Diagnostic_Relevance_and_June_Lit

data/STRchive-citations.json

@@ -162938,6 +162938,255 @@
   "language": "eng",
   "note": "PMID: 20301458\nThis CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: url:https://www.ncbi.nlm.nih.gov/books/NBK1281"
 },
+{
+  "id": "pmid:40015980",
+  "manubot_success": true,
+  "link": "https://www.ncbi.nlm.nih.gov/pubmed/40015980",
+  "title": "A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia.",
+  "type": "article-journal",
+  "doi": "10.1101/gr.279634.124",
+  "authors": [
+    ["Haloom", "Rafehi"],
+    ["Liam G", "Fearnley"],
+    ["Justin", "Read"],
+    ["Penny", "Snell"],
+    ["Kayli C", "Davies"],
+    ["Liam", "Scott"],
+    ["Greta", "Gillies"],
+    ["Genevieve C", "Thompson"],
+    ["Tess A", "Field"],
+    ["Aleena", "Eldo"],
+    ["Simon", "Bodek"],
+    ["Ernest", "Butler"],
+    ["Luke", "Chen"],
+    ["John", "Drago"],
+    ["Himanshu", "Goel"],
+    ["Anna", "Hackett"],
+    ["G Michael", "Halmagyi"],
+    ["Andrew", "Hannaford"],
+    ["Katya", "Kotschet"],
+    ["Kishore R", "Kumar"],
+    ["Smitha", "Kumble"],
+    ["Matthew", "Lee-Archer"],
+    ["Abhishek", "Malhotra"],
+    ["Mark", "Paine"],
+    ["Michael", "Poon"],
+    ["Kate", "Pope"],
+    ["Katrina", "Reardon"],
+    ["Steven", "Ring"],
+    ["Anne", "Ronan"],
+    ["Matthew", "Silsby"],
+    ["Renee", "Smyth"],
+    ["Chloe", "Stutterd"],
+    ["Mathew", "Wallis"],
+    ["John", "Waterston"],
+    ["Thomas", "Wellings"],
+    ["Kirsty", "West"],
+    ["Christine", "Wools"],
+    ["Kathy H C", "Wu"],
+    ["David J", "Szmulewicz"],
+    ["Martin B", "Delatycki"],
+    ["Melanie", "Bahlo"],
+    ["Paul J", "Lockhart"]
+  ],
+  "publisher": "Genome research",
+  "issn": "1549-5469",
+  "date": "2025-04-14",
+  "abstract": "The cerebellar ataxias (CAs) are a heterogeneous group of disorders characterized by progressive incoordination. Seventeen repeat expansion (RE) loci have been identified as the primary genetic cause and account for >80% of genetic diagnoses. Despite this, diagnostic testing is limited and inefficient, often utilizing single gene assays. This study evaluates the effectiveness of long- and short-read sequencing as diagnostic tools for CA. We recruited 110 individuals (48 females, 62 males) with a clinical diagnosis of CA. Short-read genome sequencing (SR-GS) was performed to identify pathogenic RE and also non-RE variants in 356 genes associated with CA. Independently, long-read sequencing with adaptive sampling (LR-AS) was performed to identify pathogenic RE. SR-GS provided a genetic diagnosis for 38% of the cohort (40/110) including seven non-RE pathogenic variants. RE causes disease in 33 individuals, with the most common condition being SCA27B (",
+  "language": "en",
+  "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:40015980"
+},
+{
+  "id": "pmid:39996131",
+  "manubot_success": true,
+  "link": "https://www.ncbi.nlm.nih.gov/pubmed/39996131",
+  "title": "Redefining the Pathogenic CAG Repeat Units Threshold in",
+  "type": "article-journal",
+  "doi": "10.1212/nxg.0000000000200245",
+  "authors": [
+    ["Yuya", "Hatano"],
+    ["Tomohiko", "Ishihara"],
+    ["Sachiko", "Hirokawa"],
+    ["Hidetoshi", "Date"],
+    ["Yuji", "Takahashi"],
+    ["Hidehiro", "Mizusawa"],
+    ["Osamu", "Onodera"]
+  ],
+  "publisher": "Neurology. Genetics",
+  "issn": "2376-7839",
+  "date": "2025-02-21",
+  "abstract": "Spinocerebellar ataxia type 6 (SCA6) is caused by expansion of CAG repeat units (RUs) in",
+  "language": "en",
+  "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:39996131"
+},
+{
+  "id": "pmid:41285770",
+  "manubot_success": true,
+  "link": "https://www.ncbi.nlm.nih.gov/pubmed/41285770",
+  "title": "Targeted sequencing and iterative assembly of near-complete genomes.",
+  "type": "article-journal",
+  "doi": "10.1038/s41467-025-65410-x",
+  "authors": [
+    ["Hasindu", "Gamaarachchi"],
+    ["Igor", "Stevanovski"],
+    ["Jillian M", "Hammond"],
+    ["Andre L", "M Reis"],
