Search Results for: Variants

02/28/2020 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/play/e688e94d71934c4183480167b05f0f67 The CIViC knowledgebase (www.civicdb.org) is an open access, open source, community-driven resource for Clinical Interpretation of Read More...

01/07/2020 - The CIViC knowledgebase (www.civicdb.org) is an open access, open source, community-driven resource for Clinical Interpretation of Variants in Cancer. The goal of CIViC is to enable precision medicine by providing an educational Read More...

09/20/2022 - Dr. Mikhail Kolmogorov, Stadtman Investigator, Cancer Data Science Laboratory, NCI (guest of Pedro Batista) will present a lecture: Please join us for a hybrid LCB seminar/webinar via ZoomGov and in Conference Room 37/2041 Meeting Read More...

07/27/2022 - Many recent studies highlighted the improved capability of long-read sequencing to detect structural variation in the human genome. For example, these technologies was also recently utilized to produce the first complete assembly of the Read More...

02/28/2020 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/e688e94d71934c4183480167b05f0f67/playback

08/22/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/c1bf64260cba42daa17b673022ac1f45/playback

Variants are usually called from alignment (BAM) files. Here is the process: 1. Align reads to the reference. 2. Correct and refine alignments (optional). 3. Determine variants from the alignments. 4. Filter the resulting variants for the desired characteristics. 5. Read More...

10/07/2020 - QIAGEN’s Ingenuity Variant Analysis (IVA) combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based on published Read More...

10/12/2018 - QIAGEN’s Ingenuity Variant Analysis (IVA) combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based on published Read More...

08/04/2021 - This class introduces mutation types and how to identify the mutations from DNA sequences. Additionally, it describes resources to access information about the impact of variants on proteins associated with drug response guidelines. This Read More...

03/03/2021 - Register This class introduces mutation types and how to identify the mutations from DNA sequences. Additionally, it describes resources to access information about the impact of variants on proteins associated with drug response guidelines. Read More...

09/02/2020 - This class introduces mutation types and how to identify the mutations from DNA sequences. Additionally, it describes resources to access information about the impact of variants on proteins associated with drug response guidelines. This Read More...

05/07/2020 - This class introduces mutation types and how to identify the mutations from DNA sequences. Additionally, it describes resources to access information about the impact of variants on proteins associated with drug response guidelines. This Read More...

04/02/2020 - This class introduces mutation types and how to identify the mutations from DNA sequences. Additionally, it describes resources to access information about the impact of variants on proteins associated with drug response guidelines. This Read More...

The Pharmacogenetics Core is responsible for correlating outcome observations (toxicity, efficacy, survival, PK/PD) with genetic variants (germline or somatic) to identify key genetic determinants and biomarkers that predict response to specific treatments. We also Read More...

07/09/2024 - Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This workshop will cover exome sequencing data Read More...

Filtering is done to keep or remove variants to satisfy certain constraints. Make a new directory and download the example data (VCF file and index). This file contains variants in chromosome 19:400kb-500kb mkdir hg19 Read More...

There are a number of specific solutions that have been devised to address the issues created by attempting to map mRNA to DNA genomes. Each of these has its advantages and disadvantages. Align against the Read More...

Genomic variations are typically categorized into different classes and are often denoted with a shortened acronym: SNP, a single nucleotide polymorphism - A change of a single base. INDEL, an insertion or a deletion - Read More...

07/14/2023 - Galaxy is a scientific workflow, data integration, data analysis, and publishing platform that makes computational biology accessible to research scientists that do not have computer programming experience. This workshop will cover exome sequencing data Read More...

07/13/2022 - This training will provide an introduction to exome sequencing data analysis followed by tutorials showing the use of exome analysis workflow and preparing participants to independently run basic exome analysis for variant detection using Read More...

06/28/2021 - This training will provide an introduction to exome sequencing data analysis followed by tutorials showing the use of exome analysis workflow and preparing participants to independently run basic exome analysis for variant detection using Read More...

09/28/2020 - Register/Join This webinar is intended for cancer researchers and bioinformaticians who are interested in learning more about the NCI Genomic Data Commons’ (GDC’s) bioinformatics pipelines for data harmonization. The GDC DNA-Seq analysis Read More...

