Internal Citation List

LePichon JB, Saunders CJ, Soden SE. The Future of Next Generation Sequencing in Neurology. JAMA Neurology. Published online July 16, 2015. doi:10.1001/jamaneurol.2015.1076
Thiffault I, Wolf N., Forget D., Guerrero K., Tran L., Choquet K., Lavallée-Adam M., Poitras C., Brais B., Yoon G., Sztriha L., Webster R., Timmann D., van de Warrenburg B., Seeger J., Zimmermann A., Máté A., Goizet C., Fung E., van der Knaap M., Fribourg S., Vanderver A., Simons C., Taft R., Yates J., Coulombe B., and Bernard G. (2015)Recessive mutations in POLR1C cause a leukodystrophy by impairing biogenesis of RNA polymerase III Nature Communications, MS ID#NCOMMS-14-18725B in press
Gutierrez M, Thiffault I., Guerrero k., Martos-Moreno G.A/, Tran L.T., Benko W., van der Knaap M.S., van Spaendonk R., Wolf N., Bernard G. (2015) Large exonic deletions in POLR3B gene cause POLR3-related leukodystrophy, Orphanet Journal of Rare Diseases. 2015 Jun 5;10(1):69. PMID: 26045207
Thiffault I, Saunders C, Jenkins J, Raje N, Canty K, Sharma M, Grote L, Welsh HI, Farrow E, Twist G, Miller N, Zwick D, Zellmer L, Kingsmore SF,, Safina NP. (2015) A patient with polymerase E1 deficiency (POLE1): clinical features and overlap with DNA breakage/instability syndromes. BMC Med Genet. 2015 May 7;16(1):31. doi: 10.1186/s12881-015-0177-y. PMID: 25948378
Saunders C, Smith L, Wibrand F, Ravn K, Bross P, Thiffault I, Christensen M, Atherton A, Farrow E, Miller N, Kingsmore SF,, Ostergaard E (2015) CLPB variants associated with autosomal-recessive mitochondrial disorder with cataract, neutropenia, epilepsy and methylglutaconic aciduria. Am J Hum Genet. 2015 Jan 15. pii: S0002-9297(14)00526-6. doi: 10.1016/j.ajhg.2014.12.020. [Epub ahead of print]. PMID: 25597511.
Sasarman F, Thiffault I, Weraarpachai W, Salomon S, Maftei C, Gauthier J, Ellazam B, Webb N, Antonicka H, Janer A, Brunel-Guitton C, Elpeleg O, Mitchell G, Shoubridge EA. (2015) The 3' addition of CCA to mitochondrial tRNASer(AGY) is specifically impaired in patients with mutations in the tRNA nucleotidyl transferase TRNT1. Hum Mol Genet. 2015 May 15;24(10):2841-7.
Willig LK, Petrikin JE, Smith LD, Saunders CJ, Thiffault I, Miller NA, Soden SE, Cakici JA, Herd SM, Twist G, Noll A, Creed M, Alba PM, Carpenter SL, Clements MA, Fischer RT, Hays JA, Kilbride H, McDonough RJ, Rosterman JL, Tsai SL, Zellmer L, Farrow EG, Kingsmore SF,. (2015) Whole-genome sequencing for identification of Mendelian disorders in critically ill infants: a retrospective analysis of diagnostic and clinical findings. Lancet Respir Med 3(5):377-87. doi: 10.1016/S2213-2600(15)00139-3. Epub 2015 Apr 27. PMID: 25937001
Saunders CJ, Moon SH, Liu X, Thiffault I, Coffman K, LePichon JB, Taboada E, Smith LD, Farrow EG, Miller N, Gibson M, Patterson M, Kingsmore SF,, Gross RW.(2015) Loss of function variants in human PNPLA8 encoding calcium-independent phospholipase A2 γ recapitulate the mitochondriopathy of the homologous null mouse. Hum Mutat. 2015 Mar;36(3):301-6. doi: 10.1002/humu.22743. PMID: 25512002
Milner JD, Vogel TP, Forbes L, Ma CA, Stray-Pedersen A, Niemela JE, Lyons JJ, Engelhardt KR, Zhang Y, Topcagic N, Roberson ED, Matthews H, Verbsky JW, Dasu T, Vargas-Hernandez A, Varghese N, McClain KL, Karam LB, Nahmod K, Makedonas G, Mace EM, Sorte HS, Perminow G, Rao VK, O'Connell MP, Price S, Su HC, Butrick M, McElwee J, Hughes JD, Willet J, Swan D, Xu Y, Santibanez-Koref M, Slowik V, Dinwiddie DL, Ciaccio CE, Saunders CJ, Septer S, Kingsmore SF,, White AJ, Cant AJ, Hambleton S, Cooper MA. (2015) Early-onset lymphoproliferation and autoimmunity caused by germline STAT3 gain-of-function mutations. Blood. 2015 Jan 22;125(4):591-9. doi: 10.1182/blood-2014-09-602763. Epub 2014 Oct 30. PMID: 25359994
Tsalik EL, Willig LK, Rice BJ, van Velkinburgh JC, Mohney RP, McDunn JE, Dinwiddie DL, Miller NA, Mayer ES, Glickman SW, Jaehne AK, Glew RH, Sopori ML, Otero RM, Harrod KS, Cairns CB, Fowler VG, Rivers EP, Woods CW, Kingsmore SF,, Langley RJ. Renal systems biology of patients with systemic inflammatory response syndrome. Kidney Int. 2015 May 20. doi: 10.1038/ki.2015.150. [Epub ahead of print] PubMed PMID: 25993322.
