15136 results for "cancer studies using rna-seq"

in 40.30 milliseconds.

• Molecular analysis in bowel malignancies in cancer survivors vs. primary malignancies

  Study EGAS00001005940

• Deep whole genome ctDNA chronology of treatment-resistant prostate cancer

  Study EGAS00001005783

• Identification of novel colorectal cancer predisposition genes

  Study EGAS00001005118

• Genome analysis of early onset sporadic rectal cancer

  Study EGAS00001005970

• RNAseq

  RNAseq of pancreatic cancer organoids.

  Study EGAS00001007212

• Identifying autosomal recessive mutations causing neurological disorders

  The objective of this study is to resequence of targeted intervals containing autosomal recessive variants causing neurological disorders in consanguineous pedigrees. Using homozygosity mapping, three intervals of very different sizes have previously been unambiguously mapped for three different neurological diseases: 2.4Mb, 8Mb and 14.3Mb in size, for Microlissencephaly, Severe Mental Retardation and Complicated hereditary spastic paraplegia respectively. This study is a pilot to assess how well custom targeted resequencing performs across a broad size range of intervals. The study design is to use a different custom capture probe set for each interval, pulldown from a single patient from each family, and sequence 1 lane using Illumina paired-reads for each sample. Candidate variants will be followed up in the families themselves, and in patients with similar phenotypes from outbred populations.

  Study EGAS00001000023

• Somatic Mutations in Epilepsy: Whole Genome Sequence Analysis of Single Neurons

  Low-coverage whole-genome sequencing was performed on single-cells from resected brain tissues obtained from an individual with hemimegalencephaly (HMG) along with a somatic copy number variant (sCNV) of chromosome 1q in order to characterize the sCNV at the single cell level. Single neuronal nuclei and non-neuronal nuclei were isolated by fluorescence-activated cell sorting (FACS) using NeuN immunoreactivity to identify neurons. 46 neurons and 30 non-neuronal cells, as well as a batch of 10 and a batch of 100 cells from each group, were genome amplified using multiple displacement amplification (MDA) and sequenced on an Illumina HiSeq 2000 sequencer. Thirty-two samples were multiplexed into each HiSeq lane for single-end 50 bp runs, obtaining ~5 million pass-filter reads per sample.

  Study phs002615

• UAMS Smoldering Myeloma Timeline Cohort

  To better understand the pattern of genetic changes over time, we performed whole exome sequencing of sequential bone marrow samples from 9 patients taken overtime including some paired SMM/newly diagnosed MM/Relapse MM samples. Samples from 9 patients (9 controls and 53 tumors) underwent whole exome sequencing with an additional capture for the IGH, IHK, IGL, and MYC loci. DNA was obtained from either CD138+ cells from the bone marrow of smoldering myeloma patients through time (tumor) or from stem cell harvests or peripheral blood cells from the same patient (control). 100 ng of DNA was fragmented, end-repaired, and adapters ligated using NimbleGen's MedExome. After PCR amplification hybridized libraries underwent further amplification before being sequenced on a NextSeq500 (Illumina) using 75 bp paired end reads.

  Study EGAS00001003687

• Breast Cancer Follow Up Series

  This study's purpose is to use data generated in whole genome and exome Breast Cancer sequencing to target specific areas in multiple other Breast Cancer samples. These areas will then be subjected to PCR in multiple cases, tagged and then pool the resultant amplicons. These amplicons will then be sequenced on the Illumina GAII. This is hoped to show the prevalence of previous findings in multiple individuals in a high throughput method.

  Study EGAS00001000002

• Breast Cancer Family Registry Early-onset Breast Cancer GWAS

  In order to enhance our understanding of the genetic etiology of breast cancer, this study analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 age-matched population control women, all of whom were age 50 or younger at enrollment. Subjects were recruited from the eight sites, some of which oversampled cases with a personal or family history of breast cancer.

  Study phs001589

• Prognostic whole-genome and transcriptome signatures in colorectal cancers

  Colorectal cancer (CRC) is caused by a sequence of somatic genomic alterations affecting driver genes in core cancer pathways1. To understand the functional and prognostic impact of cancer-causing somatic mutations, we analysed the whole genomes and transcriptomes of 1,063 primary CRCs in a population-based cohort with long-term follow-up. This study constitutes the largest integrated genome and transcriptome analysis of CRC to date, and links mutations, gene expressions and patient outcomes.

