Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana

Array-based comparative genomic hybridization (Array-CGH) is an important technology in molecular biology for the detection of DNA copy number polymorphisms between closely related genomes. Hidden Markov Models (HMMs) are popular tools for the analysis of Array-CGH data, but current methods are only based on first-order HMMs having constrained abilities to model spatial dependencies between measurements of closely adjacent chromosomal regions. Here, we develop parsimonious higher-order HMMs enabling the interpolation between a mixture model ignoring spatial dependencies and a higher-order HMM exhaustively modeling spatial dependencies. We apply parsimonious higher-order HMMs to the analysis of Array-CGH data of the accessions C24 and Col-0 of the model plant Arabidopsis thaliana. We compare these models against first-order HMMs and other existing methods using a reference of known deletions and sequence deviations. We find that parsimonious higher-order HMMs clearly improve the identification of these polymorphisms. Moreover, we perform a functional analysis of identified polymorphisms revealing novel details of genomic differences between C24 and Col-0. Additional model evaluations are done on widely considered Array-CGH data of human cell lines indicating that parsimonious HMMs are also well-suited for the analysis of non-plant specific data. All these results indicate that parsimonious higher-order HMMs are useful for Array-CGH analyses. An implementation of parsimonious higher-order HMMs is available as part of the open source Java library Jstacs (www.jstacs.de/index.php/PHHMM)

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Impact of COVID-19 on cardiovascular testing in the United States versus the rest of the world

Objectives: This study sought to quantify and compare the decline in volumes of cardiovascular procedures between the United States and non-US institutions during the early phase of the coronavirus disease-2019 (COVID-19) pandemic. Background: The COVID-19 pandemic has disrupted the care of many non-COVID-19 illnesses. Reductions in diagnostic cardiovascular testing around the world have led to concerns over the implications of reduced testing for cardiovascular disease (CVD) morbidity and mortality. Methods: Data were submitted to the INCAPS-COVID (International Atomic Energy Agency Non-Invasive Cardiology Protocols Study of COVID-19), a multinational registry comprising 909 institutions in 108 countries (including 155 facilities in 40 U.S. states), assessing the impact of the COVID-19 pandemic on volumes of diagnostic cardiovascular procedures. Data were obtained for April 2020 and compared with volumes of baseline procedures from March 2019. We compared laboratory characteristics, practices, and procedure volumes between U.S. and non-U.S. facilities and between U.S. geographic regions and identified factors associated with volume reduction in the United States. Results: Reductions in the volumes of procedures in the United States were similar to those in non-U.S. facilities (68% vs. 63%, respectively; p = 0.237), although U.S. facilities reported greater reductions in invasive coronary angiography (69% vs. 53%, respectively; p < 0.001). Significantly more U.S. facilities reported increased use of telehealth and patient screening measures than non-U.S. facilities, such as temperature checks, symptom screenings, and COVID-19 testing. Reductions in volumes of procedures differed between U.S. regions, with larger declines observed in the Northeast (76%) and Midwest (74%) than in the South (62%) and West (44%). Prevalence of COVID-19, staff redeployments, outpatient centers, and urban centers were associated with greater reductions in volume in U.S. facilities in a multivariable analysis. Conclusions: We observed marked reductions in U.S. cardiovascular testing in the early phase of the pandemic and significant variability between U.S. regions. The association between reductions of volumes and COVID-19 prevalence in the United States highlighted the need for proactive efforts to maintain access to cardiovascular testing in areas most affected by outbreaks of COVID-19 infection

Tuberculosis presenting as a pancreatic cystic neoplasm

A 33-year-old Thai born woman was referred to our tertiary referral hospital with back and epigastric pain. Investigations included abdominal ultrasound and CT scan of the abdomen which demonstrated a 3 cm cystic lesion in the head of the pancreas, most likely a mucinous cystadenoma. Because of its malignant potential resection was advised. During surgical exploration, the tumour appeared unresectable, due to involvement of the common hepatic artery. PCR on biopsy revealed Mycobacterium tuberculosis The patient was referred to an infectious disease specialist, and a full recovery was achieved after 6 months of antimicrobials

Repeatability and correlations of dynamic contrast enhanced and T2* MRI in patients with advanced pancreatic ductal adenocarcinoma

