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Genome Research

Baudhuin LM, Funke BH, Bean LH, Deignan JL, Hofherr S, Miller DT, Nagan N, Santani A, Saunders C., 2016. Classifying Germline Sequence Variants in the Era of Next-Generation Sequencing. Clin Chem Feb 9.

Flex E, Niceta M, Cecchetti S, Thiffault I, Au MG, Capuano A, Piermarini E Ivanova AA, Francis JW, Chillemi G, Chandramouli B, Carpentieri G, Haaxma CA,Ciolfi A, Pizzi S, Douglas GV, Levine K, Sferra A, Dentici ML, Pfundt RR, Le Pichon JB, Farrow E, Baas F, Piemonte F, Dallapiccola B, Graham JM Jr, Saunders CJ, Bertini E, Kahn RA, Koolen DA, Tartaglia M. Biallelic Mutations in TBCD, Encoding the Tubulin Folding Cofactor D, Perturb Microtubule Dynamics and Cause Early-Onset Encephalopathy. Am J Hum Genet. 2016 Oct 6;99(4):962-973. doi:10.1016/j.ajhg.2016.08.003. PubMed PMID: 27666370; PubMed Central PMCID:PMC5065658.

Gallo V, Dotta L, Giardino G, Cirillo E, Lougaris V, D'Assante R, Prandini A, Consolini R, Farrow EG, Thiffault I, Saunders CJ, Leonardi A, Plebani A, BadolatoR, Pignata C. Diagnostics of Primary Immunodeficiencies through Next-Generation Sequencing. Front Immunol. 2016 Nov 7;7:466. PubMed PMID: 27872624

Giardino G, Gallo V, Somma D, Farrow EG, Thiffault I, D'Assante R, Donofrio V, Paciolla M, Ursini MV, Leonardi A, Saunders CJ, Pignata C. 2016. Targeted next-generation sequencing revealed MYD88 deficiency in a child with chronic yersiniosis and granulomatous lymphadenitis. J Allergy Clin Immunol. May;137(5):1591-1595.

Jay AM, Conway RL, Thiffault I, Saunders C, Farrow E, Adams J, Toriello HV.Neonatal progeroid syndrome associated with biallelic truncating variants in POLR3A. Am J Med Genet A. 2016 Dec;170(12):3343-3346. doi: 10.1002/ajmg.a.37960. PubMed PMID: 27612211.

Job F, Mizumoto S, Smith L, Couser N, Brazil A, Saal H, Patterson M, GibsonMI, Soden S, Miller N, Thiffault I, Saunders C, Yamada S, Hoffmann K, Sugahara K,Farrow E. Functional validation of novel compound heterozygous variants in B3GAT3resulting in severe osteopenia and fractures: expanding the disease phenotype.BMC Med Genet. 2016 Nov 21;17(1):86. PubMed PMID: 27871226; PubMed Central PMCID:PMC5117547.

K. Kernohan, D. Dyment, M. Pupavac, Z. Cramer, A. McBride, G. Bernard, I. Straub, M. Tetreault, T. Hartley, L. Huang, E. Sell, J. Majewski, D. S. Rosenblatt, E. Shoubridge, A. Mhanni, T. Myers, V. Proud, S. Vergano, B. Spangler, E. Farrow, J.Kussman, N. Safina, Care4Rare Consortium, C. Saunders, K. M. Boycott, I. Thiffault. Matchmaking facilitates the diagnosis of an autosomal-recessive mitochondrial disease caused by biallelic mutation of the tRNA isopentenyltransferase (TRIT1) gene. Under press humu-2016-0478.R1. Human Mutation 2017

The Challenge of Analyzing the Results of Next-Generation Sequencing in Children. Thiffault I, Lantos J. Pediatrics. 2016 Jan;137 Suppl 1:S3-7. doi: 10.1542/peds.2015-3731C. PMID: 26729700

Thiffault I, Bernard G. Expert opinion and caution are imperative for interpretation of next generation sequencing data. Eur J Med Genet. 2016 Oct;59(10):519-21.

Thiffault, B. Zuccarelli, H. Welsh, Xuan Yuan, E. Farrow, L. Zellmer, N. Miller, S. Soden, A. Abdelmoity, RA. Brodsky, C. Saunders. Hypotonia and intellectual disability without dysmorphic features in a patient with PIGN-related disease. Accepted MGTC-D-16-00182. BMC Medical Genetics

Thiffault, I., Farrow, E., Smith, L., Lowry, J., Zellmer, L., Black, B., Abdelmoity A., Miller, N., Soden, S., Saunders, C. (2016). PCDH19-related epileptic encephalopathy in a male mosaic for a truncating variant. American Journal of Medical Genetics. Part A, 170(6), 1585–9.

