Rare Disease

Research

Advancing Understanding
of Rare Disease

Annually, up to 10 percent of the nearly 4 million babies born in the US are hospitalized in an intensive care unit due to an underlying rare genetic disease. Without proper diagnosis and treatment, some such disorders can lead to permanent disability or even death.

Many rare genetic diseases are never seen by most physicians, as they affect very few children worldwide. This creates challenges in recognizing the condition and knowing how to treat it.

At RCIGM, we want to provide accurate information when a rare disorder is diagnosed to enable families and their healthcare teams to make informed decisions about treatment. 

Knowledge Generation

  • We identify new diseases.
  • We study the normal disease progression of the rare diseases we diagnose.
  • We evaluate treatments for rare disease, including trying medicines not previously used in children, and participating in research with drug companies to evaluate the efficacy of potential new therapies.

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Key Facts

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Publications

Addressing the needs of nano-rare patients: the n-Lorem experience

  • Crooke ST, Glass S, Gleeson JG, Mignon L, Skourti-Stathaki K, Douville J, Knutsen M, Pu H, Bain JM, Berry-Kravis E, Shneider NA, Kim-McManus O, Eichler FS, Chung WK, Nagy A, Kaufmann H, Gonzalez-Duarte A, Oskarsson B, McCourt EA, Leung N.

Nucleic Acids Res. 2026 May 20;54(10):gkag504. doi: 10.1093/nar/gkag504.

ABSTRACT

Patients with extremely rare pathogenic variants pose unique challenges to current healthcare systems. Nano-rare mutations have been defined as mutations with a known prevalence of <30 patients worldwide, but because of the small fraction of humans who have undergone genetic testing, neither the precise prevalence of individual mutations nor the total prevalence of patients with nano-rare mutations is known. n-Lorem is a non-profit founded in 2020 with the mission of equitably discovering, developing, and providing bespoke experimental antisense oligonucleotides (ASOs) for free, for life, to patients with nano-rare mutations that are amenable to ASO treatment. In this perspective, we provide an overview of the n-Lorem processes and systems, the characteristics of the first 329 patients who have applied for treatment for whom initial assessment was completed and suitability for ASO treatment determined, and a summary of the results of ASO treatment for patients treated to date. Detailed data on individual patients and the overall clinical safety and tolerability profiles of the ASOs for which there are clinical data are the subjects of other manuscripts.

PMID:42227334 | DOI:10.1093/nar/gkag504

Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations

  • Kobren SN, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Corona RI, Carvalho Neto GV, Willett J, Berselli M, Ronchetti W, Nelson SF, Martinez-Agosto JA, Sherwood R, Krier J, Kohane IS; Undiagnosed Diseases Network; Sunyaev SR.

Nat Commun. 2025 Aug 7;16(1):7267. doi: 10.1038/s41467-025-61712-2.

ABSTRACT

Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform in-depth analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development. The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale case-based diagnostic analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser ( https://dbmi-bgm.github.io/udn-browser/ ). These results show that case-level diagnostic efforts should be supplemented by a joint genomic analysis across cohorts.

PMID:40770127 | DOI:10.1038/s41467-025-61712-2

The contribution of de novo coding mutations to meningomyelocele

  • Ha YJ, Nisal A, Tang I, Lee C, Jhamb I, Wallace C, Howarth R, Schroeder S, Vong KL, Meave N, Jiwani F, Barrows C, Lee S, Jiang N, Patel A, Bagga K, Banka N, Friedman L, Blanco FA, Yu S, Rhee S, Jeong HS, Plutzer I, Major MB, Benoit B, Poüs C, Heffner C, Kibar Z, Bot GM, Northrup H, Au KS, Strain M, Ashley-Koch AE, Finnell RH, Le JT, Meltzer HS, Araujo C, Machado HR, Stevenson RE, Yurrita A, Mumtaz S, Ahmed A, Khara MH, Mutchinick OM, Medina-Bereciartu JR, Hildebrandt F, Melikishvili G, Marwan AI, Capra V, Noureldeen MM, Salem AMS, Issa MY, Zaki MS, Xu L, Lee JE, Shin D, Alkelai A, Shuldiner AR, Kingsmore SF, Murray SA, Gee HY, Miller WT, Tolias KF, Wallingford JB; Spina Bifida Sequencing Consortium; Kim S, Gleeson JG. The contribution of de novo coding mutations to meningomyelocele. Nature. 2025 Mar 26. doi: 10.1038/s41586-025-08676-x. Epub ahead of print. PMID: 40140573.

