Homologous Recombination Deficiency Landscape of Breast Cancers and Real-World Effectiveness of Poly ADP-Ribose Polymerase Inhibitors in Patients With Somatic BRCA1/2, Germline PALB2, or Homologous Recombination Deficiency Signature.

PURPOSE: Poly ADP-ribose polymerase inhibitors (PARPi) are approved for patients with human epidermal growth factor receptor 2-negative metastatic breast cancer (mBC) and germline pathogenic/likely pathogenic variant (hereafter mutation) in the BRCA1/2 genes (gBRCA); however, clinical benefit has also been demonstrated in mBC with somatic BRCA1/2 mutations (sBRCA) or germline PALB2 mutations (gPALB2). This study aims to describe the genomic landscape of homologous recombination repair (HRR) gene alterations in mBC and assess PARPi treatment outcomes for patients with gBRCA compared with other HRR genes and by status of a novel homologous recombination deficiency signature (HRDsig). METHODS: A real-world (RW) clinico-genomic database (CGDB) of comprehensive genomic profiling (CGP) linked to deidentified, electronic health record-derived clinical data was used. CGP was analyzed for HRR genes and HRDsig. The CGDB enabled cohort characterization and outcomes analyses of 177 patients exposed to PARPi. RW progression-free survival (rwPFS) and RW overall survival (rwOS) were compared. RESULTS: Of 28,920 patients with mBC, gBRCA was detected in 3.4%, whereas the population with any BRCA alteration or gPALB2 increased to 9.5%. HRDsig+ represented 21% of patients with mBC. BRCA and gPALB2 had higher levels of biallelic loss and HRDsig+ than other HRR alterations. Outcomes on PARPi were assessed for 177 patients, and gBRCA and sBRCA/gPALB2 cohorts were similar: gBRCA versus sBRCA/gPALB2 rwPFS was 6.3 versus 5.4 months (hazard ratio [HR], 1.37 [0.77-2.43]); rwOS was 16.2 versus 21.2 months (HR, 1.45 [0.74-2.86]). Additionally, patients with HRDsig+ versus HRDsig- had longer rwPFS (6.3 v 2.8 months; HR, 0.62 [0.42-0.92]) and numerically longer rwOS (17.8 v 13.0 months; HR, 0.72 [0.46-1.14]). CONCLUSION: Patients with sBRCA and gPALB2 derive similar benefit from PARPi as those with gBRCA alterations. In combination, HRDsig+, sBRCA, and gPALB2 represent an additional 19% of mBC that can potentially benefit from PARPi. Randomized trials exploring a more inclusive biomarker such as HRDsig are warranted.

Pan-Cancer Analysis of Copy-Number Features Identifies Recurrent Signatures and a Homologous Recombination Deficiency Biomarker to Predict Poly (ADP-Ribose) Polymerase Inhibitor Response.

PURPOSE: Copy-number (CN) features reveal the molecular state of cancers and may have predictive and prognostic value in the treatment of cancer. We sought to apply published CN analysis methods to a large pan-cancer data set and characterize ubiquitous CN signatures across tumor types, including potential utility for treatment selection. METHODS: We analyzed the landscape of CN features in 260,333 pan-cancer samples. We examined the association of 10 signatures with genomic alterations and clinical characteristics and trained a machine learning classifier using CN and insertion and deletion features to detect homologous recombination deficiency signature (HRDsig) positivity. Clinical outcomes were assessed using a real-world clinicogenomic database (CGDB) of comprehensive genomic profiling linked to deidentified, electronic health record-derived clinical data. RESULTS: CN signatures were prevalent across cancer types and associated with diverse processes including focal tandem duplications, seismic amplifications, genome-wide loss of heterozygosity (gLOH), and HRD. Our novel HRDsig outperformed gLOH in predicting BRCAness and effectively distinguished biallelic BRCA and homologous recombination-repair wild-type (HRRwt) samples pan-tumor, demonstrating high sensitivity to detect biallelic BRCA in ovarian (93%) and other HRD-associated cancers (80%-87%). Pan-tumor prevalence of HRDsig was 6.4%. HRRwt cases represented a significant fraction of the HRDsig-positive cohort, likely reflecting a population with nongenomic mechanisms of HRD. In ovarian and prostate CGDBs, HRDsig identified more patients than gLOH and had predictive value for poly (ADP-ribose) polymerase inhibitor (PARPi) benefit. CONCLUSION: Tumor CN profiles are informative, revealing diverse processes active in cancer. We describe the landscape of 10 CN signatures in a large pan-cancer cohort, including two associated with HRD. We trained a machine learning-based HRDsig that robustly identified BRCAness and associated with biallelic BRCA pan-tumor, and was predictive of PARPi benefit in real-world ovarian and prostate data sets.

