Grants

11000.050.01  (Farrell)

10/13/2017 – 10/13/2020                                               
The Legacy of Angels Foundation
Assessing the Added value of Whole Genome Sequencing in Cystic Fibrosis Newborn Screening
Whole genome sequencing, analysis, and interpretation to identified variants associated with non responder status and altered outcomes in a pediatric CF patient cohort.

Ramsay Award (Worthey)

09/17/2019 – 08/16/2020    
Solve ME/CFS Foundation
Whole genome sequencing and analysis of ME/CFS
WGS and RNA sequencing and analysis of myalgic encephalomyelitis/chronic fatigue syndrome cases and controls to identify causal molecular variants and genetic risk factors.1R35-CA220502

1R35-CA220502 (Bhatia)

09/01/2018 – 08/31/2025   
NIH
Mitigating long-term treatment related morbidity in Childhood Cancer survivors
Whole exome based secondary and tertiary analysis and interpretation of Dr. Smita Bhatia’s pediatric cancer long term survival cohort to identify common and rare molecular variation associated with treatment related morbidity.

R01-PA-18-003 (Bhatia)

09/01/2018 – 08/30/2023   
NIH
Predicting Risk of Anthracycline-related Cardiotoxicity in Childhood Cancer Survivors
Whole exome based secondary and tertiary analysis and interpretation of Dr. Smita Bhatia’s pediatric cancer long term survival cohort to identify common and rare molecular variation associated cardiotoxicity.

CFF 19A0 2019 (Worthey)

09/01/2019 – 08/30/2023    
CF foundation
Finding and Integrating Pharma and Nutrition Linked Genomic Variation in CF
Whole genome sequencing and analysis and polygenic risk analysis to identify molecular variation associated with growth, vitamin D status and EFA status in a cohort of CF patients.

FPWR (Worthey)

01/01/2020 – 12/31/2021  
The Foundation for Prader-Willi Research
Whole Genome Sequence Analysis in Prader-Willi Syndrome
Whole genome sequencing and interpretation to identify causal and polygenic variation outside of the PWS region on chromosome 15 capable of influencing personal risk in individuals with PWS.

UW-Madison (Greenspan)

01/01/2020 – 06/31/2020   
UW-Madison Research Foundation
Identification of causal variants in a family with Ehlers-Danlos Syndrome type 3.
Whole exome based secondary and tertiary analysis and interpretation to identify causal variants in a family with Ehlers-Danlos Syndrome.

NIH OT2 (Byrd and Might)       

01/24/2020-05/31/2020 
NCATS
Doc Sherlock: An autonomous relay agent for discovering the unknown knowns in precision medicine 
Consultation on molecular data use and interpretation for precision medicine applications.

