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restrictedFeb 2022View details →

Dataset related to article "Impact of Antibiotic Therapy and Metabolic Parameters in Non-Small Cell Lung Cancer Patients Receiving Checkpoint Inhibitors"

This record contains raw data related to article “Impact of Antibiotic Therapy and Metabolic Parameters in Non-Small Cell Lung Cancer Patients Receiving Checkpoint Inhibitors" Introduction: In the current study, we aimed to assess the impact of antibiotics (ATB) and metabolic parameters on clinical outcome of non-small cell lung carcinoma (NSCLC) patients treated with immune checkpoint inhibitors (ICI). Methods: Data from fifty NSCLC patients referred for ICI between December 2015 and May 2019 were analyzed. All patients underwent 18F-fluorodeoxyglucose positron emission tomography computed tomography (18F-FDG PET/CT) and contrast-enhanced CT at baseline and for response assessment after 6-8 weeks. Patients who received ATB within 1 month before or after the first dose of ICI were compared with those who did not. Response assessment according to iRECIST and EORTC was evaluated, as well as progression-free survival (PFS) and overall survival (OS). For semi-quantitative parameters, we computed metabolic tumor volume (MTV), total lesion glycolysis (TLG) and their variations (∆). Results: Twenty NSCLC cases of 50 (40%) had received ATB. Patients receiving ATB had a higher number of metastases (p = 0.046), and were associated with an elevated tumor burden, expressed by TLG (687 vs. 235.3, p = 0.007) and MTV (125.6 vs. 40.6, p = 0.002), compared to no-ATB patients. According to iRECIST, progressive disease rate was significantly higher for ATB group (64.7% vs. 27.6%, p = 0.029). Likewise, PFS was shorter for ATB compared to no-ATB (median 4.1 vs. 12.4 months, p = 0.004), while no difference for OS was detected. On multivariate analysis, the effect of ATB remained significant for poor PFS along with performance status (ECOG ≥ 1), and ∆SUVmax. Conclusions: ATB therapy seems to be associated with a worse treatment response, PFS, and higher metabolic tumor burden in NSCLC patients treated with ICI.

