Tag: COSMIC

[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-azure-5.15/5.15.0.1056.64~20.04.45)

All autopkgtests for the newly accepted linux-meta-azure-5.15 (5.15.0.1056.64~20.04.45) for focal have finished running. The following regressions have been reported in tests triggered by the package: systemd/245.4-4ubuntu3.23 (arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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Mutational signatures of cancer: Can passenge

“[…] mutational signatures are not only genomic noise of passenger mutations, but they provide etiological and biological information on carcinogenesis.” BUFFALO, NY- January 19, 2024 – A new editorial paper was recently published in Oncoscience (Volume 10), by researcher Peeter Karihtala from the University of Helsinki and University Hospital Comprehensive…

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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…

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The science events to watch for in 2024

AI advances The rise of ChatGPT had a profound effect on science this year. Its creator, OpenAI in San Francisco, California, is expected to release GPT-5, the next generation of the artificial intelligence (AI) model that underpins the chatbot, late next year. GPT-5 is likely to showcase more advanced capabilities…

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Troynorth Cosmos Epsilon Cord Trim, Cosmic

Troynorth Cosmos Epsilon Cord Trim, 0.8cm diameter in Cosmic colourway. The Cosmos Epsilon Cord trim is the perfect way to enhance your Curtains, Blinds, Pelmets, Cushions etc. The Cord trim is available in 20 different colourways with a matt finish. From Subtle tones to vivid pinks there is something to…

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Randomized phase II study of preoperative afatinib in untreated head and neck cancers: predictive and pharmacodynamic biomarkers of activity

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

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Arsenic is a potent co-mutagen of ultraviolet light

Barnes, J. L., Zubair, M., John, K., Poirier, M. C. & Martin, F. L. Carcinogens and DNA damage. Biochem. Soc. Trans. 46, 1213–1224 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Ames, B. N., Durston, W. E., Yamasaki, E. & Lee, F. D. Carcinogens are mutagens: a simple test system…

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Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma

Whole-genome sequencing (WGS) analysis of early and advanced adenocarcinomas Whole-genome short read and long read sequencing datasets of 76 lung cancer specimens were analyzed. The datasets included newly generated data for 48 early small-sized lung adenocarcinoma cases (collectively called “Early-Ad” hereafter). These cases included 26 AIS (9 and 17 cases…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-nvidia-tegra/5.15.0.1020.20)

All autopkgtests for the newly accepted linux-meta-nvidia-tegra (5.15.0.1020.20) for jammy have finished running. The following regressions have been reported in tests triggered by the package: linux-nvidia-tegra/5.15.0-1020.20 (arm64) wireguard/unknown (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…

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Bioinformatics Engineer – Lifelancer | Career Page

What you will do Work with other engineers and scientists to build Isos platform, applying AI to biological systems. Design, develop and maintain bioinformatics pipelines for the ingestion, management and analysis of biological datasets, especially -omics, imaging, and clinical data. Perform data analysis and data quality assurance according to best…

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Human hg38 chr6:31,165,200-31,165,800 UCSC Genome Browser v457

     Custom Tracks ac4C-RIP-seq peaks, hESC CTL-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC CTL-2hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-1hidedensesquishpackfull ac4C-RIP-seq peaks, hESC NAT10-KD-2hidedensesquishpackfull    Mapping and Sequencing Base Positionhidedensefull p14 Fix Patcheshidedensesquishpackfull p14 Alt Haplotypeshidedensesquishpackfull Assemblyhidedensesquishpackfull Centromereshidedensesquishpackfull Chromosome Bandhidedensesquishpackfull Clone Endshidedensesquishpackfull Exome Probesetshidedensesquishpackfull FISH Cloneshidedensesquishpackfull Gaphidedensesquishpackfull GC Percenthidedensefull GRC Contigshidedensefull GRC Incidenthidedensesquishpackfull Hg19…

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Faith Meets Byte: Unraveling the Holy Code of Blockchain and Scriptures | by Cindrum Official | Dec, 2023

Throughout the time, religion and science have choreographed a dance of discord, from the historic Galileo to contemporary debates on evolution and cosmic creation. This dance revolves around the perceived threat scientific discoveries pose to sacred scripts, challenging religious doctrines entrenched in the binary code of belief. In this techno-theological…

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Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression

B cells undergo a series of programmed genomic alterations that enable the immunoglobulin light and heavy chain loci to generate high-affinity antibodies against invading pathogens. First, B cells undergo variability, diversity and joining (VDJ) recombination in the bone marrow with subsequent somatic hypermutation (SHM) and class switch recombination (CSR) occurring…

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EMBL’s European Bioinformatics Institute (EMBL-EBI) in 2023 | Nucleic Acids Research

