Scientific Publications

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Detection of Neisseria gonorrhoeae from Joint Aspirate by Metagenomic Sequencing in Disseminated Gonococcal Infection

Asmerom B, Drobish I, Winckler B, Chiang L, Farnaes L, Beauchamp-Walters J, Bradley JS, Ramchandar N.

J Pediatric Infect Dis Soc. 2021 Apr 3;10(3):367-369. doi: 10.1093/jpids/piaa108. ABSTRACT Disseminated gonococcal infection (DGI) often manifests as gonococcal arthritis and may carry significant morbidity. However, diagnosis remains elusive due to limited sensitivity of available diagnostic tests. We used metagenomic next-generation sequencing to detect Neisseria gonorrhoeae from culture-negative joint aspirates of 2 patients with clinically diagnosed DGI. PMID:32964934 | DOI:10.1093/jpids/piaa108

September 23, 2020

A New Standard in Graft-versus-Host Disease Prophylaxis? An Introduction to Blood and Marrow Transplant Clinical Trials Network 1703

DeFilipp Z, Burns LJ, Jaglowski SM, Leppin AL, Pavletic S, Waldman B, Weisdorf DJ, Wood WA, Khera N.

Biol Blood Marrow Transplant. 2020 Dec;26(12):e305-e308. doi: 10.1016/j.bbmt.2020.08.029. Epub 2020 Sep 10. ABSTRACT Effective immunosuppressive regimens to prevent the development of graft-versus-host disease (GVHD) are essential to the success of allogeneic hematopoietic cell transplantation (HCT). After revolutionizing haploidentical transplantation, post-transplantation cyclophosphamide (PTCy) is now being evaluated for HCT performed from related and unrelated donors. In this setting, 2 recent randomized studies have demonstrated lower rates of GVHD and superior GVHD-free, relapse-free survival with PTCy compared with conventional GVHD prophylaxis. The Blood and Marrow Transplant Clinical Trials Network (BMT CTN) is currently conducting a large, randomized phase III, multicenter trial (BMT CTN 1703) comparing PTCy/tacrolimus/mycophenolate mofetil to tacrolimus/methotrexate as GVHD prophylaxis regimens in reduced-intensity allogeneic HCT. Here we review the ongoing study, highlight its importance to the field, and explore the possible implications of its results on clinical practice. PMID:32920205 | PMC:PMC7735536 | DOI:10.1016/j.bbmt.2020.08.029

September 13, 2020

A relatively common homozygous TRAPPC4 splicing variant is associated with an early-infantile neurodegenerative syndrome

Ghosh SG, Scala M, Beetz C, Helman G, Stanley V, Yang X, Breuss MW, Mazaheri N, Selim L, Hadipour F, Pais L, Stutterd CA, Karageorgou V, Begtrup A, Crunk A, Juusola J, Willaert R, Flore LA, Kennelly K, Spencer C, Brown M, Trapane P, Hurst ACE, Lane Rutledge S, Goodloe DH, McDonald MT, Shashi V, Schoch K; Undiagnosed Diseases Network, Tomoum H, Zaitoun R, Hadipour Z, Galehdari H, Pagnamenta AT, Mojarrad M, Sedaghat A, Dias P, Quintas S, Eslahi A, Shariati G, Bauer P, Simons C, Houlden H, Issa MY, Zaki MS, Maroofian R, Gleeson JG. 

Eur J Hum Genet. 2021 Feb;29(2):271-279. doi: 10.1038/s41431-020-00717-5. Epub 2020 Sep 8. ABSTRACT Trafficking protein particle (TRAPP) complexes, which include the TRAPPC4 protein, regulate membrane trafficking between lipid organelles in a process termed vesicular tethering. TRAPPC4 was recently implicated in a recessive neurodevelopmental condition in four unrelated families due to a shared c.454+3A>G splice variant. Here, we report 23 patients from 17 independent families with an early-infantile-onset neurodegenerative presentation, where we also identified the homozygous variant hg38:11:119020256 A>G (NM_016146.5:c.454+3A>G) in TRAPPC4 through exome or genome sequencing. No other clinically relevant TRAPPC4 variants were identified among any of over 10,000 patients with neurodevelopmental conditions. We found the carrier frequency of TRAPPC4 c.454+3A>G was 2.4-5.4 per 10,000 healthy individuals. Affected individuals with the homozygous TRAPPC4 c.454+3A>G variant showed profound psychomotor delay, developmental regression, early-onset epilepsy, microcephaly and progressive spastic tetraplegia. Based upon RNA sequencing, the variant resulted in partial exon 3 skipping and generation of an aberrant transcript owing to use of a downstream cryptic splice donor site, predicting a premature stop codon and nonsense mediated decay. These data confirm the pathogenicity of the TRAPPC4 c.454+3A>G variant, and refine the clinical presentation of TRAPPC4-related encephalopathy. PMID:32901138 | PMC:PMC7868361 | DOI:10.1038/s41431-020-00717-5