  Study EGAS50000000124

• In this study, we performed exon sequencing (WXS) of 80 paired Brain cancer tumors and adjacent normal tissues to identify novel potential biomarkers. We extracted mutational signatures which induce somatic mutations . Our study covers a comprehensive genetic framework that can be used in clinical trials and treatment modalities in Brain cancer.

  In this study, we performed exon sequencing (WXS) of 80 paired Brain cancer tumors and adjacent normal tissues to identify novel potential biomarkers. We extracted mutational signatures which induce somatic mutations . Our study covers a comprehensive genetic framework that can be used in clinical trials and treatment modalities in Brain cancer.

  Study EGAS00001002352

• Hyperdiploidy impairs fetal hematopoietic progenitor cell fitness and differentiation enabling persistence of rare preleukemic aneuploid clones

  Cells previously cryopreserved in FBS-10%DMSO were thawed and resuspended in 1mL of cold lysis buffer (10 mM Tris-HCl pH 7.4, 154 mM NaCl, 0.2% BSA, 0.1% NP-40, 1 mM CaCl₂, 0.5 mM MgCl₂ in ultra-pure water) to lyse the cell membrane and release intact nuclei. The nuclei were stained with propidium iodide (10 µg/mL) and Hoechst 33258 (10µg/mL) to facilitate sorting based on cell cycle state and viability. Single nuclei from 48 cells per sample were isolated into 96-well plates containing 5µL of freeze buffer (1X PBS, 7.5% DMSO, and 40% ProFreeze freezing medium (Lonza)) using a MoFlo Astrios cell sorter (Beckman Coulter) at the Flow Cytometry Unit of the University Medical Center Groningen (UMCG), Netherlands. The plates were centrifuged at 500 g and stored at -80°C until library preparation. Single-nuclei libraries were prepared using a Bravo Automated Liquid Handling Platform (Agilent Technologies). Nuclei were lysed, and DNA was labelled with unique 10 bp dual barcodes and amplified as previously described. Sequencing was performed on an Illumina NextSeq 2000 platform with 77bp single end reads. The generated data were subsequently demultiplexed using sample-specific barcodes and converted to FASTQ files with bcl2fastq. Sequencing reads were aligned to the GRCh38/hg38 human reference genome using Bowtie2 (v2.2.4), and duplicate reads were marked with BamUtil (v1.0.3). Single-cell karyotypes were determined by performing copy number analysis using AneuFinder (v4.3.3) (https://github.com/ataudt/aneufinder). The analysis included GC-content correction and blacklisting of artifact regions identified from euploid controls. Copy number calling was conducted with the dnacopy and edivisive algorithms, employing a bin size of 1 Mb and a step size of 500 Kb. Libraries with an average of fewer than 10 reads per chromosome copy per bin or less than 95% concordance between the two algorithms were excluded from analysis. Whole-chromosome aneuploidies were identified when over 95% of bins exhibited deviation from the disomic state. Aneuploidy scores were calculated as weighted averages of absolute copy number deviations from the euploid state. 

  Dataset EGAD50000002314

• Genomics of Prostate Cancer

  This dataset includes genomic data from patients with prostate cancer. Specimens include archival active surveillance biopsies, radical prostatectomy specimens selected based on evidence of PD-L1 expression and/or T lymphocyte infiltrates, and rapid autopsy material from patients deceased of prostate cancer. These data include low pass whole genome sequencing and targeted sequencing with matched normal.

  Study phs002398

• Identifying and Reducing Disparities in Patient-Reported Outcomes Among African American Prostate Cancer Survivors

  This research study aimed to identify disparities in prostate cancer symptom burden and their contributors among African American, Hispanic, and non-Hispanic White prostate cancer survivors. We collected patient-reported outcomes data, focusing on various aspects of the survivors' health and well-being, clinical data, demographics data, and germline genomic data.

  Study phs003745

• Target sequencing of 11 hereditary breast cancer genes in Japanese

  We performed a case control association study for variants in coding regions of 11 hereditary breast cancer genes in 7,051 female unselected breast cancer patients, 11,241 female controls, 53 male patients, and 12,490 male controls of Japanese ancestry. The 11 genes were ATM, BRCA1, BRCA2, CDH1, CHEK2, NBN, NF1, PALB2, PTEN, STK11, and TP53.