Abstract The European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) is one of the world’s leading sources of public biomolecular data. Based at the Wellcome Genome Campus in Hinxton, UK, EMBL-EBI is one of six sites of the European Molecular Biology Laboratory (EMBL), Europe’s only intergovernmental life sciences organisation. This…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-raspi/6.5.0.1008.9)

All autopkgtests for the newly accepted linux-meta-raspi (6.5.0.1008.9) for mantic have finished running. The following regressions have been reported in tests triggered by the package: acpi-call/unknown (arm64) adv-17v35x/unknown (arm64) backport-iwlwifi-dkms/unknown (arm64) bbswitch/unknown (arm64) dahdi-linux/unknown (arm64) ddcci-driver-linux/unknown (arm64) digimend-dkms/unknown (arm64) dm-writeboost/unknown (arm64) dpdk-kmods/unknown (arm64) evdi/unknown (arm64) falcosecurity-libs/unknown (arm64) fwts/unknown (arm64) glibc/unknown…

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Molecular complexity of diffuse large B-cell lymphoma: a molecular perspective and therapeutic implications

Agarwal P, Kabir FM, DeInnocentes P, Bird RC (2012) Tumor suppressor gene p16/INK4A/CDKN2A and its role in cell cycle exit, differentiation, and determination of cell fate. Tumor Suppressor Genes 3(10):27882 Google Scholar  Alaggio R, Amador C, Anagnostopoulos I, Attygalle AD, Araujo IBO, Berti E et al (2022) The 5th edition…

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Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA

Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA 0 Dear Biostar Community I’m currently trying to generate a protein FASTA containing all known variants from HeLa (from Cosmic CellLinesProject) for variant detection in proteomics measurements. For this, I’ve downloaded the variants file (VCF) and the…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-raspi/5.4.0.1099.129)

All autopkgtests for the newly accepted linux-meta-raspi (5.4.0.1099.129) for focal have finished running. The following regressions have been reported in tests triggered by the package: nvidia-graphics-drivers-390/390.157-0ubuntu0.20.04.1 (armhf) openafs/unknown (arm64) openrazer/unknown (arm64) systemd/unknown (arm64) west-chamber/unknown (arm64) wireguard/unknown (arm64) wireguard-linux-compat/unknown (arm64) xtables-addons/unknown (arm64) zfs-linux/unknown (arm64) Please visit the excuses page listed below…

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Bioconductor – GenomicRanges

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges. Representation and manipulation of genomic intervals Bioconductor version: 2.14 The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing…

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Whole genome sequencing in high-grade cervical intraepitheli… : Medicine

1. Introduction Cervical cancer (CC) is the third most common cancer in women worldwide and has a high mortality rate among women. In 2008, CC was responsible for 275,000 deaths, thereby being the fourth leading cause of cancer death in females worldwide.[1,2] In China, CC is the second most…

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Decoding the Best IDE for You in 2024

Navigate the coding landscape with our comprehensive comparison of RStudio vs VSCode. Uncover the strengths, weaknesses, and unique features of each IDE to make an informed choice for your programming needs. Explore the showdown between RStudio and VSCode to optimize your coding experience. Embarking on a coding venture often feels…

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Growing Supermassive Black Hole Detected in Early Universe

Observations of quasars reveal that many supermassive black holes were in place less than 700 million years after the Big Bang. However, the origin of the first black holes remains a mystery. Seeds of the first black holes are postulated to be either light (that is, 10-100 solar masses), remnants…

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vcf – VEP annotation INFO field Ensembl IDs and locations

I have a vcf file that I annoteted with VEP, for human data. I have run VEP to annotate my files with some additional parameters (as shown below in the ##VEP-command-line). However, my output is rather strange (mainly the INFO column). ##VEP=”v108″ time=”2023-04-27 15:13:08″ cache=”workflow/resources/variants/cache_vep/homo_sapiens/108_GRCh38″ ensembl-funcgen=108.56bb136 ensembl-variation=108.a885ada ensembl-io=108.58d13c1 ensembl=108.d8a9c80 1000genomes=”phase3″…

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Characterization of the genomic alterations in poorly differentiated thyroid cancer

Cancer Genome Atlas Research, N. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159, 676–690. doi.org/10.1016/j.cell.2014.09.050 (2014). Sherman, S. I. Thyroid carcinoma. Lancet 361, 501–511. doi.org/10.1016/s0140-6736(03)12488-9 (2003). Article  PubMed  Google Scholar  Tong, J. et al. Poorly differentiated thyroid carcinoma: a clinician’s perspective. Eur. Thyroid J. 11, doi.org/10.1530/ETJ-22-0021 (2022). Asioli, S….

