Determining the Dosimetric Accuracy of Deep Learning-Based Fully Automated Registration-Segmentation Approach for Thoracic Cancer Organs-at-Risk Contouring

PURPOSE/OBJECTIVE(S)

For adaptive radiation therapy (ART), the contours on the planning CT (pCT) are frequently propagated to cone-beam CT (CBCT) via deformable image registration and manually edited, which is observer-dependent and time-consuming. To automate this process, we created a fully automated workflow by combining a deep learning (DL)-based pCT segmentation model with a CT-to-CBCT registration-segmentation DL model. The purpose of our research is to determine how using the proposed workflow's automatically generated contours affects thoracic organs-at-risk sparing (OAR).

MATERIALS/METHODS

Seven patients with locally advanced non-small cell lung cancer who underwent treatment with intensity modulated radiation therapy were included in this study. Each patient's pCT was segmented using a published DL model that has been used for generating thoracic OAR segmentation and radiotherapy planning in the clinic since July of 2020. Next, pCT was deformably registered using a published recurrent deep registration-segmentation method. Whereas the original method's segmentation sub-network was only trained to segment esophagus, the registration sub-network was used to propagate contours for heart, esophagus, and the proximal bronchial tree (PBT). Geometric segmentation accuracy using the Dice Similarity Coefficient (DSC) and the 95th percentile Hausdorff Distance (HD) and dose metrics including the mean esophageal dose (MED) and D90% of the heart (D90) were computed from the total accumulated dose for the first two weeks of treatment.

RESULTS

The esophagus had a high DSC and a low HD (0.93 and 2.85mm) and conversely, the heart had lower accuracy (DSC = 0.85, HD = 22.06mm). PBT showed relatively high performance as well, with DSC of 0.91 and HD of 2.28mm, owing to its proximity to the esophagus. The accumulated MED for manual contour was slightly lower than AI-contours (11.34 vs 11.83 Gy), suggesting reliability of the proposed workflow. The reverse is seen for the D90 of the heart (manual = 1.74 and AI-contour = 1.56 Gy), likely due to the heart not being included in the original DL framework.

CONCLUSION

This study reported preliminary results on the feasibility of using a fully automated and patient-specific workflow for CBCT auto-segmentation in ART, confirming its role as a geometrically and dosimetrically accurate solution for thoracic OARs. However, because it is currently limited to the esophagus, we believe that re-training the algorithm will increase confidence in other OARs such as the heart and lungs.

Clinical Feasibility of Deep Learning-Based CT during Treatment CBCT Tumor Registration-Segmentation in Thoracic Radiotherapy (RT)

PURPOSE/OBJECTIVE(S)

Accurate tumor segmentation on weekly cone-beam computed tomography (CBCT) images is critical for image-guided and adaptive radiation therapy (ART). In thoracic RT, low image contrast, imaging artifact, and geometry and image modality differences from the planning CT (pCT) typically limits accurate tumor segmentation and registration. Here, we explored the clinical feasibility of using 3D recurrent registration-segmentation deep learning (DL) that combines patient-specific anatomic and shape context from higher contrast pCT and planning contours (PACs) for tumor segmentation on during treatment CBCTs.

MATERIALS/METHODS

We included the pCT and CBCTs from six patients with locally advanced non-small cell lung cancer (LA-NSCLC) who had underwent RT. Cases were selected with a primary GTV contoured and labeled separately from the nodal GTV. Using rigidly aligned pCT and CBCT as inputs, DL auto-segmented the GTV on week 1 and 6 CBCTs, and these auto-segmented contours were manually inspected by a radiation oncologist that edited the GTV according to clinical standard quality. The Dice similarity coefficient (DSC), Hausdorff distance (HD95), mean surface distance (MSD), surface DSC (sDSC) and added path length (APL) were used to quantitively compare the DL and the edited GTV.

RESULTS

The primary GTV was in the right lung in five cases, and left lung in one case. Manual adjustments were typically made at the interface of GTV and lung parenchyma with partial inclusion of adjacent vessels. Hypodensities within the GTV were sometimes not segmented in all axial slices resulting in discontinuous components. The quantitative comparison between the edited and DL-generated GTV is shown in Table 1. For week 1, the average DSC and HD95 were 0.87 and 6.94 mm, respectively. The performance for week 6 was slightly lower than week 1, with a DSC of 0.85 and HD95 of 7.22 mm.