+    ["Melissa", "Rapadas"],
+    ["Kavindu", "Jayasooriya"],
+    ["Tonia", "Russell"],
+    ["Dennis", "Yeow"],
+    ["Yvonne", "Hort"],
+    ["Chirag", "Patel"],
+    ["Andrew J", "Mallett"],
+    ["Elaine", "Stackpoole"],
+    ["Lauren", "Roman"],
+    ["Luke W", "Silver"],
+    ["Carolyn J", "Hogg"],
+    ["Louise M", "Streeting"],
+    ["Ozren", "Bogdanovic"],
+    ["Renata", "Coelho Rodrigues Noronha"],
+    ["Lu\u00eds Adriano", "Santos do Nascimento"],
+    ["Adauto", "Lima Cardoso"],
+    ["Arthur", "Georges"],
+    ["Haoyu", "Cheng"],
+    ["Hardip R", "Patel"],
+    ["Kishore Raj", "Kumar"],
+    ["Amali C", "Mallawaarachchi"],
+    ["Ira W", "Deveson"]
+  ],
+  "publisher": "Nature communications",
+  "issn": "2041-1723",
+  "date": "2025-11-24",
+  "abstract": "Advances in long-read sequencing (LRS) and assembly algorithms have made it possible to create highly complete genome assemblies for humans, animals and plants. However, ongoing development is needed to improve accessibility, affordability, and assembly quality and completeness. 'Cornetto' is a new strategy in which we use programmable selective nanopore sequencing to focus LRS data production onto the unsolved regions of a nascent assembly. This improves assembly quality and streamlines the process, both for humans and non-human vertebrates. Cornetto enables us to generate highly complete diploid human genome assemblies using only nanopore LRS data, surpassing the quality of previous efforts at a fraction of the cost. Cornetto enables genome assembly from challenging sample types like human saliva. Finally, we obtain accurate assemblies for clinically-relevant repetitive loci at the extremes of the genome, demonstrating valid approaches for genetic diagnosis in facioscapulohumeral muscular dystrophy (FSHD) and MUC1-autosomal dominant tubulointerstitial kidney disease (MUC1-ADTKD).",
+  "language": "en",
+  "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:41285770"
+},
+{
+  "id": "pmid:40751262",
+  "manubot_success": true,
+  "link": "https://www.ncbi.nlm.nih.gov/pubmed/40751262",
+  "title": "A CGG Repeat Expansion in CSNK1E Associated with Progressive Myoclonic Epilepsy with Incomplete Penetrance.",
+  "type": "article-journal",
+  "doi": "10.1002/mds.30326",
+  "authors": [
+    ["Fulya", "Ak\u00e7imen"],
+    ["Pilar", "Alvarez Jerez"],
+    ["Ulviyya", "Guliyeva"],
+    ["Jasmine", "Lee"],
+    ["Laksh", "Malik"],
+    ["Breeana", "Baker"],
+    ["Kamran", "Salayev"],
+    ["Sughra", "Guliyeva"],
+    ["Kimberley J", "Billingsley"],
+    ["Henry", "Houlden"],
+    ["Andrew B", "Singleton"],
+    ["Cornelis", "Blauwendraat"],
+    ["Sara", "Bandres-Ciga"],
+    ["Rauan", "Kaiyrzhanov"]
+  ],
+  "publisher": "Movement disorders : official journal of the Movement Disorder Society",
+  "issn": "1531-8257",
+  "date": "2025-08-01",
+  "abstract": "Progressive myoclonic epilepsy is a heterogeneous neurodegenerative disorder characterized by early-onset myoclonus, epilepsy, generalized tonic-clonic seizures, and progressive neurological deterioration. Recently, a CGG repeat expansion and increased CSNK1E DNA methylation have been shown to be associated with developmental and epileptic encephalopathies.",
+  "language": "en",
+  "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:40751262"
+},
+{
+  "id": "pmid:39107278",
+  "manubot_success": true,
+  "link": "https://www.ncbi.nlm.nih.gov/pubmed/39107278",
+  "title": "Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement.",
+  "type": "article-journal",
+  "doi": "10.1038/s41467-024-50159-6",
+  "authors": [
+    ["Christy W", "LaFlamme"],
+    ["Cassandra", "Rastin"],
+    ["Soham", "Sengupta"],
+    ["Helen E", "Pennington"],
+    ["Sophie J", "Russ-Hall"],
+    ["Amy L", "Schneider"],
+    ["Emily S", "Bonkowski"],
+    ["Edith P", "Almanza Fuerte"],
+    ["Talia J", "Allan"],
+    ["Miranda Perez-Galey", "Zalusky"],
+    ["Joy", "Goffena"],
+    ["Sophia B", "Gibson"],
+    ["Denis M", "Nyaga"],
