Neurogenomics

Research

Cracking
the Code

Identifying the cause of neurological disorders and early intervention are key to reducing the devastating brain damage that can occur. 

Neurological disorders can be caused both by inherited and random gene variations. Often, the first sign of a disorder in a newborn is unexplained seizures. 

RCIGM is involved in both foundational and translational research.

Neurodevelopmental Genetics

RCIGM investigations into inherited brain disorders focus on poorly understood conditions in neuronal development where the application of human genetics, wet-lab disease modeling and cell biology can be used to develop new treatments.
190227RadySeminar

Joseph Gleeson, MD

RCIGM Director of Neurodevelopmental Genetics Endowed Chair

Joseph Gleeson, MD, is the RCIGM Director of Neurodevelopmental Genetics Endowed Chair. Among his current research projects is a genetic investigation of the genetic mechanisms underlying spina bifida, the most common structural defect of the central nervous system.

In 2020 Dr. Gleeson along with other researchers at UC San Diego School of Medicine, in collaboration with Rady Children’s Institute for Genomic Medicine, were awarded an $8.3 million grant from the National Institutes of Health’s Eunice Kennedy Shriver National Institute of Child Health and Human Development to further illuminate the causes of spina bifida.

Dr. Gleeson also heads the Neurogenetics Laboratory at UC San Diego and is the Director of the Center for Brain Development. He is the 2020 recipient of the Bernard Sachs Award from the Child Neurology Society. In 2017, he was the first recipient of the Constance Lieber Prize for Innovation in Developmental Neuroscience.

Publications

COXFA4L2 upregulation preserves residual cytochrome c oxidase activity in COXFA4-related Leigh-like encephalopathy

  • Falabella M, Lopez Calcerrada S, Aref J, Gao J, Macken WL, Pizzamiglio C, Kabiljo R, Francavilla AL, Gaignard P, Pouzet A, Levy J, Barcia G, Leighton JK, Chronopoulou E, Pierre G, Köksal Özgül R, Dursun A, Halligan R, Mundy H, Raza Alvi J, Sultan T, Craigen WJ, Emrick L, Rosenfeld JA, Elmakkawy G, Kim J, Gleeson JJ, Rad A, Oprea G, Hussain M, Rehman KU, Riaz S, Taylor RW, Procaccio V, Zaki MS, Fernandez-Vizarra E, Pierri CL, Hanna MG, Houlden H, Maroofian R, Ugalde C, Taanman JW, Pitceathly RDS.

Nat Commun. 2026 May 30. doi: 10.1038/s41467-026-73455-9. Online ahead of print.

ABSTRACT

Primary mitochondrial diseases (PMDs) affect approximately 1 in 4300 individuals and cause early-onset neuromuscular and multisystem dysfunction with reduced lifespan. They result from pathogenic variants in mitochondrial or nuclear DNA that impair oxidative phosphorylation. Cytochrome c oxidase (COX; complex IV) deficiency is a well-established cause of PMD, leading to a broad spectrum of phenotypes. COXFA4 (cytochrome c oxidase subunit FA4), formerly NDUFA4, is a nuclear-encoded COX subunit, but its role in disease remains poorly defined. We report the largest genetically confirmed cohort of COXFA4-related PMD to date, comprising 13 individuals from 12 families with biallelic pathogenic COXFA4 variants. All present with Leigh-like encephalopathy and complete loss of COXFA4 protein; however, patient-derived fibroblasts retain residual COX activity, with upregulation of COXFA4L2 (cytochrome c oxidase subunit FA4-like 2), a poorly characterised paralog. Here, we show that COXFA4 is a late-stage COX assembly subunit and identify a paralog-mediated compensatory mechanism with translational potential.

PMID:42218136 | DOI:10.1038/s41467-026-73455-9

Essential genetic testing in movement disorders – results from a Delphi study

  • Carvalho V, Guedes LC, Gatto E, Rodriguez-Violante M, Klein C, Rodriguez-Porcel F, Morgante F, Rossi M, Miranda M, Ganos C, Riboldi GM, Cesarini M, Darling A, Skorvanek M, van de Warrenburg B, Shalash A, Cossu G, Friedman J, Albanese A, Cardozo A, Lohmann K, Thaler A, Stamelou M, Saunders-Pullman R, Marras C, Sarva H, Bhatia KP, Ferreira JJ.