CONCLUSION

The agreement with the generated DL GTV and the edited GTV was high in week 1 and decreased somewhat later during the treatment course possibly due to a higher impact of geometric changes in tumor and adjacent structures. The proposed DL algorithm showed reasonable performance throughout the treatment, supporting its potential for use into clinical routine for LA-NSCLC.

Influence of Body Posture on Internal Organ Dosimetry: Radiocesium Exposure Modeling Using Novel Posture-dependent Mesh Computational Phantoms

ABSTRACT

Current practice in reference internal dosimetry assumes a fixed upright standing posture is maintained throughout the dose-integration period. Recently, the mesh-type ICRP adult reference computational phantoms were transformed into different body postures (e.g., sitting, squatting) for use in occupational dose reconstruction applications. Here, for the first time, we apply this phantom series to the study of organ dose estimates following radionuclide intake. We consider the specific cases of 137 Cs and 134 Cs ingestion (accidental/occupational intake) with attention to variability in absorbed dose as a function of posture. The ICRP Publication 137 systemic biokinetic model for soluble cesium ingestion was used to compute organ-level time-integrated activity coefficients for reference adults, over a 50-y dose-integration period, for 134 Cs and 137 Cs (and its radioactive progeny 137m Ba). Mean posture time-allocations (h d -1 for standing, sitting, and lying) were taken from published survey data. In accord with modern dosimetry formalisms (e.g., MIRD, ICRP), a posture weighting factor was introduced that accounts for the fraction of time spent within each independent posture. Absorbed dose coefficients were computed using PHITS Monte Carlo simulations. ICRP 103 tissue weighting factors were applied along with the posture weighting factors to obtain committed effective dose per unit intake (Sv Bq -1 ). For 137 Cs ingestion, most organ absorbed dose coefficients were negligibly to marginally higher (< ~3%) for sitting or crouched (lying fetal/semi-fetal) postures maintained over the dose commitment period, relative to the upright standing posture. The committed effective dose coefficients were 1.3 × 10 -8 Sv Bq -1 137 Cs for standing, sitting, or crouched postures; thus, the posture-weighted committed effective dose was not significantly different than the committed effective dose for a maintained upright standing posture. For 134 Cs ingestion, most organ absorbed dose coefficients for the sitting and crouched postures were significantly larger than the standing posture, but the differences were still considered minor (< ~8% for most organs). The committed effective dose coefficients were 1.2 × 10 -8 Sv Bq -1 134 Cs for the standing posture and 1.3 × 10 -8 Sv Bq -1 134 Cs for the sitting or crouched posture. The posture-weighted committed effective dose was 1.3 × 10 -8 Sv Bq -1 134 Cs. Body posture has minor influence on organ-level absorbed dose coefficients and committed effective dose for ingestion of soluble 137 Cs or 134 Cs.

The value of performing cerebrovascular CT angiography in major trauma patients: a 5-year retrospective review

AIM

To assess whether routine cerebrovascular imaging is required in all major trauma (MT) patients.

MATERIALS AND METHODS

All MT patients with cerebrovascular imaging between January 2015 and December 2020 were included in the study. Data were collated regarding the type of indication for computed tomography (CT) angiography imaging, time interval from the initial trauma, relevant trauma diagnoses on initial trauma imaging, and CT angiography. Findings, such as aneurysms, vascular malformations, luminal thrombus, venous sinus thrombosis, or vascular injury, were collated. Subsequent treatment with anti-coagulants/anti-platelets or surgical/radiological intervention was noted. Follow-up imaging was assessed for residual injury or complications.

RESULTS

Two hundred and fifty of the 6,251 MT patients underwent dedicated cerebrovascular imaging and were included in the study. Of these 41 (16.4%) had cervical artery or venous sinus injury. Further positive vascular findings were identified in 25/250 patients who presented with an incidental stroke or a vascular abnormality and were mislabelled as MT patients at presentation. One patient with a carotid injury subsequently died following a large infarction. Another patient with vertebral artery injury suffered a non-lethal stroke. No patients underwent surgery or intervention.

