Tag: nevin manimala

Bioinformatics. 2023 Apr 21:btad280. doi: 10.1093/bioinformatics/btad280. Online ahead of print.

ABSTRACT

MOTIVATION: Missense variants are a frequent class of variation within the coding genome, and some of them cause Mendelian diseases. Despite advances in computational prediction, classifying missense variants into pathogenic or benign remains a major challenge in the context of personalized medicine. Recently, the structure of the human proteome was derived with unprecedented accuracy using the artificial intelligence system AlphaFold2. This raises the question of whether AlphaFold2 wild-type structures can improve the accuracy of computational pathogenicity prediction for missense variants.

IMPLEMENTATION: To address this, we first engineered a set of features for each amino acid from these structures. We then trained a random forest to distinguish between relatively common (proxy-benign) and singleton (proxy-pathogenic) missense variants from gnomAD v3.1. This yielded a novel AlphaFold2-based pathogenicity prediction score, termed AlphScore.

RESULTS: Important feature classes used by AlphScore are solvent accessibility, amino acid network related features, features describing the physicochemical environment, and AlphaFold2’s quality parameter (pLDDT). AlphScore alone showed lower performance than existing in silico scores used for missense prediction, such as CADD or REVEL. However, when AlphScore was added to those scores, the performance increased, as measured by the approximation of deep mutational scan data, as well as the prediction of expert-curated missense variants from the ClinVar database. Overall, our data indicate that the integration of AlphaFold2 predicted structures can improve pathogenicity prediction of missense variants.

AVAILABILITY: AlphScore, combinations of AlphScore with existing scores, as well as variants used for training and testing are publicly available.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:37084271 | DOI:10.1093/bioinformatics/btad280

Bioinformatics. 2023 Apr 21:btad192. doi: 10.1093/bioinformatics/btad192. Online ahead of print.

ABSTRACT

SUMMARY: The discovery of differential gene-gene correlations across phenotypical groups can help identify the activation/deactivation of critical biological processes underlying specific conditions. The presented R package, provided with a count and design matrix, extract networks of group-specific interactions that can be interactively explored through a shiny user-friendly interface. For each gene-gene link, differential statistical significance is provided through robust linear regression with an interaction term.

AVAILABILITY: DEGGs is implemented in R and available on GitHub at https://github.com/elisabettasciacca/DEGGs. The package is also under submission on Bioconductor.

PMID:37084249 | DOI:10.1093/bioinformatics/btad192

Eur J Cardiothorac Surg. 2023 Apr 21:ezad160. doi: 10.1093/ejcts/ezad160. Online ahead of print.

ABSTRACT

OBJECTIVES: We aim to develop the first risk prediction models for 30-day mortality for benchmarking outcomes specifically for the Australian and New Zealand patient populations and examine whether machine learning algorithms outperform traditional statistical approaches.

METHODS: Data from the Australia New Zealand Congenital Outcomes Registry for Surgery, which contains information on every paediatric cardiac surgical encounter in Australian and New Zealand for patients aged <18 years between January 2013 to December 2021 was analysed (n = 14,343). The outcome was mortality within the 30-day period following a surgical encounter, with approximately 30% of the observations randomly selected to be used for validation of the final model. Three different ML methods were used, all of which employed 5-fold cross-validation to prevent overfitting, with model performance judged primarily by the area under the receiver operating curve (AUC).

RESULTS: Among the 14,343 30-day periods there were 188 deaths (1.3%). In the validation data, the gradient boosted tree obtained the best performance [AUC = 0.87, 95% CI = (0.82, 0.92); calibration = 0.97 95% confidence intervals = (0.72, 1.27)], outperforming penalised logistic regression and artificial neural networks [AUC of 0.82 and 0.81 respectively]. The strongest predictors of mortality in the GBT were patient weight, STAT score, age, and gender.

CONCLUSIONS: Our risk prediction model outperformed logistic regression and achieved a level of discrimination comparable to the PRAiS2 and STS-CHSD mortality risk models (both which obtained AUC = 0.86). Non-linear ML methods can be used to construct accurate clinical risk prediction tools.

