Laboratory evaluation of next-generation backfill materials and methods for airfield damage repair

Abstract Background The EMERGEncy ID Net Study Group is investigating whether advanced molecular tests (AMT) increase the detection of causative agents in the CSF of patients presenting with meningoencephalitis (ME). We report findings from a pilot study using AMT on 18 CSF samples from 10 US Urban Emergency Departments. The purpose of the pilot was to compare the performance of these four AMT to established clinical laboratory methods. Methods We investigated four AMT: (1) BioFire FilmArray ME Panel targeting 14 causative agents; (2) an in-house target-directed next generation sequencing assay targeting 25 agents; (3) a microarray capable of detecting >2,500 agents; and (4) deep metagenomic next generation sequencing. For targeted sequencing, loci from 12 DNA-based and 13 RNA-based pathogens were amplified from the extracts by multiplex PCR. All sequencing was performed on an Illumina MiSeq using 500 cycle v2 Reagent Kits. Reads from the targeted sequencing were aligned to the 25 specific reference target sequences using Bowtie2 while metagenomics reads were processed with the taxonomic sequence classifying software Kraken. For microarray analysis, Lawrence Livermore Microbial Detection Array v2 arrays were hybridized with Cy3-labeled DNA or cDNA. Scanned images of arrays were analyzed by CLiMax 3.1. Results Eight CSF samples had results positive for well-established causes of ME from prior testing (Table). The pilot study demonstrated none of the four AMT detected all causative agents in the eight CSF samples known to have well-established causes of ME. BioFire and targeted sequencing performed best, both detecting 6/8, metagenomics deep sequencing detected 3/8, and microarray detected 1/8. Conclusion Despite the sophistication of AMT, they cannot detect pathogens they do not target, that are present in small numbers, or that have been eliminated from the CSF by the immune response. Despite the theoretical potential for microarray and metagenomic sequencing to detect thousands of different agents, the agents probably must be present at high levels for detection. Disclosures All authors: No reported disclosures.

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Laboratory Evaluation of Cemented Backfill Materials for Mines

Geotechnical Testing Journal ◽

10.1520/gtj11070j ◽

2000 ◽

Vol 23 (4) ◽

pp. 496 ◽

Cited By ~ 1

Author(s):

RC Chaney ◽

KR Demars ◽

E Unal ◽

G Cakmakci

Keyword(s):

Laboratory Evaluation ◽

Cemented Backfill ◽

Backfill Materials

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1213P Next generation sequencing of metastatic prostate cancer: Targetable alternations in DNA damage repair genes and beyond

Annals of Oncology ◽

10.1016/j.annonc.2020.08.107 ◽

2020 ◽

Vol 31 ◽

pp. S792-S793

Author(s):

B. Macanovic ◽

F. Crowley ◽

D. Collins ◽

R. Bambury

Keyword(s):

Prostate Cancer ◽

Dna Damage ◽

Next Generation Sequencing ◽

Metastatic Prostate Cancer ◽

Dna Damage Repair ◽

Next Generation ◽

Damage Repair ◽

Repair Genes ◽

Generation Sequencing

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Identification of Variants Associated With Rare Hematological Disorder Erythrocytosis Using Targeted Next-Generation Sequencing Analysis

Frontiers in Genetics ◽

10.3389/fgene.2021.689868 ◽

2021 ◽

Vol 12 ◽

Author(s):

Aleša Kristan ◽

Tadej Pajič ◽

Aleš Maver ◽

Tadeja Režen ◽

Tanja Kunej ◽

...

Keyword(s):

