Search Results - "Klee, Eric W."

Comment on Australian public perspectives on genomic data governance by Lynch et al. in the EJHG by Houwink, Elisa J F, Klee, Eric W

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Bi-allelic Alterations in AEBP1 Lead to Defective Collagen Assembly and Connective Tissue Structure Resulting in a Variant of Ehlers-Danlos Syndrome by Blackburn, Patrick R., Xu, Zhi, Tumelty, Kathleen E., Zhao, Rose W., Monis, William J., Harris, Kimberly G., Gass, Jennifer M., Cousin, Margot A., Boczek, Nicole J., Mitkov, Mario V., Cappel, Mark A., Francomano, Clair A., Parisi, Joseph E., Klee, Eric W., Faqeih, Eissa, Alkuraya, Fowzan S., Layne, Matthew D., McDonnell, Nazli B., Atwal, Paldeep S.

“…AEBP1 encodes the aortic carboxypeptidase-like protein (ACLP) that associates with collagens in the extracellular matrix (ECM) and has several roles in…”
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LeafCutterMD: an algorithm for outlier splicing detection in rare diseases by Jenkinson, Garrett, Li, Yang I, Basu, Shubham, Cousin, Margot A, Oliver, Gavin R, Klee, Eric W

“…Abstract Motivation Next-generation sequencing is rapidly improving diagnostic rates in rare Mendelian diseases, but even with whole genome or whole exome…”
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HELLO: improved neural network architectures and methodologies for small variant calling by Ramachandran, Anand, Lumetta, Steven S, Klee, Eric W, Chen, Deming

“…Modern Next Generation- and Third Generation- Sequencing methods such as Illumina and PacBio Circular Consensus Sequencing platforms provide accurate…”
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Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma by Borad, Mitesh J, Champion, Mia D, Egan, Jan B, Liang, Winnie S, Fonseca, Rafael, Bryce, Alan H, McCullough, Ann E, Barrett, Michael T, Hunt, Katherine, Patel, Maitray D, Young, Scott W, Collins, Joseph M, Silva, Alvin C, Condjella, Rachel M, Block, Matthew, McWilliams, Robert R, Lazaridis, Konstantinos N, Klee, Eric W, Bible, Keith C, Harris, Pamela, Oliver, Gavin R, Bhavsar, Jaysheel D, Nair, Asha A, Middha, Sumit, Asmann, Yan, Kocher, Jean-Pierre, Schahl, Kimberly, Kipp, Benjamin R, Barr Fritcher, Emily G, Baker, Angela, Aldrich, Jessica, Kurdoglu, Ahmet, Izatt, Tyler, Christoforides, Alexis, Cherni, Irene, Nasser, Sara, Reiman, Rebecca, Phillips, Lori, McDonald, Jackie, Adkins, Jonathan, Mastrian, Stephen D, Placek, Pamela, Watanabe, Aprill T, Lobello, Janine, Han, Haiyong, Von Hoff, Daniel, Craig, David W, Stewart, A Keith, Carpten, John D

“…Advanced cholangiocarcinoma continues to harbor a difficult prognosis and therapeutic options have been limited. During the course of a clinical trial of whole…”
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Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy by Kendig, Katherine I, Baheti, Saurabh, Bockol, Matthew A, Drucker, Travis M, Hart, Steven N, Heldenbrand, Jacob R, Hernaez, Mikel, Hudson, Matthew E, Kalmbach, Michael T, Klee, Eric W, Mattson, Nathan R, Ross, Christian A, Taschuk, Morgan, Wieben, Eric D, Wiepert, Mathieu, Wildman, Derek E, Mainzer, Liudmila S

“…As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important. The…”
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OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks by Tang, Xiaojia, Prodduturi, Naresh, Thompson, Kevin J, Weinshilboum, Richard, O'Sullivan, Ciara C, Boughey, Judy C, Tizhoosh, Hamid R, Klee, Eric W, Wang, Liewei, Goetz, Matthew P, Suman, Vera, Kalari, Krishna R

“…The OmicsFootPrint framework addresses the need for advanced multi-omics data analysis methodologies by transforming data into intuitive two-dimensional…”
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Confirming Variants in Next-Generation Sequencing Panel Testing by Sanger Sequencing by Baudhuin, Linnea M, Lagerstedt, Susan A, Klee, Eric W, Fadra, Numrah, Oglesbee, Devin, Ferber, Matthew J

“…Current clinical laboratory practice guidelines for next-generation sequencing (NGS) do not provide definitive guidance on confirming NGS variants. Sanger…”
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Global Methylation Profiling for Risk Prediction of Prostate Cancer by MAHAPATRA, Saswati, KLEE, Eric W, YOUNG, Charles Y. F, ZHIFU SUN, JIMENEZ, Rafael E, KLEE, George G, TINDALL, Donald J, VANAJA DONKENA, Krishna

“…The aim of this study was to investigate the promoter hypermethylation as diagnostic markers to detect malignant prostate cells and as prognostic markers to…”
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Computational Detection of Known Pathogenic Gene Fusions in a Normal Tissue Database and Implications for Genetic Disease Research by Oliver, Gavin Robert, Jenkinson, Garrett, Klee, Eric W