Nature. 2025 Mar 26. doi: 10.1038/s41586-025-08676-x. Online ahead of print.

ABSTRACT

Meningomyelocele (also known as spina bifida) is considered to be a genetically complex disease resulting from a failure of the neural tube to close. Individuals with meningomyelocele display neuromotor disability and frequent hydrocephalus, requiring ventricular shunting. A few genes have been proposed to contribute to disease susceptibility, but beyond that it remains unexplained1. We postulated that de novo mutations under purifying selection contribute to the risk of developing meningomyelocele2. Here we recruited a cohort of 851 meningomyelocele trios who required shunting at birth and 732 control trios, and found that de novo likely gene disruption or damaging missense mutations occurred in approximately 22.3% of subjects, with 28% of such variants estimated to contribute to disease risk. The 187 genes with damaging de novo mutations collectively define networks including actin cytoskeleton and microtubule-based processes, Netrin-1 signalling and chromatin-modifying enzymes. Gene validation demonstrated partial or complete loss of function, impaired signalling and defective closure of the neural tube in Xenopus embryos. Our results indicate that de novo mutations make key contributions to meningomyelocele risk, and highlight critical pathways required for neural tube closure in human embryogenesis.

PMID:40140573 | DOI:10.1038/s41586-025-08676-x

The growing research toolbox for SLC13A5 citrate transporter disorder: a rare disease with animal models, cell lines, an ongoing Natural History Study and an engaged patient advocacy organization

  • Brown TL, Bainbridge MN, Zahn G, Nye KL, Porter BE.

Ther Adv Rare Dis. 2024 Jul 31;5:26330040241263972. doi: 10.1177/26330040241263972. eCollection 2024 Jan-Dec.

ABSTRACT

TESS Research Foundation (TESS) is a patient-led nonprofit organization seeking to understand the basic biology and clinical impact of pathogenic variants in the SLC13A5 gene. TESS aims to improve the fundamental understanding of citrate’s role in the brain, and ultimately identify treatments and cures for the associated disease. TESS identifies, organizes, and develops collaboration between researchers, patients, clinicians, and the pharmaceutical industry to improve the lives of those suffering from SLC13A5 citrate transport disorder. TESS and its partners have developed multiple molecular tools, cellular and animal models, and taken the first steps toward drug discovery and development for this disease. However, much remains to be done to improve our understanding of the disorder associated with SLC13A5 variants and identify effective treatments for this devastating disease. Here, we describe the available SLC13A5 resources from the community of experts, to foundational tools, to in vivo and in vitro tools, and discuss unanswered research questions needed to move closer to a cure.

PMID:39091896 | PMC:PMC11292725 | DOI:10.1177/26330040241263972

Biallelic Loss of Function Variants in SENP7 Cause Immunodeficiency with Neurologic and Muscular Phenotypes

  • Kobayashi ES, Lotan NS, Schejter YD, Makowski C, Kraus V, Ramchandar N, Meiner V, Thiffault I, Farrow E, Cakici J, Kingsmore S, Wagner M, Rieber N, Bainbridge M.

J Pediatr. 2024 Jul 4:114180. doi: 10.1016/j.jpeds.2024.114180. Online ahead of print.

ABSTRACT

To evaluate a novel candidate disease gene, we engaged international collaborators and identified rare, biallelic, specifically homozygous, loss of function variants in SENP7 in four children from three unrelated families presenting with neurodevelopmental abnormalities, dysmorphism, and immunodeficiency. Their clinical presentations were characterized by hypogammaglobulinemia, intermittent neutropenia, and ultimately death in infancy for all four patients. SENP7 is a sentrin-specific protease involved in posttranslational modification of proteins essential for cell regulation, via a process referred to as deSUMOylation. We propose that deficiency of deSUMOylation may represent a novel mechanism of primary immunodeficiency.