Next Generation Sequencing ◽

Cell Mass ◽

Laboratory Evaluation ◽

Future Research ◽

Sequencing Analysis ◽

Next Generation ◽

Enhanced Production ◽

Hematological Disorder ◽

Unknown Significance ◽

Generation Sequencing

An erythrocytosis is present when the red blood cell mass is increased, demonstrated as elevated hemoglobin and hematocrit in the laboratory evaluation. Congenital predispositions for erythrocytosis are rare, with germline variants in several genes involved in oxygen sensing (VHL, EGLN1, and EPAS1), signaling for hematopoietic cell maturation (EPOR and EPO), and oxygen transfer (HBB, HBA1, HBA2, and BPGM) that were already associated with the eight congenital types (ECYT1–8). Screening for variants in known congenital erythrocytosis genes with classical sequencing approach gives a correct diagnosis for only up to one-third of the patients. The genetic background of erythrocytosis is more heterogeneous, and additional genes involved in erythropoiesis and iron metabolism could have a putative effect on the development of erythrocytosis. This study aimed to detect variants in patients with yet unexplained erythrocytosis using the next-generation sequencing (NGS) approach, targeting genes associated with erythrocytosis and increased iron uptake and implementing the diagnostics of congenital erythrocytosis in Slovenia. Selected 25 patients with high hemoglobin, high hematocrit, and no acquired causes were screened for variants in the 39 candidate genes. We identified one pathogenic variant in EPAS1 gene and three novel variants with yet unknown significance in genes EPAS1, JAK2, and SH2B3. Interestingly, a high proportion of patients were heterozygous carriers for two variants in HFE gene, otherwise pathogenic for the condition of iron overload. The association between the HFE variants and the development of erythrocytosis is not clearly understood. With a targeted NGS approach, we determined an actual genetic cause for the erythrocytosis in one patient and contributed to better management of the disease for the patient and his family. The effect of variants of unknown significance on the enhanced production of red blood cells needs to be further explored with functional analysis. This study is of great significance for the improvement of diagnosis of Slovenian patients with unexplained erythrocytosis and future research on the etiology of this rare hematological disorder.

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Pan-cancer Analysis of Tumor Mutational Burden and Homologous Recombination DNA Damage Repair Using Targeted Next-Generation Sequencing

Cancer Research and Treatment ◽

10.4143/crt.2020.798 ◽

2021 ◽

Author(s):

Hai-Yun Wang ◽

Ling Deng ◽

Ying-Qing Li ◽

Xiao Zhang ◽

Ya-Kang Long ◽

...

Keyword(s):

Dna Damage ◽

Next Generation Sequencing ◽

Homologous Recombination ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Mutational Burden ◽

Damage Repair ◽

Tumor Mutational Burden ◽

Pan Cancer ◽

Generation Sequencing

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Evaluation of geocell-reinforced backfill for airfield pavement repair

10.21079/11681/42550 ◽

2021 ◽

Author(s):

Lyan Garcia ◽

James Rowland ◽

Jeb Tingle

Keyword(s):

Field Experiments ◽

Crushed Stone ◽

Flight Operations ◽

Damage Repair ◽

Flowable Fill ◽

Backfill Materials ◽

Specific Material ◽

Temporary Airfield ◽

Weak Subgrades ◽

Aircraft Loads

After an airfield has been attacked, temporary airfield pavement repairs should be accomplished quickly to restore flight operations. Often, the repairs are made with inadequate materials and insufficient manpower due to limited available resources. Legacy airfield damage repair (ADR) methods for repairing bomb damage consist of using bomb damage debris to fill the crater, followed by placement of crushed stone or rapid-setting flowable fill backfill with a foreign object debris (FOD) cover. While these backfill methods have provided successful results, they are heavily dependent on specific material and equipment resources that are not always readily available. Under emergency conditions, it is desirable to reduce the logistical burden while providing a suitable repair, especially in areas with weak subgrades. Geocells are cellular confinement systems of interconnected cells that can be used to reinforce geotechnical materials. The primary benefit of geocells is that lower quality backfill materials can be used instead of crushed stone to provide a temporary repair. This report summarizes a series of laboratory and field experiments performed to evaluate different geocell materials and geometries in combinations with a variety of soils to verify their effectiveness at supporting heavy aircraft loads. Results provide specific recommendations for using geocell technology for backfill reinforcement for emergency airfield repairs.

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Abstract B07: Prospective germline next-generation sequencing in pediatric patients with neuroblastoma identifies frequent alterations in genes involved in DNA damage repair

10.1158/1538-7445.pedca19-b07 ◽

2020 ◽

Author(s):

Sarah Cohen-Gogo ◽

Karin Langenberg-Ververgaert ◽

Anita Villani ◽

Winnie Lo ◽

Ted Young ◽

...

Keyword(s):

Dna Damage ◽

Next Generation Sequencing ◽

Pediatric Patients ◽

Dna Damage Repair ◽

Next Generation ◽

Damage Repair ◽

Generation Sequencing

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Genomic determinants of sensitivity to bipolar androgen therapy (BAT) in castrate-resistant prostate cancer (CRPC).

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.7_suppl.200 ◽

2019 ◽

Vol 37 (7_suppl) ◽

pp. 200-200

Author(s):

Michael Thomas Schweizer ◽

Emmanuel S. Antonarakis ◽

Mario A. Eisenberger ◽

Peter Nelson ◽

Jun Luo ◽

...

