525 results for "retinitis+pigmentosa+2017+surgery+blog+"my+twin+died+at+birth""

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• OCCAMS_Oesophageal Cancer Organoids_1

  ***THIS DATA CAN ONLY BE USED FOR NON-COMMERCIAL CANCER RESEARCH*** Sequencing of organoid cell lines derived from oesophageal tumour sections taken from patients diagnosed with primary oesophageal cancer who underwent tumour resection surgery.

  Dataset EGAD00001001889

• Final results and ctDNA analyses from the randomized phase 3 IMpassion031 trial evaluating peri-operative atezolizumab for early-stage triple-negative breast cancer

  In IMpassion031, adding atezolizumab to neoadjuvant chemotherapy significantly improved pathologic complete response (pCR) rate (primary endpoint) for stage II/III triple-negative breast cancer (TNBC). Patients with stage II/III TNBC were randomized 1:1 to neoadjuvant chemotherapy plus peri-operative atezolizumab or pre-operative placebo. Descriptive secondary endpoints included event-free, disease-free, and overall survival. Long-term outcomes favored the atezolizumab group (event-free survival HR 0.76, 95% CI: 0.47–1.21). Among patients without pCR, 14/70 (20%) atezolizumab-treated and 33/99 (33%) placebo-treated patients received additional adjuvant therapy, frequently capecitabine. In exploratory analyses, pCR was prognostic for long-term outcome. Patients with baseline ctDNA-negative status (6%) had excellent long-term outcomes. Most patients (87%) had cleared ctDNA at surgery. ctDNA-positive status at surgery identified a subset of non-pCR patients with poorest prognosis. Long-term safety was consistent with primary results. Adding atezolizumab to chemotherapy for stage II/III TNBC is associated with more favorable long-term outcomes. ctDNA dynamics provide prognostic value beyond pCR. ClinicalTrials.gov identifier: NCT03197935

  Study EGAS50000000974

• Whole genome and transcriptome analysis of medullary thyroid cancer

  Medullary thyroid cancer is the neoplasm of the calcitonin-producing parafollicular cells of the thyroid gland. The hormone calcitonin acts to lower the blood calcium level, counteracting the effects of the parathyroid hormone; it can also serve as a biomarker for the presence or recurrence of medullary thyroid cancer. Surgery is the only curative treatment for this cancer. Targeted therapeutics vandetanib and cabozantinib are approved for the treatment of aggressive and metastatic tumors that are not amenable to surgery. The use of these multikinase inhibitors are supported by the observed overactivation of the RET oncoprotein in a large sub-population of medullary thyroid cancers; however, not all patients carry oncogenic alterations of this kinase. Hence, there is a need for molecular characterization of medullary tumors on the genomic scale with the aim of identifying targetable mutations. Here, we describe the genomic profiles of two medullary thyroid cancers and report the presence of a putative oncogenic BRAF fusion in one. Such alterations previously observed in other malignancies and known targets of available drugs, can benefit patients who currently have no therapy options.

  Study EGAS00001001473

• Monotherapy Breast Cancer

  These samples are from locally advanced breast cancers that have been treated with epirubicin monotherapy before surgery. We will sequence some samples from patients with good response to the therapy and some with poor response to the therapy.

  Dataset EGAD00001000349

• PRADO trial - Personalized response-directed surgery and adjuvant therapy after neoadjuvant ipilimumab plus nivolumab in stage III melanoma

  The dataset includes RNA sequencing data on PRE- treatment biopsies of lymph node metastasis (n=80) The technology used for sequencing is llumina HiSeq 2500

  Dataset EGAD00001012116

• Single-cell RNA-sequencing of nivolumab-treated glioblastoma

  Single-cell RNA-sequencing of 8 patients, from primary and relapse tumour (total of 16 samples). Patients were treated with nivolumab prior to relapse surgery.

  Dataset EGAD00001010843

• Bulk RNA-sequencing of nivolumab-treated glioblastoma

  Bulk RNA-sequencing of 30 relapse tumour samples. 20 patients were treated with nivolumab prior to relapse surgery, while 10 patients are control patients.