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No magic to green lights over Phetchaburi, says prof

Consequently, they congregate around the light source and end up being trapped in nets. Scientists have pinpointed the optimal wavelength range of these green lights, falling within the range of 495 and 570 nanometres, which they say is effective in attracting squid. In stark contrast, the mesmerising “northern lights” or…

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Where Cosmic Wonders and Tech Wackiness Collide

In a world where tech ‘game-changers’ are as common as memes, Apple has just dropped a bombshell- the new MacBook Pro line-up, featuring the magnificent M3 chips. So, let’s get ready as I am about to take you on a rollercoaster of information and some laughter as we dive into…

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Quantification of rare somatic single nucleotide variants by droplet digital PCR using SuperSelective primers

Primary samples and nucleic acid extraction A cohort of 48 patients diagnosed with advanced adenoma (AAD), defined by size > 20 mm, or colorectal carcinoma (CRC) were collected between 2013 and 2016. The study was approved by the institutional ethics committee of Hospital General Universitario de Alicante (Ref. CEICPI2013/01), and written informed consent…

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WellSpan peers into patient DNA as part of effort to detect and prevent diseases earlier

The York Dispatch receives a ‘cosmic check-in’ from Hanover shop targeted by obscure law Reporter Tina Locurto sat down with Beck Lawrence to receive a tarot reading and learn more about what the practice is. New advancements in genealogy research at WellSpan Health could help patients detect diseases and disorders…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta/6.5.0.12.14)

All autopkgtests for the newly accepted linux-meta (6.5.0.12.14) for mantic have finished running. The following regressions have been reported in tests triggered by the package: network-manager/1.44.2-1ubuntu1.2 (arm64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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ftsj3 Summary

Gene Symbol:  ftsj3 Gene Name:  FtsJ RNA methyltransferase homolog 3 Synonyms: ( Nomenclature history ) Gene Function: Putative SAM-dependent rRNmethyltransferase SPB1 Protein Function : Probable…

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NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology

Patient characteristics and tissue context The clinical interpretation of molecular alterations starts with evaluating relevant patient characteristics and the tissue context in which a genetic profile occurs. The former relates, in particular, to previous therapies, in addition to disease stage and clinical performance status. For example, prior targeted therapies warrant…

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Public Kaggle Competition “IceCube – Neutrinos in Deep ice”

Abstract: The reconstruction of neutrino events in the IceCube experiment is crucial for many scientific analyses, including searches for cosmic neutrino sources. The Kaggle competition “IceCube – Neutrinos in Deep ice” was a public machine learning challenge designed to encourage the development of innovative solutions to improve the accuracy and…

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Detailed Results from Phase 3 CABINET Pivotal Trial Evaluating Cabozantinib in Advanced Neuroendocrine Tumors Presented at ESMO 2023

ALAMEDA, Calif.–(BUSINESS WIRE)– Exelixis, Inc. (Nasdaq: EXEL) today announced detailed results from CABINET, a phase 3 pivotal trial evaluating cabozantinib (CABOMETYX®) compared with placebo in two cohorts of patients with previously treated neuroendocrine tumors: one cohort of patients with advanced pancreatic neuroendocrine tumors (pNET) and a second cohort of patients…

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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…

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E-IT hiring Bioinformatics Business Analyst in United States

Company Description E-IT Professionals Corp. (EIT) is an award-winning IT consulting, recruitment, management, and staffing organization founded in 1999. EIT is comprised of around 320 Information Technology Consultants and boasts revenues approaching $21M overall. Our dedicated team of professionals in the US and India serves clients from various geographies. We…

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Comparative study on the mutation spectrum of L-MYC and C-MYC genes of blood cfDNA in patients with ovarian cancer and healthy females

doi: 10.1111/jog.15808. Online ahead of print. Affiliations Expand Affiliations 1 Centre for Interdisciplinary Biomedical Research, Adesh University, Bathinda, India. 2 Department of Clinical Biochemistry, Govt. College for Women, M. A. Road, Srinagar, Cluster University Srinagar, Kashmir, India. Item in Clipboard Saba Shabir et al. J Obstet Gynaecol Res. 2023. Show details…

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USC Aiken biology students use cutting-edge technology to sequence DNA of the South Carolina state tree

University of South Carolina Aiken Associate Professor Nathan Hancock and his students are using breakthrough technology to decode the DNA sequence of the Sabal palmetto tree through a partnership with the American Campus Tree Genomes (ACTG) Project. In doing so, students can enhance their bioinformatic skills, giving them an advantage…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-nvidia-tegra/5.15.0.1018.18)

All autopkgtests for the newly accepted linux-meta-nvidia-tegra (5.15.0.1018.18) for jammy have finished running. The following regressions have been reported in tests triggered by the package: wireguard/unknown (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1]. people.canonical.com/~ubuntu-archive/proposed-

