Categories
Tag: PIK3CA
cfDNA Extraction Sensitivity Controls – cfDNA Extraction Sensitivity Controls
Does your cfDNA extraction process affect the Limit of Detection (LOD) of a particular gene target? Our new products, cfDNA Extraction Sensitivity Panels and Extraction Low Positive Controls, can help your research and development for liquid biopsy assays. NEW PRODUCTS: cfDNA EXTRACTION SENSITIVITY PANELS & CONTROLS The Extraction Sensitivity Controls…
Association of PIK3CA Mutation With Pathologic Complete Response and Outcome by Hormone Receptor Status and Intrinsic Subtype in Early-Stage ERBB2/HER2-Positive Breast Cancer | Oncology | JAMA Network Open
Key Points Question What is the association of PIK3CA mutations, response to therapy, and outcome by hormone receptor (HR) status and intrinsic subtype among patients with ERBB2/HER2-positive early breast cancer (EBC) treated in a clinical trial? Findings In this cohort study of 184 patients enrolled in the phase 3 trial…
R ComplexHeatmap – Adujusting the cell size in heatmap
I think the main thing is not to use “width = width/2” in cell_fun1. Using ComplexHeatmap 2.14.0 on R 4.2.1 i was able to modify cell width and height via width and height params in call to Heatmap. I tried a few different widths and heights and each time the…
HER2 low expression breast cancer subtyping and their correlation with prognosis and immune landscape based on the histone modification related genes
Barzaman, K. et al. Breast cancer: Biology, biomarkers, and treatments. Int. Immunopharmacol. 84, 106535 (2020). Article CAS PubMed Google Scholar Siegel, R. L., Miller, K. D., Wagle, N. S. & Jemal, A. Cancer statistics, 2023. CA Cancer J. Clin. 73(1), 17–48 (2023). Article PubMed Google Scholar Mueller, C., Haymond, A.,…
Bioinformatics analysis of immune characteristics in tumors with alternative carcinogenesis pathways induced by human papillomaviruses | Virology Journal
de Martel C, Georges D, Bray F, Ferlay J, Clifford GM. Global burden of cancer attributable to infections in 2018: a worldwide incidence analysis. Lancet Glob Health. 2020;8:e180–90. Article PubMed Google Scholar McKaig RG, Baric RS, Olshan AF. Human papillomavirus and head and neck cancer: epidemiology and molecular biology. Head…
Roche’s bid to build a better Piqray yields phase 3 breast cancer win, opening door to regulators
Roche’s pitch to reset the standard of care in a breast cancer population has cleared a late-phase hurdle. The drugmaker’s attempt to improve on Novartis’ Piqray and deliver a first-line PI3K inhibitor has yielded an improved progression-free survival (PFS) in phase 3, teeing up talks with regulatory authorities. The investigational…
New Study Shows Neratinib, Fulvestrant, Trastuzumab Combo as Effective Treatment for Metastatic Breast Cancer
TUESDAY, Nov. 28, 2023 (HealthDay News) — For patients with hormone receptor (HR)-positive HER2-mutant metastatic breast cancer (MBC) with progression on cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) therapy, neratinib + fulvestrant + trastuzumab (N + F + T) is beneficial, according to a study published in the October issue of the…
Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations
Adams, R. H. & Eichmann, A. Axon guidance molecules in vascular patterning. Cold Spring Harb. Perspect. Biol. 2, a001875 (2010). Article PubMed PubMed Central Google Scholar Fish, J. E. & Wythe, J. D. The molecular regulation of arteriovenous specification and maintenance. Dev. Dyn. 244, 391–409 (2015). Article CAS PubMed Google…
Truqap Plus Fulvestrant Approved for HR-Positive Advanced Breast Cancer
The Food and Drug Administration (FDA) has approved Truqap™ (capivasertib) in combination with fulvestrant for the treatment of adults with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative, locally advanced or metastatic breast cancer with 1 or more PIK3CA/AKT1/PTEN-alterations, as detected by an FDA-approved test, following progression on…
Personalized Treatment Sequencing Is a New Way of Thinking in Breast Cancer
Sara M. Tolaney, MD, MPH, chief of the Division of Breast Oncology and associate director of the Susan F. Smith Center for Women’s Cancers, senior physician at Dana-Farber Cancer Institute, and associate professor of medicine at Harvard Medical School, all in Boston, Massachusett In a rapidly evolving field, new strides…