restrictedJun 2022View details →

cfDNA methylome profiling for detection and subtyping of Small Cell Lung Cancers

Methyl-Binding Domain protein sequencing (MBD-Seq) was applied to samples derived from patients with small cell lung cancer (SCLC), as well as non-cancerous controls. This included circulating tumour cell derived explants (CDX) or patient derived Xenograft (PDX) preclinical models derived from 33 patients with SCLC, circulating cell-free DNA (cfDNA) from 78 patients with SCLC, cfDNA from 79 non-cancer controls and 13 non-cancerous lung tissue samples. The objects deposited here include R data files containing qseaSets from the R package qsea, which includes the read counts per sample per 300 base pair window across the genome, as well as information on copy number variation and metadata tables and the scripts used to generate and analyse them. Details of files: DX_All_min50_max1000_w300_q10.rds   A qseaSet containing all 97 CDX/PDX samples (including replicates) and the 13 normal lung tissue samples. Note that min50_max1000_w300_q10 refers to including paired reads with between 50 and 1000 base pairs (bp), a window size of 300bp and a minimum MAPQ score of 10. DX_merged.rds   A qseaSet with the biological replicates of each CDX merged together (formed from the above dataset). cfDNA_All_min50_max1000_w300_q10.rds   A qseaSet containing 157 cfDNA samples used in the main body of the paper. NCCsForTrain_All_min50_max1000_w300_q10.rds   A qseaSet containing the 38 NCC cfDNA samples used in the mixture sets for training the tumour/normal classifier. These samples are a subset of those in the cfDNA_All_min50_max1000_w300_q10.rds object. ValidationSet_All_min50_max1000_w300_q10.rds   A qseaSet containing the 41 NCC cfDNA samples and 78 SCLC cfDNA samples used to validate the tumour/normal classifier. A subset of the cfDNA_All_min50_max1000_w300_q10.rds object. cfDNApostTreatment_All_min50_max1000_w300_q10.rds   A qseaSet containing 7 cfDNA samples which were collected at a later, post-treatment, timepoint (mostly disease progression) from the same patients as in the main cfDNA object. Used only for Extended Figure 5, not any other part of the manuscript. varyDNAinput_All_min50_max1000_w300_q10.rds   A qseaSet containing independent replicates of the cell line H1975, with different ng amounts of starting DNA (1-75ng). Used only for Figure 1B. TNmixSets_combined_regionsFiltered_redo2.rds   A qseaSet containing the synthetic mixture sets generated by mixing either a CDX/PDX sample and a NCC sample or two NCC samples. Used to train the tumour/normal classifier. This object is restricted to only the windows used in the classifier for size regions, but the original mixtures are across the whole genome. CDXarrayWide.csv   Pre-processed 450k Infinium Methylation array beta values for 8 CDX samples which were previously sequenced. Used for Supplementary Table 7 only. ArrayCDXs_percent100.rds   A qseaSet containing the 8 CDX samples processed on 450k Infinium Methylation arrays (CDXarrayWide.csv) converted to estimated reads.   KeyTFsincYAP.csv   Variance stabilised transform (vst) values generated from RNASeq for the CDX/PDX samples, for the key genes involved in the subtype classifications. infinium-methylationepic-v-1-0-b5-manifest-file.csv   A lookup file for the Infinium EPIC arrays, as downloaded from https://emea.support.illumina.com/downloads/infinium-methylationepic-v1-0-product-files.html. SCLC_transcript_expression_adjusted_for_batch_effects.csv SCLC_methylation_beta_values_of_individual_probes_after_QC_and_filtering_out_SNVs.csv   Pre-processed transcript and methylation beta values from Infinium EPIC arrays for SCLC cell lines, as downloaded from sclccelllines.cancer.gov/sclc/downloads.xhtml (data timestamped as December 2019). CellLine_100percent.rds   A qseaSet containing the SCLC cell lines converted to estimated MBD-Seq reads. Cellline_mixtureSets.rds   A qseaSet containing the synthetic mixture sets generated by mixing converted cell lines with a NCC sample. Used to train the subtype classifier.  DilutionSeries_CDX13_min50_max1000_w300_q10.rds DilutionSeries_CDX29_min50_max1000_w300_q10.rds DilutionSeries_CDX32_min50_max1000_w300_q10.rds   Three qseaSets containing the results of an in silico dilution of a CDX (CDX13 = POU2F3, CDX29 = NEUROD1, CDX32 = ASCL1) with a single NCC, used to test limit of detection of the subtype classifier. Reads were mixed at the fastq level, prior to the NextFlow pipeline being used. DilutionSeries_H446_Rep*_min50_max1000_w300_q10.rds   Eleven qseaSets containing the results of an in silico dilution of a SCLC cell line H446 with a single NCC (not used to build the classifier), used to determine limit of detection of the tumour/normal classifier. Reads were mixed at the fastq level with different random seeds, prior to a NextFlow pipeline being used. poirier_oncogene.rda PoirierEtAl_Oncogene2015_SuppTab1.csv PoirierEtAl_Oncogene2015_SuppTab2.csv   Processed data object for the 2015 Oncogene paper Poirier et al (PMID:25746006), with 450k array data for SCLC tumours and normal lungs, along with two of the supplementary tables from that paper.

restrictedOct 2022View details →

Dataset related to article "Locally Advanced Non-Small Cell Lung Cancer: Clinical Outcome, Toxicity and Predictive Factors in Patients Treated with Hypofractionated Sequential or Exclusive Radiotherapy "