CONCLUSION

The present study showed that the overall incidence of detected blunt cerebrovascular injuries was very low (0.6%) and even lower for symptomatic vascular injury (0.03%). Routine cerebrovascular imaging is not recommended in all MT trauma patients, but instead, a continued case-by-case basis should be considered.

Mechanical Testing of Artificial Vessels and Tissues for Photoplethysmography Phantoms

Various studies have looked at the efficiency of artificial vessel and tissue networks in the study of photoplethysmography (PPG) in an effort to better understand the origin of various morphological features present in the signal. Whilst there are all reasonable attempts made to replicate geometrical features such as vessel depth, vessel wall thickness and diameter etc., not many studies have attempted to replicate the mechanical properties such as vessel elasticity and tissue compressibility. This study reports two methods for tissue mechanical testing for the analysis of vessel elasticity and tissue compressibility. A two-part polydimethylsiloxane (PDMS) was used as a base material for both tissue and vessel construction, and the properties altered by changing the curing component ratio. Tissue compression properties were investigated using an industrially calibrated materials testing device using the protocol from the ASTM 0575-91 testing method. Vessel elasticity was investigated using a custom method and apparatus to report vessel diameter and length change simultaneously. Tissue compressive properties proved reasonably easy to replicate through catalyst alteration, however the vessel elasticity properties were found to be higher than expected at all reasonable catalyst ratios. The property of hyper-elasticity was observed in the artificial vessels though, leading to the conclusion that alternative material recipes or construction methods may be needed to correctly replicate the expected mechanical characteristics. Clinical Relevance- The latest generation of health monitoring devices, especially those that are wearable and used widely by individuals wishing to monitor their health daily are becoming smarter and more sophisticated in their functionality. The majority of such devices use photoplethysmography (PPG) as their primary monitoring technique. Being able to replicate the PPG in a phantom allows the continued study and development of devices, and to improve their functionality without the continued need for extensive user-testing.

Bibliometric analysis of manuscript characteristics that influence citations: A comparison of ten major dermatology journals

BACKGROUND

The number of citations an article receives is a reassuring marker for its influence in the academic world.

OBJECTIVE

We aimed to discover characteristics of dermatology articles that may impact their citation.

METHODS

This cross-sectional study collected and analyzed articles published between January and June 2013 from ten highest impact dermatology journals. The study included manuscript characteristics i.e. the length of an article, the presence of visual aids, accessibility, originality, and clarity. Citation analysis statistics required multiple tools such as linear regression, point-biserial correlation, Spearman's rank-order correlation, and Kruskal-Wallis to determine the association between these study variables and the number of citations of articles.

RESULTS

Of 748 articles included in our study, the number of citations ranged from 0 to 814 (median: 18), with weak positive correlations to the length of manuscript (word count: r_s 0.3, p<0.001; pages: r_s 0.3, p<0.001). Having a structured abstract (r_pb -0.15, p<0.001) and increasing number of references (r_s -0.26, p<0.001) showed a negative correlation. Studies originating in North America were associated with higher citations, followed by Europe and Asia (p<0.001). Review articles had a higher number of citations (p<0.001).

CONCLUSIONS

We found that the number of words and the number of pages within a dermatology manuscript had the strongest positive correlation for a higher citation count. The results of this study can benefit authors who may improve the citation of their articles by utilizing this bibliometric study when assembling their manuscript.

Correlation of ROS1 Immunohistochemistry With ROS1 Fusion Status Determined by Fluorescence In Situ Hybridization

CONTEXT.—

The ability to determine ROS1 status has become mandatory for patients with lung adenocarcinoma, as many global authorities have approved crizotinib for patients with ROS1-positive lung adenocarcinoma.

OBJECTIVE.—

To present analytical correlation of the VENTANA ROS1 (SP384) Rabbit Monoclonal Primary Antibody (ROS1 [SP384] antibody) with ROS1 fluorescence in situ hybridization (FISH).