Cloves Syndrome Market Share And Industry Trends 2023-2030
North America Accounted for Approximately 39.2% of the Market Share in 2022, Owing to the Increasing Funding, and Availability of Targeted Treatments. Cloves Syndrome Market Outlook Congenital Lipomatous Overgrowth, Vascular Malformations, Epidermal Nevis, Spinal/Skeletal Anomalies/Scoliosis (CLOVES) syndrome is a very rare congenital (present at birth) disorder characterized by a combination…
Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations,Nature Communications
Cerebral Cavernous Malformations (CCMs) are vascular malformations of the central nervous system which can lead to moderate to severe neurological phenotypes in patients. A majority of CCM lesions are driven by a cancer-like three-hit mutational mechanism, including a somatic, activating mutation in the oncogene PIK3CA, as well as biallelic loss-of-function…
Single-nucleus DNA sequencing reveals hidden somatic loss-of-heterozygosity in Cerebral Cavernous Malformations
Ethical statement Our research complies with all relevant ethical regulations, including the Declaration of Helsinki and has been approved by the Institutional Review Boards of University of Chicago, Duke University and the Alliance to Cure Cavernous Malformations. Cerebral cavernous malformation lesions All human CCM tissue specimens have been previously reported18,19…
Pathway-driven analysis of synthetic lethal interactions in cancer using perturbation screens
Introduction Cancer cells are characterized by unrestrained proliferation and dysregulated growth, which lead to the formation of malignant neoplasms (Hanahan & Weinberg, 2023). The development and progression of cancer have been linked to the dysregulation of multiple signaling pathways, including MAPK/ERK, Wnt/β-catenin, PI3K/AKT/mTOR, and NF-kB, which are among crucial pathways…
PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer: a retrospective study | BMC Gastroenterology
Tissue samples A total of 84 analytic samples from surgical or biopsy specimens were collected from 84 patients who underwent radical surgery for CRC at Saitama Medical University International Medical Center between January and December 2016. One case was excluded because the specimen was too small; therefore, we used a…
Identifying ESR1 Mutations to Determine Resistance in HR+ Metastatic Breast Cancer
The global disease burden of breast cancer (BC) is a serious health concern worldwide, especially among women. Globally, about 2.3 million women were diagnosed with BC in 2020, and there were 685,000 deaths from BC.1 Various BC subtypes have been identified based on the expression of genes encoding hormone receptors…
Breast Cancer Detected in Breast Milk Earlier Than in Plasma
Researchers say they have detected breast cancer in circulating tumor DNA (ctDNA) from breast milk, and breast milk may allow for earlier cancer detection than plasma. These results “open up the potential” to use breast milk as a new source for liquid biopsy for breast cancer detection, according to the…
Real world evidence reveals improved survival outcomes in biliary tract cancer through molecular matched targeted treatment
Patient characteristics In our analysis, we included patients with biliary tract cancer and available comprehensive molecular characterization data from five Austrian cancer centers. The data cut-off date was September 2022 (Fig. 1). Figure 1 Trial design: Flow chart depicting patient allocation. In total, the molecular profile of 159 patients with biliary…
A biobank of pediatric patient-derived-xenograft models in cancer precision medicine trial MAPPYACTS for relapsed and refractory tumors
Patient characteristics and PDX establishment Between February 2016 and July 2020, 787 pediatric, adolescent and young adult patients with recurrent or refractory malignancies were enrolled in the MAPPYACTS trial;2 756 (96%) patients and their parents consented to the optional ancillary study of preclinical model development (Fig. 1a). 744 patients had a…
DNA/RNA Sequencing Aids Subsequent Treatment Selection in HCC/H-CCK Post Atezolizumab/Bevacizumab
Tissue- and blood-based molecular analysis could help match patients with advanced hepatocellular carcinoma (HCC) or hepatocholangiocarcinoma (H-CCK) following disease progression on frontline atezolizumab (Tecentriq) and bevacizumab (Avastin) to targeted therapy or another TKI based on identified genomic alterations, according to retrospective findings from a single-center study presented at the 2023…