  Dataset EGAD00001010844

• NEOPREDICT-Lung: Neoadjuvant Immunotherapy for Resectable NSCLC

  Links via: DOI: https://doi.org/10.1038/s41591-024-02965-0 PubMed: https://pubmed.ncbi.nlm.nih.gov/38689060/ Journal: https://www.nature.com/articles/s41591-024-02965-0 Abstract Antibodies targeting the immune checkpoint molecules PD-1, PD-L1 and CTLA-4 administered alone or in combination with chemotherapy are standard of care in most patients with metastatic non-small cell lung cancers. When given prior to curative surgery, tumor responses and improved event-free survival are achieved. New antibody combinations may be more efficacious and tolerable. In an ongoing, open-label phase II study, 60 biomarker-unselected, treatment-naïve patients with resectable non-small cell lung cancer were randomized to receive two preoperative doses of nivolumab (anti-PD-1) with or without relatlimab (anti-LAG-3) antibody therapy. The primary study endpoint was feasibility of surgery within 43 days, which was met by all patients. Curative resection was achieved in 95% of patients. Secondary endpoints included pathological and radiographic response rates, pathologically complete resection rates, disease-free and overall survival rates, and safety. Major pathological (≤10% viable tumor cells) and objective radiographic responses were achieved in 27% and 10% (nivolumab), and 30% and 27% (nivolumab and relatlimab) of patients, respectively. In 100% (nivolumab) and 90% (nivolumab and relatlimab) of patients tumors and lymph nodes were pathologically completely resected. With 12 months median duration of follow-up, disease-free survival and overall survival rates at 12 months were 89% and 93% (nivolumab), and 93% and 100% (nivolumab and relatlimab). Both treatments were safe with grade ≥ 3 treatment-emergent adverse events reported in 10% and 13% of patients per study arm. Exploratory analyses provided insights into biological processes triggered by preoperative immunotherapy. This study establishes the feasibility and safety of dual targeting of PD-1 and LAG-3 prior to lung cancer surgery.

  Study EGAS00001007753

• NCT03343197: Clinical Biomarker Data

  Patients with IDH1-mutated low-grade glioma were treated with AG-120 (ivosidenib), AG-881 (vorasidenib), or Placebo for 28 days before surgical resection. A portion of the surgical sample was submitted for exome capture-based transcriptome sequencing (Personalis ACE Whole Transcriptome). Following surgery, subjects had the option to continue (or initiate) treatment with AG-120 or AG-881.This dataset comprises next-generation sequencing data from biopsies obtained in the clinical trial: NCT03343197 (Study of AG-120 and AG-881 in Subjects with Low Grade Glioma).

  Study phs003148

• African American Adolescent Idiopathic Scoliosis Whole Genome and Whole Exome Study

  Adolescent idiopathic scoliosis (AIS) is the most common pediatric spinal deformity. The causes of scoliosis are only now being discovered yet are important for predicting outcome and need for surgery. Prior studies have investigated the causes of scoliosis, including common and rare variant risk factors, but have mostly used populations consisting of Asian or European ancestry. It is essential that we determine what the risk factors are in all populations so that we can delivery equitable care to all individuals.

  Study phs003136

• Characterization of the Gut-Associated Microbiome in Inflammatory Pouch Complications Following Ileal Pouch-Anal Anastomosis

  This study involved evaluation of the tissue associated microbiome of the ileal pouch following surgery for ulcerative colitis (UC) or familial adenomatous polyposis (FAP). Individuals were recruited, with biopsies taken from the ileal pouch and the pre-pouch ileum, microbial DNA was extracted and sequenced using 454 pyrosequencing. Total bacterial community structure and abundance were evaluated to determine which changes were characteristic of inflammatory phenotypes including pouchitis (inflammation of the ileal pouch) and a Crohn's disease-like phenotype.

  Study phs000659

• Single Suture Craniosynostosis: Gene and Pathway Discovery

  Craniosynostosis is the premature fusion of one or more of the calvarial sutures. In this work, we used genomics and network modeling to reveal genetic and developmental pathways which, when disrupted, result in premature calvarial fusion. Calvarial bone explants were obtained from children undergoing surgery for single suture craniosynostosis. Primary osteoblast cell lines were established from calvarial explants and used as an RNA source.  The data available includes subject sex, affected suture, RNA sequence variants and counts.

  Study phs002684

• Single-cell RNA sequencing analysis of corneal and limbal epithelial cells derived from a patient with congenital aniridia

  Aniridia-associated keratopathy (AAK) is a progressive condition characterized by conjunctivalization of the cornea, yet its molecular mechanisms remain largely unknown. This study aims to elucidate the transcriptional landscape of AAK by characterizing the gene expression profiles of corneal epithelial cells in a patient with congenital aniridia. Corneal and limbal epithelial tissues were collected from the patient during the cultivated oral mucosal epithelial transplantation (COMET) surgery. The tissues were dissociated into single cells and subjected to single-cell RNA-seq.