DESIGN.—

The immunohistochemistry (IHC) and FISH analytical comparison was assessed by using 122 non-small cell lung cancer samples that had both FISH (46 positive and 76 negative cases) and IHC staining results available. In addition, reverse transcription-polymerase chain reaction (RT-PCR) as well as DNA and RNA next-generation sequencing (NGS) were used to further examine the ROS1 status in cases that were discrepant between FISH and IHC, based on staining in the cytoplasm of 2+ or above in more than 30% of total tumor cells considered as IHC positive. Here, we define the consensus status as the most frequent result across the 5 different methods (IHC, FISH, RT-PCR, RNA NGS, and DNA NGS) we used to determine ROS1 status in these cases.

RESULTS.—

Of the IHC scoring methods examined, staining in the cytoplasm of 2+ or above in more than 30% of total tumor cells considered as IHC positive had the highest correlation with a FISH-positive status, reaching a positive percentage agreement of 97.8% and negative percentage agreement of 89.5%. A positive percentage agreement (100%) and negative percentage agreement (92.0%) was reached by comparing ROS1 (SP384) using a cutoff for staining in the cytoplasm of 2+ or above in more than 30% of total tumor cells to the consensus status.

CONCLUSIONS.—

Herein, we present a standardized staining protocol for ROS1 (SP384) and data that support the high correlation between ROS1 status and ROS1 (SP384) antibody.

Abstract 755: AVENIO Tumor Tissue Analysis Kits performance across Illumina sequencing platforms

Introduction: Genomic profiling of tumors is an important clinical tool for biomarker discovery and therapy selection. Tumor profiling often relies on formalin-fixed, paraffin-embedded (FFPE) tissue which is challenging because of fragmentation, cross-linking, and nucleotide modifications that arise from the fixation process. AVENIO Tumor Tissue Analysis Kits (For Research Use Only. Not for use in diagnostic procedures) provide an end-to-end solution for FFPE tumor tissue genomic profiling using hybrid-capture next-generation sequencing (NGS). Three panel options (Targeted, Expanded, and Surveillance Kits) provide flexibility in gene coverage with accurate detection of four major types of cancer mutations: single nucleotide variants (SNVs), insertions/deletions (indels), fusions and copy number variations (CNVs). AVENIO Tumor Tissue Analysis Kits were verified and validated on the Illumina NextSeq 500/550 sequencers but there is a need to show comparable performance on alternative NGS platforms. Confirmation of equivalent performance on the HiSeq 4000 allows for sequencing of up to sixteen multiplexed library pools, and simultaneous sequencing of samples analyzed using the AVENIO Tumor Tissue Analysis Kits and the AVENIO ctDNA Analysis Kits.

Methods: In this study, we compared the performance of the three panel options for the AVENIO Tumor Tissue Analysis Kits (For Research Use Only. Not for use in diagnostic procedures) across three Illumina NGS platforms: Illumina NextSeq 500, Illumina HiSeq 4000, and Illumina HiSeq 2500. Ninety libraries containing variants at targeted limit of detection (5% allele frequency for SNV, Fusions, and Indels, and 4-5 copies for CNV) were prepared, sequenced, and analyzed using an internal analysis pipeline equivalent to the commercially available AVENIO Oncology Analysis Software. The total number of reads per sample were normalized across sequencers, and sequencing metrics and variant calls were compared.

Results: The libraries that were prepared using the AVENIO Tumor Tissue Analysis Kits (For Research Use Only. Not for use in diagnostic procedures) and sequenced on the Nextseq 500 demonstrate sensitivities of &gt;99% for SNVs, &gt;99% for Indels, &gt;99% for CNVs, and &gt;99% for Fusions and &gt;99% specificity for all variant types. We found that overall sensitivity and specificity performance were comparable when the samples were subsampled at the same level across the three Illumina platforms. Key sequencing metrics such as sequencing depth, on-target rate, error rate, and uniformity were also similar across the platforms. This study demonstrates that the high assay performance of the AVENIO Tumor Tissue Analysis Kits is consistent across multiple Illumina sequencing platforms.