RefSeq: NP_001154929
LOCUS NP_001154929 155 aa linear ROD 03-MAY-2023 DEFINITION core-binding factor subunit beta isoform 3 [Mus musculus]. ACCESSION NP_001154929 VERSION NP_001154929.1 DBSOURCE REFSEQ: accession NM_001161457.1 KEYWORDS RefSeq. SOURCE Mus musculus (house mouse) ORGANISM Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus;…
Unraveling variant misclassification: Insights from ClinVar and HGMD databases
Cardiac Comprehensive Kit analyzes 292 genes and covers major inherited cardiovascular disorders. Genes Tested AARS2, ABCA1, ABCC6, ABCC9, ABCG5, ABCG8, ACAD9, ACADVL, ACTA1, ACTA2, ACTC1, ACTN2, ACVR1, ACVR2B, ACVRL1, ADAMTS2, AFF4, AGK, AKAP9, AKT3, ALDH18A1, ALMS1, ALPK3, ANK2, ANKRD1, APOA5, APOB, APOE, ATP6V0A2, ATP6V1A, ATP6V1E1, B3GALT6, B4GALT7, BAG3, BGN,…
Assessing Factors for Sequencing Therapies in ER+ Advanced Breast Cancer
CASE SUMMARY A 62-year-old woman presented with a 6 cm right breast mass, which has been slowly growing for 1 year with palpable axillary nodes. Her liver function test was within normal limits and a CT scan showed 2 liver nodules, with the largest being 2 cm. A bone scan showed…
Subclonal accumulation of immune escape mechanisms in microsatellite instability-high colorectal cancers
Saito T, Niida A, Uchi R, Hirata H, Komatsu H, Sakimura S, et al. A temporal shift of the evolutionary principle shaping intratumor heterogeneity in colorectal cancer. Nat Commun. 2018;9:2884. Article PubMed PubMed Central Google Scholar Uchi R, Takahashi Y, Niida A, Shimamura T, Hirata H, Sugimachi K, et al….
Innovative research on schistosomiasis-associ | EurekAlert!
image: Genomic landscape of schistosomiasis-associated colorectal cancer. (A) Genetic characteristics of the SA-CRC. The number of mutations, the tumor mutation burden, the estimated MSI scores, and the predicted number of neo-epitopes of each sample were present. (B) Mutational landscape of recurrently mutated genes in SA-CRCs. Red arrow corresponds to the known…
Unique Genetic Insights Revolutionize SA-CRC Treatment
In a study published in the journal Genes & Diseases, researchers from Naval Medical University and Soochow University conducted an in-depth investigation into the genomic landscape of schistosomiasis-associated colorectal cancer (SA-CRC). By utilizing whole exome sequencing on tumor tissues and their non-tumor counterparts obtained from thirty SA-CRC patients diagnosed at…
Endometrial Cancer Subtypes, Treatment-Related Clues Uncovered in Multiomic Study
NEW YORK – With a combination of multiomic analyses and machine learning, an international team has tracked down endometrial carcinoma (EC) subtypes, along with potential predictive models, treatment targets, and markers for treatment response. “Analysis of this independent cohort, incorporating pre-existing EC tumor and cell line cohorts, has not only…
Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics | Cancer Research
We observed a total of 4,510 true somatic mutations in 3,391 genes in the 146 primary breast tumors (Supplementary Table S2). The number of mutations per individual varied from 2 to 225. Using MutSigCV, we found that mutations in PIK3CA, TP53, GATA3, MAP3K1, CDH1, CBFB, PTEN, and RUNX1 were significant…
Analysis Helps Distinguish the Molecular Profile of Intraductal Carcinoma of the Prostate
Patients with intraductal carcinoma of the prostate harbored several alterations in DNA damage repair (DDR) genes that may be clinically actionable, and they had high frequency of alterations associated with poor disease prognosis, according to a molecular analysis presented at the 2023 ASCO Annual Meeting. Better understanding the genetic profile…
Detection of low-frequency mutations in clinical samples by increasing mutation abundance via the excision of wild-type sequences
Vogelstein, B. et al. Genetic alterations during colorectal-tumor development. N. Engl. J. Med. 319, 525–532 (1988). Article CAS PubMed Google Scholar Abascal, F. et al. Somatic mutation landscapes at single-molecule resolution. Nature 593, 405–410 (2021). Diaz, L. A. & Bardelli, A. Liquid biopsies: genotyping circulating tumor DNA. J. Clin. Oncol….