  Study JGAS000140

• Cell_Line_Sub_Clone_Rearrangement_Screen

  Genomic libraries (500 bps) will be generated from total genomic DNA cancer samples and subjected to paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions.

  Study EGAS00001000178

• Genomic landscape of inflammatory breast cancer by whole-genome sequencing

  Inflammatory breast cancer (IBC) is the most aggressive form of breast cancer, characterized by a highly invasive and metastatic phenotype, but little is known about its genetic drivers. Here we report whole-genome sequencing (WGS) of 20 newly diagnosed IBC biopsies to characterize for the first time the entire genomic landscape of this disease.

  Study EGAS00001004117

• Whole-exome sequencing of paired tumour/blood of 58 T1 stage bladder cancer patients

  To understand the molecular determinants that underpin the clinical heterogeneity of non-muscle-invasive bladder cancer (NMIBC) we carried out whole-exome sequencing (WES) of stage T1 bladder tumours to identify prognostic biomarkers and novel therapeutic targets. The study includes paired tumour/blood samples of 58 T1 stage bladder cancer patients.

  Study EGAS00001005765

• Molecular Profiles of BRCA1-Associated Ovarian Cancer Treated by Platinum-Based Therapy

  Study EGAS00001003980

• Genotyping by array

  Expression profiling by Nanostring cancer pathway

  Dataset EGAD00010001276

• Genomic profiling of patient-derived xenografts and organoids in prostate cancer

  Study EGAS00001004673

• Prostate Cancer mitochondrial DNA heteroplasmies and mitochondrial gene expression

  Study EGAS00001004186

• Validation of cfDNA fragmentome analyses for early detection of liver cancer

  Study EGAS00001008111

• Light at Night and Prostate Cancer in the Health Professionals Follow-Up Study

  The Health Professionals Follow-Up Study (HPFS) is a prospective cohort study of men designed to evaluate hypotheses about men's health related to diet and lifestyle to the incidence of serious illnesses, such as cancer, heart disease, and other vascular diseases. It consisted of 51,529 U.S. male health professionals who were 40-75 years old at baseline in 1986 and completed a mailed six-page baseline questionnaire. Information on age, height, weight, ancestry, medications, disease history, physical activity, lifestyle factors, and diet were gathered, with follow-up questionnaires sent biennially to update information and record health outcomes with every four years to update their diet. Light at Night and Prostate Cancer project uses HPFS participants to conduct research assessing the impact of light at night on prostate cancer incidence, with follow-up from baseline in 1986 to 2016. Average annual outdoor light at night (exposure) was derived from satellite imagery data from the US Defense Meteorological Satellite Program's Operational Linescan System (maintained by the National Oceanic and Atmospheric Administration's Earth Observation Group). Prostate cancer cases (outcome) were self-reported by study participants, and then confirmed by the HPFS team through medical record and pathology report review. The data for this project are arranged in a long format, meaning that there are multiple rows for each subject ID. The various rows correspond to different questionnaire periods. Because the exposure in this dataset, light at night, and several important covariates are time-varying variables, the format of this dataset captures the variation in exposure status by questionnaire period. The outcome variables are incidence of prostate cancer, including incidence of prostate cancer clinical subtypes, such as advanced, aggressive, high- and low-grade prostate cancer. For the published study, please see Chowdhury-Paulino et al.'s 2023 publication in Cancer Epidemiology Biomarkers and Prevention entitled, “Association between Outdoor Light at Night and Prostate Cancer in the Health Professionals Follow-up Study.” (PMID: 37462694).

  Study phs003538

• Molecular Tumor Board to Inform on Personalized Medicine for a Man with Advanced Prostate Cancer

  Purpose: Molecular profiling of cancer is increasingly common as part of routine care in oncology, and germline and somatic profiling may provide insights and actionable targets for men with metastatic prostate cancer. However, all reported cases are of deidentified individuals without full medical and genomic data available in the public domain. Patient and Methods: We present a case of whole genome tumor and germline sequencing in a patient with advanced prostate cancer, who has agreed to make his genomic and clinical data publicly available in an accompanying personal testimonial. Results: We describe an 84-year-old Caucasian male with a Gleason 10 oligometastastic hormone-sensitive prostate cancer. Whole-genome sequencing provided insights into his tumor’s underlying mutational processes and the development of an SPOP mutation. It also revealed an androgen-receptor dependency of his cancer which was reflected in his durable response to radiation and hormonal therapy. Potentially actionable genomic lesions in the tumor were identified through a personalized medicine approach for potential future therapy, but at the moment, he remains in remission, illustrating the hormonal sensitivity of his SPOP-driven prostate cancer. We also placed this patient in the context of a large prostate-cancer cohort from the PCAWG (Pan-cancer Analysis of Whole Genomes) group. In this comparison, the patient's cancer appears typical in terms of the number and type of somatic mutations, but it has a somewhat larger contribution from the mutational process associated with aging. Conclusion: We combined the expertise of medical oncology and genomics approaches to develop a molecular tumor board to integrate the care and study of this patient, who continues to have an outstanding response to his combined modality treatment. This identifiable case potentially helps overcome barriers to clinical and genomic data sharing.

