Publications

Publications

Rapid whole genome sequencing identifies a novel homozygous NPC1 variant associated with Niemann-Pick Type C1 Disease in a 7 week old male with cholestasis

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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Rapid whole genome sequencing identifies a novel GABRA1 variant associated with West syndrome

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
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POLR2C Mutations Are Associated With Primary Ovarian Insufficiency in Women

Mika Moriwaki, Barry Moore, Timothy Mosbruger, Deborah W. Neklason, Mark Yandell, Lynn B. Jorde, Corrine K. Welt

Data was analyzed using Omicia Opal (now known as Fabric Genomics) in a three-person cohort analysis including the proband, mother, and daughter. The software prioritizes variants using the Variant Annotation, Analysis and Search Tool (VAAST)...Mutations were prioritized by the Fabric Genomics' score (aka Omicia score) which ranks variants according to expected protein effects using SIFT (http://sift.jcvi.org/), Mutation Taster (http://www.mutationtaster.org/), PolyPhen (http://genetics.bwh.harvard.edu/pph2), and phyloP [17–19]. In both analyses, the Phenotype Driven Variant Ontological Re-ranking tool (Phevor) feature was used to further prioritize genes for analysis using premature ovarian failure and POI as filters [8, 20].

J. Endocr. Soc. (2017) 1 (3): 162-173, Feb. 2017
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Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth: a case–control study

TA Manuck, WS Watkins, MS Esplin, J Biggio, R Bukowski, S Parry, H Zhan, H Huang, W Andrews, G Saade, Y Sadovsky, UM Reddy, J Ilekis, M Yandell, MW Varner, LB Jorde, and for the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Genomics and Proteomics Network for Preterm Birth Research (GPN-PBR)

Read how Fabric Genomics' (formerly Omicia) VAAST algorithm was used to determine genetic differences in women with recurrent preterm birth despite 17-P treatment.  

BJOG 2017; DOI: 10.1111/1471-0528.14485.
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Targeted next generation sequencing of a panel of autism-related genes identifies an EHMT1 mutation in a Kleefstra syndrome patient with autism and normal intellectual performance

István Bocka, Krisztina Némethb, Klára Pentelényic, Péter Baliczac, Anna Balázsb, Mária Judit Molnárc, Viktor Románd, József Nagye, György Lévayf, Julianna Koboláka, András Dinnyésa

Fabric Genomics' (formerly Omicia) Opal clinical genetic interpretation software was used to identify an EHMT1 mutation in autism.  "Phenotypic effects of the final candidate variants were evaluated using the ACMG guidelines & Omicia Opal."  Opal has integrated the most up-to-date ACMG classification guidelines in the software.

Gene, Volume 595, Issue 2, 31 December 2016, Pages 131–141
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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

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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Unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data

Hao Hu, Jared C. Roach, Hilary Coon, Stephen L. Guthery, Karl V. Voelkerding, Rebecca L. Margraf, Jacob D. Durtschi, Sean V. Tavtigian, Shankaracharya, Wilfred Wu, Paul Scheet, Shuoguo Wang, Jinchuan Xing, Gustavo Glusman, Robert Hubley, Hong Li, Vidu Garg, Barry Moore, Leroy Hood, David J Galas, Deepak Srivastava, Martin G Reese, Lynn B Jorde, Mark Yandell, Chad D. Huff

Nat Biotechnol. 2014 May 18. doi: 10.1038/nbt.2895.
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