PMID:37084239 | DOI:10.1093/ejcts/ezad160

Clin Exp Ophthalmol. 2023 Apr 21. doi: 10.1111/ceo.14231. Online ahead of print.

ABSTRACT

BACKGROUND: Current modalities for diagnosing carotid cavernous fistula (CCF) are inaccurate in analysing retinal microcirculations and nerve fibre changes. Retinal microvascular and neural alterations occur in CCF patients and can be quantitatively measured using optical coherence tomography angiography (OCTA). We measured the neurovascular changes in the eyes of CCF patients and used OCTA as a supplementary method.

METHODS: This cross-sectional study studied 54 eyes of 27 unilateral CCF subjects and 54 eyes of 27 healthy age- and sex-matched controls. OCTA parameters in the macula and optic nerve head (ONH) were analysed using a one-way analysis of variance with further Bonferroni corrections. Parameters with statistical significance were included in a multivariable binary logistic regression analysis and receiver operating characteristic (ROC) curves were generated.

RESULTS: There was significantly less deep-vessel density (DVD) and ONH-associated capillary density in both eyes of CCF patients than in controls, while the differences between the affected and contralateral eyes were insignificant. The retinal nerve fibre layer and ganglion cell complex thickness were lower in the affected eyes than in the contralateral or controlled eyes. ROC curves identified DVD and ONH-associated capillary density as significant parameters in both eyes of CCF patients.

CONCLUSION: The retinal microvascular circulation was affected in both eyes of unilateral CCF patients. Microvascular alterations occurred before retinal neural damage. This quantitative study suggests a supplementary measurement for diagnosing CCF and detecting early neurovascular impairments.

PMID:37084233 | DOI:10.1111/ceo.14231

Cancer Med. 2023 Apr 21. doi: 10.1002/cam4.5905. Online ahead of print.

ABSTRACT

BACKGROUND: Effective noninvasive biomarkers of gastric cancer (GC) are critical for early detection and improvement of prognosis. We performed genome-wide long non-coding RNA (lncRNA) microarray analysis to identify and validate novel GC biomarkers depending on a high-risk population cohort.

METHODS: LncRNA profiles were described using the Human LncRNA Microarray between GC and control plasma samples. The differential candidate lncRNAs were validated in two stages by quantitative reverse transcription polymerase chain reaction (qRT-PCR). We further evaluated the joint effect between the GC-associated lncRNA and Helicobacter pylori (H. pylori) infection on the risk of cardia and non-cardia GC, respectively.

RESULTS: Different lncRNA expression profiles were identified between GC and control plasma with a total of 1206 differential lncRNAs including 470 upregulated and 736 downregulated in GC compared with the control group. The eight significantly upregulated lncRNAs (RP11-521D12.1, AC011995.3, RP11-5P4.3, RP11-244 K5.6, RP11-422 J15.1, CTD-2306 M5.1, CTC-428G20.2, and AC009133.20) in GC cases both in the present study and a similar microarray screening study by our collaborative team were selected for a two-stage validation. After the large sample size validation, the subjects with higher expression of RP11-244 K5.6 showed a significantly increased risk of GC with an adjusted odds ratio (OR) as 2.68 and 95% confidence interval (CI) as 1.15-6.24. Joint effects between RP11-244 K5.6 expression and H. pylori infection on the risk of GC were evaluated with no statistical significance.

CONCLUSIONS: Our study found different lncRNA expression profiles between GC and control plasma and preliminarily identified RP11-244 K5.6 as a potential noninvasive biomarker for GC screening.

PMID:37084181 | DOI:10.1002/cam4.5905

Head Neck. 2023 Apr 21. doi: 10.1002/hed.27376. Online ahead of print.

ABSTRACT

BACKGROUND: Most of the studies on salivary gland cancers are limited for various reasons such as being single-center, small number of patients, including only major or minor SGCs, or only including epidemiological data.

METHODS: A total of 37 medical oncology clinics from different regions of Turkey participated in this retrospective-multicenter study. The analyzed data included clinical and demographical features, primary treatment, metastasis localizations, and treatments and includes certain pathologic features.