Team Research

Liz Worthey’s citations per year as of 8/10/2020

Published in 2020

  • Basu MK, Massicano F, Yu L, Halkidis K, Pillai V, Cao W, Zheng L, Zheng XL. Exome Sequencing Identifies Abnormalities in Glycosylation and ANKRD36C in Patients with Immune-Mediated Thrombotic Thrombocytopenic Purpura. Thromb Haemost. 2020 Nov 12. doi: 10.1055/s-0040-1719030. Epub ahead of print. PMID: 33184803.
  • Werling DM, Pochareddy S., Choi J., An JY, Sheppard B., Peng M., … & Tebbenkamp AT. (2020). Whole-genome and RNA sequencing reveal variation and transcriptomic coordination in the developing human prefrontal cortex. Cell Rep, 31(1):107489
  • Wilk MA, Braun AT, Farrell PM, Laxova A, Brown DM, Holt JM, Birch CL, Sosonkina N, Wilk BM, Worthey EA. Applying whole-genome sequencing in relation to phenotype and outcomes in siblings with cystic fibrosis. Cold Spring Harb Mol Case Stud. 2020 Feb;6(1). doi: 10.1101/mcs.a004531. Print 2020 Feb. PubMed PMID: 32014855; PubMed Central PMCID: PMC6996517
  • Aday AW, Krier JB, Pallais JC, Fieg EL, MacRae CA, Loscalzo J. The Undiagnosed Diseases Network as a Tool for Graduate Medical Education. Am J Med. 2020 Feb;133(2):e18-e22. doi: 10.1016/j.amjmed.2019.06.034. Epub 2019 Jul 10. PubMed PMID: 31301294
  • Johnson BV, Kumar R, Oishi S, Alexander S, Kasherman M, Vega MS, Ivancevic A, Gardner A, Domingo D, Corbett M, Parnell E, Yoon S, Oh T, Lines M, Lefroy H, Kini U, Van Allen M, Grønborg S, Mercier S, Küry S, Bézieau S, Pasquier L, Raynaud M, Afenjar A, Billette de Villemeur T, Keren B, Désir J, Van Maldergem L, Marangoni M, Dikow N, Koolen DA, VanHasselt PM, Weiss M, Zwijnenburg P, Sa J, Reis CF, López-Otín C, Santiago-Fernández O, Fernández-Jaén A, Rauch A, Steindl K, Joset P, Goldstein A, Madan-Khetarpal S, Infante E, Zackai E, Mcdougall C, Narayanan V, Ramsey K, Mercimek-Andrews S, Pena L, Shashi V, Schoch K, Sullivan JA, Pinto E Vairo F, Pichurin PN, Ewing SA, Barnett SS, Klee EW, Perry MS, Koenig MK, Keegan CE, Schuette JL, Asher S, Perilla-Young Y, Smith LD, Rosenfeld JA, Bhoj E, Kaplan P, Li D, Oegema R, van Binsbergen E, van der Zwaag B, Smeland MF, Cutcutache I, Page M, Armstrong M, Lin AE, Steeves MA, Hollander ND, Hoffer MJV, Reijnders MRF, Demirdas S, Koboldt DC, Bartholomew D, Mosher TM, Hickey SE, Shieh C, Sanchez-Lara PA, Graham JM Jr, Tezcan K, Schaefer GB, Danylchuk NR, Asamoah A, Jackson KE, Yachelevich N, Au M, Pérez-Jurado LA, Kleefstra T, Penzes P, Wood SA, Burne T, Pierson TM, Piper M, Gécz J, Jolly LA. Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor β Signaling. Biol Psychiatry. 2020 Jan 15;87(2):100-112. doi: 10.1016/j.biopsych.2019.05.028. Epub 2019 Jun 29. PubMed PMID: 31443933; PubMed Central PMCID: PMC6925349

Published in 2019

  • Holt J, Birch C, Brown D, Gajapathy M, Sosonkina N, Wilk B, Wilk M, Spillmann R, Stong N, Lee H, Huang A, Bonner D, Kohler J, Macnamara E, , Nelson S, Shashi V, Worthey E. Identification of Pathogenic Structural Variants in Rare Disease Patients through Genome Sequencing. 2019/01; :627661. doi: 10.1101/627661
  • Holt J, Wilk B, Birch C, Brown D, Gajapathy M, Moss A, Sosonkina N, Wilk M, Anderson J, Harris J, Kelly J, Shaterferdosian F, Uno-Antonison A, Weborg A, , Worthey E. VarSight: Prioritizing Clinically Reported Variants with Binary Classification Algorithms. 2019/01; :532440. doi: 10.1101/532440
  • Handoko M, Emrick LT, Rosenfeld JA, Wang X, Tran AA. Recurrent mosaic MTOR c.5930C > T (p.Thr1977Ile) variant causing megalencephaly, asymmetric polymicrogyria, and cutaneous pigmentary mosaicism: Case report and review of the literature. Am J Med Genet A. 2019 Mar;179(3):475-9
  • Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet. 2019 Jan 3;104(1):164-78
  • Holt JM, Wilk B, Birch CL, Brown DM, Gajapathy M, Moss AC, Sosonkina N, Wilk MA, Anderson JA, Harris JM, Kelly JM, Shaterferdosian F, Uno-Antonison AE, Weborg A, Worthey EA. VarSight: prioritizing clinically reported variants with binary classification algorithms. BMC Bioinformatics. 2019 Oct 15;20(1):496. doi: 10.1186/s12859-019-3026-8. PubMed PMID: 31615419; PubMed Central PMCID: PMC6792253
  • Bhatia A, Mobley BC, Cogan J, Koziura ME, Brokamp E, Phillips J, Newman J, Moore SA, Hamid R. Magnetic Resonance Imaging characteristics in case of TOR1AIP1 muscular dystrophy. Clin Imaging. 2019 Nov – Dec;58:108-113. doi: 10.1016/j.clinimag.2019.06.010. Epub 2019 Jun 21. PubMed PMID: 31299614; PubMed Central PMCID: PMC6893088

