Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation Michelle M. Clark, Amber Hildreth, Sergey Batalov, Yan Ding, Shimul Chowdhury, Kelly Watkins, Katarzyna Ellsworth, Brandon Camp, Cyrielle I. Kint, Calum Yacoubian, Lauge Farnaes, Matthew N. Bainbridge, Curtis Beebe, Joshua J. A. Braun, Margaret Bray, Jeanne Carroll, Julie A. Cakici, Sara A. Caylor, Christina Clarke, Mitchell P. Creed, Jennifer Friedman, Alison Frith, Richard Gain, Mary Gaughran, Shauna George, Sheldon Gilmer, Joseph Gleeson, Jeremy Gore, Haiying Grunenwald, Raymond L. Hovey, Marie L. Janes, Kejia Lin, Paul D. McDonagh, Kyle McBride, Patrick Mulrooney, Shareef Nahas, Daeheon Oh, Albert Oriol, Laura Puckett, Zia Rady, Martin G. Reese, Julie Ryu, Lisa Salz, Erica Sanford, Lawrence Stewart, Nathaly Sweeney, Mari Tokita, Luca Van Der Kraan, Sarah White, Kristen Wigby, Brett Williams, Terence Wong, Meredith S. Wright, Catherine Yamada, Peter Schols, John Reynders, Kevin Hall, David Dimmock, Narayanan Veeraraghavan, Thomas Defay and Stephen F. Kingsmore Sci Transl Med. 2019 Apr 24;11(489). pii: eaat6177. doi: 10.1126/scitranslmed.aat6177
Biallelic mutations in valyl-tRNA synthetase gene VARS, are associated with a progressive neurodevelopmental epileptic encephalopathy Jennifer Friedman, Desiree Smith, Mahmoud Issa, Valentina Stanley, Rengang Wang, Marisa Mendes, Meredith Wright, Kristen Wigby, Amber Hildreth, John Crawford, Alanna Koehler, Shimul Chowdhury, Shareef Nahas, Liting Zhai, Zhiwen Xu, Wing-Sze Lo, Kiely James, Damir Musaev, Andrea Accogli, Kether Guerrero, Luan Tran, Tarek Omar, Tawfeg Ben-Omran, David Dimmock, Stephen Kingsmore, Gajja Salomons, Maha Zaki, Geneviève Bernard, and Joseph Gleeson Nat Commun. 2019 Feb 12;10(1):707. doi: 10.1038/s41467-018-07067-3.
Effect of sociodemographic factors on uptake of a patient-facing information technology family health history risk assessment platform R Ryanne Wu, MD, MHS1, Rachel A Myers, PhD1, Adam H Buchanan, MS, MPH2 , David Dimmock, MD3, et.al. Appl Clin Inform 2019; 10(02): 180-188 doi: 10.1055/s-0039-1679926
A meta-analysis of the diagnostic and clinical utility of genome and exome sequencing and chromosomal microarray in children with suspected genetic diseases Clark MM, Stark Z, Farnaes L, Tan TY, White SM, Dimmock D, Kingsmore SF npj Genomic Medicine volume 3, Article number: 16 (2018) doi: 10.1038/s41525-018-0053-8
Implementation, adoption, and utility of family health history risk assessment in diverse care settings: evaluating implementation processes and impact with an implementation framework. Wu RR, Myers RA, Sperber N, Voils CI, Neuner J, McCarty CA, Haller IV, Harry M, Fulda KG, Cross D, Dimmock D, Rakhra-Burris T, Buchanan AH, Ginsburg GS, Orlando LA. Genet Med. 2018 Jun 6. doi: 10.1038/s41436-018-0049-x. [Epub ahead of print] PMID: 29875427
Rapid whole genome sequencing identifies a novel AIRE variant associated with Autoimmune Polyendocrine Syndrome Type 1 Sanford E, Watkins K, Nahas S, Gottschalk M, Coufal NG, Farnaes L, Dimmock D, Kingsmore SF; RCIGM Investigators. Cold Spring Harb Mol Case Stud. 2018 Jun 1;4(3). pii: a002485. doi: 10.1101/mcs.a002485. Print 2018 Jun. PMID: 29437776