+    ["Nico", "Lieffering"],
+    ["Malavika", "Hebbar"],
+    ["Emily V", "Walker"],
+    ["Daniel", "Darnell"],
+    ["Scott R", "Olsen"],
+    ["Pandurang", "Kolekar"],
+    ["Mohamed Nadhir", "Djekidel"],
+    ["Wojciech", "Rosikiewicz"],
+    ["Haley", "McConkey"],
+    ["Jennifer", "Kerkhof"],
+    ["Michael A", "Levy"],
+    ["Raissa", "Relator"],
+    ["Dorit", "Lev"],
+    ["Tally", "Lerman-Sagie"],
+    ["Kristen L", "Park"],
+    ["Marielle", "Alders"],
+    ["Gerarda", "Cappuccio"],
+    ["Nicolas", "Chatron"],
+    ["Leigh", "Demain"],
+    ["David", "Genevieve"],
+    ["Gaetan", "Lesca"],
+    ["Tony", "Roscioli"],
+    ["Damien", "Sanlaville"],
+    ["Matthew L", "Tedder"],
+    ["Sachin", "Gupta"],
+    ["Elizabeth A", "Jones"],
+    ["Monika", "Weisz-Hubshman"],
+    ["Shamika", "Ketkar"],
+    ["Hongzheng", "Dai"],
+    ["Kim C", "Worley"],
+    ["Jill A", "Rosenfeld"],
+    ["Hsiao-Tuan", "Chao"],
+    ["Geoffrey", "Neale"],
+    ["Gemma L", "Carvill"],
+    ["Zhaoming", "Wang"],
+    ["Samuel F", "Berkovic"],
+    ["Lynette G", "Sadleir"],
+    ["Danny E", "Miller"],
+    ["Ingrid E", "Scheffer"],
+    ["Bekim", "Sadikovic"],
+    ["Heather C", "Mefford"]
+  ],
+  "publisher": "Nature communications",
+  "issn": "2041-1723",
+  "date": "2024-08-06",
+  "abstract": "Sequence-based genetic testing identifies causative variants in ~\u200950% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850\u2009K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.",
+  "language": "en",
+  "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:39107278"
+},
+{
+  "id": "pmid:41929128",
+  "manubot_success": true,
+  "link": "https://www.ncbi.nlm.nih.gov/pubmed/41929128",
+  "title": "Muscleblind-like proteins dimerize by forming disulfide bonds to regulate alternative splicing and pathogenic RNA foci formation.",
+  "type": "article-journal",
+  "doi": "10.64898/2026.03.24.714019",
+  "authors": [
+    ["Luke A", "Knudson"],
+    ["Adam", "Kosti"],
+    ["Kathryn R", "Moss"],
+    ["Liang", "Shi"],
+    ["GiaLinh N", "Nguyen"],
+    ["Aleksandra", "Janusz-Kaminska"],
+    ["Eric X", "Zhou"],
+    ["Ryan P", "Hildebrandt"],
+    ["Eric T", "Wang"],
+    ["Gary J", "Bassell"]
+  ],
+  "publisher": "bioRxiv : the preprint server for biology",
+  "issn": "2692-8205",
+  "date": "2026-03-26",
+  "abstract": "Muscleblind-like (MBNL) RNA-binding proteins (RBPs) possess modular domains that mediate regulation of alternative splicing and RNA localization. Myotonic Dystrophy Type 1 is a CTG repeat expansion disorder where MBNL is sequestered into intranuclear RNA foci, impairing its function. Previous studies found that MBNL self-associates through its exon 7, but the nature of this interaction is not well understood. We identified a cysteine in MBNL1 exon 7 that enables dimerization through formation of an intermolecular disulfide bond. We likewise demonstrate that MBNL2 dimerizes by forming disulfide bonds between multiple cysteines in its carboxy-terminus. Nucleocytoplasmic fractionation revealed a greater proportion of MBNL1 dimer in the nucleus, suggesting a nuclear function for the MBNL1 dimer. We investigated a connection between MBNL1 dimerization and MBNL1-mediated regulation of alternative splicing. To accomplish this, we mutated the MBNL1 cysteine in question to alanine (C325A) and performed RNAseq. We uncovered novel splicing events sensitive to MBNL1 dimerization. We also found that MBNL1 C325A, when co-expressed with expanded CTG repeats, produces smaller, more numerous foci, suggesting a role for the MBNL1 dimer in maintaining foci integrity. These results provide insight into biological and pathological mechanisms of MBNL1 dimerization and suggest other RBPs might similarly dimerize to regulate function.",
+  "language": "en",
+  "note": "This CSL Item was generated by Manubot v0.6.1 from its persistent identifier (standard_id).\nstandard_id: pubmed:41929128"
+},
 {
   "id": "omim:309548",
   "manubot_success": false,