Robert Wappel

Unearthing soil biodiversity through collaborative genomic research and education

Jefferson Rogério Marques da Silva, Senem Mavruk Eskipehlivan, Lindsay Zirkle, Tristen Alberts et autres

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Unearthing soil biodiversity through collaborative genomic research and education

Tristen Alberts, Claude F. Albritton, Rosa Alcazar, Zainab AlJabri et autres

Exploring the genetic and epigenetic underpinnings of early-onset cancers: Variant prioritization for long read whole genome sequencing from family cancer pedigrees

Melissa Kramer, Sara Goodwin, Robert Wappel, Matilde Borio et autres

Abstract Despite significant advances in our understanding of genetic cancer susceptibility, known inherited cancer predisposition syndromes explain at most 20% of early-onset cancers. As early-onset cancer prevalence continues to increase, the need to assess previously inaccessible areas of the human genome, harnessing …

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Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq

Bernardo Aguzzoli Heberle, J. Anthony Brandon, Madeline L. Page, Kayla A. Nations et autres

Determining whether the RNA isoforms from medically relevant genes have distinct functions could facilitate direct targeting of RNA isoforms for disease treatment. Here, as a step toward this goal for neurological diseases, we sequenced 12 postmortem, aged human frontal cortices (6 Alzheimer …

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Direct sequencing of insect symbionts via nanopore adaptive sampling

Jonathan H. Badger, Rosanna Giordano, Aleksey V. Zimin, Robert Wappel et autres

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Using deep long-read RNAseq in Alzheimer’s disease brain to assess medical relevance of RNA isoform diversity

Bernardo Aguzzoli Heberle, J. Anthony Brandon, Madeline L. Page, Kayla A. Nations et autres

Abstract Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical …

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High resolution copy number inference in cancer using short-molecule nanopore sequencing

Timour Baslan, Sam Kovaka, Fritz J. Sedlazeck, Yanming Zhang et autres

Genome copy number is an important source of genetic variation in health and disease. In cancer, Copy Number Alterations (CNAs) can be inferred from short-read sequencing data, enabling genomics-based precision oncology. Emerging Nanopore sequencing technologies offer the potential for broader clinical utility, …

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High resolution copy number inference in cancer using short-molecule nanopore sequencing

Timour Baslan, Sam Kovaka, Fritz J. Sedlazeck, Yanming Zhang et autres

ABSTRACT Genome copy number is an important source of genetic variation in health and disease. In cancer, clinically actionable Copy Number Alterations (CNAs) can be inferred from short-read sequencing data, enabling genomics-based precision oncology. Emerging Nanopore sequencing technologies offer the potential for …

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Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing

Sergey Aganezov, Sara Goodwin, Rachel M. Sherman, Fritz J. Sedlazeck et autres

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of the disease and its progression. We performed whole-genome sequencing of the SKBR3 breast cancer cell line and …

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Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing

Sergey Aganezov, Sara Goodwin, Rachel M. Sherman, Fritz J. Sedlazeck et autres

Improved identification of structural variants (SVs) in cancer can lead to more targeted and effective treatment options as well as advance our basic understanding of disease progression. We performed whole genome sequencing of the SKBR3 breast cancer cell-line and patient-derived tumor and …

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1D Genome Sequencing on the Oxford Nanopore MinION

Sara Goodwin, Robert Wappel, W. Richard McCombie

Today's short-read sequencing instruments can generate read lengths between 50 bp and 700 bp depending on the specific instrument. These high-throughput sequencing approaches have revolutionized genomic science, allowing hundreds of thousands of full genomes to be sequenced, and have become indispensable tools …

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Multi-parameter in vitro toxicity testing of crizotinib, sunitinib, erlotinib, and nilotinib in human cardiomyocytes

Kimberly R. Doherty, Robert Wappel, Dominique R. Talbert, Patricia B. Trusk et autres

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