The case for early use of rapid whole genome sequencing in management of critically ill infants: Late diagnosis of Coffin-Siris syndrome in an infant with left congenital diaphragmatic hernia, congenital heart disease and recurrent infections Sweeney NM, Nahas SA, Chowdhury S, Campo MD, Jones MC, Dimmock DP, Kingsmore SF; RCIGM Investigators. Cold Spring Harb Mol Case Stud. 2018 Jun 1;4(3). pii: a002469. doi: 10.1101/mcs.a002469. Print 2018 Jun. PMID:29549119
Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters. Sweeney TE, Azad TD, Donato M, Haynes WA, Perumal TM, Henao R, Bermejo-Martin JF, Almansa R, Tamayo E, Howrylak JA, Choi A, Parnell GP, Tang B, Nichols M, Woods CW, Ginsburg GS, Kingsmore SF, Omberg L, Mangravite LM, Wong HR, Tsalik EL, Langley RJ, Khatri P. Crit Care Med. 2018 Jun;46(6):915-925. doi: 10.1097/CCM.0000000000003084. PMID: 29537985
Sdha+/- Rats Display Minimal Muscle Pathology Without Significant Behavioral or Biochemical Abnormalities. Siebers EM, Choi MJ, Tinklenberg JA, Beatka MJ, Ayres S, Meng H, Helbling DC, Takizawa A, Bennett B, Garces AM, Dias Duarte Machado LG, Dimmock D, Dwinell MR, Geurts AM, Lawlor MW. J Neuropathol Exp Neurol. 2018 May 8. doi: 10.1093/jnen/nly042. [Epub ahead of print] PMID: 29850869
RGC-32 induces transition of pancreatic cancer to epithelial mesenchyme in vivo. Zhu L, Ding Y. Pancreatology. 2018 May 18. pii: S1424-3903(18)30586-6. doi: 10.1016/j.pan.2018.05.480. [Epub ahead of print] PMID:29886073
Comprehensive profiling of DNA repair defects in breast cancer identifies a novel class of endocrine therapy resistance drivers. Anurag M, Punturi N, Hoog J, Bainbridge MN, Ellis MJ, Haricharan S. Clin Cancer Res. 2018 May 23. pii: clincanres.3702.2017. doi: 10.1158/1078-0432.CCR-17-3702. [Epub ahead of print] PMID: 29793947
Syndromic congenital myelofibrosis associated with a loss-of-function variant in RBSN. Magoulas PL, Shchelochkov OA, Bainbridge MN, Ben-Shachar S, Yatsenko S, Potocki L, Lewis RA, Searby C, Marcogliese AN, Elghetany MT, Zapata G, Hernández PP, Gadkari M, Einhaus D, Muzny DM, Gibbs RA, Bertuch AA, Scott DA, Corvera S, Franco LM. Blood. 2018 May 21. pii: blood-2017-12-824433. doi: 10.1182/blood-2017-12-824433. [Epub ahead of print] No abstract available. PMID:29784638
Molecular subtyping of tumors from patients with familial glioma. Ruiz VY, Praska CE, Armstrong G, Kollmeyer TM, Yamada S, Decker PA, Kosel ML, Eckel-Passow JE, Lachance DH, Bainbridge MN, Melin BS, Bondy ML, Jenkins RB; Gliogene Consortium. Neuro Oncol. 2018 May 18;20(6):810-817. doi: 10.1093/neuonc/nox192. PMID: 29040662
Pegvaliase for the treatment of phenylketonuria: Results of a long-term phase 3 clinical trial program (PRISM). Thomas J, Levy H, Amato S, Vockley J, Zori R, Dimmock D, Harding CO, Bilder DA, Weng HH, Olbertz J, Merilainen M, Jiang J, Larimore K, Gupta S, Gu Z, Northrup H; PRISM investigators. Mol Genet Metab. 2018 May;124(1):27-38. doi: 10.1016/j.ymgme.2018.03.006. Epub 2018 Mar 31.