  Study EGAS00001004648

• Genomic-Enabled Medicine for Recurrent Glioblastoma

  In this prospective study, we performed genome-wide tumor/normal exome sequencing and tumor RNA-sequencing for recurrent glioblastoma patients. A subset of patients had both enhancing tumor and non-enhancing tissue sequenced to investigate spatial heterogeneity of this disease. Together, this information builds our understanding of the genomic underpinnings of glioblastoma, and contributes toward the knowledge base for identifying and developing more effective treatments for patients with glioblastoma.

  Study phs001460

• Pilot Sequencing Study: DNA Hydroxymethylation and Gene Expression in Peripheral Blood Mononuclear Cells in Healthy Human Aging

  This study was a pilot analysis of samples of human peripheral blood mononuclear cell (PBMCs) from 10 young (23-30 years) and 10 older (68-76 years) healthy Caucasian female volunteers. Whole genome sequencing was performed to assess multiple epigenetic mechanisms and gene expression, including 5hmC-capture sequencing and RNA-sequencing, followed by integrative analyses to identify regions and genes associated with age.

  Study phs001916

• Cellular Origins and Genetic Landscape of Cutaneous GD T Cell Lymphoma

  Cutaneous gamma-delta T cell lymphomas are a rare and aggressive subtype of cutaneous lymphoma. In the present study, we analyzed these cancers by DNA and RNA sequencing in order to illuminate the genetic landscape for this rare disease. We obtained tumor samples from multiple institutions, including Northwestern University (Chicago, IL), University of Chicago (Chicago, IL), University of Virginia (Charlottesville, VA), and Massachusetts General Hospital (Boston, MA).

  Study phs001969

• Single Cell Analysis of Healthy and Diseased Temporomandibular Joint Synovial Fluid

  Temporomandibular joint disorders (TMJDs) are a set of complex, poorly understood painful conditions that negatively affect many children and adults in the US. In this study, we establish a protocol to utilize irrigation fluid from TMJ arthrocentesis to perform single-cell RNA sequencing on cells contained in TMJ synovial fluid. Our results should help investigators better understand these conditions and identify novel therapeutic options.

  Study phs003645

• Molecular Correlatives from SU2C-SARC032

  SU2C-SARC032 was a phase II international, randomized trial for patients with localized, high-risk undifferentiated pleomorphic sarcoma or dedifferentiated or pleomorphic liposarcoma of the extremity and limb girdle. On the trial, the addition of perioperative pembrolizumab to preoperative radiotherapy and surgery improved disease-free survival compared to preoperative radiotherapy and surgery alone. Bulk RNA-sequencing was performed on pre-treatment and surgically resected tumor specimens.

  Study phs003921

• RNA004 DRS METTL5 variant

  RNA004 is a method for direct RNA sequencing (DRS) that holds promise to enhance the detection of modopathies. To this end, we provide DRS data for a patient sample harboring heterozygous inactivating SNPs for the methyltransferase METTL5, which modifies m6A on 18S rRNA. Companion datasets are 1) EGAS50000001201 for DRS of a healthy control with intact METTL5 and 2) PRJEB74238 for IVT 18S rRNA vector data as unmodified control.

  Study EGAS50000001321

• RNA_expression_profiling_of_melanoma_patient_derived_xenograft

  Patient-derived xenografts (n=96) were derived from metastatic melanoma patients. RNA expression profiling will be preformed to study 1. HLA-typing and 2. the effect of the tumour microenvironment on tumour growthThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Study EGAS00001001537

• RNAseq Iron-Treated iPSC-derived Microglia

  Iron accumulation in microglia has been observed in Alzheimer’s disease and other neurodegenerative disorders and is thought to contribute to disease progression through various mechanisms including neuroinflammation. To study the interaction between iron accumulation and inflammation, we treated human induced pluripotent stem cell-derived microglia (iPSC-MG) with an increasing concentration of iron, in combination with inflammatory stimuli such as interferon gamma and amyloid β, and performed RNA sequencing.