Diagnosis of PTEN mosaicism: the relevance of additional tumor DNA sequencing. A case report and review of the literature | BMC Medical Genomics
Mosaicism is very rare in PTHS and only a few cases have been published. Most of these were reported in the study of Rofes et al.[13], that included six patients, and three another cases were reported in the studies of Steffan et al. and Hendricks et al. [13,14,15,16,17,18,19,20] (Table 2)….
CDK4/6 Inhibitor Selection and Sequencing Continue to Evolve in HR+ Breast Cancer
Selection and sequencing of CDK4/6 inhibitors in patients with metastatic hormone receptor (HR)–positive, HER2-negative breast cancer hinge on the maturation of data in the first-line setting and beyond, and these decisions need to account for patient concerns and preferences, according to Sarah Sammons, MD. Primary results from the phase 3…
From the cancer research bench to the vascular disease bedside
From penicillin to CRISPR, the greatest scientific discoveries often have the humblest origin stories. Who knew that a little fungal contamination or a bacterial defense system would revolutionize human health and medicine? Pau Castel, a cancer researcher at New York University, has experienced this serendipity in his own lab. When…
Genomic characteristics of triple negative apocrine carcinoma: a comparison to triple negative breast cancer
Baseline characteristics We described the baseline clinical and pathological characteristics of TNAC and LK-TNBC in Supplementary Table 1. Only stage at diagnosis was different between TNAC and LK-TNBC (P = 0.03), while no significant differences were observed in other characteristics, including nuclear grade, histologic grade, Ki-67, and status of (neo)adjuvant treatment. Somatic…
New Test for HER2+ Breast Cancer to Personalize Therapy
A new test for HER2+ breast cancer allows delivery of more personalized treatment, say researchers at the Baylor College of Medicine in Houston. The group developed and validated a multiparameter molecular classifier test that predicts which patients with HER2-positive breast cancer are candidates for treatment with targeted anti-HER treatment, and…
DNA Fragment Enrichment for High-Throughput Sequencing
Lesnik E.A., Freier S.M. 1995. Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: relationship with base composition and structure. Biochemistry. 34, 10807‒10815. Article CAS PubMed Google Scholar Okou D.T., Steinberg K.M., Middle C., Cutler D.J., Albert T.J., Zwick M.E. 2007. Microarray-based genomic selection for high-throughput resequencing. Nat. Methods….
The NCI-MATCH trial: lessons for precision oncology
Jabbour, E. & Kantarjian, H. Chronic myelogenous leukemia: 2020 update on diagnosis, therapy and monitoring. Am. J. Hematol. 95, 691–709 (2020). Article CAS PubMed Google Scholar Waarts, M. R., Stonestrom, A. J., Park, Y. C. & Levine, R. L. Targeting mutations in cancer. J. Clin. Invest. 132, e154943 (2022). Article …
Genomic Heterogeneity as a Barrier to Precision Oncology in Urothelial Cancer
Read the Full Video Transcript Sam Chang: Hello everyone, I’m Sam Chang. I’m a urologist at Vanderbilt University in Nashville, Tennessee and we’re quite fortunate to have a rising superstar in urologic oncology, Dr. Tim Clinton. Tim was a resident at UT Southwestern and finished his fellowship at Memorial Sloan…
Burning Rock’s precision oncology diagnostics product supports advancement in late-stage … | News
GUANGZHOU, China, June 08, 2023 (GLOBE NEWSWIRE) — Burning Rock Biotech Limited (NASDAQ: BNR and LSE: BNR, the “Company” or “Burning Rock”) is pleased to announce that our flagship comprehensive genomic profiling (CGP) product, OncoScreenTM Plus, was featured in a phase 3 multi-regional clinical trial (MRCT), along with FoundationOneCDx, in…
PFS Improvement Seen With Capivasertib/Fulvestrant in HR+/HER2- Breast Cancer
Hope S. Rugo, MD, FASCO, director of Breast Oncology and Clinical Trials Education and professor of medicine in the Division of Hematology and Oncology at the University of California San Francisco (UCSF) Helen Diller Family Comprehensive Cancer Center, discusses the methods, design, and key findings from the phase 3 CAPItello-291…