RESULTS: The study included data from a total of 443 SGCs. 56.7% was in major salivary glands and 43.3% was in minor salivary glands. Distant metastasis in the major SGCs was statistically significantly more common than in the minor SGCs, locoregional recurrence was statistically significantly more common in the minor SGCs than in the major SGCs (p = 0.003).

CONCLUSIONS: Epidemiological information, metastasis and recurrence patterns, treatment modalities, and survival analysis of the patients over 20 years of follow-up are presented.

PMID:37084179 | DOI:10.1002/hed.27376

Spec Care Dentist. 2023 Apr 21. doi: 10.1111/scd.12869. Online ahead of print.

ABSTRACT

OBJECTIVE: The purpose of this study was to evaluate the maxillary protraction effect of facemask therapy with and without skeletal anchorage in growing Class III patients with unilateral cleft lip and palate (UCLP).

MATERIALS AND METHODS: Thirty patients (aged 9-13 years) with UCLP having a GOSLON score 3 were selected for this prospective clinical study. The patients were allocated into two groups using computer generated random number table. Group I (facemask therapy along with two I shaped miniplates, FM + MP) and Group II (facemask mask along with tooth-anchored appliance, FM). Skeletal and dental parameters were evaluated on pre- and post-treatment lateral cephalograms and pharyngeal airway on cone-beam computed tomography systems (CBCT) for assessment of the treatment changes.

RESULTS: Both methods proved to be effective with statistically significant improvements in skeletal and dental parameters (p < .05). Skeletal parameters (e.g., SNA, convexity-point A, ANB) with the FM + MP group showed greater change compared to those with FM group (SNA, 2.56°; convexity-point A, 1.22°; ANB, 0.35°). Significant proclination of maxillary incisors was observed in the FM group as compared to FM + MP group (U1 to NA, 5.4°; 3.37 mm). A statistically significant increase in pharyngeal airway volume was noted in both groups (p < .05).

CONCLUSION: While both therapies are effective in protracting the maxilla in growing patients with UCLP, the FM + MP allows for a greater skeletal correction, minimizing the dental side effects seen with FM therapy alone. Thus, FM + MP appears to be a promising adjunct in reducing the severity of Class III skeletal correction needed in patients with cleft lip and palate (CLP).

PMID:37084175 | DOI:10.1111/scd.12869

Breast Cancer Res Treat. 2023 Apr 21. doi: 10.1007/s10549-023-06931-1. Online ahead of print.

ABSTRACT

PURPOSE: To determine the genetic and immune features associated with the recurrence of human epidermal growth factor receptor2-positive (HER2 +) breast cancer (BC) after trastuzumab-based treatment.

METHODS: A retrospective cohort study of 48 patients who received trastuzumab-based treatment was divided into recurrent and non-recurrent groups according to clinical follow-up. Baseline samples from all 48 patients were analyzed for genetic variation, HLA allele type, gene expression, and immune features, which were linked to HER2 + BC recurrence. Statistics included logistic regression models, Kaplan-Meier plots, and Univariate Cox proportional hazards models.

RESULTS: Compared with the non-recurrent group, the extracellular matrix-related pathway and 3 Hallmark gene sets were enriched in the recurrent group. The infiltration levels of immature B cells and activated B cells were significantly increased in the non-recurrent group, which correlated remarkably with improved overall survival (OS) in two other published gene expression datasets, including TCGA and METABRIC. In the TCGA cohort (n = 275), activated B cells (HR 0.23, 95%CI 0.13-0.43, p < 0.0001), and immature B cells (HR 0.26, 95%CI 0.12-0.59, p < 0.0001). In the METABRIC cohort (n = 236), activated B cells (HR 0.60, 95%CI 0.43-0.83, p = 0.002), and immature B cells (HR 0.65, 95%CI 0.47-0.91, p = 0.011). Cox regression suggested that immature B cells and activated B cells were protective factors for outcome OS.

CONCLUSIONS: Aberrant activation of multiple pathways and low baseline tumor-infiltrating B cells are related to HER2 + BC trastuzumab-based recurrence, which primarily affects the antitumor activity of trastuzumab.