September 9, 2020

Moving Genomics to Routine Care: An Initial Pilot in Acute Cardiovascular Disease

Aryan Z, Szanto A, Pantazi A, Reddi T, Rheinstein C, Powers W, Wilson E, Deo RC, Chowdhury S, Salz L, Dimmock D, Nahas S, Benson W, Kingsmore SF, MacRae CA, Vuzman D.

Circ Genom Precis Med. 2020 Oct;13(5):406-416. doi: 10.1161/CIRCGEN.120.002961. Epub 2020 Aug 26. ABSTRACT BACKGROUND: Whole-genome sequencing (WGS) costs are falling, yet, outside oncology, this information is seldom used in adult clinics. We piloted a rapid WGS (rWGS) workflow, focusing initially on estimating power for a feasibility study of introducing genome information into acute cardiovascular care. METHODS: A prospective implementation study was conducted to test the feasibility and clinical utility of rWGS in acute cardiovascular care. rWGS was performed on 50 adult patients with acute cardiovascular events and cardiac arrest survivors, testing for primary and secondary disease-causing variants, cardiovascular-related pharmacogenomics, and carrier status for recessive diseases. The impact of returning rWGS results on short-term clinical care of participants was investigated. The utility of polygenic risk scores to stratify coronary artery disease was also assessed. RESULTS: Pathogenic variants, typically secondary findings, were identified in 20% (95% CI, 11.7-34.3). About 60% (95% CI, 46.2-72.4) of participants were carriers for one or more recessive traits, most commonly in HFE and SERPINA1 genes. Although 64% (95% CI, 50.1-75.9) of participants carried at least one pharmacogenetic variant of cardiovascular relevance, these were actionable in only 14% (95% CI, 7-26.2). Coronary artery disease prevalence among participants at the 95th percentile of polygenic risk score was 88.2% (95% CI, 71.8-95.7). CONCLUSIONS: We demonstrated the feasibility of rWGS integration into the inpatient management of adults with acute cardiovascular events. Our pilot identified pathogenic variants in one out of 5 acute vascular patients. Integrating rWGS in clinical care will progressively increase actionability. PMID:32847406 | DOI:10.1161/CIRCGEN.120.002961

August 28, 2020

Partially automated whole-genome sequencing reanalysis of previously undiagnosed pediatric patients can efficiently yield new diagnoses

James KN, Clark MM, Camp B, Kint C, Schols P, Batalov S, Briggs B, Veeraraghavan N, Chowdhury S, Kingsmore SF. 

NPJ Genom Med. 2020 Aug 11;5:33. doi: 10.1038/s41525-020-00140-1. eCollection 2020. ABSTRACT To investigate the diagnostic and clinical utility of a partially automated reanalysis pipeline, forty-eight cases of seriously ill children with suspected genetic disease who did not receive a diagnosis upon initial manual analysis of whole-genome sequencing (WGS) were reanalyzed at least 1 year later. Clinical natural language processing (CNLP) of medical records provided automated, updated patient phenotypes, and an automated analysis system delivered limited lists of possible diagnostic variants for each case. CNLP identified a median of 79 new clinical features per patient at least 1 year later. Compared to a standard manual reanalysis pipeline, the partially automated pipeline reduced the number of variants to be analyzed by 90% (range: 74%-96%). In 2 cases, diagnoses were made upon reinterpretation, representing an incremental diagnostic yield of 4.2% (2/48, 95% CI: 0.5-14.3%). Four additional cases were flagged with a possible diagnosis to be considered during subsequent reanalysis. Separately, copy number analysis led to diagnoses in two cases. Ongoing discovery of new disease genes and refined variant classification necessitate periodic reanalysis of negative WGS cases. The clinical features of patients sequenced as infants evolve rapidly with age. Partially automated reanalysis, including automated re-phenotyping through CNLP, has the potential to identify molecular diagnoses with reduced expert labor intensity. PMID:32821428 | PMC:PMC7419288 | DOI:10.1038/s41525-020-00140-1