Burning Rock Biotech highlights breast cancer study using its genomic profiling test
Precision oncology firm Burning Rock Biotech on Thursday announced that its genomic profiling test, OncoScreen Plus, was used in a phase III multiregional breast cancer clinical trial, alongside Foundation Medicine’s FoundationOneCDx. In the study, OncoScreen Plus was used to determine activating mutations in PIK3CA and AKT1 and inactivating alterations in…
Updates in soft tissue sarcoma
Sarcoma describes a broad group of cancers that originate in the bones and soft or connective tissues, forming in the blood vessels, nerves, muscle, fat, tendons and the lining of the joints. With over 70 types of sarcomas, treatment for this unique cancer depends on the sarcoma type, its location…
IL5RA as an immunogenic cell death-related predictor in progression and therapeutic response of multiple myeloma
Differential expression analysis We downloaded GSE125361 (n = 48) microarray data from the Gene Expression Omnibus (GEO) database, which included 45 myeloma samples and 3 controls, for expression analysis of IL5RA in cancer16. Additionally, we analyzed the expression of IL5RA in smoldering myeloma (SMM) patients who progressed to active MM (n = 10) and…
Identification of acquired Notch3 dependency in metastatic Head and Neck Cancer
Molecular profiling reveals common changes in matched pairs of HNSCC primary tumor and metastasis-derived cell lines Identification of both genetic and functional differences between primary and metastatic variants of HNSCC would be enabled by in vitro models derived independently from these sites from the same patient. Unfortunately, HNSCC tumor cells…
New Trials in Breast Cancer: Could Your Patient Benefit?
Several new clinical trials in breast cancer have opened in recent months. Maybe one of your patients could benefit from enrolling. Locally advanced unresectable or metastatic HR-positive, HER2-negative, PIK3CA-mutated breast cancer. Adults with this type of breast cancer whose disease has progressed despite treatment with a cyclin-dependent kinase 4/6 inhibitor…
Novel Method for Detection of PIK3CA Mutations in Circulating Tumor DNA of Patients with Colorectal Cancer
Karakas, B., Bachman, K. E., & Park, B. H. (2006). British Journal of Cancer, 94, 455–459. Article CAS PubMed PubMed Central Google Scholar Bamford, S., Dawson, E., Forbes, S., Clements, J., Pettett, R., Dogan, A., et al. (2004). British Journal of Cancer, 91, 355–358. Article CAS PubMed PubMed Central Google…
Physicians Discuss Role of Elacestrant in ER+ Metastatic Breast Cancer
Claudine Isaacs, MD (Moderator) Medical Director Jess and Mildred Fisher Center for Hereditary Cancer and Clinical Genomics Research Professor of Medicine and Oncology Associate Director of Clinical Research and Leader, Clinical Breast Cancer Program Lombardi Comprehensive Cancer Center at Georgetown University Washington, DC DISCUSSION QUESTIONS What are your reactions to…
Analysis of the Fecal Metagenome in Long-Term Survivors of Pancreas Cancer
Analysis of the Fecal Metagenome in Long-Term Survivors of Pancreas Cancer | PracticeUpdate …
Convergent genomic diversity and novel BCAA metabolism in intrahepatic cholangiocarcinoma
Multi-omics analyses of the ICC samples Following multiregional sampling of primary ICC cases, we performed multi-omics analyses, including genome, transcriptome, proteome, and metabolome analysis. We used 10 (67 samples), 11 (88 samples), 10 (49 samples) and 10 (49 samples) ICC cases for WES, whole-transcriptome sequencing, proteomic analysis, and metabolomic analysis,…
ctDNA Genomic Profiling Can Guide Targeted Therapy in Advanced Cancer
Genomic profiling of circulating tumor DNA (ctDNA) with a large panel appeared feasible in a routine setting and helped to obtain relevant molecular information that could inform strategies with targeted therapies for patients with metastatic solid tumors, according to findings from the prospective PRISM study published in Annals of Oncology….