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UCSC Genome Browser hg38 and COSMIC v98 records

Hello, I have a question; why are the v98 COSMIC records for these two variants: NM_005228.5(EGFR):c.2062-3del NM_005228.5(EGFR):c.2062-3dup displayed in different coordinates in the UCSC genome browser hg38? (The Position: and Genomic coordinates also differ here: Genome Browser …919-…919 and COSMIC …918-…919 Additionally, for…

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We may have just found evidence of a cosmic string. This is kind of a fold of the universe

A team of scientists led by Margarita Safonova of the Indian Institute of Astrophysics described their research and doubts Latest articles Published in the Société Royale des Sciences de Liège. The hero of the article is a strange pair of galaxies located several billion light years away from us. Read…

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Molecular classification of hormone receptor-positive HER2-negative breast cancer

Siegel, R. L., Miller, K. D. & Jemal, A. Cancer statistics, 2020. CA Cancer J. Clin. 70, 7–30 (2020). Article  PubMed  Google Scholar  Huppert, L. A., Gumusay, O., Idossa, D. & Rugo, H. S. Systemic therapy for hormone receptor-positive/human epidermal growth factor receptor 2-negative early stage and metastatic breast cancer….

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KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas

Introduction The KCNQ (potassium voltage-gated channel subfamily Q) family of ion channels encode potassium transporters (1). KCNQ proteins typically repolarise the plasma membrane of a cell after depolarisation by allowing the export of potassium ions, and are therefore involved in wide-ranging biological functions including cardiac action potentials (2), neural excitability…

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60 Years in the Making: AlphaFold’s Historical Breakthrough in Protein Structure Prediction

It had only been a few days since the world shook with news of a scientific triumph in protein structure prediction. Word had spread about an insurmountable biological puzzle that had tormented scientists for decades, and lo and behold, they cracked it. The hot topic on everyone’s lips was protein…

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Mismatch repair deficiency is not sufficient to elicit tumor immunogenicity

Mice All animal use was approved by the Department of Comparative Medicine at the Massachusetts Institute of Technology (MIT) and the Institutional Animal Care and Use Committee under protocol no. 0714-076-17. Mice were housed with a 12-h light/12-h dark cycle with temperatures in the range 20–22 °C and 30–70% humidity. KrasLSL-G12D…

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Science Information that People Will Love to Learn About: Currently Trending in the World | by AutoWealth | Sep, 2023

In a world driven by curiosity and innovation, science continually pushes the boundaries of what’s possible. From space exploration to cutting-edge technologies, there’s an array of trending science topics that captivate minds worldwide. Let’s embark on a journey through some of the most exciting and thought-provoking developments in the realm…

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Houston Methodist hiring Bioinformatician – Urology – Chan lab in Houston, Texas, United States

Job SummaryAt Houston Methodist, the Bioinformatician position is responsible for managing all aspects of data analysis, data storage and bioinformatics support. This position specifically performs bioinformatics and statistical analysis for Next Generation Sequencing (NGS) experiments as well as develops pipelines, application tools for laboratory scientists, and administrating local and remote…

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Top 25 Bioconductor Interview Questions and Answers

Bioconductor is an open-source software project that provides tools for the analysis and comprehension of high-throughput genomic data. It’s a powerful tool, widely used in bioinformatics and computational biology to process and analyze intricate biological data. Bioconductor’s strength lies in its vast array of packages specifically tailored for genomics research,…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-azure/5.4.0.1115.108)

All autopkgtests for the newly accepted linux-meta-azure (5.4.0.1115.108) for focal have finished running. The following regressions have been reported in tests triggered by the package: dahdi-linux/1:2.11.1~dfsg-1ubuntu6.3 (amd64) v4l2loopback/0.12.3-1ubuntu0.4 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…

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Confusion about transcript ablation

I’m analyzing the WES data of a patient, after calling variants by GATK, I use Ensembl Variant Effect Predictor (VEP) to annotate my vcf file. Here is one record from the output file: #Uploaded_variation Location Allele Gene Feature Feature_type Consequence cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Extra chr11_64341844_GTTGTGGTCTGAGGTCTTGGGCCATCAGTGATGTCACAACCAGATGGCCCAAGACCCCAGACCACAACCCCATGTCTGGT/- chr11:64341844-64341923- ENSG00000278359…

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Exelixis and Ipsen Announce Positive Results from Phase 3

– Cabozantinib in combination with atezolizumab demonstrated a statistically significant reduction in the risk of disease progression or death compared with a second novel hormonal therapy in patients with metastatic castration-resistant prostate cancer  – A trend toward improvement in overall survival was observed at first interim analysis  – Findings will…