August 22, 2020

Loss of NARS1 impairs progenitor proliferation in cortical brain organoids and leads to microcephaly

Wang L, Li Z, Sievert D, Smith DEC, Mendes MI, Chen DY, Stanley V, Ghosh S, Wang Y, Kara M, Aslanger AD, Rosti RO, Houlden H, Salomons GS, Gleeson JG. 

Nat Commun. 2020 Aug 12;11(1):4038. doi: 10.1038/s41467-020-17454-4. ABSTRACT Asparaginyl-tRNA synthetase1 (NARS1) is a member of the ubiquitously expressed cytoplasmic Class IIa family of tRNA synthetases required for protein translation. Here, we identify biallelic missense and frameshift mutations in NARS1 in seven patients from three unrelated families with microcephaly and neurodevelopmental delay. Patient cells show reduced NARS1 protein, impaired NARS1 activity and impaired global protein synthesis. Cortical brain organoid modeling shows reduced proliferation of radial glial cells (RGCs), leading to smaller organoids characteristic of microcephaly. Single-cell analysis reveals altered constituents of both astrocytic and RGC lineages, suggesting a requirement for NARS1 in RGC proliferation. Our findings demonstrate that NARS1 is required to meet protein synthetic needs and to support RGC proliferation in human brain development. PMID:32788587 | PMC:PMC7424529 | DOI:10.1038/s41467-020-17454-4

August 14, 2020

Biallelic loss of function variants in SYT2 cause a treatable congenital onset presynaptic myasthenic syndrome

Donkervoort S, Mohassel P, Laugwitz L, Zaki MS, Kamsteeg EJ, Maroofian R, Chao KR, Verschuuren-Bemelmans CC, Horber V, Fock AJM, McCarty RM, Jain MS, Biancavilla V, McMacken G, Nalls M, Voermans NC, Elbendary HM, Snyder M, Cai C, Lehky TJ, Stanley V, Iannaccone ST, Foley AR, Lochmüller H, Gleeson J, Houlden H, Haack TB, Horvath R, Bönnemann CG.

Am J Med Genet A. 2020 Oct;182(10):2272-2283. doi: 10.1002/ajmg.a.61765. Epub 2020 Aug 10. ABSTRACT Synaptotagmins are integral synaptic vesicle membrane proteins that function as calcium sensors and regulate neurotransmitter release at the presynaptic nerve terminal. Synaptotagmin-2 (SYT2), is the major isoform expressed at the neuromuscular junction. Recently, dominant missense variants in SYT2 have been reported as a rare cause of distal motor neuropathy and myasthenic syndrome, manifesting with stable or slowly progressive distal weakness of variable severity along with presynaptic NMJ impairment. These variants are thought to have a dominant-negative effect on synaptic vesicle exocytosis, although the precise pathomechanism remains to be elucidated. Here we report seven patients of five families, with biallelic loss of function variants in SYT2, clinically manifesting with a remarkably consistent phenotype of severe congenital onset hypotonia and weakness, with variable degrees of respiratory involvement. Electrodiagnostic findings were consistent with a presynaptic congenital myasthenic syndrome (CMS) in some. Treatment with an acetylcholinesterase inhibitor pursued in three patients showed clinical improvement with increased strength and function. This series further establishes SYT2 as a CMS-disease gene and expands its clinical and genetic spectrum to include recessive loss-of-function variants, manifesting as a severe congenital onset presynaptic CMS with potential treatment implications. PMID:32776697 | PMC:PMC7959540 | DOI:10.1002/ajmg.a.61765

August 11, 2020

Correction to: Consensus guideline for the diagnosis and treatment of tetrahydrobiopterin (BH4) deficiencies

