Suicide is an urgent public health crisis that claimed over 49,000 lives in the US in 2023. While genome-wide association studies of suicide are beginning to reveal genetic risk attributable to common variants with small effects on liability, these results explain only a fraction of the substantial proportion of risk due to genetics known to contribute to suicide mortality. As with other complex health conditions, some of this unexplained genetic risk is likely due to rarer variants with larger effects on liability. Using whole genome sequencing data from 1,054 population-ascertained suicide deaths from the Utah Suicide Mortality Research Study (USMRS) jointly processed with 1,230 controls, we investigated intragenic deletions as a class of genomic variation likely to disrupt gene function. To minimize false positives, deletions were limited to those found in large publicly available control datasets (1000 Genomes, GnomAD, and Centers for Common Disease Genomics) and where replication of deletions occurred across two cohorts within the USMRS suicides. Deletions meeting these filters were manually validated. Eleven deletions had at least 2-fold increase in frequency in suicide deaths vs. controls (range 2.28 to 4.46). Implicated genes were associated with mental health conditions (MPST, IL4R, CDH13), epilepsy (CLCA4), intellectual disability (ZNF44), neuronal function (OSBPL2), metabolic function (FBOX36), lipid metabolism (TM9SF3), immune functions (PIPOX, IL4R), and Alzheimer's disease (ZHX3, LMNTD1). Pending replication, these results may help prioritize biological pathways for future functional studies with the goal of increasing our understanding of risk mechanisms leading to suicide mortality.

We present the X-ray polarization observation of G21.5−0.9, a young Galactic supernova remnant (SNR), conducted with the Imaging X-ray Polarimetry Explorer (IXPE) in 2023 October, with a total livetime of approximately 837 ks. Using different analysis methods, such as a space-integrated study of the entire region of the pulsar wind nebula (PWN) and a space-resolved polarization map, we detect significant polarization from the PWN at the center of the SNR, with an average polarization degree of ∼10% oriented at ∼33° (north through east). No significant energy-dependent variation in polarization is observed across the IXPE band (2–8 keV). The polarization map, corrected for the effect of polarization leakage, reveals a consistent pattern in both degree and angle, with little change across the nebula. Our findings indicate the presence of a highly polarized central torus, suggesting low levels of turbulence at particle acceleration sites. Unlike Vela, but similar to the Crab Nebula, we observe substantial differences between radio and X-ray polarization maps. This suggests a clear separation in energy of the emitting particle populations and hints at an important, yet poorly understood, role of instabilities in the turbulence dynamics of PWNe.

Fifty years after the very first sounding rocket measurement of cosmic X-ray polarization, the Imaging X-ray Polarimetry Explorer (IXPE) mission has effectively opened a new window into the X-ray sky. Prior to launch of IXPE, an extensive calibration campaign was carried out to fully characterize the response of this new type of instrument. Specifically, the polarization-sensitive detectors were intensively calibrated in Italy, where they were developed and built. The X-ray optics, which collect and focus X-rays onto the detectors, were built and calibrated in the USA. A key question was whether the telescope (optics + detectors) calibrations could be synthesized from the individual component calibrations, avoiding time consuming and costly end-to-end calibrations for a flight program with a fixed schedule. The data presented here are from a calibration of the flight spare telescope utilizing the flight spare detector and flight spare mirror assembly combined. These data show that the presence of the mirror module does not affect the polarization response of the detectors (within the required calibration accuracy) and that the angular resolution of the telescopes could be accurately determined. Thus, the original extensive stand-alone ground calibration data of all the flight detectors and all the flight optic can be utilized in full to derive the flight telescopes calibrations.

The NFIX gene encodes a DNA-binding protein belonging to the nuclear factor one (NFI) family of transcription factors. Pathogenic variants of NFIX are associated with two autosomal dominant Mendelian disorders, Malan syndrome (MIM 614753) and Marshall-Smith syndrome (MIM 602535), which are clinically distinct due to different disease-causing mechanisms. NFIX variants associated with Malan syndrome are missense variants mostly located in exon 2 encoding the N-terminal DNA binding and dimerization domain or are protein-truncating variants that trigger nonsense-mediated mRNA decay (NMD) resulting in NFIX haploinsufficiency. NFIX variants associated with Marshall-Smith syndrome are protein-truncating and are clustered between exons 6 and 10, including a recurrent Alu-mediated deletion of exons 6 and 7, which can escape NMD. The more severe phenotype of Marshall-Smith syndrome is likely due to a dominant-negative effect of these protein-truncating variants that escape NMD. Here, we report a child with clinical features of Malan syndrome who has a de novo NFIX intragenic duplication. Using genome sequencing, exon-level microarray analysis, and RNA sequencing, we show that this duplication encompasses exons 6 and 7 and leads to NFIX haploinsufficiency. To our knowledge, this is the first reported case of Malan Syndrome caused by an intragenic NFIX duplication.