This record contains raw data related to article “Locally Advanced Non-Small Cell Lung Cancer: Clinical Outcome, Toxicity and Predictive Factors in Patients Treated with Hypofractionated Sequential or Exclusive Radiotherapy" Abstract: Background: This study evaluated the outcome, toxicity and predictive factors in patients unfit for concurrent chemo-radiotherapy (CT-RT) treated with hypofractionated sequential CT-RT or exclusive radiotherapy (RT) for locally advanced non-small cell lung cancer (LA-NSCLC). Methods: We included patients affected by LA-NSCLC (stage IIA-IVA) treated with a total dose of 50-60 Gy in 20 fractions. The primary outcomes were local control (LC), distant metastasis-free survival (DMFS), progression-free survival (PFS) and overall survival (OS). Univariate analysis was used to correlate outcomes with prognostic factors. Results: Between 2011 and 2019, 210 patients were treated, 113 (53.8%) with sequential CT-RT and 97 (46.2%) with exclusive RT. After a median follow-up of 15.3 months, 74 patients (35.2%) had a local progression and 133 (63.3%) had a distant progression. The one-, two- and five-year LC were 73.6%, 55.3% and 47.9%, respectively. At the time of analysis, 167 patients (79.5%) died. The one-, two- and five-year OS were 64.7%, 36% and 20%, respectively. PTV volume correlated with PFS (p = 0.001) and LC (p = 0.005). Acute and late toxicity occurred in 82% and 26% of patients. Conclusions: Albeit with the known limitations of a retrospective and heterogeneous study, our work shows that hypofractionated sequential CT-RT or exclusive RT offer a good local control and toxicity profile and a promising survival rate in LA-NSCLC patients unfit for the concurrent CT-RT scheme.

restrictedcc-by-4.0May 2024View details →

Single-cell spatial profiling of small cell lung cancer suggests clinical outcome related tumor heterogeneity and immune colony niche

High-dimension processed tif images of the publication "Spatial evolution and colony landscape of small cell lung cancer". The code used to produce the results of this study is available at <a href="https://github.com/ wangjun-hub/CODEX_SCLC">https://github.com/ wangjun-hub/CODEX_SCLC</a>.

restrictedcc-by-4.0Jun 2024View details →

Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer

The dataset contains the imaging mass cytometry data associated with Enfield et al., Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer. The patient and sample information has been previously described in Frankell et al., The evolution of lung cancer and impact of subclonal selection in TRACERx and has been deposited on https://zenodo.org/records/7822002. A description of the deposited raw and process data is provided on https://tracerx-phlex.readthedocs.io/en/main/quickstart.html#data-repository.

restrictedOct 2022View details →

Dataset related to article "Locally Advanced Non-Small Cell Lung Cancer: Clinical Outcome, Toxicity and Predictive Factors in Patients Treated with Hypofractionated Sequential or Exclusive Radiotherapy"

This record contains data related to article "Locally Advanced Non-Small Cell Lung Cancer: Clinical Outcome, Toxicity and Predictive Factors in Patients Treated with Hypofractionated Sequential or Exclusive Radiotherapy" Background: This study evaluated the outcome, toxicity and predictive factors in patients unfit for concurrent chemo-radiotherapy (CT-RT) treated with hypofractionated sequential CT-RT or exclusive radiotherapy (RT) for locally advanced non-small cell lung cancer (LA-NSCLC). Methods: We included patients affected by LA-NSCLC (stage IIA-IVA) treated with a total dose of 50–60 Gy in 20 fractions. The primary outcomes were local control (LC), distant metastasis-free survival (DMFS), progression-free survival (PFS) and overall survival (OS). Univariate analysis was used to correlate outcomes with prognostic factors. Results: Between 2011 and 2019, 210 patients were treated,113 (53.8%) with sequential CT-RT and 97 (46.2%) with exclusive RT. After a median follow-up of 15.3 months, 74 patients (35.2%) had a local progression and 133 (63.3%) had a distant progression. The one-, two- and five-year LC were 73.6%, 55.3% and 47.9%, respectively. At the time of analysis, 167 patients (79.5%) died. The one-, two- and five-year OS were 64.7%, 36% and 20%, respectively. PTV volume correlated with PFS (p = 0.001) and LC (p = 0.005). Acute and late toxicity occurred in 82% and 26% of patients. Conclusions: Albeit with the known limitations of a retrospective and heterogeneous study, our work shows that hypofractionated sequential CT-RT or exclusive RT offer a good local control and toxicity profile and a promising survival rate in LA-NSCLC patients unfit for the concurrent CT-RT scheme.

restrictedcc-by-4.0Dec 2022View details →

Is cell line a good model for human cancer?