Citation Format: Isabel Soto, Lewyn Li, Cindy Choi, Garima Kushwaha, Jingchuan Li, Bosun Min, Laura Qin, Seng Salee, Liang Feng, Gregory Turenchalk, Jing Li. AVENIO Tumor Tissue Analysis Kits performance across Illumina sequencing platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 755.

Detection of viable but nonculturable Vibrio parahaemolyticus induced by prolonged cold-starvation using propidium monoazide real-time polymerase chain reaction

Viable but nonculturable (VBNC) Vibrio parahaemolyticus cannot be detected by the standard cultivation-based methods. In this study, commonly used viability assessment methods were evaluated for the detection of V. parahaemolyticus in a VBNC state. Vibrio parahaemolyticus cells exposed to nutrient deficiency at cold temperature were used for epifluorescence microscopy with SYTO₉ and propidium iodide (PI) staining and real-time polymerase chain reaction (qPCR) with propidium monoazide (PMA), and its resuscitative ability was determined by a temperature upshift in freshly prepared artificial sea water (ASW; pH 7) fluids. Viable cells with intact membranes always exceeded 5·0 log CFU per ml in ASW microcosms at 4°C. After 80 days, cycle thresholds for V. parahaemolyticus ATCC 27969 were 16·15-16·69. During cold-starvation, PMA qPCR selectively excluded DNAs from heat-killed cells. However, there may be some penetration of PMA into undamaged cells that persisted in ASW for 150 days, as evidenced by their ability to resuscitate from a VBNC state after a temperature upshift (25°C); V. parahaemolyticus ATCC 33844 and V. parahaemolyticus ATCC 27969 were successfully reactivated from a VBNC state in ASW microcosms containing <5% NaCl, following enrichment in ASW medium (pH 7). SIGNIFICANCE AND IMPACT OF THE STUDY: Few studies have evaluated the characteristics of and detection methods for viable but nonculturable (VBNC) Vibrio parahaemolyticus induced by cold-starvation. Currently, VBNC cells are routinely detected by SYTO₉ and propidium iodide double staining. However, viable cell counts might be overestimated by this approach, suggesting that the fluorescence dyes may be ineffective for accurately determining the viability of bacterial cells. We demonstrated that quantitative real-time polymerase chain reaction with propidium monoazide, which selectively permeates damaged cell membranes, can be used to obtain viable cell counts of V. parahaemolyticus after its evolution to a VBNC state under cold-starvation conditions.

New mesh-type phantoms and their dosimetric applications, including emergencies

Committee 2 of the International Commission on Radiological Protection (ICRP) has constructed mesh-type adult reference computational phantoms by converting the voxel-type ICRP Publication 110 adult reference computational phantoms to a high-quality mesh format, and adding those tissues that were below the image resolution of the voxel phantoms and therefore not included in the Publication 110 phantoms. The new mesh phantoms include all the necessary source and target tissues for effective dose calculations, including the 8-40-µm-thick target layers of the alimentary and respiratory tract organs, thereby obviating the need for supplemental organ-specific stylised models (e.g. respiratory airways, alimentary tract organ walls and stem cell layers, lens of the eye, and skin basal layer). To see the impact of the new mesh-type reference phantoms, dose coefficients for some selected external and internal exposures were calculated and compared with the current reference values in ICRP Publications 116 and 133, which were calculated by employing the Publication 110 phantoms and the supplemental stylised models. The new mesh phantoms were also used to calculate dose coefficients for industrial radiography sources near the body, which can be used to estimate the organ doses of the worker who is accidentally exposed by an industrial radiography source; in these calculations, the mesh phantoms were deformed to reflect the size of the worker, and also to evaluate the effect of posture on dose coefficients.