A Novel HRD Signature Is Predictive of FOLFIRINOX Benefit in Metastatic Pancreatic Cancer.

BACKGROUND: Pancreatic cancer (PC) represents an aggressive disease with median overall survival (OS) of less than 1 year in the front-line setting. FOLFIRINOX and gemcitabine and paclitaxel (GP) are standard of care options for these patients; however, optimal selection of therapy is challenging. METHODS: Comprehensive genomic profiling was performed on 8358 PC patients. Outcomes were available for 1149 metastatic PC patients treated with 1L FOLFIRINOX or GP. A scar-based measure of HRD was called using a machine learning-based algorithm incorporating copy number and indel features. RESULTS: A scar-based HRD signature (HRDsig) was identified in 9% of patients. HRDsig significantly co-occurred with biallelic alterations in BRCA1/2, PALB2, BARD1, and RAD51C/D, but encompassed a larger population than that defined by BRCA1/BRCA2/PALB2 (9% vs. 6%). HRDsig was predictive of 1L FOLFIRNOX chemotherapy benefit with doubled OS relative to gemcitabine and paclitaxel (GP) (rwOS aHR 0.37 [0.22-0.62]), including 25% of the population with long-term (2 year+) survival in a real-world cohort of patients. Less benefit from FOLFIRINOX was observed in the HRDsig(-) population. Predictive value was seen in both the BRCA1/2/PALB2 mutant and wildtype populations, suggesting additional value to mutational profiling. CONCLUSION: A scar-based HRD biomarker was identified in a significant fraction of PC patients and is predictive of FOLFIRINOX benefit. Incorporating a biomarker like HRDsig could identify the right patients for platinum chemotherapy and potentially reduce FOLFIRINOX use by over 40%, minimizing toxicities with similar survival outcomes. Confirmatory studies should be performed.

Ultraviolet-C AlGaN Resonant-Cavity Light-Emitting Diodes with Thermal Stability Pipe-AlGaN-Distributed Bragg Reflectors.

Ultraviolet-C AlGaN resonant-cavity light-emitting diodes with top and bottom pipe-AlGaN-distributed Bragg reflectors (DBRs) have been demonstrated. For the top/bottom DBR structures, 20 pairs of n+-AlGaN:Si/n-AlGaN:Si stack structures were transformed into the pipe-AlGaN:Si/n-AlGaN:Si DBRs through a doping-selective electrochemical wet etching process. The reflectivity of the pipe-AlGaN DBR structure was measured as 90% at 276.7 nm with a 20.9 nm flat stopband width. The anisotropic optical properties of the pipe-AlGaN DBR structure had been analyzed through the polarization-dependent reflectance spectra. For temperature-dependent reflectance spectra, the central wavelengths were slightly redshifted from 275 nm (100 K) to 281 nm (600 K) due to thermal expansion, refractive index increase, and partial strain release phenomena in the pipe-DBR structure. High photoluminescence emission intensity and line-width reducing phenomena were observed at 10 K in the UVC-LED with the resonant-cavity structure, which has potential for high-efficiency UV-C light source applications.

Molecular Characterization of Mesothelioma: Impact of Histologic Type and Site of Origin on Molecular Landscape.

PURPOSE: Mesothelioma is an aggressive malignancy with heterogeneous outcomes that are partly driven by the differential efficacy of existing therapies across histologic types and sites of origin. Large-scale molecular analysis of mesothelioma and its subtypes has the potential to inform future therapeutic strategies. MATERIALS AND METHODS: We analyzed 1,294 mesotheliomas {980 pleural (malignant pleural mesothelioma [MPM]) and 314 peritoneal (malignant peritoneal mesothelioma [MPeM])} using next-generation sequencing, determined programmed death ligand-1 (PD-L1) expression and histology in a subset of cases, and assessed MTAP/CDKN2A copy-number status by fluorescence in situ hybridization and T-cell infiltration in an independent cohort. RESULTS: The molecular landscape of MPM was characterized by inactivating alterations in CDKN2A (49%), BAP1 (44%), CDKN2B (42%), MTAP (34%), and NF2 (33%). Compared with epithelioid MPM, nonepithelioid (ie, biphasic and sarcomatoid) MPM had identical tumor mutational burden (median 1.25 mut/Mb, P = .63), more commonly expressed PD-L1 (74% v 51%, P = .02), and was more likely to harbor MTAP, CDKN2A, and CDKN2B copy loss (P < .05). Fluorescence in situ hybridization confirmed that homozygous MTAP loss was enriched in nonepithelioid MPM. Relative to MPM, MPeM had comparable tumor mutational burden and PD-L1 expression. The molecular profile of MPeM was similar to MPM, with the distinction that PBRM1 alterations occurred at higher frequency (16% v 7%, P < .01). ALK rearrangements were only observed in MPeM. CONCLUSION: Regardless of histology and location, the molecular landscape of mesothelioma primarily consists of inactivating alterations in tumor suppressor genes, with enrichment of certain alterations in distinct subsets (eg, MTAP loss in nonepithelioid tumors). Given the limited efficacy of current therapies for this disease, novel approaches targeting recurring alterations should be explored.