06/26/2020 - This training will provide an introduction to exome sequencing data analysis followed by tutorials showing the use of exome analysis workflow and preparing participants to independently run basic exome analysis for variant detection using Read More...

06/23/2020 - This training will provide an introduction to exome sequencing data analysis followed by tutorials showing the use of exome analysis workflow and preparing participants to independently run basic exome analysis for variant detection using Read More...

02/27/2020 - The Annotation, Visualization and Impact Analysis (AVIA) is an application developed to guide, prioritize and summarize genomic variants. AVIA maintains and aggregates dozens of publicly available variant annotation databases and predictions from impact analysis Read More...

05/01/2025 - In this talk, Dr. Stergachis will present data on using Fiber-seq and deaminase-assisted Fiber-seq (DAF-seq) to resolve the functional impact of both germline and somatic genetic variants, as well as to identify somatic epimutations Read More...

03/25/2025 - Dr. Ben Raphael will describe computational methods developed in his lab to analyze large-scale biological data related to cancer evolution, genetic variants, and structural variation in cancer genomes. He’ll share combinatorial and statistical Read More...

10/24/2024 - NIH Text Mining and Natural Language Processing SIG is pleased to welcome you to this special event featuring two extraordinary speakers focused on the applications of Deep Learning in Computational Biology.  & Read More...

02/28/2024 - In this seminar, you'll learn about the somatic variant caller named Lancet. This accurate, open-source tool leverages local assembly and joint analysis of tumor-normal, paired, high-throughput sequence data. New York Genome Center& Read More...

Past versions of dplyr included powerful variants of filter , select , and other functions to help perform tasks across columns. You may see functions such as filter_all , filter_if , and filter_at . Functions like these Read More...

11/21/2023 - Dear Colleagues,    This presentation will provide an overview of OpenCRAVAT.   Annotation and interpretation of cancer variants is critical to the design of personalized molecular therapies, and Read More...

Variant annotation means predicting the effects of genetic variants (SNPs, insertions, deletions, copy number variations (CNV) or structural variations (SV)) on the function of genes, transcripts, and protein sequence, as well as regulatory regions. The Read More...

First we will retrieve the Ebola reference genome and put it in the "refs" directory. Next we need to create the index for the aligner (bwa index) and for IGV (samtools faidx). Let' Read More...

Multi-sample variant calling is an extension of single sample variant calling, where all samples are evaluated together, and the presence or absence of a variant is shown for all samples in parallel. We will perform Read More...

Variant normalization involves the simplification of variant representation to follow these rules: * Represent the variant with as few letters as possible. * No allele may be zero length. * Variant must be "left aligned" Some Read More...

Your answers to the following questions will dictate many of your choices with respect of the appropriate methodologies to be employed. Which gene are expressed? Which genes are differentially expressed? Are different splicing isoforms expressed? Read More...

VCF files are produced by running a variant caller on one or more BAM alignment files. We will download the ebola genome (AF086833) into a "refs" directory, create a "bwa index" Read More...

06/06/2023 - Dr. Maximilian Haeussler is the co-PI for the  UCSC Genome Browser , an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with Read More...

06/30/2022 - Experimental Design Considerations in Variant Analysis Germline vs Somatic WGS vs WES Sample sizes and statistical power QC, variant annotation, and analysis considerations Beyond GATK! A survey of variant calling tools The  actual  Best Read More...

09/16/2021 - As a continuation of the NHGRI seminar series focused on the “Bold Predictions for Human Genomics by 2030,” please join us for the seventh seminar in the series on Thursday, September 16 from 3:00 – 4:30 pm ET. This Read More...

12/03/2020 - Register Registration is required to join this event. If you have not registered, please do so now. It has been established that over half of all cancer types are driven by DNA Copy Number Read More...

06/28/2020 - The overarching goal of our work is to implement data analysis and informatics tools for integration of biological mass spectrometry data (proteomics and metabolomics) with genomic / transcriptomic information to advance cancer research. We are Read More...