Opladen T, López-Laso E, Cortès-Saladelafont E, Pearson TS, Sivri HS, Yildiz Y, Assmann B, Kurian MA, Leuzzi V, Heales S, Pope S, Porta F, García-Cazorla A, Honzík T, Pons R, Regal L, Goez H, Artuch R, Hoffmann GF, Horvath G, Thöny B, Scholl-Bürgi S, Burlina A, Verbeek MM, Mastrangelo M, Friedman J, Wassenberg T, Jeltsch K, Kulhánek J, Kuseyri Hübschmann O; International Working Group on Neurotransmitter related Disorders (iNTD).

Orphanet J Rare Dis. 2020 Aug 5;15(1):202. doi: 10.1186/s13023-020-01464-y. ABSTRACT An amendment to this paper has been published and can be accessed via the original article. PMID:32758270 | PMC:PMC7409715 | DOI:10.1186/s13023-020-01464-y

August 8, 2020

Clinician-centric diagnosis of rare genetic diseases: performance of a gene pertinence metric in decision support for clinicians

Segal MM, George R, Waltman P, El-Hattab AW, James KN, Stanley V, Gleeson J. 

Orphanet J Rare Dis. 2020 Jul 22;15(1):191. doi: 10.1186/s13023-020-01461-1. ABSTRACT BACKGROUND: In diagnosis of rare genetic diseases we face a decision as to the degree to which the sequencing lab offers one or more diagnoses based on clinical input provided by the clinician, or the clinician reaches a diagnosis based on the complete set of variants provided by the lab. We tested a software approach to assist the clinician in making the diagnosis based on clinical findings and an annotated genomic variant table, using cases already solved using less automated processes. RESULTS: For the 81 cases studied (involving 216 individuals), 70 had genetic abnormalities with phenotypes previously described in the literature, and 11 were not described in the literature at the time of analysis (“discovery genes”). These included cases beyond a trio, including ones with different variants in the same gene. In 100% of cases the abnormality was recognized. Of the 70, the abnormality was ranked #1 in 94% of cases, with an average rank 1.1 for all cases. Large CNVs could be analyzed in an integrated analysis, performed in 24 of the cases. The process is rapid enough to allow for periodic reanalysis of unsolved cases. CONCLUSIONS: A clinician-friendly environment for clinical correlation can be provided to clinicians who are best positioned to have the clinical information needed for this interpretation. PMID:32698834 | PMC:PMC7374885 | DOI:10.1186/s13023-020-01461-1

July 24, 2020

Pathogenic ARH3 mutations result in ADP-ribose chromatin scars during DNA strand break repair

Hanzlikova H, Prokhorova E, Krejcikova K, Cihlarova Z, Kalasova I, Kubovciak J, Sachova J, Hailstone R, Brazina J, Ghosh S, Cirak S, Gleeson JG, Ahel I, Caldecott KW.

Nat Commun. 2020 Jul 7;11(1):3391. doi: 10.1038/s41467-020-17069-9. ABSTRACT Neurodegeneration is a common hallmark of individuals with hereditary defects in DNA single-strand break repair; a process regulated by poly(ADP-ribose) metabolism. Recently, mutations in the ARH3 (ADPRHL2) hydrolase that removes ADP-ribose from proteins have been associated with neurodegenerative disease. Here, we show that ARH3-mutated patient cells accumulate mono(ADP-ribose) scars on core histones that are a molecular memory of recently repaired DNA single-strand breaks. We demonstrate that the ADP-ribose chromatin scars result in reduced endogenous levels of important chromatin modifications such as H3K9 acetylation, and that ARH3 patient cells exhibit measurable levels of deregulated transcription. Moreover, we show that the mono(ADP-ribose) scars are lost from the chromatin of ARH3-defective cells in the prolonged presence of PARP inhibition, and concomitantly that chromatin acetylation is restored to normal. Collectively, these data indicate that ARH3 can act as an eraser of ADP-ribose chromatin scars at sites of PARP activity during DNA single-strand break repair. PMID:32636369 | PMC:PMC7341855 | DOI:10.1038/s41467-020-17069-9

July 9, 2020

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