These are the data for reproducing the results presented in the manuscript "Is cell line a good model for human cancer?"

Donor White Blood Cell Infusion in Treating Patients With Metastatic or Unresectable Cancer

ClinicalTrials.gov study NCT00607802. IPD Sharing: Not stated. Countries: 0. Publications: 0.

Zalutumumab in Non-Small Cell Lung Cancer (NSCLC) Patients Refractory to Tyrosine Kinase Inhibitors

ClinicalTrials.gov study NCT01449357. IPD Sharing: Not stated. Countries: 0. Publications: 0.

Treatment Plan CINC280A02001M to Provide Access to Capmatinib, for MET Exon 14 Skipping Non-Small Cell Lung Cancer (NSCLC)

ClinicalTrials.gov study NCT04741789. IPD Sharing: Not stated. Countries: 0. Publications: 0.

Expanded Access to Trilaciclib for Patients Receiving Chemotherapy for Small Cell Lung Cancer

ClinicalTrials.gov study NCT04504513. IPD Sharing: Not stated. Countries: 0. Publications: 0.

An Expanded Access Protocol for Mobocertinib in Refractory Non-small Cell Lung Cancer (NSCLC) Participants With Epidermal Growth Factor Receptor (EGFR) Exon20 Insertion Mutations

ClinicalTrials.gov study NCT04535557. IPD Sharing: Not stated. Countries: 0. Publications: 0.

Can Epidermal Growth Factor Receptor Improve the Postoperative Survivorship for Inoperable Non-small Cell Lung Cancer With Spinal Metastasis ?

ClinicalTrials.gov study NCT02740894. IPD Sharing: Not stated. Countries: 0. Publications: 0.

TS Stratified Chemotherapy and VEGF Inhibition in Non-Squamous Non-Small Cell Lung Cancer - Stage IV

ClinicalTrials.gov study NCT01674738. IPD Sharing: Not stated. Countries: 0. Publications: 0.

A Study of Conventional 3D Radiation vs. Intensity-Modulated Radiation in Squamous Cell Cancer of the Head and Neck

ClinicalTrials.gov study NCT00363441. IPD Sharing: Not stated. Countries: 0. Publications: 0.

64CuATSM and Hypoxia in Stage IV Non-small Cell Lung Cancer With Carboplatin, Paclitaxel, and Bevacizumab

ClinicalTrials.gov study NCT01006226. IPD Sharing: Not stated. Countries: 0. Publications: 0.

Chemotherapy Plus Peripheral Stem Cell Transplantation in Treating Patients With Advanced Hematologic Cancer

ClinicalTrials.gov study NCT00004114. IPD Sharing: Not stated. Countries: 0. Publications: 0.

Gemcitabine Hydrochloride and Carboplatin With or Without MK-0646 as First-Line Therapy in Treating Patients With Stage IIIB or Stage IV Non-Small Cell Lung Cancer

ClinicalTrials.gov study NCT00951444. IPD Sharing: Not stated. Countries: 0. Publications: 0.

Liposomal SN-38 in Treating Patients With Small Cell Lung Cancer

ClinicalTrials.gov study NCT00104754. IPD Sharing: Not stated. Countries: 0. Publications: 0.

Expanded Access Program for Pirtobrutinib for Participants With B-Cell Cancer

ClinicalTrials.gov study NCT05172700. IPD Sharing: Not stated. Countries: 0. Publications: 0.