01/29/2020 - NCI Shady Grove, 9609 Medical Center Drive, Room 2W032/034, and via Webinar Rachel Karchin, Ph.D., and Kym Pagel, Ph.D. Dr. Karchin and Dr. Pagel will present OpenCRAVAT, a new open source, scalable decision Read More...

11/04/2019 - This is a hands-on demo, please bring your laptop or let us know if you need to borrow one.  The field of genomics has matured to a stage where organizations are sequencing DNA at Read More...

10/24/2019 - ** Registration is not necessary for members of the public**NIH employees please register**Thank you** Re-assessing the Human Gene Catalog and the Human Genome: How much are we missing?   Steven L. Salzberg, Ph.D. Read More...

11/05/2018 - This introductory lecture will provide an overview of RNA-Seq technology, its various application and shortcomings, as well as detailing the steps involved in analyzing the resulting data. The specific topics covered include: What is Read More...

The goals of the Bioinformatics Training and Education Program within NCI/CCR are: To make researchers aware of the bioinformatics resources available to them, To provide training and guidance on these resources regularly and at Read More...

We are a bioinformatics team within the Center for Biomedical Informatics and Information Technology’s (CBIIT’s) Cancer Informatics Branch (CIB)—soon to be referred to as the Informatics and Data Science (IDS) Program. Headed Read More...

CREx Monthly Newsletter Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More. New Resources on CREx NIMH Human Brain Collection Core (HBCC) The HBCC obtains human brain tissue, hair, and blood Read More...

[embed]https://youtu.be/yTl1Q0D7aZ0[/embed] 10x Genomics' supports multiple cancer research areas from single nucleotide and structural variant detection to single cell whole transcriptome gene expression analysis of thousands of individual Read More...

2025 Sebastian R, Sun EG, Fedkenheuer M, Fu H, Jung S, Thakur BL, Redon CE, Pegoraro G, Tran AD, Gross JM, Mosavarpour S, Kusi NA, Ray A, Dhall A, Pongor LS, Casellas R, Aladjem MI. Mechanism Read More...

2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...

04/16/2025 - Updated Location: ATRF, Frederick MD, Main Auditorium What to bring:  Laptop capable of connecting to internet via NIH wifi For questions or to register, please contact Amy Stonelake ( amy.stonelake@nih.gov ) Read More...

04/15/2025 - What to bring:  Laptop capable of connecting to internet via NIH  wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...

03/18/2025 - This class is not hands-on and will demonstrate to participants the use of IGV for visualizing alignment results from Next Generation Sequencing using RNA as an example. After this class, participants will be able Read More...

03/13/2025 - UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Read More...

03/13/2024 - Dear Colleagues,    UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations.   Xena showcases seminal cancer genomics datasets from Read More...

01/22/2024 - Dear Colleagues,    Optical Genome Maps (OGM) provide scaffolding information for large DNA molecules. In this talk, we describe the use of this technology for detecting structural variants and chaining them Read More...

11/29/2023 - In this seminar, you'll learn about the somatic variant caller named Lancet. This accurate, open-source tool leverages local assembly and joint analysis of tumor-normal, paired, high-throughput sequence data. New York Genome Center& Read More...

10/25/2023 - Every week, thousands of biomedical research papers are published with a portion of them containing supporting tables with data about genes, transcripts, variants, and proteins. For example, supporting tables may contain differentially expressed genes Read More...

This page uses context taken directly from the Biostar Handbook by Istvan Albert. Remember to activate the class bioinformatics environment. conda activate bioinfo Introduction to Genomic Variation Genomic variations are typically categorized into different classes Read More...

Generating VCF Files (Simulated data) VCF files are produced by running a variant caller on one or more BAM alignment files. We will download the ebola genome (AF086833) into a "refs" directory, create Read More...

STAR 2-pass mode --sjdbGTFfile is the path to the file with annotated transcripts in standard GTF format, STAR extracts splice junctions from this file, improves accuracy of mapping. Using annotations is highly recommended whenever they Read More...

