Note: List of publications from researchers at Boston Children’s Hospital who used the core facility.

2023-2024

A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. 

A Cross-Sectional Study of Nemaline Myopathy. 

A data-driven architecture using natural language processing to improve phenotyping efficiency and accelerate genetic diagnoses of rare disorders. 

A Genotype/Phenotype Study of KDM5B-Associated Disorders Suggests a Pathogenic Effect of Dominantly Inherited Missense Variants. 

Actionability of unanticipated monogenic disease risks in newborn genomic screening: Findings from the BabySeq Project. 

Acute and chronic tirasemtiv treatment improves in vivo and in vitro muscle performance in actin-based nemaline myopathy mice. 

Adenylosuccinic Acid: An Orphan Drug with Untapped Potential. 

Alternative genomic diagnoses for individuals with a clinical diagnosis of Dubowitz syndrome. 

Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases. 

Case report: A founder UGDH variant associated with developmental epileptic encephalopathy in Saudi Arabia. 

Cell-type-specific effects of autism-associated chromosome 15q11.2-13.1 duplications in human brain. 

Children with Early-Onset Psychosis Have Increased Burden of Rare GRIN2A Variants. 

Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy. 

Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species. 

Effects of participation in a U.S. trial of newborn genomic sequencing on parents at risk for depression. 

Estimation of the Quality-of-Life Impact of X-Linked Myotubular Myopathy. 

Exome copy number variant detection, analysis and classification in a large cohort of families with undiagnosed rare genetic disease. 

Exome copy number variant detection, analysis, and classification in a large cohort of families with undiagnosed rare genetic disease. 

Expanding the genetics and phenotypes of ocular congenital cranial dysinnervation disorders. 

Gene identification for ocular congenital cranial motor neuron disorders using human sequencing, zebrafish screening, and protein binding microarrays. 

Genetic Predisposition to Neurological Complications in Patients with COVID-19. 

Genome Sequencing for Diagnosing Rare Diseases. 

Genotype‒phenotype correlation in recessive DNAJB4 myopathy. 

Heterozygous loss-of-function SMC3 variants are associated with variable growth and developmental features. 

High number of candidate gene variants are identified as disease-causing in a period of 4 years. 

High resolution kinematic approach for quantifying impaired mobility of dystrophic zebrafish larvae. 

High-resolution detection of copy number alterations in single cells with HiScanner. 

INCEPTUS Natural History, Run-in Study for Gene Replacement Clinical Trial in X-Linked Myotubular Myopathy. 

Integrated multi-omics approach reveals the role of striated muscle preferentially expressed protein kinase in skeletal muscle including its relationship with myospryn complex. 

Mendelian Disorders in an Interstitial Cystitis/Bladder Pain Syndrome Cohort. 

Novel Phenotypes and Genotype-Phenotype Correlations in a Large Clinical Cohort of Patients With Kleefstra Syndrome. 

Optimizing assays of zebrafish larvae swimming performance for drug discovery. 

Phenotypic Spectrum of DNM2-Related Centronuclear Myopathy. 

PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss. 

Psychosocial Effect of Newborn Genomic Sequencing on Families in the BabySeq Project: A Randomized Clinical Trial. 

Rare De Novo and Inherited Genes in Familial and Nonfamilial Pediatric Attention-Deficit/Hyperactivity Disorder. 

RCL1 copy number variants are associated with a range of neuropsychiatric phenotypes. 

Real-world analysis of healthcare resource utilization by patients with X-linked myotubular myopathy (XLMTM) in the United States. 

Reanalysis of clinical exome identifies the second variant in two individuals with recessive disorders. 

Sarcomeres regulate murine cardiomyocyte maturation through MRTF-SRF signaling. 

Similar Rates of Deleterious Copy Number Variants in Early-Onset Psychosis and Autism Spectrum Disorder. 

Single-nucleus multi-omic profiling of polyploid heart nuclei identifies fusion-derived cardiomyocytes in the human heart. 

Structural variation in nebulin and its implications on phenotype and inheritance: establishing a dominant distal phenotype caused by large deletions. 

The natural history and genotype-phenotype correlations of TMPRSS3 hearing loss: an international, multi-center, cohort analysis. 

Titin copy number variations associated with dominant inherited phenotypes. 

Tropomyosin 3 (TPM3) function in skeletal muscle and in myopathy. 

Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study. 

Update in: Am J Hum Genet. 2024 May 2;111(5):863-876. doi: 10.1016/j.ajhg.2024.03.008

Update in: Genet Med. 2024 Jul 17:101216. doi: 10.1016/j.gim.2024.101216

Update in: Nat Commun. 2024 Sep 27;15(1):8268. doi: 10.1038/s41467-024-52463-7

X-linked hypophosphatemia in 4 generations due to an exon 13-15 duplication in PHEX, in the absence of the c.*231A>G variant. 