  Study JGAS000790

• Single-cell RNA sequencing of human omental tissue in benign and metastatic ovarian cancer

  To elucidate the cellular and molecular mechanisms underlying omental homeostasis and its transformation during ovarian cancer metastasis, a human omental cell atlas was generated encompassing both benign and metastatic conditions. Single-cell RNA sequencing was performed on freshly dissociated omental tissue samples from patients with newly diagnosed benign and malignant disease. Samples collected during diagnostic surgery covered distinct anatomical regions, enabling comparison between non-metastasized omentum and sites along the metastatic gradient, including distant, peritumoral, and tumor core areas.

  Study EGAS50000001465

• Personalized analysis of ctDNA for detection of molecular residual disease and recurrence in a cohort of surgically treated patients with head and neck squamous cell carcinoma

  Despite advances in multimodal treatment, survival for patients with advanced head and neck squamous cell carcinoma (HNSCC) has improved only modestly. The recent advent of tumor-informed assays capable of detecting circulating cell-free tumor DNA (ctDNA) has enabled early detection of molecular residual disease (MRD) and recurrence following curative therapy. We assessed ctDNA in plasma from 76 and saliva from 54 HNSCC patients, respectively, who received primary curative-intent surgery.

  Study EGAS50000001018

• Transcriptomic Profile of Colorectal Cancer Samples

  Samples encompass primary colorectal tumors or metastasis of 75 patients, collected by Medical Pathologists from surgically removed specimens. Tissues were embedded in optimal cutting temperature (OCT) medium, snapshot frozen in liquid nitrogen within 40 minutes of collection and preserved at -80ºC. Samples were collected between June 2010 and October 2017 as part of a prospective biobanking project.

  Dataset EGAD00001009506

• GCAT| ICD Disease Diagnoses

  Disease diagnoses of GCAT Cohort participants obtained from electronic health records (EHR), mainly including the time period from 2012 to 2017. Disease diagnoses are codified in ICD-9, and the position of diagnosis refers to primary/secondary diagnoses (up to 14 secondary diagnoses per visit). The date and origin of the visit are also specified (AP: primary care, UGR: emergency, AH: hospital care, SMA: outpatient medical service, SMH: hospital medical service).

  Dataset EGAD00001007731

• RNA-sequencing of six Pilocytic astrocytoma tumors

  Total stranded TruSeq RNA sequencing by Illumina of six tumor samples from six cases of pediatric Pilocytic astrocytoma. The data is published in the following paper: Tomic TT, Olausson J, Wilzen A, Sabel M, Truve K, Sjogren H, Dosa S, Tisell M, Lannering B, Enlund F, Martinsson T, Aman P, Abel F. A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS One. 2017 Apr 27;12(4):e0175638.

  Dataset EGAD00001003143

• Immediate Postoperative Minimal Residual Disease Detection with MAESTRO Predicts Recurrence and Survival in Head and Neck Cancer Patients Treated with Surgery

  We selected 24 patients with locally advanced head and neck squamous cell carcinoma (HNSCC) who were surgically treated. MAESTRO, our ultrasensitive, tumor-informed, mutation enrichment sequencing assay, was applied in a pooled format (MAESTRO-Pool) to plasma samples collected from these patients at baseline (pre-op) and postoperatively. We show that detection of circulating tumor DNA (ctDNA) 1 to 9 days after surgery is associated with significantly worse survival. Many plasma samples also had tumor fractions detected below 100 parts-per-million, the detection limit for first-generation commercial assays, highlighting the need for more sensitive ctDNA assays. Here we provide whole genome sequencing of matched tumor biopsy and normal germline DNA from 24 patients that were used to identify somatic single nucleotide variants (SNVs) to be tracked using our MAESTRO-Pool assay.

  Study phs003981

• FEGA FAQs: a summary of the Q+A session from the FEGA workshop at ELIXIR AHM 2024

