Technology

Research

Genome Sequencing is Critical for Forecasting Outcomes following Congenital Cardiac Surgery

W. Scott Watkins, E. Javier Hernandez, Thomas A. Miller, Nathan R. Blue, Raquel Zimmerman, Eric R. Griffiths, Erwin Frise, Daniel Bernstein, Marko T. Boskovski, Martina Brueckner, Wendy K. Chung, J. William Gaynor, Bruce D. Gelb, Elizabeth Goldmuntz, Peter J. Gruber, Jane W. Newburger, Amy E. Roberts, Sarah U. Morton, John E. Mayer Jr, Christine E. Seidman, Jonathan G. Seidman, Yufeng Shen, Michael Wagner, H. Joseph Yost, Mark Yandell, Martin Tristani-Firouzi
Fabric synopsis:

Fabric GEM is used to explore the predictive value of genome sequencing in forecasting clinical outcomes following surgery for congenital heart defects (CHD).

medRxiv
Pubmed Abstract

Technology

Automated prioritization of sick newborns for whole genome sequencing using clinical natural language processing and machine learning

Bennet Peterson, Edgar Javier Hernandez, Charlotte Hobbs, Sabrina Malone Jenkins, Barry Moore, Edwin Rosales, Samuel Zoucha, Erica Sanford, Matthew N. Bainbridge, Erwin Frise, Albert Oriol, Luca Brunelli, Stephen F. Kingsmore & Mark Yandell Rapidly and efficiently identifying critically ill infants for whole genome sequencing (WGS) is a costly and challenging task currently performed by scarce, highly trained experts and is a major bottleneck for application of WGS in the NICU. There is a dire need for automated means to prioritize patients for WGS.
Fabric synopsis:

Using Artificial Intelligence (AI) to address the costly and human intensive bottleneck of identifying and prioritizing critically ill infants for whole genome sequencing (WGS) in the NICU.

Genome Medicine; 16 March 2023
Pubmed Abstract
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Technology

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases

Francisco M. De La Vega , Shimul Chowdhury, Barry Moore, Erwin Frise, Jeanette McCarthy, Edgar Javier Hernandez, Terence Wong, Kiely James, Lucia Guidugli, Pankaj B. Agrawal, Casie A. Genetti, Catherine A. Brownstein, Alan H. Beggs, Britt-Sabina Löscher, Andre Franke, Braden Boone, Shawn E. Levy, Katrin Õunap, Sander Pajusalu, Matt Huentelman, Keri Ramsey, Marcus Naymik, Vinodh Narayanan, Narayanan Veeraraghavan, Paul Billings, Martin G. Reese, Mark Yandell and Stephen F. Kingsmore
Fabric synopsis:

Fabric GEM ranks >90% of causal genes in top 2 candidates and breaks ground by incorporating SVs and phenotypes in automated AI-driven analysis.

Genome Medicine; October 14, 2021
Pubmed Abstract
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Technology

The VAAST Variant Prioritizer (VVP): ultrafast, easy to use whole genome variant prioritization tool

Steven Flygare, Edgar Javier Hernandez, Lon Phan, Barry Moore, Man Li, Anthony Fejes, Hao Hu, Karen Eilbeck, Chad Huff, Lynn Jorde, Martin G. Reese and Mark Yandell Read how VVP outperforms other methods to score genetic variants with respect to their disease-causing potential, whether they are coding or non-coding, leveraging population-scale databases. Coupled with Fabric Genomics platform, VVP facilitates fast and accurate genetic disease diagnostics sequencing data.

BMC Bioinformatics

Technology

Non-Profit Patient Research Services from Rare Genomics Institute Enable Insight into Rare Diseases through Genome Sequencing and Cloud Collaboration

Brady Tucker, Elizabeth Aguilar and Daniel Gurnon
Fabric synopsis:

See how the Rare Genomics Institute (RGI) is using Fabric Genomics' (formerly Omicia) Opal interpretation platform for exome analysis of 3 patients.  "Data analysis is performed with Omicia Opal, a web-based genome interpretation and reporting software platform integrating the machine learning algorithms VAAST and Phevor. We summarize our use of the Omicia Opal platform in three cases that represent the range of outcomes that can result from exome analysis; in one case we identified a likely pathogenic variant in the RDH12, associated with Leber’s congenital amourosis; in a second case we identified a possibly pathogenic variant in IFT140, associated with Jeune syndrome; and in a third case we identified variants of uncertain significance in genes associated with Sotos and Weaver syndrome. Opal integrates VAAST and Phevor algorithms."


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Technology

Assuring the quality of next-generation sequencing in clinical laboratory practice

Fabric synopsis:

Amy S. Gargis, Lisa Kalman, Meredith W Berry, David P. Bick, David P. Dimmock, Tina Hambuch, Fei Lu, Elaine Lyon, Karl V. Voelkerding, Barbara A. Zehnbauer, Richa Agarwala, Sarah F. Bennett, Bin Chen, Ephrem L. H. Chin, John G. Compton, Soma Das, Daniel H. Farkas, Matthew J. Ferber, Birgit H. Funke, Manohar R. Furtado, Lilia M. Ganova-Raeva, Ute Geigenmüller, Sandra J. Gunselman, Madhuri R. Hegde, Philip L. F. Johnson, Andrew Kasarskis, Shashikant Kulkarni, Thomas Lenk, C. S. Jonathan Liu, Megan Manion, Teri A. Manolio, Elaine R. Mardis, Jason D. Merker, Mangalathu S. Rajeevan, Martin G. Reese, Heidi L. Rehm, Birgitte B. Simen, Joanne M. Yeakley, Justin M. Zook, Ira M. Lubin

Nat Biotechnol. 2012 Nov;30(11):1033-6. doi: 10.1038/nbt.2403.
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Technology

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing

Kevin Judd McKernan, Heather E. Peckham, Gina L. Costa, Stephen F. McLaughlin, Yutao Fu, Eric F. Tsung, Christopher R. Clouser, Cisyla Duncan, Jeffrey K. Ichikawa, Clarence C. Lee, Zheng Zhang, Swati S. Ranade, Eileen T. Dimalanta, Fiona C. Hyland, Tanya D. Sokolsky, Lei Zhang, Andrew Sheridan, Haoning Fu, Cynthia L. Hendrickson, Bin Li, Lev Kotler, Jeremy R. Stuart, Joel A. Malek, Jonathan M. Manning, Alena A. Antipova, Damon S. Perez, Michael P. Moore, Kathleen C. Hayashibara, Michael R. Lyons, Robert E. Beaudoin, Brittany E. Coleman, Michael W. Laptewicz, Adam E. Sannicandro, Michael D. Rhodes, Rajesh K. Gottimukkala, Shan Yang, Vineet Bafna, Ali Bashir, Andrew MacBride, Can Alkan, Jeffrey M. Kidd, Evan E. Eichler, Martin G. Reese, Francisco M. De La Vega, Alan P. Blanchard

Genome Res. 2009 Sep;19(9):1527-41. doi: 10.1101/gr.091868.109.
Pubmed Abstract
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