Parkinsonism Relat Disord. 2026 May 22;148:108367. doi: 10.1016/j.parkreldis.2026.108367. Online ahead of print.

ABSTRACT

BACKGROUND: While genetic testing in Movement Disorders (MD) has expanded enormously, access to genetic testing and genetic counseling remains asymmetric at the global scale. Guidance on efficient testing strategies for clinicians, governments and stakeholders is crucial.

OBJECTIVES: Establish a list of genetic movement disorders considered essential as determined by a group of MD experts.

METHODS: All genes associated with MD were searched using the OMIM and MDS Gene database. We collected all additional tests available at 4 different laboratories from the EuroGentest database. The results were compiled in 6 questionnaires. A genetic test was considered essential if molecular testing had a direct impact in the management of the patient, including treatment of the disease or its comorbidities, or genetic counseling of the patient and family members. Two Delphi rounds were conducted asking MD experts which specific tests they considered essential in an adult MD clinic.

RESULTS: Fifty-nine disorders were considered essential to genetically identify by the MD experts. This included 25 genes associated with ataxia, 15 with parkinsonism, 14 with dystonia, eight with chorea, five with paroxysmal disorders, four with myoclonus, four with hereditary spastic paraparesis, and one with tremor. Sixteen disorders reached 100% consensus among experts: Huntington’s disease, PxMD-PPRT2, Wilson’s disease, DYT-SGCE, DYT-THAP1, DYT-TOR1A, DYT/PARK-GCH1, Fragile-X Tremor-ataxia syndrome, PARK-GBA, PARK-LRRK2, PARK-PINK1, PARK-PRKN, PARK-SNCA, Cerebrotendinous Xanthomatosis, Ataxia-Telangiectasia, and Niemann-Pick disease type C.

CONCLUSION: This study provides a list of genetic MD that should be molecularly tested in adult centers with a compatible phenotype according to a group of MD experts.

PMID:42202611 | DOI:10.1016/j.parkreldis.2026.108367

Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism

  • Mortazavi M, Guevara J, Diaz J, Tran S, Ziaei Jam H, Reeves C, Batalov S, Jepsen K, Bainbridge M, Besterman AD, Gymrek M, Palmer AA, Sebat J.

Cell Genom. 2026 Mar 9:101186. doi: 10.1016/j.xgen.2026.101186. Online ahead of print.

ABSTRACT

Long-read whole-genome sequencing (LR-WGS) technologies enhance the discovery of structural variants (SVs) and tandem repeats (TRs). We performed LR-WGS on 267 individuals from 63 autism spectrum disorder (ASD) families and generated an integrated call set combining long- and short-read data. LR-WGS increased detection of gene-disrupting SVs and TRs by 33% and 38%, respectively, and enabled identification of novel exonic de novo germline and somatic SVs. We observed complex SV patterns, including a class of nested duplication-deletion events. By joint analysis of phased genetic variation and DNA methylation, we identified deletions of imprinted genes and demonstrated the effect of intermediate TR expansions (35-54 CGG) on the methylation of FMR1 promoter. Rare SVs, TRs, and damaging SNVs together accounted for 7.4% (95% confidence interval [CI], 2.7%-17%) of the heritability of ASD. These findings demonstrate how LR-WGS can resolve complex genetic variation and its functional consequences and regulatory effects in a single assay.

PMID:41806827 | DOI:10.1016/j.xgen.2026.101186

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Genetic Neurologic Disease

Neurologic Movement Disorders

RCIGM focuses on translational research in pediatric neurologic movement disorders, particularly those resulting from genetic or metabolic conditions. 

Investigations into genetic underpinnings of neurologic movement disorders is led by Jennifer Friedman, MD. Her work involves sequencing children with unexplained neurologic disease to identify diagnosis and treatment options.

Dr. Friedman’s research is aimed at ending the diagnostic odyssey by bringing diagnoses to patients and families; shortening the therapeutic odyssey by delivering precision neurologic care and identifying novel genes for rare neurologic disorders.

headshot of Dr. Jenni Friedman

Jennifer Friedman, MD

Dr. Jennifer Friedman is the Translational Medicine Director for the Precision Medicine Clinic at Rady Children’s Hospital, where she is also a senior staff neurologist. In addition, she serves as clinical professor in the UC San Diego Departments of Neurosciences and Pediatrics. 

