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Case Studies

Our case studies are designed to showcase decision points and background content about the analysis workflows provided to our clients.

 

WES and RNA-seq analysis of patients treated with menin inhibitor compound SNDX-5613 

The following case study features data published from Issa, G.C., Aldoss, I., DiPersio, J. et al. The menin inhibitor revumenib in KMT2A-rearranged or NPM1-mutant leukaemia. Nature 615, 920–924 (2023). https://doi.org/10.1038/s41586-023-05812-3

A Bioinformatic Approach to the Clinical Evaluation of Hematopoiesis Models using Blood Cell Count Data from Patients Enrolled in Clinical Trials of Plinabulin 

The following case study features data presented at the 64th Annual Meeting of the American Society of Hematology.

Exploring Changes in Gene Expression and Associated Biological Pathways in Individuals with COVID-19

This case study focusing on gene expression changes in individuals with COVID-19 features published data from Ziegler et al., 2021, Cell.

Identifying Baseline Plasma Biomarkers Associated With Survival in Previously Treated Advanced Hepatocellular carcinoma

The following case study focusing on plasma biomarkers features published data from Rimassa et al., 2021, Liver Cancer. This study aimed to identify baseline plasma biomarkers associated with survival in HCC.

Using NanoString Data to Identify Immune Signatures in Patients With Mild to Moderate, Severe or Critical Cases of COVID-19

This study aimed to identify characteristic immune signatures in whole blood samples from patients at Cochin Hospital (Paris, France) with “mild to moderate”, “severe” or “critical” cases of COVID-19.

Transcriptome Profiling in Multiple Tumour Types

The aim of this study was to exploit the publicly available datasets of The Cancer Genome Atlas (TGCA) PanCanAtlas and Cancer Cell Line Encyclopaedia (CCLE) in order to extend transcriptomic and prognostic profiling.

Tumour Fusion Burden (TFB) in Prostate Cancer

Prostate cancer is the second leading cause of cancer-associated death in men. Following conventional hormone and chemotherapy treatment, castration-resistant prostate cancer (CRPC) may emerge. CRPC is an aggressive form of prostate cancer.

Determining Mode of Action of a Compound and Genomic Changes

This case study shows that gene expression with associated pathway analysis can be used to both identify the mechanism of action of a compound and also highlight genomic changes which may give rise to side effects following prolonged use.

Predictive Toxicity

RNA samples were hybridised to Affymetrix Rat 230 2.0 whole rat genome arrays. Samples were normalised using RMA (robust multi-chip average). Pairwise comparisons were undertaken on linear model fitted data, using empirical Bayesian approaches, with correction for multiple testing. Treated samples were normalised by comparison with timed control samples. Measures of differential expression were obtained through comparisons within a given timepoint and/or drug concentration series.

Determining Immunity Pathways

In this case study, bioinformatics supported group-wise comparisons to identify differences, functional enrichment analysis of robust markers and other markers implicated in immunity.

Posters

Transcriptome profiling of ST3GAL4 and FUT7 in multiple tumor types and prognostic value in adult acute myeloid leukemia

AACR Virtual Meeting II 2020

This poster is the outcome of our collaboration with GlycoMimetics.

E-selectin is a cell adhesion glycoprotein expressed on endothelial cells and participates in the development of environmental-mediated drug resistance and poor clinical outcomes in cancer.  Collectively, these studies extend the prognostic importance of the E-selectin ligand glycosylation genes, ST3GAL4 and FUT7, to adult AML where these genes may be useful as predictive biomarkers.

Lerociclib (G1T38), a continuously dosed oral CDK4/6 inhibitor, with fulvestrant in HR+/HER2- advanced breast cancer patients: updated Phase 2 results and dose selection

ESMO Congress 2020

This poster is the outcome of our collaboration with G1 Therapeutics, Inc.

Endocrine therapy is an established treatment for patients with hormone receptor–positive (HR+) human epidermal growth factor receptor 2–negative (HER2-) advanced breast cancer (ABC); however, endocrine resistance remains a serious challenge in the clinic. Preliminary results of this study demonstrated continuous dosing of lerociclib with fulvestrant was generally well tolerated and showed early evidence of antitumor activity.

Rintodestrant (G1T48), an oral selective estrogen receptor degrader, in ER+/HER2 locally advanced or metastatic breast cancer: updated phase 1 results and dose selection

San Antonio Breast Cancer Symposium 2020

This poster is the outcome of our collaboration with G1 Therapeutics, Inc.

Rintodestrant is a potent oral selective estrogen receptor (ER) degrader that competitively binds to the ER and blocks ER signaling in tumors resistant to other endocrine therapies. Preliminary results from part 1 dose escalation showed robust target engagement, a favorable safety profile, and encouraging antitumor activity in patients with heavily pretreated ER-positive (ER+)/human epidermal growth factor receptor 2–negative (HER2–) advanced breast cancer (ABC), including those with ESR1 variants

Pharmacodynamic analysis from a phase 1 study of rintodestrant (G1T48), an oral selective estrogen receptor degrader, in ER+/HER 2 locally advanced or metastatic breast cancer

San Antonio Breast Cancer Symposium 2020

This poster is the outcome of our collaboration with G1 Therapeutics, Inc.

Rintodestrant is an orally bioavailable, potent, and selective estrogen receptor (ER) degrader that inhibits ER gene transcription, degrades the ER, and delays tumor proliferation in preclinical models. Preliminary data from a first-in-human, open-label study of rintodestrant in patients with ER-positive (ER+)/human epidermal growth factor receptor 2–negative (HER2–) advanced breast cancer (ABC; NCT03455270) demonstrated that rintodestrant has a favorable safety profile and encouraging antitumor activity.

Trilaciclib improves overall survival when given with gemcitabine/carboplatin in patients with metastatic triple negative breast cancer: final analysis of a randomized phase 2 trial

San Antonio Breast Cancer Symposium 2020

This poster is the outcome of our collaboration with G1 Therapeutics, Inc.

Chemotherapy remains the mainstay of treatment for most patients with metastatic triple-negative breast cancer (mTNBC). Chemotherapy-induced damage to hematopoietic stem and progenitor cells (HSPCs) can lead to depletion of lymphocyte populations, which may adversely affect the ability of the patient’s immune system to mount an effective antitumor response. Preliminary data from a phase 2 trial showed that administering trilaciclib prior to gemcitabine plus carboplatin (GCb) significantly increased OS compared with GCb alone among patients with mTNBC.

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