun eruption, central Iceland: compositional and mineralogical characteristics, temporal variability and magma storage

The 2014–2015 Holuhraun fissure eruption provided a rare opportunity to study in detail the magmatic processes and magma plumbing system dynamics during a 6-month-long, moderate- to large-volume basaltic fissure eruption. In this contribution, we present a comprehensive dataset, including major and trace elements of whole-rock and glassy tephra samples, mineral chemistry, and radiogenic and oxygen isotope analyses from an extensive set of samples (n = 62) that were collected systematically in several field campaigns throughout the entire eruptive period. We also present the first detailed chemical and isotopic characterization of magmatic sulfides from Iceland. In conjunction with a unique set of geophysical data, our approach provides a detailed temporal and spatial resolution of magmatic processes before and during this eruption. The 2014–2015 Holuhraun magma is compositionally indistinguishable from recent basalts erupted from the Bárðarbunga volcanic system, consistent with seismic observations for magma ascent close to the Bárðarbunga central volcano, followed by dyke propagation to the Holuhraun eruption site. Whole-rock elemental and isotopic compositions are remarkably constant throughout the eruption. Moreover, the inferred depth of the magma reservoir tapped during the eruption is consistently 8 ± 5 km, in agreement with geodetic observations and melt inclusion entrapment pressures, but inconsistent with vertically extensive multi-tiered magma storage prior to eruption. The near constancy in the chemical and isotopic composition of the lava is consistent with the efficient homogenization of mantle-derived compositional variability. In contrast, occurrence of different mineral populations, including sulfide globules, which display significant compositional variability, requires a more complex earlier magmatic history. This may include sampling of heterogeneous mantle melts that mixed, crystallized and finally homogenized at mid- to lower-crustal conditions.</p

Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer

Abstract Genome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer

Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer

AbstractGenome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer.</jats:p