PMID:37084155 | DOI:10.1007/s10549-023-06931-1

Clin Transl Oncol. 2023 Apr 21. doi: 10.1007/s12094-023-03179-5. Online ahead of print.

ABSTRACT

PURPOSE: Neoadjuvant chemotherapy (NAC) significantly improved the prognosis of patients with locally advanced gastric cancer (LAGC). Several biomarkers, including HER2 and MMR/MSI are crucial for treatment decisions in the advanced stage but, currently, no biomarkers can guide the choice of NAC in clinical practice. Our aim was to evaluate the role of MSI and HER2 status on clinical outcomes.

METHODS: We retrospectively collected LAGC patients treated with NAC and surgery +/- adjuvant chemotherapy from 2006 to 2018. HER2 and MSI were assessed on endoscopic and surgical samples. Pathologic complete response (pCR) rate, overall survival (OS), and event-free survival (EFS) were estimated and evaluated for association with downstaging and MSI.

RESULTS: We included 76 patients, 8% were classified as MSI-H, entirely consistent between endoscopic and surgical samples. Six percent of patients were HER2 positive on endoscopic and 4% on surgical samples. Tumor downstaging was observed in 52.5% of cases, with three pCR (5.1%), none in MSI-H cancers. According to MSI status, event-free survival (EFS) and overall survival (OS) were higher for MSI-H patients to MSS [EFS not reached vs 30.0 months, p = 0.08; OS not reached vs 39.6 months, p = 0.10].

CONCLUSION: Our work confirms the positive prognostic effect of MSI-H in the curative setting of LAGC, not correlated with pathologic tumor downstaging. Prospective ad-hoc trial and tumor molecular profiling are eagerly needed.

PMID:37084152 | DOI:10.1007/s12094-023-03179-5

Pediatr Cardiol. 2023 Apr 21. doi: 10.1007/s00246-023-03156-3. Online ahead of print.

ABSTRACT

After Fontan operation, decreased venous capacitance and venoconstriction are adaptive mechanisms to maintain venous return and cardiac output. The consequent higher venous pressure may adversely impact end-organ function, exercise capacity and result in worse clinical outcomes. This pilot study evaluated the safety and effect of isosorbide dinitrate (ISDN), a venodilator, on exercise capacity, peripheral venous pressure (PVP), and liver stiffness in patients with Fontan circulation. In this prospective single-arm trial, 15 individuals with Fontan circulation were evaluated at baseline and after 4 weeks of therapeutic treatment with ISDN. Primary aims were to assess the safety of ISDN and the effect on maximal exercise. We also aimed to evaluate the effect of ISDN on ultrasound-assessed liver stiffness, markers of submaximal exercise, and PVP at rest and peak exercise. Repeated measures t-tests were used to assess change in variables of interest in response to ISDN. Mean age was 23.5 ± 9.2 years (range 11.2-39.0 years), and 10/15 (67%) were male. There was no statistically significant change in peak VO₂ (1401 ± 428 to 1428 ± 436 mL/min, p = 0.128), but VO₂ at the anaerobic threshold increased (1087 ± 313 to 1115 ± 302 mL/min, p = 0.03). ISDN was also associated with a lower peak exercise PVP (22.5 ± 4.5 to 20.6 ± 3.0 mmHg, p = 0.015). Liver stiffness was lower with ISDN, though the difference was not statistically significant (2.3 ± 0.4 to 2.1 ± 0.5 m/s, p = 0.079). Of the patients completing the trial, mild headache was common (67%), but there were no major adverse events. Treatment with ISDN for 4 weeks is well-tolerated in patients with a Fontan circulation. ISDN is associated with an increase in VO₂ at anaerobic threshold, lower peak PVP, and a trend toward lower liver stiffness. Larger, longer duration studies will be necessary to define the impact of ISDN on clinical outcomes in the Fontan circulation.Clinical Trial Registration: URL: https://clinicaltrials.gov . Unique identifier: NCT04297241.

PMID:37084132 | DOI:10.1007/s00246-023-03156-3