Alignment RNASeq Mapping Challenges The majority of mRNA derived from eukaryotes is the result of splicing together discontinuous exons, and this creates specific challenges for the alignment of RNASEQ data. Mapping Challenges Reads not perfect Read More...

06/09/2023 - Dr. Nara Sobreira will present "PhenoDB, a phenotypic and genotypic data sharing tool" at the monthly Data Sharing and Reuse Seminar on June 9, 2023, at 12 p.m. EST. About the Seminar This seminar Read More...

Bioinformatics Training and Education Program 15 January – 15 February 2023 BTEP Bulletin Contact us at ncibtep@nih.gov FEATURED BIOINFORMATICS EVENTS Data Management Sharing: Part 1 and Part 2 DOE-NCI Collaboration: MOSSAIC for Advancing Computational Models for Cancer Research Variation Read More...

11/14/2022 - During this webinar, the  Genomic Data Commons ’ (GDC’s) Drs. Zhenyu Zhang and Bill Wysocki will review the different types of harmonized data that the GDC makes available for the cancer research community. The Read More...

10/31/2022 - UCSC Xena is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as well as Read More...

07/14/2022 - The efforts of our laboratory are split evenly between experimental and computational biology.  We develop new experimental methods to sequence single cells and isolate rare subpopulations and develop new analytical approaches to detect variants Read More...

07/14/2022 - Nicholas Navin, Ph.D. Professor, Department of Genetics, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center Grady F. Saunders, Ph.D. Distinguished Professorship for Molecular Biology, Department of Genetics, Read More...

06/15/2022 - During this seminar, Washington University in St. Louis’ Dr. Obi L. Griffith will present  CIViC : an  open access , open source, community-driven web resource for clinical interpretation of variants in cancer. The goal of this Read More...

09/14/2021 - OpenCRAVAT is an open source variant annotation and decision support software to support cancer variant and gene prioritization. It offers both command line functionality and a dynamic biologist-friendly GUI, allowing users to install with Read More...

06/10/2021 - Meeting Link:  https://cbiit.webex.com/cbiit/j.php?MTID=mc11b56eb7f7e732aa44c78427402dd2e Abstract: Long read, single molecule sequencing from Pacific Biosciences (PacBio) and Oxford Nanopore are revolutionizing Read More...

06/09/2021 - The CCR Office of Science and Technology Resources (OSTR) is pleased to host a virtual technology seminar given by Advanced Cell Diagnostics (ACD) and NCI Cores at FNLCR. Presenters: Jyoti Phatak, MS | Advanced Cell Read More...

06/04/2021 - Speaker: Rangan Sreenivas Sukumar Distinguished Technologist Hewlett Packard Enterprise (HPE) Abstract: In March of 2020, the “Force for Good” pledge of intellectual property to fight COVID-19 brought into action HPE products, resources and expertise to Read More...

05/26/2021 - Register Description: This webinar will highlight UCSC Xena's newest features including genome-wide differential gene expression analysis, violin plots, and a simpler way to filter and subgroup. UCSC Xena ( http://xena.ucsc.edu/ ) is Read More...

05/03/2021 - Abstract: We will discuss technical advantages of a personalized and tumor-informed multiplex PCR next generation sequencing assay, called Signatera™, that enables a sensitive, specific, and dynamic detection of molecular disease burden in cell-free DNA ( Read More...

02/17/2021 - Speaker is Dr. Michal Linial from the Hebrew University of Jerusalem, Israel. Abstract: Incredible progress has also been made in the field of cancer genetics with the sequencing and molecular profiling of tens of Read More...

10/22/2020 - Register Presenter: Dr. Sam Dougaparsad Field Application Scientist It has been established that over half of all cancer types are driven by DNA Copy Number Variants (CNVs). In this presentation, we will demonstrate the Read More...

09/04/2020 - Speakers: Dave Clements, Galaxy Community Manager, Johns Hopkins University, Steven Weaver, Senior Programmer Analyst, Temple University Galaxy is an open web-based platform for data integration and analysis in the life sciences. Galaxy makes sophisticated Read More...