X-linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition. 

Zebrafish and cellular models of SELENON-Related Myopathy exhibit novel embryonic and metabolic phenotypes. 

2018/2019 papers

Patient-Customized Oligonucleotide Therapy for a Rare Genetic Disease.

Kim J, Hu C, Moufawad El Achkar C, Black LE, Douville J, Larson A, Pendergast MK, Goldkind SF, Lee EA, Kuniholm A, Soucy A, Vaze J, Belur NR, Fredriksen K, Stojkovska I, Tsytsykova A, Armant M, DiDonato RL, Choi J, Cornelissen L, Pereira LM, Augustine EF, Genetti CA, Dies K, Barton B, Williams L, Goodlett BD, Riley BL, Pasternak A, Berry ER, Pflock KA, Chu S, Reed C, Tyndall K, Agrawal PB, Beggs AH, Grant PE, Urion DK, Snyder RO, Waisbren SE, Poduri A, Park PJ, Patterson A, Biffi A, Mazzulli JR, Bodamer O, Berde CB, Yu TW

N Engl J Med. 2019 Oct 24;381(17):1644-1652. doi: 10.1056/NEJMoa1813279. Epub 2019 Oct 9.

PMID: 3159703

Different neuronal activity patterns induce different gene expression programs

Kelsey M. Tyssowski,1,6 Nicholas R. DeStefino,1,6 Jin-Hyung Cho,1 Carissa J. Dunn,2 Robert G. Poston,2 Crista E. Carty,3 Richard D. Jones,1 Sarah M. Chang,1 Palmyra Romeo,4 Mary K. Wurzelmann,4 James M. Ward,5 Mark L. Andermann,3 Ramendra N. Saha,2,4,7 Serena M. Dudek,4,7 and Jesse M. Gray1,7,8

Transcriptional Profiling of Articular Cartilage in a Porcine Model of Early Post-traumatic Osteoarthritis

Jakob T. Sieker,1 Benedikt L. Proffen,1 Kimberly A. Waller,2 Kaitlyn Chin,2 Naga P. Karamchedu,2 Matthew R. Akelman,2 Gabriel S. Perrone,1 Ata M. Kiapour,1 Johannes Konrad,1 Martha M. Murray,1 and Braden C. Fleming2

Transcriptional Profiling of Synovium in a Porcine Model of Early Post-traumatic Osteoarthritis

Jakob T. Sieker,1 Benedikt L. Proffen,1 Kimberly A. Waller,2 Kaitlyn E. Chin,2 Naga Padmini Karamchedu,2 Matthew R. Akelman,2 Gabriel S. Perrone,1 Ata M. Kiapour,1 Johannes Konrad,1 Braden C. Fleming,2 and Martha M. Murray1

Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface

Xavier Carette, John Platig, David C. Young, Michaela Helmel, Albert T. Young, Zhe Wang, Lakshmi-Prasad Potluri, Cameron Stuver Moody, Jumei Zeng, Sladjana Prisic, Joseph N. Paulson, Jan Muntel, Ashoka V. R. Madduri, Jorge Velarde, Jacob A. Mayfield, Christopher Locher, Tiansheng Wang, John Quackenbush, Kyu Y. Rhee, D. Branch Moody, Hanno Steen, Robert N. Husson

Association of Somatic GNAQ Mutation With Capillary Malformations in a Case of Choroidal Hemangioma

Colette A. Bichsel, PhD,1,2 Jeremy Goss, MD,3 Mohammed Alomari, MD,3 Sanda Alexandrescu, MD,4 Richard Robb, MD,5 Lois E. Smith, MD, PhD,5 Marcelo Hochman, MD,6 Arin Greene, MD, MMSc,3 and Joyce Bischoff, PhD1,2

De novo variant of TRRAP in a patient with very early onset psychosis in the context of non-verbal learning disability and obsessive-compulsive disorder: a case report.

Mavros CF, Brownstein CA, Thyagrajan R, Genetti CA, Tembulkar S, Graber K, Murphy Q, Cabral K, VanNoy GE, Bainbridge M, Shi J, Agrawal PB, Beggs AH, D'Angelo E, Gonzalez-Heydrich J.

BMC Med Genet. 2018 Nov 13;19(1):197. doi: 10.1186/s12881-018-0711-9.

PMID: 30424743

Methods for differentiation 

United States Patent Application 20190106677

Kind Code:

A1

Inventors: LI, Victor Chun (Boston, MA, US), Kirschner, Marc W. (Newton, MA, US)

DNA Gene Expression to Study Immunologic Mechanisms for the Long-Term Cure of Malaria in Babies and Children in South-Western Nigeria

Jerry T. Thornthwaite, Akanni E. Olufemi, Ayankunle A. Ademola, O. A. T. Alli