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Exome sequencing identifies breast cancer susceptibility genes and defines the contribution of coding variants to breast cancer risk

UKB The UKB is a population-based prospective cohort study of more than 500,000 subjects. More detailed information on the UKB is given elsewhere34,35. The study received ethics approval from the North West Multi-center Research Ethics Committee. All participants signed written informed consent before participating. WES data for 450,000 subjects were…

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Long-molecule scars of backup DNA repair in BRCA1- and BRCA2-deficient cancers

Pan-cancer WGS data sources GrCh37/hg19 BAM alignments for 2,489 primary tumour and matched normal whole-genome sequencing data were obtained as previously described18. In brief, 989 tumour–normal (T/N) pairs were obtained from The Cancer Genome Atlas (TCGA) Research Network (Genomic Data Commons at portal.gdc.cancer.gov/, accession: phs000178.v11.p8). Additional WGS data were obtained for 874 T/N pairs…

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The European Union Is Finally Coming Around to Gene-Edited Seeds

In 2021, the European Union announced that it would be reviewing its 2001-era legislation governing genetically modified (GM) organisms, so as to properly account for the recent development of “gene-edited” crops, which are produced using what’s known as New Genomic Techniques. To laypeople, the distinction between the various technology types…

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Bioconductor – deepSNV

DOI: 10.18129/B9.bioc.deepSNV     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see deepSNV. Detection of subclonal SNVs in deep sequencing data. Bioconductor version: 3.15 This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV…

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Characterizing the role of Phlda3 in the development of acute toxicity and malignant transformation of hematopoietic cells induced by total-body irradiation in mice

Mouse strains and procedures All animal procedures for this study were approved by the Institutional Animal Care and Use Committee (IACUC) at Duke University (protocol number A215-20-11 was approved on November 9, 2020). All methods were performed in accordance with the relevant guidelines and regulations. The study is reported in…

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Bioinformatics Position – IEO – European Institute of Oncology, Milan

Bioinformatics Position – IEO – European Institute of Oncology, Milan Bioinformatics Position IEO – European Institute of Oncology Milan, Italy ACC genomics is seeking a motivated bioinformatician to coordinate the bioinformatics efforts within the multiple projects. The candidate will be based at the IEO in Milan, where he/she will also…

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Effect of mutations in cancer-driving genes across human cancers

In a recent study published in Scientific Reports, researchers used multiple publically available cancer sequencing project datasets encompassing 20,331 primary tumor genomic sequences representing 41 different human cancers to detect and understand the extent of genetic mutations in 727 known cancer genes and their association with patient outcomes. The source of cancer…

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Postdoctor in bioinformatics at Karolinska Institutet

Do you want to contribute to top quality medical research? The research group of Professor Johan Hartman at the Oncology-Pathology departmentperforms clinical and translational studies for breast cancer, with a special focus on precisionmedicine. The aim is to predict the individual patients’ unique treatment response, as well asto understand the…

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Strategies to therapeutically modulate cytokine action

Cohen, S., Bigazzi, P. E. & Yoshida, T. Commentary. Similarities of T cell function in cell-mediated immunity and antibody production. Cell Immunol. 12, 150–159 (1974). Article  CAS  PubMed  Google Scholar  Keegan, A. D. & Leonard, W. J. in Paul’s Fundamental Immunology 8th edn, ch. 9 (eds Flajnik, M. F., Singh,…

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Myeloid Cancer Panel cfDNA Reference Standard

The Myeloid Cancer Panel cfDNA reference standard is a well-characterized cell line-derived control which contains 15 clinically-relevant variants across 14 genes. This cell-free DNA reference material allows labs to perform reliable and cost-effective validations of myeloid cancer liquid biopsy assays. QC pipelines are supported by controls manufactured under ISO:13485 with…

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NGS Analysis of Plasma cfDNA and cfmiRNA Signatures in Melanoma Brain Metastasis Patients

Gardner, L.J., Ward, M., Andtbacka, R.H.I., Boucher, K.M., Bowen, G.M., Bowles, T.L., Cohen, A.L., Grossmann, K., Hitchcock, Y.J., Holmen, S.L., Hyngstrom, J., Khong, H., McMahon, M., Monroe, M.M., Ross, C.B., Suneja, G., Wada, D., Grossman, D.: Risk factors for development of melanoma brain metastasis and disease progression: a single-center retrospective…

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Exelixis Announces Second Quarter 2023 Financial Results and Provides Corporate Update

– Total Revenues of $469.8 million, Cabozantinib Franchise U.S. Net Product Revenues of $409.6 million – – GAAP Diluted EPS of $0.25, Non-GAAP Diluted EPS of $0.31 – – Conference Call and Webcast Today at 5:00 PM Eastern Time – ALAMEDA, Calif., August 01, 2023–(BUSINESS WIRE)–Exelixis, Inc. (Nasdaq: EXEL) today…