IJMS | Free Full-Text | Surveillance of cfDNA Hot Spot Mutations in NSCLC Patients during Disease Progression
1. Introduction Lung cancer is the second most frequent cancer and the leading cause of cancer death in 2020, representing approximately 1 in 10 (11.4%) cancers diagnosed and 1 in 5 (18.0%) deaths [1]. In Lithuania, with a population of 2.7 million, a rough number of 1500 new cases of…
Cancer Tumor Profiling Global Market Report 2023
ReportLinker Major players in the cancer tumor profiling market are F. Hoffmann-La Roche Ltd., Caris Life Sciences, Thermo Fisher Scientific Inc., Illumina Inc., QIAGEN, Ribomed Biotechnologies Inc., HTG Molecular Diagnostics Inc. New York, March 03, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Cancer Tumor Profiling Global…
Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously
We aimed to assess the extent to which it was possible to effectively normalize and combine microarray and RNA-seq data with existing methods for use as a training set for machine learning applications. We assessed performance on holdout sets composed entirely of microarray data and entirely of RNA-seq data. To…
Relay Therapeutics: It Could Be Time To ‘Be Greedy When Others Are Fearful’ (NASDAQ:RLAY)
domoyega/E+ via Getty Images Investment Overview – Cash Intensive But Cash Rich – At Current Price Relay Offers The Patient Investor Value I have covered Relay Therapeutics (NASDAQ:RLAY) several times for Seeking Alpha since the company completed what was, at the time, the third largest biotech IPO in history, raising…
IJMS | Free Full-Text | Endothelial Differentiation of CCM1 Knockout iPSCs Triggers the Establishment of a Specific Gene Expression Signature
1. Introduction Cerebral cavernous malformations (CCMs) are capillary–venous lesions which are primarily found in the brain and spinal cord [1]. The familial form of this neurovascular disorder is inherited in an autosomal dominant manner with incomplete penetrance. Pathogenic variants in the CCM1 gene (also known as KRIT1) can be identified…
Comparison of the mutation patterns between tumor tissue and cell-free DNA in stage IV gastric cancer
Clinicopathological characteristics The clinicopathological features of the 56 stage IV GC patients are shown in Table 1. There were 29 males and 27 females. The mean age was 65.8 years old. The tumor was located mostly in the middle third of the stomach. Approximately 69.6% of the 56 patients had…
Table of Pharmacogenomic Biomarkers in Drug Labeling
Abacavir Infectious Diseases HLA-B Boxed Warning, Dosage and Administration, Contraindications, Warnings and Precautions Abemaciclib (1) Oncology ESR(Hormone Receptor) Indications and Usage, Adverse Reactions, Clinical Studies Abemaciclib (2) Oncology ERBB2(HER2) Indications and Usage, Adverse Reactions, Clinical Studies Abemaciclib (3) Oncology MKI67 Indications and Usage, Dosage and Administration,…
Oppenheimer Says These 2 Stocks Have Double-Digit Gains in Sight
2023 is well underway now, and the key story is the sudden change in sentiment on the financial front. Last year’s bearish trend and headwinds are well known. Stubborn inflation, the Fed’s rapid increase in interest rates, the risk of recession, China’s shutdowns, and Russia’s Ukraine invasion; they all weighed…
CfDNA Alterations in 1671 Patients with Advanced BTC: A Clinical Landscape
The following is the summary of “Clinical landscape of cell-free DNA alterations in 1671 patients with advanced biliary tract cancer” published in the December 2022 issue of Oncology by Berchuck, et al. Targeted medicines have revolutionized clinical care of advanced biliary tract cancer (BTC). In contrast to conventional tissue analysis,…
APOBEC mutagenesis is a common process in normal human small intestine
The landscape of somatic mutation in normal human small intestinal crypts The base of each small intestinal crypt is occupied by stem cells, and the descendants of a single recent ancestor stem cell comprise most cells in each crypt19,20. Therefore, isolation of single crypts provides relatively homogeneous clones of cells…
Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer
Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…