The Undiagnosed Disease Network, a National Institutes of Health-sponsored research program with 14 centers across the United States, addresses the diagnostic challenges faced by individuals with rare diseases. RNA-sequencing (RNA-seq) has become a powerful tool in clinical genetics, offering insights into transcriptome and genome complexity. RNA-seq provides valuable information on gene expression, allele-specific expression, and alternative splicing, aiding in unraveling the intricacies of genetic variants identified by exome or genome sequencing and serving as functional evidence for variant pathogenicity.

Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess de novo mutations (DNMs) and recombination. From this family, we estimate an average of 192 DNMs per generation, including 75.5 de novo single-nucleotide variants (SNVs), 7.4 non-tandem repeat indels, 79.6 de novo indels or structural variants (SVs) originating from tandem repeats, 7.7 centromeric de novo SVs and SNVs, and 12.4 de novo Y chromosome events per generation. STRs and VNTRs are the most mutable with 32 loci exhibiting recurrent mutation through the generations. We accurately assemble 288 centromeres and six Y chromosomes across the generations, documenting de novo SVs, and demonstrate that the DNM rate varies by an order of magnitude depending on repeat content, length, and sequence identity. We show a strong paternal bias (75-81%) for all forms of germline DNM, yet we estimate that 17% of de novo SNVs are postzygotic in origin with no paternal bias. We place all this variation in the context of a high-resolution recombination map (~3.5 kbp breakpoint resolution). We observe a strong maternal recombination bias (1.36 maternal:paternal ratio) with a consistent reduction in the number of crossovers with increasing paternal (r=0.85) and maternal (r=0.65) age. However, we observe no correlation between meiotic crossover locations and de novo SVs, arguing against non-allelic homologous recombination as a predominant mechanism. The use of multiple orthogonal technologies, near-telomere-to-telomere phased genome assemblies, and a multi-generation family to assess transmission has created the most comprehensive, publicly available "truth set" of all classes of genomic variants. The resource can be used to test and benchmark new algorithms and technologies to understand the most fundamental processes underlying human genetic variation.

BACKGROUND AND AIMS:In the classical form of α1-antitrypsin deficiency, a misfolded variant α1-antitrypsin Z accumulates in the endoplasmic reticulum of liver cells and causes liver cell injury by gain-of-function proteotoxicity in a sub-group of affected homozygotes but relatively little is known about putative modifiers. Here, we carried out genomic sequencing in a uniquely affected family with an index case of liver failure and 2 homozygous siblings with minimal or no liver disease. Their sequences were compared to sequences in well-characterized cohorts of homozygotes with or without liver disease, and then candidate sequence variants were tested for changes in the kinetics of α1-antitrypsin variant Z degradation in iPS-derived hepatocyte-like cells derived from the affected siblings themselves. APPROACH AND RESULTS:Specific variants in autophagy genes MTMR12 and FAM134A could each accelerate the degradation of α1-antitrypsin variant Z in cells from the index patient, but both MTMR12 and FAM134A variants were needed to slow the degradation of α1-antitrypsin variant Z in cells from a protected sib, indicating that inheritance of both variants is needed to mediate the pathogenic effects of hepatic proteotoxicity at the cellular level. Analysis of homozygote cohorts showed that multiple patient-specific variants in proteostasis genes are likely to explain liver disease susceptibility at the population level. CONCLUSIONS:These results validate the concept that genetic variation in autophagy function can determine susceptibility to liver disease in α1-antitrypsin deficiency and provide evidence that polygenic mechanisms and multiple patient-specific variants are likely needed for proteotoxic pathology.