InGaN light emitting diodes with a nanopipe layer formed from the GaN epitaxial layer.

A Si-heavy doped GaN:Si epitaxial layer is transformed into a directional nanopipe GaN layer through a laser-scribing process and a selectively electrochemical (EC) etching process. InGaN light-emitting diodes (LEDs) with an EC-treated nanopipe GaN layer have a high light extraction efficiency. The direction of the nanopipe structure was directed perpendicular to the laser scribing line and was guided by an external bias electric field. An InGaN LED structure with an embedded nanopipe GaN layer can enhance external quantum efficiency through a one-step epitaxial growth process and a selective EC etching process. A birefringence optical property and a low effective refractive index were observed in the directional-nanopipe GaN layer.

InGaN Light-Emitting Diodes with an Embedded Nanoporous GaN Distributed Bragg Reflectors.

InGaN light emitting diodes (LED) structure with an embedded 1/4λ-stack nanoporous-GaN/undoped-GaN distributed Bragg reflectors (DBR) structure have been demonstrated. Si-heavily doped GaN epitaxial layers (n(+)-GaN) in the 12-period n(+)-GaN/u-GaN stack structure are transformed into low refractive index nanoporous GaN structure through the doping-selective electrochemical wet etching process. The central wavelength of the nanoporous DBR structure was located at 442.3 nm with a 57 nm linewidth and a 97.1% peak reflectivity. The effective cavity length (6.0λ), the effective penetration depth (278 nm) in the nanoporous DBR structure, and InGaN active layer matching to Fabry-Pérot mode order 12 were observed in the far-field photoluminescence radiative spectra. High electroluminescence emission intensity and line-width narrowing effect were measured in the DBR-LED compared with the non-treated LED structure. Non-linear emission intensity and line-width reducing effect, from 11.8 nm to 0.73 nm, were observed by increasing the laser excited power. Resonant cavity effect was observed in the InGaN LED with bottom nanoporous-DBR and top GaN/air interface.

InGaN light emitting diodes with a laser-treated tapered GaN structure.

InGaN light-emitting diode (LED) structures get an air-void structure and a tapered GaN structure at the GaN/sapphire interface through a laser decomposition process and a lateral wet etching process. The light output power of the treated LED structure had a 70% enhancement compared to a conventional LED structure at 20 mA. The intensities and peak wavelengths of the micro-photoluminescence spectra were varied periodically by aligning to the air-void (461.8nm) and the tapered GaN (459.5nm) structures. The slightly peak wavelength blueshift phenomenon of the EL and the PL spectra were caused by a partial compressed strain release at the GaN/sapphire interface when forming the tapered GaN structure. The relative internal quantum efficiency of the treated LED structure (70.3%) was slightly increased compared with a conventional LED (67.8%) caused by the reduction of the piezoelectric field in the InGaN active layer.

InGaN-based light-emitting diodes with an embedded conical air-voids structure.

The conical air-void structure of an InGaN light-emitting diode (LEDs) was formed at the GaN/sapphire interface to increase the light extraction efficiency. The fabrication process of the conical air-void structure consisted of a dry process and a crystallographic wet etching process on an undoped GaN layer, followed by a re-growth process for the InGaN LED structure. A higher light output power (1.54 times) and a small divergent angle (120°) were observed, at a 20 mA operation current, on the treated LED structure when compared to a standard LED without the conical air-void structure. In this electroluminescence spectrum, the emission intensity and the peak wavelength varied periodically by corresponding to the conical air-void patterns that were measured through a 100 nm-optical-aperture fiber probe. The conical air-void structure reduced the compressed strain at the GaN/sapphire interface by inducing the wavelength blueshift phenomenon and the higher internal quantum efficiency of the photoluminescence spectra for the treated LED structure.

InGaN light emitting solar cells with a roughened N-face GaN surface through a laser decomposition process.

InGaN-based light-emitting solar cell (LESC) structure with an inverted pyramidal structure at GaN/sapphire interface was fabricated through a laser decomposition process and a wet crystallographic etching process. The highest light output power of the laser-treated LESC structure, with a 56% backside roughened-area ratio, had a 75% enhancement compared to the conventional device at a 20 mA operating current. By increasing the backside roughened area, the cutoff wavelength of the transmittance spectra and the wavelength of the peak photovoltaic efficiency had a redshift phenomenon that could be caused by increasing the light absorption at InGaN active layer.