Publications

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.

Genome Medicine; 16 March 2023
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Publications

Yan Ding, Mallory Owen, Jennie Le, Sergey Batalov, Kevin Chau, Yong Hyun Kwon, Lucita Van Der Kraan, Zaira Bezares-Orin, Zhanyang Zhu, Narayanan Veeraraghavan, Shareef Nahas, Matthew Bainbridge, Joe Gleeson, Rebecca J. Baer, Gretchen Bandoli, Christina Chambers & Stephen F. Kingsmore

Archived DBS appear to be a suitable sample type for WGS in population genomic studies.

npj Genomic Medicine; 14 February, 2023
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Publications

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 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
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Publications

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.

Publications

Abdulmoein Eid Al-Agha, Ihab Abdulhamed Ahmed, Esther Nuebel, Mika Moriwaki, Barry Moore, Katherine A Peacock, Tim Mosbruger, Deborah W Neklason, Lynn B Jorde, Mark Yandell, Corrine K Welt

"Genomic Analysis Data were analyzed using Opal 4.15 (Fabric Genomics, Inc., Oakland, CA) in a four-person VAAST cohort
analysis including the affected sisters (https://app.omicia.com/) …Clinical analysis of genome next-generation sequencing data using the Omicia platform."

"The Phenotype Driven Variant Ontological Re-ranking tool (Phevor)(26) was used to re-rank the prioritized genes using premature ovarian failure and POI as
Human Phenotype Ontology seed terms (27)."

"Intervention DNA was subjected to whole genome sequencing. Shared regions of homozygosity were identified using Truploidy and prioritized using the Variant Annotation, Analysis and Search Tool (VAAST) with control data from 387 healthy subjects …"

The Journal of Clinical Endocrinology & Metabolism, jc.2017-01966, Dec. 12, 2017
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Publications

Amber Hildreth, Kristen Wigby, Shimul Chowdhury, Shareef Nahas, Jaime Barea, Paulina Ordonez, Serge Batalov, David M Dimmock, RCIGM Investigators and Stephen F Kingsmore

Variants were annotated and analyzed in Opal Clinical (Fabric Genomics- formerly Omicia.)

Cold Spring Harbor Molecular Case Studies; May 2017
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Publications

Lauge Farnaes, Shareef A Nahas, Shimul Chowdhury, James Nelson, Serge Batalov, David Dimmock, Stephen F. Kingsmore, and RCIGM Investigators

Variants were annotated and analyzed in Opal Clinical (Fabric Genomics - formerly Omicia.) Clinical analysis of genome next-generation sequencing data used the Fabric Genomics- formerly Omicia platform.

Cold Spring Harbor Molecular Case Studies; May 2017
Pubmed Abstract
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