06/05/2020 - OpenCRAVAT is a an open source, scalable decision support system to support cancer variant and gene prioritization. It offers both command line functionality and a dynamic biologist-friendly GUI, allowing users to install with a Read More...

06/01/2020 - After nearly two decades of improvements, the current human reference genome is the most accurate and complete vertebrate genome ever produced. However, no one chromosome has been finished end to end, and hundreds of Read More...

05/19/2020 - UCSC Xena ( xena.ucscedu/) is a web-based visual integration and exploration tool for multi-omic data and associated clinical and phenotypic annotations. Xena showcases seminal cancer genomics datasets from TCGA and the Pan-Cancer Atlas, as Read More...

09/26/2019 - Qlucore Omics Explorer is an interactive analysis and visualization tool that helps the user to find groups, structures, variable networks and discriminating variables. You can use your own data and analyze public data. Omics Read More...

05/21/2019 - This introductory lecture will provide an overview of RNA-Seq technology, its various application and shortcomings, as well as detailing the steps involved in analyzing the resulting data. The specific topics covered include: What is Read More...

05/21/2019 - This introductory lecture will provide an overview of RNA-Seq technology, its various application and shortcomings, as well as detailing the steps involved in analyzing the resulting data. The specific topics covered include: What is Read More...

10/26/2018 - Variant Analysis using Genomatix GeneGrid ** please bring laptop with Flash installed for the hands-on portion of this demo Susan M. Dombrowski, PhD and Peter Grant, Genomatix, Inc. Genomatix GeneGrid is a variant annotation and Read More...

11/13/2017 - MetaCore™ is an integrated curated knowledge database and software suite for pathway analysis of experimental data and gene lists. The scope of data types includes microarray and sequence-based gene expression, SNPs and CGH arrays, Read More...

09/27/2017 - UCSC Xena ( http://xena.ucsc.edu ) is a web-based, visual exploration tool for all modes of multi-omic data and associated annotations. Xena has several seminal cancer datasets pre-loaded and ready for visualization including TCGA, Read More...

NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to Read More...

The National Cancer Institute (NCI) is developing a national repository of Patient-Derived Models (PDMs) comprised of patient-derived xenografts (PDXs), patient-derived organoids (PDOrg), and in vitro patient-derived tumor cell cultures (PDCs) and cancer-associated fibroblasts (CAFs). These Read More...

The NCI Genomic Data Commons (GDC) was established by the NCI Center for Cancer Genomics (CCG) to support the receipt, harmonization, distribution, and analysis of genomic and clinical data from cancer research programs. The GDC Read More...

CREx News & Updates October 2021 Learn about the NIH Collaborative Research Exchange (CREx), Core Facilities, Webinars, & More NIH Collaborative Research Exchange (CREx) News Site Spotlight FACILITY HIGLIGHTS Learn more about services from the CPTR Read More...

The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at Read More...

The computational chemistry and protein modeling team in the Advanced Biomedical Computational Science (ABCS) group provides novel solutions in structural modeling and computational chemistry. Computational scientists in the group collaborate with NCI researchers by using Read More...

The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: • Subject matter expertise in genomics, proteomics, and imaging. • Machine learning/ Read More...

Introduction to dplyr and the %>% Objectives Today we will begin to wrangle data using the tidyverse package, dplyr . To this end, you will learn: how to filter data frames using dplyr how to employ Read More...

RNA-SEQ Overview What is RNASEQ ? RNA-Seq (RNA sequencing), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. (Wikipedia) Strictly speaking this could be any Read More...

How to download data from the Sequence Read Archive (NCBI/SRA) to your account on NIH HPC Biowulf You will need: active, unlocked Biowulf account (hpc.nih.gov) active Globus account for transferring files OR Read More...

10/05/2022 - For our next CDSL webinar we will have presentations by two CDSL fellows:  Ekaterina Kazantseva  and Sanna Madan.  Ekaterina is a master’s student in Dr. Mikhail Kolmogorov's group and the title of Read More...

02/20/2020 - Learn how to easily analyze your gene expression data yourself - using Qlucore Omics Explorer NCI/CCR:To get access to Qlucore, put a request into NCI at Your Service under Get Help https:// Read More...

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