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problems in hg19 and b37 compatibility

Hi everybody, A bam file has been aligned using hg19 reference genome. Thus, the chromosome notation is [chrM, chr1, chr2, chr3, chr4, …, chrX,chrY]. I want to look for PMs using MuTect that requires in input vcf files from dbSNP and COSMIC. In these vcf files the chromosome notation is…

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Landscape of mSWI/SNF chromatin remodeling complex perturbations in neurodevelopmental disorders

Bailey, M. H. et al. Comprehensive characterization of cancer driver genes and mutations. Cell 173, 371–385 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Gabriele, M., Tobon, A. L., D’Agostino, G. & Testa, G. The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog. Neuropsychopharmacol….

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Evolutionary histories of breast cancer and related clones

Data reporting No statistical methods were used to determine the sample size. The experiments were not randomized. Pathologists were blinded to the genetic alterations in each sample during histopathological evaluation. Participants and materials We enroled 207 female patients with breast cancer who underwent surgery at the Kyoto University Hospital and…

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10 of Futurama’s Hardest Sci-fi Moments

These aren’t episodes of Futurama which are hard in the sense of ‘tough’, or ‘tumescent’, but in the sense of how closely a work of science fiction adheres to actual science. The harder it is, the more based in scientific fact it is – and naturally you have the counterpoint…

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2023-07-06 | NDAQ:RARE | Press Release

Pivotal Phase 3 portion of Orbit study now enrolling approximately 195 pediatric and young adult patients Newly initiated Phase 3 Cosmic study now enrolling approximately 65 younger pediatric patients NOVATO, Calif., July 06, 2023 (GLOBE NEWSWIRE) — Ultragenyx Pharmaceutical Inc. (NASDAQ: RARE) today announced that the first patients have been…

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Ultragenyx Announces Groundbreaking Development in Treating Osteogenesis Imperfecta

Ultragenyx, a leading pharmaceutical company, has recently announced a groundbreaking development in the field of medical research. On July 6, 2023, the company revealed that the first patients have been administered with Setrusumab (UX143) as part of a Phase 3 program. This program aims to evaluate the efficacy of Setrusumab…

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Ultragenyx Announces First Patients Dosed in Phase 3 Program Evaluating Setrusumab (UX143) for the Treatment of Osteogenesis Imperfecta (OI)

/EIN News/ — Pivotal Phase 3 portion of Orbit study now enrolling approximately 195 pediatric and young adult patients Newly initiated Phase 3 Cosmic study now enrolling approximately 65 younger pediatric patients NOVATO, Calif., July 06, 2023 (GLOBE NEWSWIRE) — Ultragenyx Pharmaceutical Inc. (NASDAQ: RARE) today announced that the first…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-kvm/6.2.0.1008.8)

All autopkgtests for the newly accepted linux-meta-kvm (6.2.0.1008.8) for lunar have finished running. The following regressions have been reported in tests triggered by the package: dahdi-linux/1:2.11.1.0.20170917~dfsg-8.4ubuntu1 (amd64) lttng-modules/2.13.8-1 (amd64) oss4/4.2-build2020-1ubuntu1 (amd64) sl-modem/2.9.11~20110321-16ubuntu4 (amd64) xtrx-dkms/0.0.1+git20190320.5ae3a3e-3.2 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per…

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Whole genome and RNA sequencing analyses for 254 Taiwanese hepatocellular carcinomas | Biomarker Research

Clinical data The demographic data of the 254 HCC patients are presented in Table S1. We found that treatment received by HCC patients were associated with patient survival, as shown in Fig. S1. Somatic mutations The mutational landscape is shown in Fig. 1. The top 10 most common mutated genes were…

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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…

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Genomenon Accelerates Quest to Curate Entire Human Genome With Boston Genetics Acquisition

NEW YORK – In acquiring longtime partner Boston Genomics this week, Genomenon is stepping up its efforts to become the first entity to curate the entire human genome, though it may be the only one to have declared such an intention. By adding Cambridge, Massachusetts-based Boston Genetics’ team of about…

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CRISPR prime editing for unconstrained correction of oncogenic KRAS variants

Design of universal pegRNAs for KRAS gene correction We first investigated the mutation frequency of three RAS family genes, HRAS, NRAS, and KRAS, which are involved in tumorigenesis. According to the COSMIC (Catalog Of Somatic Mutations In Cancer) database (cancer.sanger.ac.uk/)22, KRAS mutations account for the majority (81.4%) of RAS mutations,…