“…Several recent studies have demonstrated the utility of RNA-Seq in the diagnosis of rare inherited disease. Diagnostic rates 35% higher than those previously…”
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De novo DDX3X missense variants in males appear viable and contribute to syndromic intellectual disability by Nicola, Pantelis, Blackburn, Patrick R., Rasmussen, Kristen J., Bertsch, Nicole L., Klee, Eric W., Hasadsri, Linda, Pichurin, Pavel N., Rankin, Julia, Raymond, F. Lucy, Clayton‐Smith, Jill

“…DDX3X (Xp11.4) encodes a DEAD‐box RNA helicase that escapes X chromosome inactivation. Pathogenic variants in DDX3X have been shown to cause X‐linked…”
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Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease by Fadra, Numrah, Schultz-Rogers, Laura E, Chanana, Pritha, Cousin, Margot A, Macke, Erica L, Ferrer, Alejandro, Pinto E Vairo, Filippo, Olson, Rory J, Oliver, Gavin R, Mulvihill, Lindsay A, Jenkinson, Garrett, Klee, Eric W

“…X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of…”
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COVID-19 Mortality Prediction From Deep Learning in a Large Multistate Electronic Health Record and Laboratory Information System Data Set: Algorithm Development and Validation by Sankaranarayanan, Saranya, Balan, Jagadheshwar, Walsh, Jesse R, Wu, Yanhong, Minnich, Sara, Piazza, Amy, Osborne, Collin, Oliver, Gavin R, Lesko, Jessica, Bates, Kathy L, Khezeli, Kia, Block, Darci R, DiGuardo, Margaret, Kreuter, Justin, O’Horo, John C, Kalantari, John, Klee, Eric W, Salama, Mohamed E, Kipp, Benjamin, Morice, William G, Jenkinson, Garrett

“…Background COVID-19 is caused by the SARS-CoV-2 virus and has strikingly heterogeneous clinical manifestations, with most individuals contracting mild disease…”
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Recommendations for performance optimizations when using GATK3.8 and GATK4 by Heldenbrand, Jacob R, Baheti, Saurabh, Bockol, Matthew A, Drucker, Travis M, Hart, Steven N, Hudson, Matthew E, Iyer, Ravishankar K, Kalmbach, Michael T, Kendig, Katherine I, Klee, Eric W, Mattson, Nathan R, Wieben, Eric D, Wiepert, Mathieu, Wildman, Derek E, Mainzer, Liudmila S

“…Use of the Genome Analysis Toolkit (GATK) continues to be the standard practice in genomic variant calling in both research and the clinic. Recently the…”
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Editorial: Clinical Genome Sequencing: Bioinformatics Challenges and Key Considerations by Tian, Shulan, Tu, Zheng Jin, Yan, Huihuang, Klee, Eric W

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A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease by Oliver, Gavin R, Tang, Xiaojia, Schultz-Rogers, Laura E, Vidal-Folch, Noemi, Jenkinson, W Garrett, Schwab, Tanya L, Gaonkar, Krutika, Cousin, Margot A, Nair, Asha, Basu, Shubham, Chanana, Pritha, Oglesbee, Devin, Klee, Eric W

“…RNA sequencing has been proposed as a means of increasing diagnostic rates in studies of undiagnosed rare inherited disease. Recent studies have reported…”
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Next Generation Sequencing of Sporadic Vestibular Schwannoma: Necessity of Biallelic NF2 Inactivation and Implications of Accessory Non-NF2 Variants by Carlson, Matthew L, Smadbeck, James B, Link, Michael J, Klee, Eric W, Vasmatzis, George, Schimmenti, Lisa A

“…OBJECTIVES:1) Describe the genetic alterations discovered in a series of sporadic vestibular schwannomas (VS). 2) Identify if more clinically aggressive…”
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3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer by Asmann, Yan W, Klee, Eric W, Thompson, E Aubrey, Perez, Edith A, Middha, Sumit, Oberg, Ann L, Therneau, Terry M, Smith, David I, Poland, Gregory A, Wieben, Eric D, Kocher, Jean-Pierre A

“…Massive parallel sequencing has the potential to replace microarrays as the method for transcriptome profiling. Currently there are two protocols: full-length…”
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Pathogenic mutations in the chromokinesin KIF22 disrupt anaphase chromosome segregation by Thompson, Alex F, Blackburn, Patrick R, Arons, Noah S, Stevens, Sarah N, Babovic-Vuksanovic, Dusica, Lian, Jane B, Klee, Eric W, Stumpff, Jason

“…The chromokinesin KIF22 generates forces that contribute to mitotic chromosome congression and alignment. Mutations in the α2 helix of the motor domain of…”
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Design considerations for workflow management systems use in production genomics research and the clinic by Ahmed, Azza E., Allen, Joshua M., Bhat, Tajesvi, Burra, Prakruthi, Fliege, Christina E., Hart, Steven N., Heldenbrand, Jacob R., Hudson, Matthew E., Istanto, Dave Deandre, Kalmbach, Michael T., Kapraun, Gregory D., Kendig, Katherine I., Kendzior, Matthew Charles, Klee, Eric W., Mattson, Nate, Ross, Christian A., Sharif, Sami M., Venkatakrishnan, Ramshankar, Fadlelmola, Faisal M., Mainzer, Liudmila S.

“…The changing landscape of genomics research and clinical practice has created a need for computational pipelines capable of efficiently orchestrating complex…”
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