Dr. Friedman is a diplomate of the American Board of Psychiatry and Neurology. She is a member of the American Academy of Neurology, the Movement Disorder Society, the Tourette Syndrome Association, and the Phi Beta Kappa National Honor Society. 

Publications

Disease insights from brain somatic mosaicism

  • Chung C, Nedunuri R, Gleeson JG.

Exp Mol Med. 2026 Apr 8. doi: 10.1038/s12276-024-01331-x. Online ahead of print.

ABSTRACT

Brain somatic mosaicism (BSM) refers to genome variation within brain cells that results from accumulated postzygotic mutations. These mutations can be used to understand cell lineage, molecular dynamics and disease processes. Unlike most other organs, brain cells are mostly fixed in position and not replaced throughout life. Thus, assessing mosaic variants (MVs) within the brain, including their spread and cell type-specific distributions and correlations with aging and cellular health, can reveal insights into neurodevelopmental, neuropsychiatric and neurodegenerative diseases. Extracting genetic material from human surgical brain resections, pregnancy remnants, or postmortem samples can reveal the origins of brain cells and uncover the effects of aging and disease on genomic integrity. Technological advances combining high-read-depth bulk sequencing, isolation of specific brain cell types, and single-cell multiomics can both detect and quantify MVs with good precision and recall. Research exploiting brain MVs is revolutionizing the understanding of the origins, mechanisms and potential treatments for brain conditions.

PMID:41951903 | DOI:10.1038/s12276-024-01331-x

Systematic analysis of snRNA genes reveals frequent RNU2-2 variants in dominant and recessive developmental and epileptic encephalopathies

  • Leitão E, Santini A, Cogne B, Essid M, Athanasiadou M, LaFlamme CW, Marijon P, Bernard V, Jousselin K, Chatron N, Barcia G, Keren B, Mignot C, Charles P, Besnard T, Paluch R, de Sainte Agathe JM, Almanza Fuerte EP, Sengupta S, Milh M, Ramond F, Allan T, An I, Araujo C, Arpin S, Austin-Tse C, Auvin S, Baer S, Bahi-Buisson N, Bak M, Barth M, Baulac S, Bednarek-Weirauch N, Begemann M, Bennett MF, Bensabath U, Bézieau S, Bhouri R, Biehler M, Hammer TB, Bogoin J, Bonanno E, Boussion S, Bris C, Brosseau-Beauvir A, Bruel AL, Briand-Suleau A, Buratti J, Celse T, Chambon P, Chemaly N, Chesneau B, Colin E, Colmard M, Colson C, Conrad S, Courtin T, Creveaux I, Cullier AC, Dang LT, de Saint Martin A, de Vanssay de Blavous Legendre C, Demeer B, Denommé-Pichon AS, Diekhoff P, DiTroia S, Doco-Fenzy M, Dubourg C, Dubucs C, Ducreux S, Dufour L, Duquet R, Durand B, El Chehadeh S, Elbracht M, Faivre L, Faoucher M, Faudet A, Forlani S, Fradin M, Gaignard P, Ganne B, Garde A, Géraud J, Gill D, Goldenberg A, Grabli D, Grisel C, Gueden S, Gueguen P, Guerrot AM, Guichet A, Haack TB, Härting N, Häusler MG, Heide S, Herget T, Héron B, Héron D, Herwig J, Heulin M, Holling T, Houdayer C, Isidor B, Jacquette A, Januel L, Jean-Marçais N, Kaiser FJ, Kaya S, King C, Konyukh M, Kraft F, Krause J, Kirstetter R, Kuechler A, Kurth I, Kutsche K, Labalme A, Laloy JS, Laugel V, Le Bricquir F, Lèbre AS, Lebrun M, Leguern E, Levy J, Lieffering N, Lyonnet S, Lüthy K, Macdonald SMW, Mansour-Hendili L, Maraval J, Marquardt I, Mattausch C, Mercier S, Messaoud O, Morel G, Mortreux J, Munnich A, Nabbout R, Nambot S, Navarro V, Neale A, Nguyen L, Nizon M, Nowak F, O'Leary MC, Odent S, Ojeda NM, Olin V, Olivieri S, Õunap K, Pais LS, Panagiotakaki E, Patat O, Perrin-Sabourin L, Petit F, Philippe C, Piton A, Planes M, Poirsier C, Pouzet A, Prouteau C, Quéméner-Redon S, Renaud M, Richard AC, Rio M, Rivier C, Robin-Renaldo F, Rollier P, Rossi M, Roubertie A, Ruault V, Rupin-Mas M, Saugier-Veber P, Saunier A, Saneto R, Sarrazin E, Sarret C, Schaefer E, Schluth-Bolard C, Schneider A, Schumann I, Seplyarskiy VB, Spranger S, Smol T, Sturm M, Sunyaev SR, Sperelakis-Beedham B, Stenton SL, Stock F, Tharreau M, Torun D, Toulouse J, Thiyagarajah H, Valence S, Valleix S, Van-Gils J, Villard L, Ville D, Villeneuve N, Vitobello A, Waernessyckle A, Wagner J, Weber Y, Wieczorek D, Witkowski T, Yadavilli M, Yammine T, Zaafrane-Khachnaoui K, Zaki MS, Ziegler A, Bramswig NC, Lermine A, Nicolas G, Gleeson JG, Sadleir LG, Hildebrand MS, Scheffer IE, Whiffin N, O'Donnell-Luria A, Mefford HC, Blanc P, Thevenon J, Charbonnier C, Charenton C, Depienne C, Lesca G, Nava C.