Saunders CJ, Moon SH, Liu X, Thiffault I, Coffman K, LePichon JB, Taboada E, Smith LD, Farrow EG, Miller N, Gibson M, Patterson M, Kingsmore SF,, Gross RW (2014) Loss of function variants in human PNPLA8 encoding calcium-dependent phospholipase A2 γ recapitulate the mitochondriopathy of the homologous null mouse. Hum Mutat 2014 Dec 16, doi: 10.1002/humu.22743. [Epub ahead of print] PMID: 25512002
Smith LD, Kingsmore SF, (2014) N-of-1 genomic medicine for the rare pediatric genetic diseases Expert Opinion on Orphan Drugs : 1–12. Posted online on 5 Nov 2014. (doi:10.1517/21678707.2014.979153).
Sarah E. Soden, Carol J. Saunders, Laurel K. Willig, Emily G. Farrow, Laurie D. Smith, Josh E. Petrikin, Jean-Baptiste LePichon, Neil A. Miller, Isabelle Thiffault, Darrell L. Dinwiddie, Greyson Twist, Aaron Noll, Bryce A. Heese, Lee Zellmer, Andrea M. Atherton, Ahmed T. Abdelmoity, Nicole Safina, Sarah S. Nyp, Britton Zuccarelli, Ingrid A. Larson, Ann Modrcin, Suzanne Herd, Mitchell Creed, Zhaohui Ye, Xuan Yuan, Robert A. Brodsky, and Stephen F. Kingsmore. Effectiveness of exome and genome sequencing guided by acuity of illness for diagnosis of neurodevelopmental disorders. Sci Transl Med 3 December 2014 6:265ra168. DOI:10.1126/scitranslmed.3010076
Tsalik EL, Langley RJ, Dinwiddie DL, Miller NA, Yoo B, van Velkinburgh JC, Smith LD, Thiffault I, Jaehne AK, Valente AM, Henao R, Yuan X, Glickman SW, Rice BJ, McClain MT, Carin K, Corey GR, Ginsburg GS, Cairns CB, Otero RM, Fowler VG, Rivers EP, Woods CW, Kingsmore SF, (2014) An integrated transcriptome and expressed variant analysis of sepsis survival and death. Genome Med. 2014 Nov 26;6(11):111. doi: 10.1186/s13073-014-0111-5. eCollection 2014, PMID:25538794
Raje N, Soden SE, Swanson D, Ciaccio CE, Kingsmore SF, Dinwiddie DL. Utility of next generation sequencing in clinical primary immunodeficiencies. Curr Allergy Asthma Rep. 2014 Oct;14(10):468. doi: 10.1007/s11882-014-0468-y.
Leeder JS, Brown JT, Soden SE. Individualizing the use of medications in children: making Goldilocks happy. Clin Pharmacol Ther. 2014 Sep;96(3):304-6. doi: 10.1038/clpt.2014.130. Epub 2014 Jun 13.
Kingsmore SF, Lantos JD, Dinwiddie DL, Miller NA, Soden SE, Farrow EG, Saunders CJ. Next-generation Community Genetics for Low- and Middle-income Countries. Genome Med 4(3):25 (2012)
Dinwiddie DL, Soden SE, Saunders CJ, Miller NA, Farrow EG, Smith LD, Kingsmore SF (2013) De novo frame shift mutation in ASXL3 in a patient with global developmental delay, microcephaly and craniofacial anomalies. BMC Medical Genomics Sep 17;6(1):32
Dinwiddie DL, Bracken JM, Bass JA, Christenson K, Soden SE, Saunders CJ, Miller NA, Singh V, Zwick DL, Roberts CC, Dalal J, Kingsmore SF. (2013) Molecular diagnosis of infantile onset inflammatory bowel disease by exome sequencing. Genomics. 2013 Nov-Dec;102(5-6):442-7. doi: 10.1016/j.ygeno.2013.08.008. Epub 2013 Aug 31. PMID: 24001973
Saunders CJ, Dinwiddie DL, Atherton AM, Miller NA, Soden SE, Farrow EG, Abdelmoity AT, Kingsmore SF (2013) Exome sequencing reveals de novo germline mutation of the mammalian target of rapamycin (MTOR) in a patient with megalencephaly and intractable seizures. J Genomes and Exomes 2: 63-72.