  Study EGAS00001006112

• Somatic L1 retrotranspositions in normal human cells

  Genomic mutations accumulate in normal cells during lifetime; however, somatic mosaicism generated by mobilization of transposable elements is not well understood. Here, we explored whole-genome sequences of single-cell expanded clones to illustrate the mutational landscape produced by L1. In addition, we analyzed promoter DNA methylation status of retrotransposition-competent L1 and read-through RNA expression profiles to investigate the epigenetic regulation of L1 activity.

  Study EGAS00001006213

• SPECIAL: Dissecting the melanoma ecosystem one cell at the time during immunotherapy

  The aim of this study was to identify potential biomarkers of response to immunotherapy (anti-PD1-based) as well as gain understanding of the biological mechanism of therapy resistance (either intrinsic or acquired) in melanoma patients. Single cell RNA sequencing was performed from pre- and on-treatment (2-3 weeks after immunotherapy) metastatic biopsies from stage III and IV melanoma patients.

  Study EGAS00001006488

• EGAD00010000387

  Cambridge control samples using a 1.2M genotyping chip from Illumina

  Dataset EGAD00010000387

• Plasma-Seq of patients with metastatic prostate cancer

  Study 1 In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We wanted to make whole-genome analysis from plasma DNA amenable to clinical routine applications and developed an approach based on a benchtop high-throughput platform, i.e. Illuminas MiSeq instrument. We performed whole-genome sequencing from plasma at a shallow sequencing depth to establish a genome-wide copy number profile of the tumor at low costs within 2 days. The genome-wide profiling in the plasma of our patients revealed multiple copy number aberrations including those previously reported in prostate tumors, such as losses in 8p and gains in 8q. High-level copy number gains in the AR locus were observed in patients with CRPC but not with CSPC disease. We identified the TMPRSS2-ERG rearrangement associated 3-Mbp deletion on chromosome 21 and found corresponding fusion plasma fragments in these cases. In an index case multiregional sequencing of the primary tumor identified different copy number changes in each sector, suggesting multifocal disease. Our plasma analyses of this index case, performed 13 years after resection of the primary tumor, revealed novel chromosomal rearrangements, which were stable in serial plasma analyses over a 9 months period, which is consistent with the presence of one metastatic clone. Our approach provides specific genomic signatures within 2 days which may therefore serve as “liquid biopsy”.

  Study EGAS00001000451

• The mutational landscape of skin tumours in CYLD cutaneous syndrome determined

  Patients with germline mutations in CYLD can develop hundreds of benign skin tumours called cylindromas. The development of multiple tumours within a single patient at sun-protected and sun-exposed sites, varying tumour histological patterns and grades of malignancy allow for the testing of several genetic hypothesis in relation to cutaneous carcinogenesis. By adopting the unprecedented approach of whole genome sequencing of multiple benign skin tumours within individuals in multigenerational families, we set out to study the impact of mutational diversity on models such as multistep carcinogenesis as well as non-sequential carcinogenesis. Using non-negative matrix factorisation (NMF) to discover mutational signatures, we found distinct mutational signatures in identical benign tumours (N=2 patients; n=11 tumours) at sun exposed and sun protected skin tumours within a mother and her daughter. We found recurrent mutations in epigenetic modifying genes in CCS tumours which are known to have an oncogenic dependency on Wnt signalling. We also demonstrate that cutaneous tumours that metastasize to the lung carry a a UV signature, supporting the origin from the skin. Distinct malignant tumours, such as BCC and malignant spiradenocarcinoma carried unique driver mutations. These findings add new dimensions to the existing paradigms of UV-induced skin cancer and highlight the utility of studying rare disease to gain novel insights into genetic mechanisms of tumour formation.

  Dataset EGAD00001004573

• Colorectal cancer functional annotation - MPRA

  We performed a Massively Parallel Reporter Assay (MPRA) in colorectal cancer (CRC) cell lines HT29 and SW403 and normal colon cell line HCEC-1CT. We specifically targeted the regions around the CRC GWAS loci to identify which variants alter transcription.