  The ELIXIR All Hands Meeting (AHM) was held in Uppsala, Sweden this June. We at EGA always look forward to this meeting as a chance to see many of our partners and colleagues face-to-face. The Federated EGA (FEGA) is one initiative that always benefits from the AHM, and this year FEGA was in the spotlight, with several questions related to the advances we've made recently. We held this year's FEGA workshop a little differently, with most time for discussions on various “hot topics”. Organised in different breakouts, over 2 rounds, participants could choose which session they wanted to attend. One breakout was a general Q+A about FEGA and the path to join. We had a diverse range of participants, including experts from Central EGA (CEGA) and FEGA inaugural nodes, people from up and coming nodes at various stages of readiness, as well as participants not directly a part of FEGA but curious to learn more. It made for a great discussion! In this blog post, we highlight some of the questions for those who didn’t have a chance to be there. What is the FEGA Collaboration Agreement? It is a legal agreement between the node and Central EGA (CEGA) where both parties agree to certain responsibilities, like what services will be provided, sharing of public metadata with CEGA, interoperable technologies and more. The agreement is for 4 years, with the expectation of long-term sustainability. If a node is made up of multiple institutes, one institute must be the signatory. This could require a legal agreement within the node. CEGA is composed of CRG and EMBL-EBI (EGA itself has its own legal agreement between these institutes) Check the FEGA Collaboration Agreement What about purely medical data? Is this accepted in FEGA? CEGA only accepts data approved for secondary research use. We do accept medical data collected in this context, as do some nodes. Nodes are able to accept any data they like, as long as it is sensitive, thus in need of controlled access. What about other data types other than genomics? Like proteomics or images? They can be accepted, although CEGA is currently not designed with those formats in mind, so they might not fit with precision in the data model. The FEGA nodes are welcome to accept any data they want. Proteomic studies generating sensitive data are increasing, and specific work will likely be developed in the near future to adress this need. Does CEGA require a certain amount or type of data to be shared by the node? No, we do not and it's up to each node to decide what specific data types they accept and in what format. Nonetheless, a FEGA node has the duty to be open to data submission from any institution of their country, and can't be limited by design to a single or limited data source. Does CEGA and FEGA require a certain amount or type of details and description on the data to be submitted to the node? Data description (technical and biological), usually called metadata in this field, is crucial for the findability of the submitted data. Thus, we highly recommend including as much information as available to maximise the discoverability of the data. Specifical minimal metadata is defined in the submission schema, and thresholds are specified by the nodes. We are currently working towards a unified FEGA metadata model. What are the geographical borders of FEGA? FEGA should make the E for Everyone, because any institute worldwide could join and we indeed do have countries and use-cases worldwide. Some of them are very close to officially joining the federation. What are the main differences between FEGA and GDI? The two networks have a lot in common and also some critical differences. You can read all about this in one of our latest blog post. If you have more questions, please consider having a look at the FEGA onboarding webpage and, of course, don't miss our workshop at the ELIXIR AHM next year!

  Blog fega-faqs-elixir-ahm-2024

• Genomics of Opioid Pharmacogenomics and Acute/Chronic Postsurgical Pain after Major Surgery in Children

  Pain management after surgery is not optimal, partly due to great interindividual variability in pain perception and coping. This can lead to persistent pain beyond the healing period and disability. Up to two-thirds of the inter-individual variability results from genetic variations in pain perception as well as response to the pain medicine. The investigators aim to identify genomic (genetic/epigenetic), psychological and drug profiles contributing to this variability. Opioids are the mainstay for treatment of postoperative pain in children. Experience dictates that opioids have narrow therapeutic indices and large inter-patient variability in response. This leads to serious side effects like respiratory depression in up to 50% of children undergoing invasive surgery, which can be fatal. It is evident that there are particular children who are more susceptible to suffering side effects and having inadequate pain relief from opioids.It is hypothesized that much of the genetic variability can be explained by gene function which is modulated by a) Single Nucleotide Polymorphisms (SNPs) in genes that encode proteins involved in pain perception, opioid transport/metabolism (pharmacokinetics), and opioid receptor signaling (pharmacodynamics); b) epigenetics which modify gene expression without structural changes to the DNA, and c) genes that influence psychological factors.The purpose of this research study is to identify factors and genes that may be associated with acute and chronic post-surgical pain, and to develop pharmacometric models for response to opioids, like morphine and hydromorphone. While children undergoing different surgeries will be recruited for acute outcomes, children undergoing spine fusion will be followed for 10-12 months for evaluation of psychological and genomic factors affecting chronic post-surgical pain, with a goal of identifying genetic and epigenetic risk models for prediction of acute and chronic post-surgical pain. Although opioids are used every day, some children have bad reactions from their use, like breathing problems, sedation, etc. The investigators want to study factors that may be associated with pain sensitivity, opioid requirements after surgery, their metabolism, efficacy and their side-effects. The investigators expect that the information obtained in this research study will help to develop effective, safer, and tailored treatment options in the future.

