Publications

Research

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)
Fabric synopsis:

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.
Pubmed Abstract
Download PDF

Genetic Disease

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 synopsis:

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
Pubmed Abstract
Download PDF

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."


Pubmed Abstract
Download PDF

Genetic Disease

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.
Pubmed Abstract
Download PDF

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.
Pubmed Abstract
Download PDF

Research

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation

Jeffrey M. Kidd, Simon Grave, Jake Byrnes, Andres Moreno-Estrada, Shaila Musharoff, Katarzyna Bryc, Jeremiah D. Degenhardt, Abra Brisbin, Vrunda Sheth, Rong Chen, Stephen F. McLaughlin, Heather E. Peckham, Larsson Omberg, Christina A. Bormann Chung, Sarah Stanley, Kevin Pearlstein, Elizabeth Levandowsky, Suehelay Acevedo-Acevedo, Adam Auton, Alon Keinan, Victor Acuña-Alonzo, Rodrigo Barquera-Lozano, Samuel Canizales-Quinteros, Celeste Eng, Esteban G. Burchard, Archie Russell, Andy Reynolds, Andrew G. Clark, Martin G. Reese, Stephen E. Lincoln, Atul J. Butte, Francisco M. De La Vega, Carlos D. Bustamante

Am J Hum Genet. 2012 Oct 5;91(4):660-71. doi: 10.1016/j.ajhg.2012.08.025.
Pubmed Abstract
Download PDF

Genetic Disease

Using VAAST to identify an X-linked disorder resulting in lethality in male infants

Alan F. Rope, Kai Wang, Rune Evjenth, Jinchuan Xing, Jennifer J. Johnston, Jeffrey J. Swensen, W. Evan Johnson, Barry Moore, Chad D. Huff, Lynne M. Bird, John C. Carey, John M. Opitz, Cathy A. Stevens, Tao Jiang, Christa Schank, Heidi Deborah Fain, Reid Robison, Brian Dalley, Steven Chin, Sarah T. South, Theodore J. Pysher, Lynn B. Jorde, Hakon Hakonarson, Johan R. Lillehaug, Leslie G. Biesecker, Mark Yandell, Thomas Arnesen, Gholson J. Lyon

Am J Hum Genet. 2011 Jul 15;89(1):28-43. doi: 10.1016/j.ajhg.2011.05.017.
Pubmed Abstract
Download PDF

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
Download PDF