In current oncological practice of pancreatic ductal adenocarcinoma (PDAC), there is a great demand for response predictors and markers for early treatment evaluation. In this study, we investigated the repeatability and the interaction of dynamic contrast enhanced (DCE) and T2* MRI in patients with advanced PDAC to enable for such evaluation using these techniques. p). Quantitative R2* (1/T2*) maps were obtained from the multi-echo T2* images. Differences between normal and cancerous pancreas were determined using a Wilcoxon matched pairs test. Repeatability was obtained using Bland-Altman analysis and relations between DCE and T2*/R2* were observed by Spearman correlation and voxel-wise binned plots of tumor voxels. e. ewith tissue T2* and R2* indicating substantial value of these parameters for detecting tumor hypoxia in future studies. The results from our study pave the way for further response evaluation studies and patient selection based on DCE and T2* parameter

Metastatic lymph nodes in hilar cholangiocarcinoma: does size matter?

To determine the diagnostic efficacy of the size criteria for the detection of metastatic lymph nodes (LN) in patients with hilar cholangiocarcinoma (HCCA). LN metastasis is one of the most significant independent prognostic factors in patients with HCCA. Presently, in spite of the well known lack of sensitivity and specificity, one of the most used clinical criteria for nodal metastases is LN size. Pathological slides of 147 patients who had undergone exploration for HCCA were assessed. The size (maximum and short axis diameter) of each single node was retrieved from the pathology report or measured from a section on the glass slide using a stereo microscope and a calibrated ruler integrated in the software. When a metastatic lesion was detected, the proportion of the lesion in relation to LN size was estimated. Out of 147 patients, 645 LN were retrieved and measured. In all, 106 nodes (16%) showed evidence of metastasis. The proportion of positive nodes was 8% in nodes 30 mm. Ten per cent of LN smaller than 10 mm were positive, whereas only 23% of LN larger than 10 mm were metastastically involved. No clear cut-off point could be found. Similar results were found for the short axis diameter. In 50% of positive LN, the metastatic lesion accounted for 10% or less of the LN size. No cut-off point could be determined for accurately predicting nodal involvement. Therefore, imaging studies should not rely on LN size when assessing nodal involvemen

Comparison of six fit algorithms for the intra-voxel incoherent motion model of diffusion-weighted magnetic resonance imaging data of pancreatic cancer patients

<div><p>The intravoxel incoherent motion (IVIM) model for diffusion-weighted imaging (DWI) MRI data bears much promise as a tool for visualizing tumours and monitoring treatment response. To improve the currently poor precision of IVIM, several fit algorithms have been suggested. In this work, we compared the performance of two Bayesian IVIM fit algorithms and four other IVIM fit algorithms for pancreatic cancer imaging. DWI data were acquired in 14 pancreatic cancer patients during two MRI examinations. Three different measures of performance of the fitting algorithms were assessed: (i) uniqueness of fit parameters (Spearman’s rho); (ii) precision (within-subject coefficient of variation, wCV); and (iii) contrast between tumour and normal-appearing pancreatic tissue. For the diffusivity D and perfusion fraction f, a Bayesian fit (IVIM-Bayesian-lin) offered the best trade-off between tumour contrast and precision. With the exception for IVIM-Bayesian-lin, all algorithms resulted in a very poor precision of the pseudo-diffusion coefficient D* with a wCV of more than 50%. The pseudo-diffusion coefficient D* of the Bayesian approaches were, however, significantly correlated with D and f. Therefore, the added value of fitting D* was considered limited in pancreatic cancer patients. The easier implemented least squares fit with fixed D* (IVIM-fixed) performed similar to IVIM-Bayesian-lin for f and D. In conclusion, the best performing IVIM fit algorithm was IVM-Bayesian-lin, but an easier to implement least squares fit with fixed D* performs similarly in pancreatic cancer patients.</p></div

The added value of systematic biopsy in men with suspicion of prostate cancer undergoing multiparametric MRI-targeted biopsy