2019 Background: Newer generation tyrosine kinase inhibitors (TKI) for NSCLC with EGFR mutations and ALK rearrangements have demonstrated encouraging central nervous system (CNS) activity with CNS objective response rates, greatly improved from 1st generation TKIs. In response to these data, guideline statements have acknowledged a strategy of CNS-penetrant TKI +/- upfront stereotactic radiosurgery (SRS) for the treatment of select patients with BM. However, optimal use of upfront SRS for BM in these patients is controversial since upfront CNS radiation has been the historical standard of care, and there are limited data guiding patient management with upfront TKI alone. Additionally, results from a large multi-institutional series reported inferior overall survival (OS) with the omission of SRS in patients with EGFR-mutated NSCLC treated with first-generation TKI. Methods: Data on TKI-naïve patients with EGFR- and ALK-driven NSCLC with BM treated with CNS-penetrant TKIs +/- upfront SRS were retrospectively collected from 7 centers in the United States. Time to CNS progression (PD), local CNS PD, and OS were analyzed, with multivariable adjustment (MVA) in Fine and Gray and Cox proportional hazards models for baseline factors including age, sex, performance status, mutation, extracranial metastases, prior therapy, neurologic symptoms, and number and size of BM. Results: We identified 317 patients (200 TKI only and 117 TKI+SRS). 250 (79%) and 61 (19%) patients received osimertinib and alectinib, respectively. Patients who received TKI+SRS were more likely to have BM ≥1 cm (p<0.001) and neurologic symptoms (p<0.001) at baseline. The median follow-up from treatment of BM was 23 months and 26 months in the TKI and TKI+SRS groups, respectively. Median OS was similar between the TKI and TKI+SRS groups (median 41 months [95% CI: 35-NR] vs 40 months [95% CI: 40-NR], respectively; p=0.5). On MVA, TKI+SRS was associated with a significant improvement in time to CNS PD (HR 0.63; 95% CI: 0.42-0.96; p=0.033). Local CNS control was significantly improved with TKI+SRS (HR 0.30, 95% CI: 0.16-0.55; p<0.001), whereas no significant differences were observed in distant CNS control. Subgroup analyses demonstrated greater CNS control benefits with TKI+SRS in patients with BM ≥1 cm. Conclusions: This is the largest multi-institutional study comparing strategies of CNS-penetrant TKIs +/- upfront SRS in TKI-naïve patients with oncogene-driven NSCLC. The addition of SRS improved time to CNS PD and local CNS control but not OS. Patients with BM ≥1 cm may benefit the most from upfront integration of SRS. [Table: see text]

Electroforming replication technology at the Marshall Space Flight Center has a long heritage of producing high-quality, full-shell X-ray mirrors for various applications. Nickel alloys are electroformed onto a super-polished mandrel in the electroforming process and then separated to form the replicated full-shell optic. Various parameters in the electroplating configuration could result in the non-uniformity of the shell's thickness. Thickness non-uniformities primarily occur due to the non-uniform electric field distribution in the electroforming tank during deposition. Using COMSOL Multiphysics simulations, we studied the electric field distributions during the deposition process. Using these studies, we optimized the electric field distribution and strength inside the tank using customized shields and insulating gaskets on the mandrel. These efforts reduced the thickness non-uniformity from over 20% to under 5%. Improving the thickness uniformity of the shell aids in better mounting and aligning shells in the optics module. Optimization of the electroforming process, in some cases, improved the optical performance of the shells. Using finite element modeling, we estimated the effect of electroforming stress on the figure errors of the replicated optics. We observed that the electroforming stress predominantly affects the figure toward the ends of the optics. We presented COMSOL optimization of the electroforming process and the experimental results validating these simulations. We also discuss modeling experimental results of the replication figure errors due to electroforming stresses.

PURPOSE:Newer-generation tyrosine kinase inhibitors (TKIs) for non-small cell lung cancer (NSCLC) with epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) rearrangements have demonstrated high CNS activity. The optimal use of up-front stereotactic radiosurgery (SRS) for brain metastases (BM) in patients eligible for CNS-penetrant TKIs is controversial, and data to guide patient management are limited. MATERIALS AND METHODS:Data on TKI-naïve patients with EGFR- and ALK-driven NSCLC with BM treated with CNS-penetrant TKIs with and without up-front SRS were retrospectively collected from seven academic centers in the United States. Time-to-CNS progression and overall survival (OS) were analyzed, with multivariable adjustment in Fine & Gray and Cox proportional hazards models for clinically relevant factors. RESULTS:From 2013 to 2022, 317 patients were identified (200 TKI-only and 117 TKI + SRS). Two hundred fifty (79%) and 61 (19%) patients received osimertinib and alectinib, respectively. Patients receiving TKI + SRS were more likely to have BM ≥1 cm (P < .001) and neurologic symptoms (P < .001) at presentation. Median OS was similar between the TKI and TKI + SRS groups (median 41 v 40 months, respectively; P = .5). On multivariable analysis, TKI + SRS was associated with a significant improvement in time-to-CNS progression (hazard ratio [HR], 0.63 [95% CI, 0.42 to 0.96]; P = .033). Local CNS control was significantly improved with TKI + SRS (HR, 0.30 [95% CI, 0.16 to 0.55]; P < .001), whereas no significant differences were observed in distant CNS control. Subgroup analyses demonstrated a greater benefit from TKI + SRS in patients with BM ≥1 cm in diameter for time-to-CNS progression and CNS progression-free survival. CONCLUSION:The addition of up-front SRS to CNS-penetrant TKI improved time-to-CNS progression and local CNS control, but not OS, in patients with BM from EGFR- and ALK-driven NSCLC. Patients with larger BM (≥1 cm) may benefit the most from up-front SRS.