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Stream Juan Pablo Moran – Nebula [Savia Park] by Savia Park

published on 2023-06-26T17:44:52Z Influenced by his beginnings in Progressive House, he is a born and frugal innovator. Founder of his label Amplusens, which remains faithful to its motto: ‘Creativity, innovation and evolution’, Juan Pablo Moran has excelled in the studio and on the dance floor. Each of Juan Pablo Moran’s…

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Get proper link to Mutation Overview webpages in COSMIC

Get proper link to Mutation Overview webpages in COSMIC 0 Hi everyone, I have a VCF annotated using COSMIC database VCFs where the ID column is now the COSV identifier for each variant and I also have the LEGACY ID in the INFO column. My question is, using either identifier…

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COSMIC Actionability data files format (mutation ID)

COSMIC Actionability data files format (mutation ID) 0 Hi all! I was trying to retrieve information from COSMIC’s Actionability project: The aim of COSMIC Mutation Actionability in Precision Oncology product (Actionability) is to indicate the availability of drugs that target mutations in cancer and track the progress of clinical studies…

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Proton and alpha radiation-induced mutational profiles in human cells

Determining proton and helium ion fraction, and irradiating the cell lines The dosage of radiation was determined experimentally in order to achieve between 40 and 50% lethality (corresponding to 50% to 60% clonogenic survival), independently across the two types of particle beams (Fig. 1a,b). Figure 1 Overview of the experimental design….

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Bioinformatics Engineer II – Hiring Now at Thermo Fisher Scientific in Bangalore

We are on the lookout for a driven Bioinformatics Engineer II to join our exceptional team at Thermo Fisher Scientific in Bangalore.Growing your career as a Full Time Bioinformatics Engineer II is a great opportunity to develop competitive skills.If you are strong in project management, communication and have the right…

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SBS Mutational Signatures aetiology

SBS Mutational Signatures aetiology 0 Hello, I was working with some mutational signatures, until now I used this cosmic page to search the signature proposed aetiology cancer.sanger.ac.uk/signatures/sbs/ I looked in the downloads but i didn’t found a table with the signature name and it’s aetiology. Is there any reference with…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-kvm/5.19.0.1025.22)

All autopkgtests for the newly accepted linux-meta-kvm (5.19.0.1025.22) for kinetic have finished running. The following regressions have been reported in tests triggered by the package: backport-iwlwifi-dkms/9904-0ubuntu3.1 (amd64) digimend-dkms/10-5 (amd64) rtl8812au/4.3.8.12175.20140902+dfsg-0ubuntu17 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding…

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Bitscopic hiring Senior Bioinformatics Pipeline Engineer in United States

We are seeking a remote full-time Bioinformatics Pipeline Engineer who has the skillset to construct and maintain scalable genomic analysis pipelines. Your role will not only be centered around development for pharmacogenomics, cancer, and infectious diseases biosurveillance. We value someone with the expertise to implement Python and shell scripting in…

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mutational signatures in different tumor samples

mutational signatures in different tumor samples 0 Dear all. I am currently researching the mutational signatures (or patterns?) in a large cohort of targeted sequencing of tumor samples. I found that the definition of “mutational signatures” in COSMIC is like this : “The profile of each signature is displayed using…

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Retrieving allele-specific information for a variant using VEP annotation

Hi all! I annotated a VCF file using VEP and noticed that it reports several variant IDs to each input variant. For example, this is an excerpt of one of the variant lines (I removed the annotation info that is not relevant to the question): 12 25398284 . C A…

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Things Phase 4 Did Perfectly

The one-two punch of Avengers: Infinity War and Avengers: Endgame firmly established the Marvel Cinematic Universe (MCU) as the biggest movie franchise in the world. What helped make the films among the biggest box-office hits ever is that they were the grand culmination of a decade’s worth of storytelling, as…

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Retrieving information from COSMIC database in an automated way

Retrieving information from COSMIC database in an automated way 0 Hi! I am performing variant calling and annotation of some cancer samples. For the moment, I am checking manually the variants with an entry in the COSMIC database and then going to the COSMIC database website to retrieve information associated…

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What Is Distributed Learning In Machine Learning?