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Paternally inherited cis-regulatory structural variants are associated with autism. Brandler WM, Antaki D, Gujral M, Kleiber ML, Whitney J, Maile MS, Hong O, Chapman TR, Tan S, Tandon P, Pang T, Tang SC, Vaux KK, Yang Y, Harrington E, Juul S, Turner DJ, Thiruvahindrapuram B, Kaur G, Wang Z, Kingsmore SF, Gleeson JG, Bisson D, Kakaradov B, Telenti A, Venter JC, Corominas R, Toma C, Cormand B, Rueda I, Guijarro S, Messer KS, Nievergelt CM, Arranz MJ, Courchesne E, Pierce K, Muotri AR, Iakoucheva LM, Hervas A, Scherer SW, Corsello C, Sebat J. Science. 2018 Apr 20;360(6386):327-331. doi: 10.1126/science.aan2261. PMID: 29674594 Free Article
Rapid Whole Genome Sequencing Decreases Morbidity and Healthcare Cost of Hospitalized Infants Farnaes L, Hildreth A, Sweeney NM, Clark MM, Chowdhury S, Nahas S, Cakici JA, Benson W, Kaplan RH, Kronick R, Bainbridge MN, Friedman J, Gold JJ, Ding Y, Veeraraghavan N, Dimmock D, Kingsmore SF. NPJ Genom Med. 2018 Apr 4;3:10. doi: 10.1038/s41525-018-0049-4. eCollection 2018. PMID: 29644095
Acute liver failure in neonates with undiagnosed hereditary fructose intolerance due to exposure from widely available infant formulas Li H, Byers HM, Diaz-Kuan A, Vos MB, Hall PL, Tortorelli S, Singh R, Wallenstein MB, Allain M, Dimmock DP, Farrell RM, McCandless S, Gambello MJ. Mol Genet Metab. 2018 Apr;123(4):428-432. doi: 10.1016/j.ymgme.2018.02.016. Epub 2018 Feb 27. PMID:29510902
Encephalitis and Thalamic Injury From Neuroinvasive West Nile Virus in Children on Treatment for Acute Lymphoblastic Leukemia. Farnaes L, Schiff D, McElroy AK, Coufal NG, Crawford JR, Cannavino C. Pediatr Neurol. 2018 Mar;80:84-87. doi: 10.1016/j.pediatrneurol.2017.11.013. Epub 2017 Dec 2. No abstract available. PMID: 29398166
A community approach to mortality prediction in sepsis via gene expression analysis. Sweeney TE, Perumal TM, Henao R, Nichols M, Howrylak JA, Choi AM, Bermejo-Martin JF, Almansa R, Tamayo E, Davenport EE, Burnham KL, Hinds CJ, Knight JC, Woods CW, Kingsmore SF, Ginsburg GS, Wong HR, Parnell GP, Tang B, Moldawer LL, Moore FE, Omberg L, Khatri P, Tsalik EL, Mangravite LM, Langley RJ. Nat Commun. 2018 Feb 15;9(1):694. doi: 10.1038/s41467-018-03078-2. PMID: 29449546 Free PMC Article
The NSIGHT1randomized controlled trial: rapid whole-genome sequencing for accelerated etiological diagnosis in critically ill infants Petrikin JE, Cakici JA, Clark MM, Willig LK, Sweeney NM, Farrow EG, Saunders CJ, Thiffault I, Miller NA, Zellmer L, Herd SM, Holmes AM, Batalov S, Veeraraghavan N, Smith LD, Dimmock DP, Leeder JS, Kingsmore SF NPJ Genom Med. 2018 Feb 9;3:6. doi: 10.1038/s41525-018-0045-8. eCollection 2018. PMID: 29449963
Patient care standards for primary mitochondrial disease: a consensus statement from the Mitochondrial Medicine Society. Parikh S, Goldstein A, Karaa A, Koenig MK, Anselm I, Brunel-Guitton C, Christodoulou J, Cohen BH, Dimmock D, Enns GM, Falk MJ, Feigenbaum A, Frye RE, Ganesh J, Griesemer D, Haas R, Horvath R, Korson M, Kruer MC, Mancuso M, McCormack S, Raboisson MJ, Reimschisel T, Salvarinova R, Saneto RP, Scaglia F, Shoffner J, Stacpoole PW, Sue CM, Tarnopolsky M, Van Karnebeek C, Wolfe LA, Cunningham ZZ, Rahman S, Chinnery PF. Genet Med. 2017 Dec;19(12). doi: 10.1038/gim.2017.107. Epub 2017 Jul 27. Review. PMID: 28749475
The humanistic burden of Pompe disease: are there still unmet needs? A systematic review. Schoser B, Bilder DA, Dimmock D, Gupta D, James ES, Prasad S. BMC Neurol. 2017 Nov 22;17(1):202. doi: 10.1186/s12883-017-0983-2. Review. PMID: 29166883 Free PMC Article
Loss of MutL Disrupts CHK2-Dependent Cell-Cycle Control through CDK4/6 to Promote Intrinsic Endocrine Therapy Resistance in Primary Breast Cancer. Haricharan S, Punturi N, Singh P, Holloway KR, Anurag M, Schmelz J, Schmidt C, Lei JT, Suman V, Hunt K, Olson JA Jr, Hoog J, Li S, Huang S, Edwards DP, Kavuri SM, Bainbridge MN, Ma CX, Ellis MJ. Cancer Discov. 2017 Oct;7(10):1168-1183. doi: 10.1158/2159-8290.CD-16-1179. Epub 2017 Aug 11. PMID: 28801307
