TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples.

In cancer genomics, variant calling has advanced, but traditional mean accuracy evaluations are inadequate for biomarkers like tumor mutation burden, which vary significantly across samples, affecting immunotherapy patient selection and threshold settings. In this study, we introduce TMBstable, an innovative method that dynamically selects optimal variant calling strategies for specific genomic regions using a meta-learning framework, distinguishing it from traditional callers with uniform sample-wide strategies. The process begins with segmenting the sample into windows and extracting meta-features for clustering, followed by using a pre-trained meta-model to select suitable algorithms for each cluster, thereby addressing strategy-sample mismatches, reducing performance fluctuations and ensuring consistent performance across various samples.

Selection of endovascular treatment strategies and analysis of the efficacy of different locations and types of splenic artery aneurysms.

Purpose: To analyze the selection of endovascular treatment strategies and the efficacy of various locations and types of splenic artery aneurysms (SAAs).

Methods: Sixty-three cases of patients diagnosed with SAA from January 2016 to October 2021 were collected, and their clinical data and follow-up results were analyzed.

Results: Among the 63 patients, 55 had true SAAs, and 8 had false SAAs.

A nomogram model based on the combination of the systemic immune-inflammation index, body mass index, and neutrophil/lymphocyte ratio to predict the risk of preoperative deep venous thrombosis in elderly patients with intertrochanteric femoral fracture: a retrospective cohort study.

Objectives: Deep vein thrombosis (DVT) has been considered as a frequent and serious consequence of intertrochanteric femoral fractures in the elderly. Several negative repercussions of DVT can be considerably mitigated by its timely recognition and treatment. The current work was aimed at exploring the factors independently predicting DVT among cases suffering from intertrochanteric femoral fractures and validate their predictive usefulness in diagnosing DVT.

What makes TMB an ambivalent biomarker for immunotherapy? A subtle mismatch between the sample-based design of variant callers and real clinical cohort.

Tumor mutation burden (TMB) is a widely recognized biomarker for predicting the efficacy of immunotherapy. However, its use still remains highly controversial. In this study, we examine the underlying causes of this controversy based on clinical needs.

Cytokine concentration in peripheral blood of patients with colorectal cancer.

Introduction: The role of tumour secretory cytokines and peripheral circulatory cytokines in tumour progression has received increasing attention; however, the role of tumour-related inflammatory cytokines in colorectal cancer (CRC) remains unclear. In this study, the concentrations of various cytokines in the peripheral blood of healthy controls and patients with CRC at different stages were compared.

Methods: Peripheral blood samples from 4 healthy participants and 22 colorectal cancer patients were examined.

Is an SV caller compatible with sequencing data? An online recommendation tool to automatically recommend the optimal caller based on data features.

A lot of bioinformatics tools were released to detect structural variants from the sequencing data during the past decade. For a data analyst, a natural question is about the selection of a tool fits for the data. Thus, this study presents an automatic tool recommendation method to facilitate data analysis.

DelInsCaller: An Efficient Algorithm for Identifying Delins and Estimating Haplotypes from Long Reads with High Level of Sequencing Errors.

Delins, as known as complex indel, is a combined genomic structural variation formed by deleting and inserting DNA fragments at a common genomic location. Recent studies emphasized the importance of delins in cancer diagnosis and treatment. Although the long reads from PacBio CLR sequencing significantly facilitate delins calling, the existing approaches still encounter computational challenges from the high level of sequencing errors, and often introduce errors in genotyping and phasing delins.

HRD-MILN: Accurately estimate tumor homologous recombination deficiency status from targeted panel sequencing data.

Homologous recombination deficiency (HRD) is a critical feature guiding drug and treatment selection, mainly for ovarian and breast cancers. As it cannot be directly observed, HRD status is estimated on a small set of genomic instability features from sequencing data. The existing methods often perform poorly when handling targeted panel sequencing data; however, the targeted panel is the most popular sequencing strategy in clinical practices.

PEcnv: accurate and efficient detection of copy number variations of various lengths.

Copy number variation (CNV) is a class of key biomarkers in many complex traits and diseases. Detecting CNV from sequencing data is a substantial bioinformatics problem and a standard requirement in clinical practice. Although many proposed CNV detection approaches exist, the core statistical model at their foundation is weakened by two critical computational issues: (i) identifying the optimal setting on the sliding window and (ii) correcting for bias and noise.

Percutaneous Ablation of Hepatic Tumors at the Hepatocaval Confluence Using Irreversible Electroporation: A Preliminary Study.

Background: Tumors at the hepatocaval confluence are difficult to treat, either surgically or ablatively.

Methods: A retrospective longitudinal study on patients ineligible for thermal ablation who underwent computed tomography-guided IRE for hepatic tumors at the hepatocaval confluence was conducted. Factors analyzed included patient and tumor characteristics, IRE procedure details, treatment-related complications, and prognosis.

Overexpression of CXCR2 predicts poor prognosis in patients with colorectal cancer.

Colorectal cancer is a heterogeneous disease. Although many risk factors are used to predict colorectal cancer patients' prognosis after surgical resection, new prognostic factors are still needed to be defined to promote predictive efficacy of prognosis and further guide therapies. Herein, we identified the prognostic significance of CXCR2 in colorectal cancer patients.