Abstract 3648: Performance of the AVENIO ctDNA assays across multiple high-throughput next-generation sequencing platforms

Introduction:

Molecular profiling of tumor samples is becoming routine practice in the clinic, particularly for therapy selection. However, in some cases, tumor tissue is not available for testing. Liquid biopsy, which enables the analysis of circulating tumor DNA (ctDNA) shed from the tumor into the blood, can be used as a surrogate for conventional tissue based testing to detect somatic mutations. Furthermore, ctDNA profiling can have potential applications in tumor burden monitoring. Some technical challenges must be overcome to accurately and sensitively detect the often low amount of ctDNA present in plasma. The AVENIO ctDNA Analysis Kits (Targeted, Expanded and Surveillance Kits; Research Use Only) were developed to sensitively detect all 4 major mutation classes: single nucleotide variants, insertions/deletions, fusions, and copy number variations, using a hybrid capture target enrichment workflow, molecular barcoding, and next generation sequencing. We previously presented a comprehensive study of 370+ samples demonstrating analytical performance of the assays on the Illumina NextSeq 500. As ctDNA based analysis becomes more prevalent in the clinical research community, there is great desire for high performing and cost-effective assays that are easy to implement and available across multiple sequencing platforms.

Methods:

We used the commercially available AVENIO ctDNA Analysis Kits (Expanded, Target and Surveillance Kits; Research Use Only) pre-sequencing workflow to process a panel of cell line blends and plasma-derived ctDNA samples in order to compare the performance of the assays on multiple Illumina sequencing platforms: NextSeq 500, HiSeq 4000 and HiSeq 2500. Ninety samples were tested across all platforms. The samples contain SNVs at 0.5% minor allele frequency (MAF), deletions at 1% MAF, selected fusions at 1% MAF, and MET amplification at 2.3 copies. Analysis was done using the AVENIO ctDNA analysis pipeline for all sequencing runs across the sequencing platforms.

Results: On the NextSeq 500, the AVENIO ctDNA Analysis Kits achieve sensitivities of &gt;99% for 0.5% SNVs, &gt;99% for 1% deletions, &gt;96% for 1% fusions, and &gt;99% for 2.3 copies of MET amplification, with 96% to &gt;99% specificity for all mutations. Similar performance is observed across additional Illumina platforms, HighSeq 4000 and HiSeq 2500. Across all platforms, key sequencing metrics are consistent to achieve required sequencing depths, on-target rates, and uniformity. Also, it is noted that in order to achieve required depths, each platform requires different levels of sample multiplexing. We demonstrated that the AVENIO ctDNA Analysis Kits achieve high sensitivity and specificity across multiple high throughput sequencing platforms. We also will highlight the key performance differences and considerations when performing the assay across these sequencing platforms.

Citation Format: Jonathan Choi, Richard Dannebaum, Ashla Singh, Rob Foley, Jorge Dinis, Cindy Choi, Bosun Min, Jingchuan Li, Liang Feng, Fergal Casey, Janet Jin. Performance of the AVENIO ctDNA assays across multiple high-throughput next-generation sequencing platforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3648.

Abstract 5677: Performance of a robust and sensitive liquid biopsy workflow for mutation detection in plasma

The discovery of circulating tumor DNA (ctDNA) and the development of highly sensitive technologies have made the utility of liquid biopsies in clinical practice more feasible. Potential applications for liquid biopsies include early cancer detection, tumor genotyping in the absence of tissue biopsies, disease monitoring, and identification of drug resistance markers. However, there is a multitude of technical challenges to accurately detect ctDNA with high sensitivity and reproducibility. Various methods have been established by research centers and companies, each with its advantages and limitations. We have developed a sensitive NGS-based liquid biopsy assay, called the AVENIO ctDNA Analysis Kits (research use only), which includes three panels targeting biomarkers for solid tumors. The AVENIO ctDNA Analysis Kits include cfDNA extraction from up to 5ml plasma input, optimized reagents and workflow for NGS library preparation and target enrichment. It is accompanied with an intuitive software and data analysis package to easily obtain results. The assay sensitively detects 4 cancer relevant mutation classes - single nucleotide variations (SNVs), insertions/deletions, copy number variations and structural rearrangements.

We conducted a study with 200+ samples of plasma-derived cfDNA, cell line blends containing relevant cancer mutations, and clinical samples, with which we demonstrate the analytical sensitivity of the three distinct AVENIO gene panels (covering 17, 77 and 197 genes). We demonstrate &gt;95% sensitivity for SNVs at 0.5% mutant allele frequency; &gt;95% sensitivity for 1% indels; &gt;95% sensitivity for 1% structural variants. We also demonstrate assay robustness through multiple replicates, day-to-day, and operator-to-operator reproducibility.