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. Hildreth A, Wigby K, Chowdhury S, Nahas S, Barea J, Ordonez P, Batalov S, Dimmock D, Kingsmore S; RCIGM Investigators. Cold Spring Harb Mol Case Stud. 2017 Sep 1;3(5). pii: a001966. doi: 10.1101/mcs.a001966. Print 2017 Sep. PMID: 28550066 Free PMC Article
Rapid whole-genome sequencing identifies a novel GABRA1 variant associated with West syndrome. Farnaes L, Nahas SA, Chowdhury S, Nelson J, Batalov S, Dimmock DM, Kingsmore SF; RCIGM Investigators. Cold Spring Harb Mol Case Stud. 2017 Sep 1;3(5). pii: a001776. doi: 10.1101/mcs.a001776. Print 2017 Sep. PMID: 28864462 Free PMC Article
Analyses of SLC13A5-epilepsy patients reveal perturbations of TCA cycle. Bainbridge MN, Cooney E, Miller M, Kennedy AD, Wulff JE, Donti T, Jhangiani SN, Gibbs RA, Elsea SH, Porter BE, Graham BH. Mol Genet Metab. 2017 Aug;121(4):314-319. doi: 10.1016/j.ymgme.2017.06.009. Epub 2017 Jun 24. PMID: 28673551
Futher delineation of a rare recessive encephalomyopathy linked to mutations in GFER thanks to data sharing of whole exome sequencing data Nambot S, Gavrilov D, Thevenon J, Bruel AL, Bainbridge M, Rio M, Goizet C, Rötig A, Jaeken J, Niu N, Xia F, Vital A, Houcinat N, Mochel F, Kuentz P, Lehalle D, Duffourd Y, Rivière JB, Thauvin-Robinet C, Beaudet AL, Faivre L. Clin Genet. 2017 Aug;92(2):188-198. doi: 10.1111/cge.12985. Epub 2017 Mar 1. PMID: 28155230
Novel Genetic Triggers and Genotype-Phenotype Correlations in Patients With Left Ventricular Noncompaction Miszalski-Jamka K, Jefferies JL, Mazur W, Głowacki J, Hu J, Lazar M, Gibbs RA, Liczko J, Kłyś J, Venner E, Muzny DM, Rycaj J, Białkowski J, Kluczewska E, Kalarus Z, Jhangiani S, Al-Khalidi H, Kukulski T, Lupski JR, Craigen WJ, Bainbridge MN. Circ Cardiovasc Genet. 2017 Aug;10(4). pii: e001763. doi: 10.1161/CIRCGENETICS.117.001763.
Haploinsufficiency of ZNF462 is associated with craniofacial anomalies, corpus callosum dysgenesis, ptosis, and developmental delay. Weiss K, Wigby K, Fannemel M, Henderson LB, Beck N, Ghali N, Study DDD, Anderlid BM, Lundin J, Hamosh A, Jones MC, Ghedia S, Muenke M, Kruszka P. Eur J Hum Genet. 2017 Aug;25(8):946-951. doi: 10.1038/ejhg.2017.86. Epub 2017 May 17. PMID: 28513610
Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic. Bick D, Fraser PC, Gutzeit MF, Harris JM, Hambuch TM, Helbling DC, Jacob HJ, Kersten JN, Leuthner SR, May T, North PE, Prisco SZ, Schuler BA, Shimoyama M, Strong KA, Van Why SK, Veith R, Verbsky J, Weborg AM Jr, Wilk BM, Willoughby RE Jr, Worthey EA, Dimmock DP. J Pediatr Genet. 2017 Jun;6(2):61-76. doi: 10.1055/s-0036-1593968. Epub 2016 Nov 28. PMID: 28496993 Free PMC Article
Gastrointestinal disorders in Curry-Jones syndrome: Clinical and molecular insights from an affected newborn. Wigby K, Twigg SRF, Broderick R, Davenport KP, Wilkie AOM, Bickler SW, Jones MC. Am J Med Genet A. 2017 Jun;173(6):1586-1592. doi: 10.1002/ajmg.a.38232. Epub 2017 Apr 6. PMID: 28386950 Free PMC Article
Common data elements for clinical research in mitochondrial disease: a National Institute for Neurological Disorders and Stroke project. Karaa A, Rahman S, Lombès A, Yu-Wai-Man P, Sheikh MK, Alai-Hansen S, Cohen BH, Dimmock D, Emrick L, Falk MJ, McCormack S, Mirsky D, Moore T, Parikh S, Shoffner J, Taivassalo T, Tarnopolsky M, Tein I, Odenkirchen JC, Goldstein A; Mito Working Group Member Participants:. J Inherit Metab Dis. 2017 May;40(3):403-414. doi: 10.1007/s10545-017-0035-5. Epub 2017 Mar 16. Erratum in: J Inherit Metab Dis. 2017 Oct 4;:. PMID: 28303425
Whole-exome sequencing in the molecular diagnosis of individuals with congenital anomalies of the kidney and urinary tract and identification of a new causative gene. Bekheirnia MR, Bekheirnia N, Bainbridge MN, Gu S, Coban Akdemir ZH, Gambin T, Janzen NK, Jhangiani SN, Muzny DM, Michael M, Brewer ED, Elenberg E, Kale AS, Riley AA, Swartz SJ, Scott DA, Yang Y, Srivaths PR, Wenderfer SE, Bodurtha J, Applegate CD, Velinov M, Myers A, Borovik L, Craigen WJ, Hanchard NA, Rosenfeld JA, Lewis RA, Gonzales ET, Gibbs RA, Belmont JW, Roth DR, Eng C, Braun MC, Lupski JR, Lamb DJ. Genet Med. 2017 Apr;19(4):412-420. doi: 10.1038/gim.2016.131. Epub 2016 Sep 22.