  Study EGAS50000000406

• Comprehensive analyses of genetic aberrations in gastroenterological tumors

  Intestinal metaplasia (IM) is a risk factor of gastric cancer in gastric mucosa with Helicobacter pylori infection. To explore the susceptibility to the cancer development in pure gastric IM, we investigated landscape of genetic alterations in gastric single-glands with IM.

  Study JGAS000269

• Multiomic cell-free DNA profiling to inform molecular classification and immunotherapy outcomes in endometrial cancer

  This study involved a cell-free DNA (cfDNA) framework integrating genomic, transcriptomic and epigenomic profiling to investigate patient response to immune checkpoint inhibitors in advanced endometrial cancer (EC) with mismatch repair deficiency (dMMR).

  Study EGAS50000001582

• Digital tEchnology For Lung Cancer Treatment

  DEFLeCT metadata: 1) A table containing the mutational profile for all human genes across the cohort of the 81 PROMOLE lung cancer samples. 2) A table containing the expression levels for all human genes across the cohort of the 81 PROMOLE lung cancer samples. 3) A table containing the clinical, histology data and follow-ups of the cohort of 81 PROMOLE lung cancer patients.

  Dataset EGAD00001010838

• Genetic alterations in benign breast biopsies of subsequent breast cancer patient

  This dataset consists of amplicon sequencing of fibrocystic breast tissues, subsequent cancer tissue and germline control of 17 patients. The target genes include all exons of 27 protein-coding genes and 2 non-coding genes, as well as mutation hotspots in three cancer genes, frequently mutated in breast cancer. Ion AmpliSeq libraries were generated and sequenced on the Ion S5 XL system.

  Dataset EGAD00001004874

• A transcriptomic approach to understand patient susceptibility to pneumonia after abdominal surgery

  Rationale Nosocomial infections are a major healthcare challenge, developing in over 20% of patients aged 45 or over undergoing major-abdominal surgery, with postoperative pneumonia associated with an almost five-fold increase in 30-day mortality. Objectives To describe immune-pathways and gene-networks altered following major-abdominal surgery and identify transcriptomic patterns associated with postoperative pneumonia. Methods and Measurements From a prospective consecutive cohort (n=150) undergoing major-abdominal surgery whole-blood RNA was collected preoperatively and at three time-points postoperatively (2-6, 24 and 48hrs). Twelve patients diagnosed with postoperative pneumonia and 27 matched patients remaining infection-free were identified for analysis with RNA-sequencing. Main Results Compared to preoperative sampling, 3,639 genes were upregulated and 5,043 downregulated at 2-6hrs. Pathway-analysis demonstrated innate-immune activation with neutrophil-degranulation and Toll-like-receptor signalling upregulation alongside adaptive-immune suppression. Cell-type deconvolution of preoperative RNA-sequencing revealed elevated S100A8/9-high neutrophils alongside reduced naïve CD4 T-cells in those later developing pneumonia. Preoperatively, a gene-signature characteristic of neutrophil-degranulation was associated with postoperative pneumonia acquisition (P=0.00092). A previously reported Sepsis Response Signature (SRSq) score, reflecting neutrophil-dysfunction and a more dysregulated host response, at 48hrs postoperatively, differed between patients subsequently developing pneumonia and those remaining infection-free (P=0.045). Analysis of the novel neutrophil gene-signature and SRSq scores in independent major-abdominal surgery and polytrauma cohorts indicated good predictive performance in identifying patients suffering later infection. Conclusions Major-abdominal surgery acutely upregulates innate-immune pathways while simultaneously suppressing adaptive-immune pathways. This is more prominent in patients developing postoperative pneumonia. Preoperative transcriptomic signatures characteristic of neutrophil-degranulation and postoperative SRSq scores may be useful predictors of subsequent pneumonia risk.

  Study EGAS00001007229

• Division of Cancer Genomics, National Cancer Center Research Institute Data Access Committee

  Dac EGAC00001000957

• Transcriptome profiling by array

  Expression profiling by Nanostring cancer immune

  Dataset EGAD00010001274

• Bone metastatic biopsies of breast cancer patients progressing on endocrine therapies.

  Study EGAS00001004268

• Detailed molecular and immune marker profiling of archival prostate cancer samples

  Study EGAS00001004396

• Tumour evolvability metrics predict recurrence in advanced localised prostate cancer (tumour data)

  Study EGAS00001006096