Jennifer McDaniel

Correction: Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

Jennifer McDaniel, Vaidehi Patel, Nathan D. Olson, Hua‐Jun He et autres

In this article the following sentence was omitted from the Usage Notes, ‘The data and alignments are publicly available on the GIAB FTP site hosted by the NIH-NCBI ( https://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/) ’. The original article has been corrected.

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Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

Jennifer McDaniel, Vaidehi Patel, Nathan D. Olson, Hua‐Jun He et autres

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a comprehensive genomic …

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Interlaboratory assessment of candidate reference materials for lentiviral vector copy number and integration site measurements

Hua‐Jun He, Zhiyong He, Steven P. Lund, Laure Turner et autres

While lentiviral vectors have played a critical role in the emergence of gene-modified cell therapies, safety concerns remain regarding potential insertional mutagenesis. Regulatory authorities strongly recommend risk assessment and management of vector copy numbers (VCNs), integration profiles, and integration sites in the …

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Small variant benchmark from a complete assembly of X and Y chromosomes

Justin Wagner, Nathan D. Olson, Jennifer McDaniel, Lindsay N. Harris et autres

The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant detection on male sex chromosomes X and …

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A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

Camille A. Daniels, Adetola Abdulkadir, Megan H. Cleveland, Jennifer McDaniel et autres

Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell populations, we developed a …

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The GIAB genomic stratifications resource for human reference genomes

Nathan Dwarshuis, Divya Kalra, Jennifer McDaniel, Philippe Sanio et autres

Despite the growing variety of sequencing and variant-calling tools, no workflow performs equally well across the entire human genome. Understanding context-dependent performance is critical for enabling researchers, clinicians, and developers to make informed tradeoffs when selecting sequencing hardware and software. Here we …

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Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

Jennifer McDaniel, Vaidehi Patel, Nathan D. Olson, Hua‐Jun He et autres

The Genome in a Bottle Consortium (GIAB), hosted by the National Institute of Standards and Technology (NIST), is developing new matched tumor-normal samples, the first to be explicitly consented for public dissemination of genomic data and cell lines. Here, we describe a …

us, ua (code pays fourni par la source)

Abstract 3551: Continued analysis of extensive data towards Genome in a Bottle benchmarks for a new tumor normal pair

Justin Wagner, Jennifer McDaniel, GAIL L. ROSEN, Nathan D. Olson et autres

Abstract Here, we detail in-progress genome-scale measurements from a variety of technologies of the first tumor normal benchmark from the Genome in a Bottle (GIAB) consortium. We created the first broadly-consented tumor cell line from a pancreatic ductal adenocarcinoma with matched normal …

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A Robust Benchmark for Detecting Low-Frequency Variants in the HG002 Genome in a Bottle NIST Reference Material

Camille A. Daniels, Adetola Abdulkadir, Megan H. Cleveland, Jennifer McDaniel et autres

Small variant benchmark from a complete assembly of X and Y chromosomes

Justin Wagner, Nathan D. Olson, Jennifer McDaniel, Lindsay N. Harris et autres

Abstract The sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To evaluate variant detection on chromosomes X and Y, we created an 111,725 variant benchmark for the Genome in …

us, es (code pays fourni par la source)

The GIAB genomic stratifications resource for human reference genomes

Nathan Dwarshuis, Divya Kalra, Jennifer McDaniel, Philippe Sanio et autres

Abstract Stratification of the genome into different genomic contexts is useful when developing bioinformatics software like variant callers, to assess performance in difficult regions in the human genome. Here we describe a set of genomic stratifications for the human reference genomes GRCh37, …

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The GIAB genomic stratifications resource for human reference genomes

Nathan Dwarshuis, Divya Kalra, Jennifer McDaniel, Philippe Sanio et autres

Stratification of the genome into different genomic contexts is useful when developing bioinformatics software like variant callers, to assess performance in different types of difficult regions in the human genome. Here we describe a set of genomic stratifications for the human reference …

us, at, in, ch (code pays fourni par la source)