Publications

Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing

Arindam Bhattacharjee,Tanya Sokolsky, Stacia K. Wyman, Martin G. Reese, Erik Puffenberger, Kevin Strauss, Holmes Morton, Richard B. Parad, Edwin W. Naylor

Genet Med. 2014 Sep 25. doi: 10.1038/gim.2014.117.  Pubmed Abstract


A 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


Using VAAST to identify disease-associated variants in next-generation sequencing data

Brett Kennedy, Zev Kronenberg, Hao Hu, Barry Moore, Steven Flygare, Martin G. Reese, Lynn B. Jorde, Mark Yandell, Chad Huff

Curr Protoc Hum Genet. 2014 Apr 24;81:6.14.1-6.14.25.  Pubmed Abstract


Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families

Marc V. Singleton, Stephen L. Guthery, Karl V. Voelkerding, Karin Chen, Brett Kennedy, Rebecca L. Margraf, Jacob Durtschi, Karen Eilbeck, Martin G. Reese, Lynn B. Jorde, Chad D. Huff, Mark Yandell

Am J Hum Genet. 2014 Apr 3;94(4):599-610. doi: 10.1016/j.ajhg.2014.03.010.  Pubmed Abstract


Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention

Tracy A. Manuck, W. Scott Watkins, Barry Moore, M. Sean Esplin, Michael W. Varner, G. Marc Jackson, Mark Yandell, Lynn Jorde

Am J Obstet Gynecol. 2014 Apr;210(4):321.e1-321.e21. doi: 10.1016/j.ajog.2014.01.013.  Pubmed Abstract


VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix

Hao Hu, Chad D. Huff, Barry Moore, Steven Flygare, Martin G. Reese, Mark Yandell

Genet Epidemiol. 2013 Sep;37(6):622-34. doi: 10.1002/gepi.21743.  Pubmed Abstract


Integrating precision medicine in the study and clinical treatment of a severely mentally ill person

Jason A. O’Rawe, Han Fang, Shawn Rynearson, Reid Robison, Edward S. Kiruluta, Gerald Higgins, Karen Eilbeck, Martin G. Reese, Gholson J. Lyon

PeerJ. 2013 Oct 3;1:e177. doi: 10.7717/peerj.177.  Pubmed Abstract


Clinical analysis of genome next-generation sequencing data using the Omicia platform

Emily M. Coonrod, Rebecca L. Margraf, Archie Russell, Karl V. Voelkerding, Martin G. Reese

Expert Rev Mol Diagn. 2013 Jul;13(6):529-40. doi: 10.1586/14737159.2013.811907.  Pubmed Abstract


Genomic diversity and evolution of the head crest in the rock pigeon

Michael D. Shapiro, Zev Kronenberg, Cai Li, Eric T. Domyan, Hailin Pan, Michael Campbell, Hao Tan, Chad D. Huff, Haofu Hu, Anna I. Vickrey, Sandra C. A. Nielsen, Sydney A. Stringham, Hao Hu, Eske Willerslev, M. Thomas P. Gilbert, Mark Yandell, Guojie Zhang, Jun Wang

Science. 2013 Mar 1;339(6123):1063-7. doi: 10.1126/science.1230422. Pubmed Abstract


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

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


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


A probabilistic disease-gene finder for personal genomes

Mark Yandell, Chad Huff, Hao Hu, Marc Singleton, Barry Moore, Jinchuan Xing, Lynn B. Jorde, Martin G. Reese

Genome Res. 2011 Sep;21(9):1529-42. doi: 10.1101/gr.123158.111.  Pubmed Abstract


Gene-based tests of association

Hailiang Huang, Pritam Chanda, Alvaro Alonso, Joel S. Bader, Dan E. Arking

PLoS Genet. 2011 Jul;7(7):e1002177. doi: 10.1371/journal.pgen.1002177.  Pubmed Abstract


Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency

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


Global analysis of disease-related DNA sequence variation in 10 healthy individuals: Implications for whole genome-based clinical diagnostics

Barry Moore, Hao Hu, Marc Singleton, Francisco M. De La Vega, Martin G. Reese, Mark Yandell

Genet Med. 2011 Mar;13(3):210-7. doi: 10.1097/GIM.0b013e31820ed321.  Pubmed Abstract


A standard variation file format for human genome sequences

Martin G. Reese, Barry Moore, Colin Batchelor, Fidel Salas, Fiona Cunningham, Gabor T. Marth, Lincoln Stein, Paul Flicek, Mark Yandell, Karen Eilbeck

Genome Biol. 2010;11(8):R88. doi: 10.1186/gb-2010-11-8-r88.  Pubmed Abstract


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

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


Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins

Mark Yandell, Barry Moore, Fidel Salas, Chris Mungall, Andrew MacBride, Charles White, Martin G. Reese

PLoS Comput Biol. 2008 Nov;4(11):e1000218. doi: 10.1371/journal.pcbi.1000218.  Pubmed Abstract


EGASP: the human ENCODE Genome Annotation Assessment Project

Roderic Guigó, Paul Flicek, Josep F. Abril1, Alexandre Reymond, Julien Lagarde, France Denoeud, Stylianos Antonarakis, Michael Ashburner, Vladimir B. Bajic, Ewan Birney, Robert Castelo, Eduardo Eyras, Catherine Ucla, Thomas R. Gingeras, Jennifer Harrow, Tim Hubbard, Suzanna E. Lewis, Martin G. Reese

Genome Biol. 2006;7 Suppl 1:S2.1-31.  Pubmed Abstract