Twist GP, Gaedigk A, Miller NA, Farrow EG, Willig LK, Dinwiddie DL, Petrikin JE, Soden SE, Herd S, Gibson M, Cakici JA, Riffel AK, Leeder JS, Dinakarpandian D, Kingsmore SF. Constellation: a tool for rapid, automated phenotype assignment of a highly polymorphic pharmacogene, CYP2D6, from whole-genome sequences. NPJ Genomic Medicine. 2016 Jan;1:15007. doi:10.1038/npjgenmed.2015.7

Willig LK. Techniques and Approaches to Genetic Analyses in Nephrological Disorders. J Pediatr Genet. 2016 Mar;5(1):2-14. doi: 10.1055/s-0035-1557108. Review. PubMed PMID: 27617137; PubMed Central PMCID: PMC4918702.

Noll AC, Miller NA, Smith LD, Yoo B, Fiedler S, Cooley LD, Willig LK, Petrikin JE, Caciki JA, Lesko J, Newton A, Detherage K, Thiffault I, Saunders CJ, Farrow EG, Kingsmore SF (2016) Clinical detection of deletion structural variants in whole-genome sequences. Nature Genomic Medicine doi: 10.1038/npgenmed.2016.26

C. Saunders. Invited platform: “Clinical Whole Genome Sequencing” Mayo Individualizing Medicine Conference, October 6, 2016, Rochester, MN.

Saunders, C., and Thiffault, I. "Casting a Broader Net: Using Genomic Medicine to Diagnose Rediatric Neurodevelopmental Disease." Presented at 7th Annual Pediatric Genomic Medicine Conference, Kansas City, MO , April 6, 2016.
Saunders, C., "Variant Interpretation and Reporting: Tools to Finding the Right Variant(s). Presented at Pre-Conference Workshop "A Deep Dive into Genome Sequencing" at 7th Annual Pediatric Genomic Medicine Conference, Kansas City, MO , April 6, 2016.

Saunders, C. Panelist for Session "Translating Regional Strengths into Treatments and Cures" for Rare Disease Day 2016. Kansas City, MO, February 29, 2016.

S. Soden. Keynote: Genome Sequencing: What It Means to You and Your Patients. Annual Pediatric Advanced Practice Nursing Conference, Children's Mercy - Kansas City, Overland Park, KS. October 7, 2016. 

S. Soden. Using Clinical Resources to Optimize the Use of Genomics in Medicine. Festival of Genomics. Boston, MA. June 29, 2016

S. Soden. The Impact of Genomics in children with developmental and psychiatric disorders: diagnosis and gene discovery. Paul Laybourne Symposium on Child Psychiatry. Overland Park, KS. April 29, 2016. 

S. Soden. Gene Discovery in Tourette Syndrome: Next Gen Sequencing and an Animal Model. Pediatric Genomic Medicine Conference, Children's Mercy - Kansas City, Kansas City, MO, April 5-7, 2016.

I.Thiffault. Introduction to Genetics. First National Conference on Leukodystrophies. McgIll University, Montreal, Quebec, Canada. September 16, 2016

I.Thiffault. The Challenge of Analyzing the Results of Next-Generation Sequencing in Children. ASBH 18th Annual Meeting, Washington DC. October 19, 2016

E Farrow: Genomics in Practice. March 3, 2016. Clinical Laboratory Management Association, Kansas City Chapter. Genomics and Molecular Medicine Summit. Kansas City, Missouri. 

E Farrow: Pediatric Genetics-Applications of Next Generation Sequencing in the Clinic. May 11, 2016. LabRoots Genetics and Genomics Virtual Event. 

N Miller: Chair for Workshop “Best Practices for Big Data in Life Sciences Research”. Bio-IT World, Boston MA April 5, 2016

N Miller: “Software for Interpretation of Next-Gen Sequencing Data in a Clinical Setting”. Bio-IT World, Boston MA April 7, 2016

S Corder: Panelist for Session “Understanding Storage Strategies – Striking the Right Balance Between the Technology and Economics of Big Data”. Leverage Big Data, Carlsbad CA, June 5, 2016

S Corder: “Advancements in Genomics at Children’s Mercy, Kansas City”. Oklahoma Supercomputing Symposium, Norman OK, September 21, 2016

S Corder: “Advancements in Genomic Analysis at Children’s Mercy, Kansas City”. Supercomputing 2016, Salt Lake City, UT November 16, 2016

G Twist: “Constellation: A Full Stack Solution for Pharmacogenomics”. Molecular Tri-Con. San Francisco, CA March 7 2016

E. Guest: Infant ALL Trio Sequencing. E Guest. Session on Relapsed Acute Lymphoblastic Leukemia. Children’s Oncology Group Fall Meeting. Atlanta, GA. September 14, 2016.

E Guest: Identifying Genomic Biomarkers of Relapse in Infant Acute Lymphoblastic Leukemia. The University of Kansas Cancer Center Research Symposium, Overland Park, KS. November 18, 2016.

LePichon JBSaunders CJSoden 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 ISaunders 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 CJThiffault 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 EGKingsmore 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 SFLantos JDDinwiddie DLMiller NASoden SEFarrow EGSaunders CJNext-generation Community Genetics for Low- and Middle-income Countries. Genome Med 4(3):25 (2012) 

Dinwiddie DL, Soden SESaunders 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 SESaunders 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 SEFarrow 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 CJSoden 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 CJFarrow EGSoden 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.