  Study phs002105

• A neoadjuvant, phase II trial demonstrates efficacy and tolerability of Talimogene laherparepvec in cutaneous basal cell carcinoma (NeoBCC trial)

  We present a single arm, phase II neoadjuvant trial with the oncolytic virus Talimogene laherparepvec (T-VEC) in 18 patients with difficult-to-resect basal cell carcinomas. Six cycles of T-VEC were applied intralesionally. The primary endpoint of the study, defined as the proportion of the patients, who after six cycles of T-VEC (13 weeks) at the time point of surgery, become resectable with primary wound closure without the need for plastic reconstructive surgery like skin flaps or skin grafts, was achieved (9/18 patients; 50.0%). Secondary endpoints also included the relapse free survival rate (100%), overall survival (100%) and biological read outs in the tumor samples. T-VEC led to a significant increase of cytotoxic T cells, B cells and myeloid cells, and a decrease of Tregs within the tumor microenvironment. We observed a potent induction of antitumoral and antiviral T cell clones, as well as a strong humoral immune response. The objective response rate was 55.6% and the complete pathological response rate was 33.3%. Only mild adverse events occurred. Together, neoadjuvant T-VEC represents a viable treatment option for patients with difficult-to-resect BCCs (EudraCT Number 2018-002165-19).

  Study EGAS50000000252

• Microbiomic and immunogenic biomarkers of adjuvant chemotherapy efficacy in stage III colorectal cancer

  The standard treatment for stage III colorectal cancer (CRC) is surgery, followed by adjuvant chemotherapy (AC). However, the efficacy of AC is limited, and approximately 30% of patients experience recurrence. Therefore, easily assessable molecular biomarkers that can predict response to AC are needed. Here, we aimed to identify predictive biomarkers of response to AC using tumor transcriptomic data. Tumor specimens from 253 patients who underwent surgery for stage III CRC between 1997 and 2019 were analyzed using RNA sequencing. Transcriptional subtyping and analyses of gut microbiome, immune cell fractions, and T-cell receptor (TCR) were performed to identify factors associated with recurrence-free survival (RFS) in patients treated with or without AC. Of 253 patients, 118 (46.6%) received AC. Twenty phyla and 799 species of the microbiomes were identified, among which Fusobacteria were identified in 247 patients (97.6%). Multivariable Cox proportional hazards regression analysis of patients who received AC showed that intratumoral Fusobacterium and M1 macrophage abundance and diversity of TCR alpha and delta (TRAD) were independently associated with RFS. Fusobacterium and M1 macrophage abundance, and TRAD diversity were associated with the response to AC, suggesting that these factors could serve as biomarkers for personalized treatment in stage III CRC.

  Study JGAS000875

• Longitudinal breast cancer cohort in SMC

  Whole transcriptome sequencing (WTS) of a longitudinal breast cancer (BC) cohort consisting of 146 cases (281 tumors, 109 pairs), including 52 (38%) that achieved pathologic complete responses (pCR) and 85 (62%) that harbored residual diseases at time of surgery.

  Dataset EGAD00001004487

• Tourette International Collaborative Genetics (TIC Genetics) Study - NJCTS and NIMH

  The Tourette International Collaborative Genetics (TIC Genetics) Study is an international collaboration of scientists and clinicians specialized in Tourette Disorder (TD) from more than 20 sites across the United States, Europe, and South Korea. The study was established to further our understanding of the genetic architecture of tic disorders by developing a large sample of genotypically and phenotypically well-characterized affected probands and their relatives. We employ state-of-the-art genetic technologies to identify major genetic variants contributing to TD and the most commonly comorbid disorders, such as Obsessive-Compulsive Disorder (OCD) and Attention-Deficit/Hyperactivity Disorder (ADHD). TIC Genetics is a direct result of work of the New Jersey Center for Tourette Syndrome (NJCTS) Sharing Repository (Heiman et. al., 2008; PMID: 19036136), funded by a grant from NJCTS Center of Excellence. Established in 2011 (Dietrich et. al., 2015; PMID: 24771252), the TIC Genetic study focuses on both on familial genetic variants with large effects within multiplex affected pedigrees and on de novo mutations ascertained through the analysis of apparently simplex parent-child trios with non-familial tics. In May 2017, we published a whole-exome sequencing study on apparently 311 parent-child trios (Willsey et. al., 2017; PMID: 28472652). These data, both phenotypes and sequencing data, are available through dbGaP. There were 120 subject samples included in the publication that did not have consent for sharing. These are excluded from dbGaP.In November 2021, we published a whole-exome sequencing study on 13 multiplex TD families (Cao et. al., 2021). These data, both phenotypes and sequencing data, are available through dbGaP.

  Study phs001423