In conclusion, the AVENIO ctDNA Analysis Kits for solid tumors encompasses a comprehensive assay and analysis workflow aimed to provide researchers with robust, reliable, highly sensitive and ease to use liquid biopsy assays to conduct the necessary studies to demonstrate the utility of circulating biomarkers in routine clinical testing.

Citation Format: Jonathan Choi, Cindy Choi, Jorge Dinis, Jingchuan Li, Sean Chien, Bosun Min, Abraham Munoz, Janet Jin, Amrita Pati, Liang Feng, Johnny Wu, Ashla Singh, Fergal Casey. Performance of a robust and sensitive liquid biopsy workflow for mutation detection in plasma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5677. doi:10.1158/1538-7445.AM2017-5677

Graphene Q-switched distributed feedback fiber lasers with narrow linewidth approaching the transform limit

A compact all-in-line graphene-based distributed feedback Bragg-grating fiber laser (GDFB-FL) with narrow linewidth of hundreds kHz is demonstrated and investigated in this study. Performing as an optical saturable absorber, graphene oscillates the initially kHz linewidth DFB-FL, and generates high-quality passively Q-switched pulses. Pumped with a 980 nm continuous-wave laser, the Q-switched GDFB-FL observes ~1 μs pulse durations, with pulse energies up to ~10 nJ and approaching the transform limit. The peak power is ~600 times higher than the original DFB-FL laser. By optimizing the cavity design and the graphene material, it is predicted that fast Q-switched pulses with more than MHz repetition rates and sub-100 ns pulse durations are achievable. Such transform-limited Q-switched GDFB-FLs with narrow linewidth of sub-MHz have long coherence length, good tunability, stability, compactness and robustness, with potential impact in optical coherent communications, metrology and sensing.

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus

BACKGROUND

The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus.

RESULTS

We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli.

CONCLUSIONS

Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

The most frequently encountered symbiont on tree roots is the ascomycete Cenococcum geophilum, the only mycorrhizal species within the largest fungal class Dothideomycetes, a class known for devastating plant pathogens. Here we show that the symbiotic genomic idiosyncrasies of ectomycorrhizal basidiomycetes are also present in C. geophilum with symbiosis-induced, taxon-specific genes of unknown function and reduced numbers of plant cell wall-degrading enzymes. C. geophilum still holds a significant set of genes in categories known to be involved in pathogenesis and shows an increased genome size due to transposable elements proliferation. Transcript profiling revealed a striking upregulation of membrane transporters, including aquaporin water channels and sugar transporters, and mycorrhiza-induced small secreted proteins (MiSSPs) in ectomycorrhiza compared with free-living mycelium. The frequency with which this symbiont is found on tree roots and its possible role in water and nutrient transport in symbiosis calls for further studies on mechanisms of host and environmental adaptation.

Analysis of 'Fuji' apple somatic variants from next-generation sequencing

The domesticated apple (Malus x domestica Borkh.) is a major fruit crop of temperate regions of the world. 'Fuji' apple (Ralls Genet x Delicious), a famous apple cultivar in Korea, has been very popular since its promotion in Japan in 1958. 'Fuji' and its bud mutant cultivars possess variable levels of genetic diversity. Nonetheless, the phenotypes of each group, which are classified into the bud mutation groups: early season, fruiting spur, and coloring, are similar. Despite attempts to identify these bud mutation cultivars, molecular markers, which were developed before the emergence of next-generation sequencing technology, have not been able to distinguish each cultivar easily. In this study, we adopted the resequencing technique using the 'Golden Delicious' (Grimes Golden x Unknown) apple genome as a reference. SNPs (single nucleotide polymorphisms) and InDels (insertions or deletions) of 'Fuji' apple and its bud mutant cultivar were detected and SNPs and unique InDels distinct to each cultivar were identified. Data from this study may be used to identify bud mutant cultivars of 'Fuji' apples and be useful for further breeding of apples.