AIFM1 mutation presenting with fatal encephalomyopathy and mitochondrial disease in an infant. Morton SU, Prabhu SP, Lidov HGW, Shi J, Anselm I, Brownstein CA, Bainbridge MN, Beggs AH, Vargas SO, Agrawal PB. Cold Spring Harb Mol Case Stud. 2017 Mar;3(2):a001560. doi: 10.1101/mcs.a001560. PMID: 28299359 Free PMC Article
Efficient Precision Genome Editing in iPSCs via Genetic Co-targeting with Selection. Mitzelfelt KA, McDermott-Roe C, Grzybowski MN, Marquez M, Kuo CT, Riedel M, Lai S, Choi MJ, Kolander KD, Helbling D, Dimmock DP, Battle MA, Jou CJ, Tristani-Firouzi M, Verbsky JW, Benjamin IJ, Geurts AM. Stem Cell Reports. 2017 Mar 14;8(3):491-499. doi: 10.1016/j.stemcr.2017.01.021. Epub 2017 Feb 24. PMID: 28238794 Free PMC Article
Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility. Kim J, Shimizu C, Kingsmore SF, Veeraraghavan N, Levy E, Ribeiro Dos Santos AM, Yang H, Flatley J, Hoang LT, Hibberd ML, Tremoulet AH, Harismendy O, Ohno-Machado L, Burns JC. PLoS One. 2017 Feb 2;12(2):e0170977. doi: 10.1371/journal.pone.0170977. eCollection 2017. PMID: 28151979 Free PMC Article
Newborn Sequencing in Genomic Medicine and Public Health Jonathan S. Berg, Pankaj B. Agrawal, Donald B. Bailey Jr., Alan H. Beggs, Steven E. Brenner, Amy M. Brower, Julie A. Cakici, Ozge Ceyhan-Birsoy, Kee Chan, Flavia Chen, Robert J. Currier, Dmitry Dukhovny, Robert C. Green, Julie Harris-Wai, Ingrid A. Holm, Brenda Iglesias, Galen Joseph, Stephen F. Kingsmore, Barbara A. Koenig, Pui-Yan Kwok, John Lantos, Steven J. Leeder, Megan A. Lewis, Amy L. McGuire, Laura V. Milko, Sean D. Mooney, Richard B. Parad, Stacey Pereira, Joshua Petrikin, Bradford C. Powell, Cynthia M. Powell, Jennifer M. Puck, Heidi L. Rehm,Neil Risch, Myra Roche, Joseph T. Shieh, Narayanan Veeraraghavan, Michael S. Watson, Laurel Willig, Timothy W. Yu, Tiina Urv, Anastasia L. Wise Pediatrics Jan 2017, e20162252; DOI: 10.1542/peds.2016-2252
Presentation and Diagnostic Evaluation of Mitochondrial Disease. Dimmock DP, Lawlor MW. Pediatr Clin North Am. 2017 Feb;64(1):161-171. doi: 10.1016/j.pcl.2016.08.011. Review. PMID: 27894442 Free PMC Article
Amphetamines promote mitochondrial dysfunction and DNA damage in pulmonary hypertension. Chen PI, Cao A, Miyagawa K, Tojais NF, Hennigs JK, Li CG, Sweeney NM, Inglis AS, Wang L, Li D, Ye M, Feldman BJ, Rabinovitch M. JCI Insight. 2017 Jan 26;2(2):e90427. doi: 10.1172/jci.insight.90427. PMID: 28138562 Free PMC Article