PMID:38972567 | DOI:10.1016/j.jpeds.2024.114180

Genome Sequencing for Diagnosing Rare Diseases

  • Wojcik MH, Lemire G, Berger E, Zaki MS, Wissmann M, Win W, White SM, Weisburd B, Wieczorek D, Waddell LB, Verboon JM, VanNoy GE, Töpf A, Tan TY, Syrbe S, Strehlow V, Straub V, Stenton SL, Snow H, Singer-Berk M, Silver J, Shril S, Seaby EG, Schneider R, Sankaran VG, Sanchis-Juan A, Russell KA, Reinson K, Ravenscroft G, Radtke M, Popp D, Polster T, Platzer K, Pierce EA, Place EM, Pajusalu S, Pais L, Õunap K, Osei-Owusu I, Opperman H, Okur V, Oja KT, O'Leary M, O'Heir E, Morel CF, Merkenschlager A, Marchant RG, Mangilog BE, Madden JA, MacArthur D, Lovgren A, Lerner-Ellis JP, Lin J, Laing N, Hildebrandt F, Hentschel J, Groopman E, Goodrich J, Gleeson JG, Ghaoui R, Genetti CA, Gburek-Augustat J, Gazda HT, Ganesh VS, Ganapathi M, Gallacher L, Fu JM, Evangelista E, England E, Donkervoort S, DiTroia S, Cooper ST, Chung WK, Christodoulou J, Chao KR, Cato LD, Bujakowska KM, Bryen SJ, Brand H, Bönnemann CG, Beggs AH, Baxter SM, Bartolomaeus T, Agrawal PB, Talkowski M, Austin-Tse C, Abou Jamra R, Rehm HL, O'Donnell-Luria A.

N Engl J Med. 2024 Jun 6;390(21):1985-1997. doi: 10.1056/NEJMoa2314761.

ABSTRACT

BACKGROUND: Genetic variants that cause rare disorders may remain elusive even after expansive testing, such as exome sequencing. The diagnostic yield of genome sequencing, particularly after a negative evaluation, remains poorly defined.

METHODS: We sequenced and analyzed the genomes of families with diverse phenotypes who were suspected to have a rare monogenic disease and for whom genetic testing had not revealed a diagnosis, as well as the genomes of a replication cohort at an independent clinical center.

RESULTS: We sequenced the genomes of 822 families (744 in the initial cohort and 78 in the replication cohort) and made a molecular diagnosis in 218 of 744 families (29.3%). Of the 218 families, 61 (28.0%) – 8.2% of families in the initial cohort – had variants that required genome sequencing for identification, including coding variants, intronic variants, small structural variants, copy-neutral inversions, complex rearrangements, and tandem repeat expansions. Most families in which a molecular diagnosis was made after previous nondiagnostic exome sequencing (63.5%) had variants that could be detected by reanalysis of the exome-sequence data (53.4%) or by additional analytic methods, such as copy-number variant calling, to exome-sequence data (10.8%). We obtained similar results in the replication cohort: in 33% of the families in which a molecular diagnosis was made, or 8% of the cohort, genome sequencing was required, which showed the applicability of these findings to both research and clinical environments.

CONCLUSIONS: The diagnostic yield of genome sequencing in a large, diverse research cohort and in a small clinical cohort of persons who had previously undergone genetic testing was approximately 8% and included several types of pathogenic variation that had not previously been detected by means of exome sequencing or other techniques. (Funded by the National Human Genome Research Institute and others.).

PMID:38838312 | DOI:10.1056/NEJMoa2314761

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Read more about this groundbreaking work.

Robert Wechler-Reva

PHD, Neuro-Oncology Program Director

Noted scientist Robert Wechsler-Reya, PhD, is also a professor and researcher at the Sanford Burnham Prebys Medical Discovery Institute (SBP) where he is focused on investigating the genes and nervous system signaling pathways that contribute to medulloblastoma, the most common malignant brain tumor in children.

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News Features

IN THE NEWS

October 22, 2020

Variety.com

Inside Our Child’s Battle With Mitochondrial Disease

“Despite a beautiful pregnancy and delivery with every prenatal screening and precaution taken, Evan was born with mitochondrial disease.” Lindzi Scharf shares a … Read More
IN THE NEWS

October 14, 2020

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