Distributed learning has emerged as a crucial technique for tackling complex problems and harnessing the power of large-scale data processing. But what exactly is distributed learning in machine learning? Why is it so important? In this article, we will explore the concept of distributed learning and its significance in the…

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open-cravat: variant annotation tool

Tool:open-cravat: variant annotation tool 3 open-cravat is an open-source platform for rapidly developing, using, and disseminating variant annotation tools. It can handle unlimited number of variants in VCF format input files as well as its own input format and produce tab-separated text output files and excel spreadsheets. It is command-line-based…

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LOINC 81874-0 SLC12A3 gene full mutation analysis in Blood or Tissue by Sequencing

81247-9 Master HL7 genetic variant reporting panel  Indent81306-3 Variables that apply to the overall study  Indent Indent53577-3 Reason for study O 0..*  Indent Indent51967-8 Genetic disease assessed [ID] O 0..*  Indent Indent51963-7 Medication assessed [ID] C 0..*  Indent Indent48018-6 Gene studied [ID] C 0..*  Indent Indent36908-2 Gene mutations tested for in Blood or Tissue by…

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Every Time Futurama Made Us Cry

Part of what made Futurama so great is its ability to combine comedy and drama. One minute we’re laughing, and the next we’re grabbing for a box of tissues. This list will focus on the latter. With the show’s revival in the works, we’re looking at some of the saddest moments…

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Revvity hiring Senior Bioinformatics Scientist in Cambridge, England, United Kingdom

About The RoleWe have an exciting opportunity for an experienced bioinformatician who is interested in working at the forefront of the gene editing (CRISPR knock-out, base editing) and gene modulation (CRISPRa, CRISPRi, RNAi) fields. We are seeking a Cambridge-based Senior Bioinformatics Scientist 1 to join our global Bioinformatics team, which…

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Astronomers find ‘largest ever’ cosmic explosion by chance

Data suggests that the explosion is roughly 8bn light years away and nearly 100 times brighter than all the stars in our galaxy combined. A new investigation has revealed a cosmic explosion that is 10 times brighter than any known supernova (exploding star). The cosmic explosion – called AT2021lwx –…

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Clonal evolution during metastatic spread in high-risk neuroblastoma

Maris, J. M. Recent advances in neuroblastoma. N. Engl. J. Med. 362, 2202–2211 (2010). Article  CAS  PubMed  PubMed Central  Google Scholar  London, W. B. et al. Historical time to disease progression and progression-free survival in patients with recurrent/refractory neuroblastoma treated in the modern era on Children’s Oncology Group early-phase trials.Cancer…

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Phase 3 data for cabozantinib triplet in kidney cancer published in NEJM

Findings from the phase 3 COSMIC-313 trial, which showed that adding cabozantinib (Cabometyx) to nivolumab (Opdivo) and ipilimumab (Yervoy) in the first-line setting significantly improved progression-free survival (PFS) in patients with intermediate- or poor-risk renal cell cancer (RCC), have been published in the New England Journal of Medicine.1 “This is…

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State of Success: National Washington Day

Historical Background  The WSU College of Agricultural, Human and Natural Resource Sciences (CAHNRS) traces its origins to our Land-grant University’s founding. Only five months after attaining statehood, the Washington State Legislature established the Washington State Agricultural College, Experiment Station and School of Sciences on March 28, 1890. Instruction began in…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-azure-fde-5.15/5.15.0.1038.45~20.04.1.17)

All autopkgtests for the newly accepted linux-meta-azure-fde-5.15 (5.15.0.1038.45~20.04.1.17) for focal have finished running. The following regressions have been reported in tests triggered by the package: dahdi-linux/1:2.11.1~dfsg-1ubuntu6.3 (amd64) nvidia-graphics-drivers-340/340.108-0ubuntu5.20.04.2 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions…

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Senior Bioinformatics Scientist @ Natera

We are seeking a bioinformatician with significant oncology or immunology experience to join a multidisciplinary team developing leading-edge genomics analysis tools to understand the immune system’s response to cancer. This highly motivated, detail-oriented individual would join a clinical genomics analysis group and will be responsible for developing and applying bioinformatics…

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New Products Posted to GenomeWeb: Roche, GeneDx

Roche Kapa HyperExome V2 Probes Roche has launched its Kapa HyperExome V2 Probes, a whole-exome sequencing panel that provides a key update to the company’s Kapa HyperCap Target Enrichment portfolio. The new panel covers recent versions of the ACMGv3.1, RefSeq, CCDS, ClinVar, Ensembl, and COSMIC genomic databases within a compact…

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Single duplex DNA sequencing with CODEC detects mutations with high sensitivity

Ethical approval, DNA samples and oligonucleotides All patients provided written informed consent to allow the collection of blood and/or tumor tissue and the analysis of clinical and genetic data for research purposes. The IRB of the Dana-Farber Cancer Institute and New York University Grossman School of Medicine approved these protocols….

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The genome-wide mutational consequences of DNA hypomethylation

Goldberg, A. D., Allis, C. D. & Bernstein, E. Epigenetics: A landscape takes shape. Cell 128, 635–638 (2007). Article  PubMed  Google Scholar  Mohn, F. & Schübeler, D. Genetics and epigenetics: Stability and plasticity during cellular differentiation. Trends Genet. 25, 129–136 (2009). Article  PubMed  Google Scholar  Takahashi, K. et al. Induction…

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