Published in 2018

  • Tebbenkamp AT, Varela L, Choi J, Paredes MI, Giani AM, Song JE., … & Li M. (2018). The 7q11. 23 protein DNAJC30 interacts with ATP synthase and links mitochondria to brain development. Cell, 175(4):1088-1104
  • Li M, Santpere G, Kawasawa YI, Evgrafov OV, Gulden FO, Pochareddy S, … & Sousa AM. (2018). Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science, 362(6420):eaat7615
  • Mamidi TKK, Wu J, Tchounwou PB, Miele L, Hicks C. Whole Genome Transcriptome Analysis of the Association between Obesity and Triple-Negative Breast Cancer in Caucasian Women. Int J Environ Res Public Health. 2018 Oct 23;15(11)
  • Johnston JJ, van der Smagt JJ, Rosenfeld JA, Pagnamenta AT, Alswaid A, Autosomal recessive Noonan syndrome associated with biallelic LZTR1 variants. Genet Med. 2018 Oct;20(10):1175-1185
  • Tan QK, Cope H, Spillmann RC, Stong N, Jiang YH, et al. Further evidence for the involvement of EFL1 in a Shwachman–Diamond-like syndrome and expansion of the phenotypic features. Cold Spring Harb Mol Case Stud. 2018 Oct 1;4(5)

Published in 2017

  • Brynedal B, Choi J, Raj T, Bjornson R, Stranger BE, Neale BM, … & Cotsapas C. (2017). Large-scale trans-eQTLs affect hundreds of transcripts and mediate patterns of transcriptional co-regulation. The Am J Hum Genet. 100(4):581-591
  • Penha ED, Iriabho E, Dussaq A, de Oliveira DM, Almeida JS Isomorphic semantic mapping of variant call format (VCF2RDF). Bioinformatics. 2017 Feb 15;33(4):547-548.
  • 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. Successful Application of Whole Genome Sequencing in a Medical Genetics Clinic. J Pediatr Genet. 2017 Jun;6(2):61-76. doi: 10.1055/s-0036-1593968. Epub 2016 Nov 28. PubMed PMID: 28496993; PubMed Central PMCID: PMC5423809

Published in 2016

  • Choi J, Shooshtari P, Samocha KE, Daly MJ, Cotsapas C. (2016). Network analysis of genome-wide selective constraint reveals a gene network active in early fetal brain intolerant of mutation. PLoS Genet, 12(6): e1006121
  • Gajapathy M. Molecular and functional analyses of inorganic pyrophosphatases. The University of Alabama in Huntsville; 2016
  • Shashi V, Pena LD, Kim K, Burton B, Hempel M, et al. De Novo Truncating Variants in ASXL2 Are Associated with a Unique and Recognizable Clinical Phenotype. Am J Hum Genet. 2016 Oct 6;99(4):991-999
  • Gahl WA, Mulvihill JJ, Toro C, Markello TC, Wise AL, Ramoni RB, Adams DR, Tifft CJ; UDN.(2016). The NIH Undiagnosed Diseases Program and Network: Applications to modern medicine. Mol Genet Metab;117(4):393-400
  • Bashamboo A, Donohoue PA, Vilain E, Rojo S, Calvel P, Seneviratne SN, Buonocore F, Barseghyan H, et. al. (in UDN) (2016). A recurrent p.Arg92Trp variant in steroidogenic factor-1 (NR5A1) can act as a molecular switch in human sex development. Hum Mol Genet. 2016 Jul 4 [Epub ahead of print]