Nat Genet. 2026 Mar 30. doi: 10.1038/s41588-026-02547-5. Online ahead of print.

ABSTRACT

Small nuclear RNAs (snRNAs) are essential components of the spliceosome. De novo variants in snRNA genes RNU4-2 (ReNU syndrome), RNU5B-1 and RNU2-2 have been linked to dominant neurodevelopmental disorders (NDDs), revealing a large unexpected contribution of noncoding RNA genes to genetic diseases. Here, through international collaborations, we analyze systematically 200 potentially functional snRNA genes in a French cohort of 34,329 people with rare disorders. We report RNU2-2 variants in 141 individuals, including 35 with recurrent dominant pathogenic variants and 91 affected members from 73 families with biallelic variants. Recessive RNU2-2 NDD is at least twice as frequent as the dominant form and often involves a de novo variant in trans with an inherited allele, consistent with the high mutability of snRNA genes. Dominant and recessive RNU2-2 NDDs share overlapping clinical features, with frequent epilepsy. Blood transcriptomics and DNA methylation analyses revealed subtle, variant-specific effects on splicing and episignatures. Our results support a gradient-of-impact model bridging dominant and recessive inheritance, and establish RNU2-2 variants as a principal contributor to NDDs, nearly as prevalent as ReNU syndrome.

PMID:41912934 | DOI:10.1038/s41588-026-02547-5

De novo mutations and environmental modifiers: lessons from neural tube defects

  • Li HY, Shen Y, Vong KI, Kahle KT, Gleeson JG.

Trends Genet. 2026 Mar 18:S0168-9525(26)00030-2. doi: 10.1016/j.tig.2026.01.011. Online ahead of print.

ABSTRACT

Spina bifida is a clinically and etiologically heterogeneous group of neural tube defects (NTDs) that includes meningomyelocele. While folic acid (FA) supplementation has reduced the incidence by 30-50%, genetic contributors remain only partially understood. New trio sequencing technology has identified de novo mutations (DNMs) in 20-25% of patients. Two recent large-scale genomic studies identified DNMs in 187 candidate genes and a recurrent 22q11.2 deletion as risk factors. Partial penetrance and variable expressivity are frequent, suggesting that risk is dependent upon FA and other modifiers. The Spina Bifida Sequencing Consortium supports large-scale data sharing for multidisciplinary approaches, emphasizing high-confidence NTD genes and moving the results toward clinical testing.

PMID:41850968 | DOI:10.1016/j.tig.2026.01.011

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Discovery of Endocannabinoid Gene Mutation Leads to Identification of  New, Rare Pediatric Neurological Disease

In a study published in the October 2022 issue of BRAIN, researchers from Rady Children’s Institute for Genomic Medicine (RCIGM®) and the University of California San Diego School of Medicine describe their discovery of a new clinical syndrome, Neuro-Ocular DAGLA-related Syndrome (NODRS), in children with termination variants in the diacylglycerol lipase alpha (DAGLA) gene which encodes an enzyme in the brain that is involved in the signaling pathway of the endocannabinoid (eCB) system.

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