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Progression Free Survival ◽

Cell Cycle Regulators ◽

Next Generation ◽

Damage Repair ◽

Somatic Alterations ◽

Castrate Resistant Prostate Cancer ◽

Castrate Resistant ◽

Next Generation Sequencing Ngs

200 Background: BAT is a promising treatment for CRPC and preclinical work has shown that its effects may be mediated by inducing DNA damage or cell cycle arrest. We sought to evaluate if mutations in DNA damage repair (DDR) genes or cell cycle regulators were associated with improved outcomes. Methods: Biospecimens from CRPC patients enrolled to studies testing BAT underwent germline or somatic next-generation sequencing (NGS). Samples tested included plasma (i.e. cell-free DNA) (N = 79), tumor tissue (N = 21) and saliva (N = 10). A variety of clinical grade NGS platforms were generally used. Given the concern for false negatives, we excluded cases if plasma NGS did not reveal a somatic alteration. Absence of a germline alteration was not assumed to indicate absence of somatic alterations. Comparative analyses to assess candidate biomarkers of BAT efficacy were performed. Results: Most patients received BAT following one or more next generation hormonal therapy, while 6 received BAT as first-line CRPC therapy. Of 65 cases where a germline or somatic pathogenic alteration in any gene was detected, 30 (46%) had evidence of homologous recombination deficiency (HRD), with mutations found in BRCA2 (N = 10), ATM (N = 8), CHEK2 (N = 5), PALB2 (N = 4), CDK12 (N = 3), CHD1 (N = 2), FANCA (N = 1), FANCD2 (N = 1) and BRCA1 (N = 1). TP53 alterations were also common (27/65; 42%). HRD mutations associated with increased PSA50 responses, with a trend toward improved PSA50 responses in TP53 mutated cases too (Table). In a combined analysis, men with HRD and/or TP53 mutations had improved PSA50 responses and near-significant improvement in progression free survival (PFS). Conclusions: These preliminary data suggest that BAT may be most efficacious in cancers harboring mutations in genes involved in DDR and/or cell cycle regulation. These results require prospective confirmation. [Table: see text]

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Genomic Characterization of Prostatic Ductal Adenocarcinoma Identifies a High Prevalence of DNA Repair Gene Mutations

JCO Precision Oncology ◽

10.1200/po.18.00327 ◽

2019 ◽

pp. 1-9 ◽

Cited By ~ 8

Author(s):

Michael T. Schweizer ◽

Emmanuel S. Antonarakis ◽

Tarek A. Bismar ◽

Liana B. Guedes ◽

Heather H. Cheng ◽

...

Keyword(s):

Dna Damage ◽

Next Generation Sequencing ◽

Mapk Pathway ◽

Dna Damage Repair ◽

Case Series ◽

Next Generation ◽

Repair Gene ◽

Damage Repair ◽

Dna Repair Gene ◽

Generation Sequencing

PURPOSE Ductal prostate cancer (dPC) is a rare variant of prostatic adenocarcinoma associated with poor outcomes. Although its histopathologic features are well characterized, the underlying molecular hallmarks of this aggressive subtype are not well described. We sought to provide a comprehensive overview of the spectrum of mutations associated with dPC. METHODS Three case series across multiple institutions were assembled. All patients had a diagnosis of dPC, and histopathologic classification was confirmed by an expert genitourinary pathologist. Case series 1 included men who were prospectively enrolled in a tumor sequencing study at the University of Washington (n = 22). Case series 2 and 3 included archival samples from men treated at Johns Hopkins Hospital (n = 21) and University of Calgary (n = 8), respectively. Tumor tissue was sequenced on a targeted next-generation sequencing assay, UW-OncoPlex, according to previously published methods. The frequency of pathogenic/likely pathogenic mutations are reported. RESULTS Overall, 25 patients (49%) had at least one DNA damage repair gene alteration, including seven (14%) with a mismatch repair gene mutation and 16 (31%) with a homologous repair mutation. Germline autosomal dominant mutations were confirmed or suspected in 10 patients (20%). Activating mutations in the PI3K pathway (n = 19; 37%), WNT pathway (n = 16; 31%), and MAPK pathway (n = 8; 16%) were common. CONCLUSION This study strongly suggests that dPCs are enriched for actionable mutations, with approximately 50% of patients demonstrating DNA damage repair pathway alteration(s). Patients with dPC should be offered next-generation sequencing to guide standard-of-care treatment (eg, immune checkpoint inhibitors) or triaged toward an appropriate clinical trial (eg, poly [ADP-ribose] polymerase inhibitors).

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