Purpose: Incorporation of multiparametric magnetic resonance imaging (mpMRI) and targeted biopsy (TBx) in the diagnostic pathway for prostate cancer (CaP) is rapidly becoming common practice. In men with a prebiopsy positive mpMRI a TBx only approach, thereby omitting transrectal ultrasound-guided systematic biopsy (SBx), has been postulated. In this study we evaluated the additional clinical relevance of SBx in men with a positive prebiopsy mpMRI (Prostate Imaging Reporting and Data System [PI-RADS] ≥ 3) undergoing TBx for CaP detection, Gleason grading and CaP localization. Material and methods: Prospective data of 255 consecutive men with a prebiopsy positive mpMRI (PI-RADS ≥ 3) undergoing 12-core SBx and subsequent MRI-transrectal ultrasound fusion TBx in 2 institutions between 2015 and 2018 was obtained. The detection rate for significant CaP (Gleason score [GS] ≥ 3 + 4) for TBx and SBx were compared. The rate of potentially missed significant CaP by a TBx only approach was determined and GS concordance and CaP localization by TBx and SBx was evaluated. Results: TBx yielded significant CaP in 113 men (44%) while SBx yielded significant CaP in 110 men (43%) (P = 0.856). Insignificant CaP was found in 21 men (8%) by TBx, while SBx detected 34 men (13%) with insignificant CaP (P = 0.035). A TBx only approach, omitting SBx, would have missed significant CaP in 13 of the 126 men (10%) with significant CaP on biopsy. Ten of the 118 men (8%), both positive on TBx and SBx, were upgraded in GS by SBx while 11 men (9%) had higher maximum tumor core involvement on SBx. Nineteen of the 97 men (20%) with significant CaP in both TBx and SBx were diagnosed with unilateral significant CaP on mpMRI and TBx while SBx demonstrated bilateral significant CaP. Conclusions: In men with a prebiopsy positive mpMRI, TBx detects high-GS CaP while reducing insignificant CaP detection as compared to SBx. SBx and TBx as stand-alone missed significant CaP in 13% and 10% of the men with significant CaP on biopsy, respectively. A combination of SBx and TBx remains necessary for the most accurate assessment of detection, grading, tumor core involvement, and localization of CaP

Pathological validation and prognostic potential of quantitative MRI in the characterization of pancreas cancer: preliminary experience

Patient stratification based on biological variation in pancreatic ductal adenocarcinoma (PDAC) subtypes could help to improve clinical outcome. However, noninvasive assessment of the entire tumor microenvironment remains challenging. In this study, we investigate the biological basis of dynamic contrast-enhanced (DCE), intravoxel incoherent motion (IVIM), and R2*-derived magnetic resonance imaging (MRI) parameters for the noninvasive characterization of the PDAC tumor microenvironment and evaluate their prognostic potential in PDAC patients. Patients diagnosed with treatment-naïve resectable PDAC underwent MRI. After resection, a whole-mount tumor slice was analyzed for collagen fraction, vessel density, and hypoxia and matched to the MRI parameter maps. MRI parameters were correlated to immunohistochemistry-derived tissue characteristics and evaluated for prognostic potential. Thirty patients were included of whom 21 underwent resection with whole-mount histology available in 15 patients. DCE K trans and v e, ADC, and IVIM D correlated with collagen fraction. DCE k ep and IVIM f correlated with vessel density and R2* with tissue hypoxia. Based on MRI, two main PDAC phenotypes could be distinguished; a stroma-high phenotype demonstrating high vessel density and high collagen fraction and a stroma-low phenotype demonstrating low vessel density and low collagen fraction. Patients with the stroma-high phenotype (high k ep and high IVIM D, n = 8) showed longer overall survival (not reached vs. 14 months, P = 0.001, HR = 9.1, P = 0.004) and disease-free survival (not reached vs. 2 months, P < 0.001, HR 9.3, P = 0.003) compared to the other patients (n = 22). Median follow-up was 41 (95% CI: 36–46) months. MRI was able to accurately characterize tumor collagen fraction, vessel density, and hypoxia in PDAC. Based on imaging parameters, a subgroup of patients with significantly better prognosis could be identified. These first results indicate that stratification-based MRI-derived biomarkers could help to tailor treatment and improve clinical outcome and warrant further research

Example parameter maps from a pancreatic cancer patient.

<p>Axial parameter maps of the fit parameters of six IVIM model fit algorithms in a 71-year-old male with pancreatic adenocarcinoma in the pancreas tail. ROIs containing pancreatic tumour are shown. The CE T1W GE is added as a reference. Note that for the Bayesian approaches, not all voxels were fitted, as including more voxels will influence the prior. This patient had D, f and D* between 1.0–1.3×10⁻³ mm²/s, 2.0–14.9% and 15–70×10⁻³ mm²/s respectively. The green arrow highlights the higher f found in IVIM-Bayesian compared to the other algorithms. The blue arrows highlight the lower f in IVIM-Bayesian-lin and IVIM-fix.</p