Langley RJ, Tsalik EL, van Velkinburgh JC, Glickman SW, Rice BJ, Wang C, Chen B, Carin L, Suarez A, Mohney RP, Freeman DH, Wang M, You J, Wulff J, Thompson JW, Moseley MA, Reisinger S, Edmonds BT, Grinnell B, Nelson DR, Dinwiddie DL, Miller NA, Saunders CJ, Soden SE, Rogers AJ, Gazourian L, Fredenburgh LE, Massaro AF, Baron RM, Choi AM, Corey GR, Ginsburg GS, Cairns CB, Otero RM, Fowler VG Jr, Rivers EP, Woods CW, Kingsmore SF. (2013) An integrated clinico-metabolomic model improves prediction of death in sepsis. Sci Transl Med. 2013 Jul 24;5(195):195ra95. doi: 10.1126/scitranslmed.3005893. PMID: 23884467
Dinwiddie DL, Saunders CJ, Farrow EG, Soden SE, Miller NA, Kingsmore SF. Structured Genome-cale Variant and Clinical Data Reporting for Meta-Analysis in an era of Genomic Medicine. J Genome Exome. 2013:2, 31-42.

External Data Sources

HPO Köhler S, Doelken SC, Mungall CJ, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res. 2014;42(Database issue):D966-74.
EVS Exome Variant Server, NHLBI GO Exome Sequencing Project (ESP), Seattle, WA (URL: http://evs.gs.washington.edu/EVS/) [18 (Aug, 2015) accessed].
ENSEMBL - Release 75_37 Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah Hunt, Nathan Johnson, Thomas Juettemann, Andreas K. Kähäri, Stephen Keenan, Eugene Kulesha, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet S. Riat, Magali Ruffier, Daniel Sheppard, Kieron Taylor, Anja Thormann, Stephen J. Trevanion, Alessandro Vullo, Steven P. Wilder, Mark Wilson, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Jennifer Harrow, Javier Herrero, Tim J.P. Hubbard, Rhoda Kinsella, Matthieu Muffato, Anne Parker, Giulietta Spudich, Andy Yates, Daniel R. Zerbino, and Stephen M.J. Searle Ensembl 2014. Nucleic Acids Res. (1 January 2014) 42 (D1): D749-D755 doi: 10.1093/nar/gkt1196
HGNC HGNC Database, HUGO Gene Nomenclature Committee (HGNC), EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK www.genenames.org. accessed:8/14/2015
OMIM Online Mendelian Inheritance in Man, OMIM®. McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD), {accessed:10/13/2015}.
ExAC Exome Aggregation Consortium (ExAC), Cambridge, MA (URL: http://exac.broadinstitute.org) [14 (Aug, 2015) accessed].
The authors would like to thank the Exome Aggregation Consortium and the groups that provided exome variant data for comparison. A full list of contributing groups can be found at http://exac.broadinstitute.org/about.
dbSNP Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11.
Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine. (dbSNP Build ID: {144}). Available from: http://www.ncbi.nlm.nih.gov/SNP/
RefSeq The NCBI handbook [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2002 Oct. Available from http://www.ncbi.nlm.nih.gov/books/NBK21101
The NCBI handbook [Internet]. Bethesda (MD): National Library of Medicine (US), National Center for Biotechnology Information; 2002 Oct. Chapter 18, The Reference Sequence (RefSeq) Project. Available from http://www.ncbi.nlm.nih.gov/books/NBK21091
BioSystems Geer LY, Marchler-Bauer A, Geer RC, Han L, He J, He S, Liu C, Shi W, Bryant SH. The NCBI BioSystems database. Nucleic Acids Res. 2010 Jan; 38(Database issue):D492-6. (Epub 2009 Oct 23) [PubMed PMID: 19854944] [Full Text] [PDF]
Gene Maglott D, et al. Gene: a gene-centered information resource at NCBI. Nucleic Acids Res. 2014. pi:gku1055.Maglott D, et al. Gene, The NCBI Handbook, 2nd Ed. NCBI, 2013. www.ncbi.nlm.nih.gov/books/NBK169435/
ClinVar Melissa Landrum, PhD, Jennifer Lee, PhD, George Riley, PhD, Wonhee Jang, PhD, Wendy Rubinstein, MD, PhD, Deanna Church, PhD, and Donna Maglott, PhD. ClinVar. The NCBI Handbook, 2nd Ed. http://www.ncbi.nlm.nih.gov/books/NBK174587/
COSMIC Simon A. Forbes*, David Beare, Prasad Gunasekaran, Kenric Leung, Nidhi Bindal, Harry Boutselakis, Minjie Ding, Sally Bamford, Charlotte Cole, Sari Ward, Chai Yin Kok, Mingming Jia, Tisham De, Jon W. Teague, Michael R. Stratton, Ultan McDermott and Peter J. Campbell COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. (28 January 2015) 43 (D1): D805-D811. doi: 10.1093/nar/gku107