A hypoxia-related signature in lung squamous cell carcinoma
Introduction Lung cancer is the major leading cause of tumour-related deaths throughout the world, while lung squamous cell carcinoma (LUSC) as the second most common histological type of lung cancer.1 Each year, almost 1.8 million people are diagnosed with lung cancer worldwide and 400,000 of these die from LUSC.2,3 Due to…
RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder
Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…
Relay Therapeutics Announces Dosing of First Patient in First-in-Human Trial of RLY-2608 and Initiation of Expansion Cohorts for First-In-Human Trial of RLY-4008
Doses first patient in first-in-human trial of RLY-2608, a pan-mutant and isoform-selective PI3Kα inhibitor Selects 70 mg once-daily dose for RLY-4008 andinitiates expansion cohorts in patients with FGFR2-altered solid tumors, including cholangiocarcinoma and breast cancer CAMBRIDGE, Mass., Jan. 04, 2022 (GLOBE NEWSWIRE) — Relay Therapeutics (Nasdaq: RLAY), a clinical-stage precision…
Characterization of Blood- Based Molecular Profiling in Pancreatic Adenocarcinoma
Introduction Most cases of pancreatic adenocarcinoma (PDAC) are diagnosed in the metastatic or locally advanced stage. It is the fourth leading cause of cancer death in the United States,1,2 with a 5-year overall survival (OS) around 10% in this country2 despite years of research and therapeutic development. For those patients…
Qiagen (QGEN) Collaborates with Denovo to Develop Companion Diagnostic Test for the Treatment of Diffuse Large B-Cell Lymphoma (DLBCL
News and research before you hear about it on CNBC and others. Claim your 1-week free trial to StreetInsider Premium here. QIAGEN (NYSE: QGEN) and Denovo Biopharma LLC today announced a collaboration to develop a blood-based companion diagnostic (CDx) test to identify patients expressing Denovo Genomic Marker 1 (DGM1TM) who…
Data Demonstrates Lucence Liquid Biopsy Test Can Track Treatment-Based ctDNA Changes
NEW YORK – At the European Society for Medical Oncology Congress this week, precision oncology assay developer Lucence presented data that demonstrated its amplicon-based LiquidHallmark assay could be used to personalize care for people with advanced urothelial carcinoma. LiquidHallmark is a laboratory-developed test based on the company’s AmpliMark next-generation sequencing platform…
The Current Molecular Treatment Landscape of Advanced Colorectal Cancer and Need for the COLOMATE Platform
Next-Generation Sequencing Utilizing Tumor Tissue and/or Blood The identification of actionable genomic alterations in tumors such as mCRC was once performed by Sanger DNA sequencing of tumor DNA that was extracted from fixed paraffin-embedded tumor tissue, but this has now been replaced by next-generation sequencing (NGS), which allows for larger-scale…
Dual Targeting of CDKN2A and PIK3CA May Offer Better Outcomes in Urothelial Carcinoma
Genomic testing varies in the academic and community setting. For community settings, commercial panels are available. However, academic settings have access to tools that provide a more comprehensive views of the genome. Investigators used patient-derived UC organoid (PDO) harboring FGFR3, PIK3CA, and CDKN2A mutations. Dose-response curves of alpelisib (Piqray), abemaciclib…
Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection | Genome Biology
Stochastic Amplicon Ligation. DNA samples for oncology sequencing are typically extracted from FFPE tissues and can have average lengths of less than 500 nt due to accumulated chemical damage [18]. We developed the Stochastic Amplicon Ligation (SAL) method to enzymatically concatenate many short DNA molecules together to utilize the long-read…
Analysis of the Prognostic Significance of Circulating Tumor DNA in Metastatic Castrate Resistant Prostate Cancer
This article was originally published here Clin Genitourin Cancer. 2021 Jul 31:S1558-7673(21)00151-8. doi: 10.1016/j.clgc.2021.07.012. Online ahead of print. ABSTRACT BACKGROUND: There has been considerable interest in ctDNA next generation sequencing platforms to assess genomic alterations in mCRPC given its accessibility and identification of temporal genomic data. PATIENTSAND METHODS: In this…