[HTML][HTML] A clinician's guide to bioinformatics for next-generation sequencing

NB Larson, AL Oberg, AA Adjei, L Wang - Journal of Thoracic Oncology, 2023 - Elsevier
Next-generation sequencing (NGS) technologies are high-throughput methods for DNA
sequencing and have become a widely adopted tool in cancer research. The sheer amount …

Ancestry-driven recalibration of tumor mutational burden and disparate clinical outcomes in response to immune checkpoint inhibitors

AH Nassar, E Adib, S Abou Alaiwi, T El Zarif, S Groha… - Cancer Cell, 2022 - cell.com
The immune checkpoint inhibitor (ICI) pembrolizumab is US FDA approved for treatment of
solid tumors with high tumor mutational burden (TMB-high;≥ 10 variants/Mb). However, the …

Tissue-based Profiling Techniques to Achieve Precision Medicine in Cancer: Opportunities and Challenges in Melanoma

TN Gide, Y Mao, RA Scolyer, GV Long… - Clinical Cancer …, 2024 - aacrjournals.org
Immunotherapies targeting the programmed cell death 1 (PD-1) and cytotoxic T lymphocyte
antigen 4 (CTLA-4) checkpoint receptors have revolutionised the treatment of metastatic …

[HTML][HTML] Tumor junction burden and antigen presentation as predictors of survival in mesothelioma treated with immune checkpoint inhibitors

F Kosari, M Disselhorst, J Yin, T Peikert, J Udell… - Journal of Thoracic …, 2022 - Elsevier
Introduction The favorable outcomes with immunotherapy for mesothelioma were somewhat
unexpected because this tumor has a low tumor mutation burden which has been …

Lower exome sequencing coverage of ancestrally African patients in The Cancer Genome Atlas

DP Wickland, ME Sherman, DC Radisky… - Journal of the …, 2022 - academic.oup.com
Abstract Background In the United States, cancer disproportionately impacts Black and
African American individuals. Identifying genetic factors underlying cancer disparities has …

RBM10 deficiency is associated with increased immune activity in lung adenocarcinoma

B Liu, Y Wang, H Wang, Z Li, L Yang, S Yan… - Frontiers in …, 2021 - frontiersin.org
Introduction RBM10 is one of the frequently mutated genes in lung adenocarcinoma (LUAD).
Previous studies have confirmed that RBM10 could suppress the disease progression and …

Integrative multi-OMICs identifies therapeutic response biomarkers and confirms fidelity of clinically annotated, serially passaged patient-derived xenografts …

PH Pandya, AJ Jannu, K Bijangi-Vishehsaraei… - Cancers, 2022 - mdpi.com
Simple Summary Solid tumors account for~ 60% of pediatric, as well as adolescent and
young adult (AYA), cancers, and outcomes for patients with these progressive diseases …

[HTML][HTML] LRP1B mutation is associated with tumor immune microenvironment and progression-free survival in lung adenocarcinoma treated with immune checkpoint …

Z He, W Feng, Y Wang, L Shi, Y Gong… - Translational Lung …, 2023 - ncbi.nlm.nih.gov
Background Only a fraction of lung adenocarcinoma (LUAD) patients are eligible for
immunotherapy. The identification of biomarkers for immunotherapy is crucial to improve …

Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning

RT McLaughlin, M Asthana, M Di Meo… - Npj Precision …, 2023 - nature.com
Accurately identifying somatic mutations is essential for precision oncology and crucial for
calculating tumor-mutational burden (TMB), an important predictor of response to …

[HTML][HTML] Dynamics and survival associations of T cell receptor clusters in patients with pleural mesothelioma treated with immunotherapy

AP Desai, F Kosari, M Disselhorst, J Yin… - … for ImmunoTherapy of …, 2023 - ncbi.nlm.nih.gov
Background Immune checkpoint inhibitors (ICIs) are now a first-line treatment option for
patients with pleural mesothelioma with the recent approval of ipilimumab and nivolumab …