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Article: Splicing in the Diagnosis of Rare Disease: Advances and Challenges.

Lord, Jenny / Baralle, Diana

2021 Volume 12, Page(s) 689892

Abstract: Mutations which affect splicing are significant contributors to rare disease, but are frequently overlooked by diagnostic sequencing pipelines. Greater ascertainment of pathogenic splicing variants will increase diagnostic yields, ending the diagnostic ... ...

Abstract	Mutations which affect splicing are significant contributors to rare disease, but are frequently overlooked by diagnostic sequencing pipelines. Greater ascertainment of pathogenic splicing variants will increase diagnostic yields, ending the diagnostic odyssey for patients and families affected by rare disorders, and improving treatment and care strategies. Advances in sequencing technologies, predictive modeling, and understanding of the mechanisms of splicing in recent years pave the way for improved detection and interpretation of splice affecting variants, yet several limitations still prohibit their routine ascertainment in diagnostic testing. This review explores some of these advances in the context of clinical application and discusses challenges to be overcome before these variants are comprehensively and routinely recognized in diagnostics.
Language	English
Publishing date	2021-07-01
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2021.689892
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Article ; Online: CI-SpliceAI-Improving machine learning predictions of disease causing splicing variants using curated alternative splice sites.

Strauch, Yaron / Lord, Jenny / Niranjan, Mahesan / Baralle, Diana

PloS one

2022 Volume 17, Issue 6, Page(s) e0269159

Abstract: Background: It is estimated that up to 50% of all disease causing variants disrupt splicing. Due to its complexity, our ability to predict which variants disrupt splicing is limited, meaning missed diagnoses for patients. The emergence of machine ... ...

Abstract	Background: It is estimated that up to 50% of all disease causing variants disrupt splicing. Due to its complexity, our ability to predict which variants disrupt splicing is limited, meaning missed diagnoses for patients. The emergence of machine learning for targeted medicine holds great potential to improve prediction of splice disrupting variants. The recently published SpliceAI algorithm utilises deep neural networks and has been reported to have a greater accuracy than other commonly used methods. Methods and findings: The original SpliceAI was trained on splice sites included in primary isoforms combined with novel junctions observed in GTEx data, which might introduce noise and de-correlate the machine learning input with its output. Limiting the data to only validated and manual annotated primary and alternatively spliced GENCODE sites in training may improve predictive abilities. All of these gene isoforms were collapsed (aggregated into one pseudo-isoform) and the SpliceAI architecture was retrained (CI-SpliceAI). Predictive performance on a newly curated dataset of 1,316 functionally validated variants from the literature was compared with the original SpliceAI, alongside MMSplice, MaxEntScan, and SQUIRLS. Both SpliceAI algorithms outperformed the other methods, with the original SpliceAI achieving an accuracy of ∼91%, and CI-SpliceAI showing an improvement at ∼92% overall. Predictive accuracy increased in the majority of curated variants. Conclusions: We show that including only manually annotated alternatively spliced sites in training data improves prediction of clinically relevant variants, and highlight avenues for further performance improvements.
MeSH term(s)	Alternative Splicing ; Humans ; Machine Learning ; Mutation ; Neural Networks, Computer ; RNA Splice Sites/genetics ; RNA Splicing
Chemical Substances	RNA Splice Sites
Language	English
Publishing date	2022-06-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0269159
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Article ; Online: Splicing in the pathogenesis, diagnosis and treatment of ciliopathies.

Wheway, Gabrielle / Lord, Jenny / Baralle, Diana

Biochimica et biophysica acta. Gene regulatory mechanisms

2019 Volume 1862, Issue 11-12, Page(s) 194433

Abstract: Primary cilia are essential signalling organelles found on the apical surface of epithelial cells, where they coordinate chemosensation, mechanosensation and light sensation. Motile cilia play a central role in establishing fluid flow in the respiratory ... ...

Abstract	Primary cilia are essential signalling organelles found on the apical surface of epithelial cells, where they coordinate chemosensation, mechanosensation and light sensation. Motile cilia play a central role in establishing fluid flow in the respiratory tract, reproductive tract, brain ventricles and ear. Genetic defects affecting the structure or function of cilia can lead to a broad range of developmental and degenerative diseases known as ciliopathies. Splicing contributes to the pathogenesis, diagnosis and treatment of ciliopathies. Tissue-specific alternative splicing contributes to the tissue-specific manifestation of ciliopathy phenotypes, for example the retinal-specific effects of some genetic defects, due to specific transcript expression in the highly specialised ciliated cells of the retina, the photoreceptor cells. Ciliopathies can arise both as a result of genetic variants in spliceosomal proteins, or as a result of variants affecting splicing of specific cilia genes. Here we discuss the opportunities and challenges in diagnosing ciliopathies using RNA sequence analysis and the potential for treating ciliopathies in a relatively mutation-neutral way by targeting splicing. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
MeSH term(s)	Ciliopathies/diagnosis ; Ciliopathies/drug therapy ; Ciliopathies/genetics ; Humans ; Molecular Targeted Therapy ; Mutation ; Organ Specificity ; Phenotype ; RNA Splicing/drug effects ; Sequence Analysis, RNA/methods
Language	English
Publishing date	2019-11-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2918786-2
ISSN	1876-4320 ; 1874-9399
ISSN (online)	1876-4320
ISSN	1874-9399
DOI	10.1016/j.bbagrm.2019.194433
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Article: Microtubule modification defects underlie cilium degeneration in cell models of retinitis pigmentosa associated with pre-mRNA splicing factor mutations.

Nazlamova, Liliya / Villa Vasquez, Suly Saray / Lord, Jenny / Karthik, Varshini / Cheung, Man-Kim / Lakowski, Jörn / Wheway, Gabrielle

Frontiers in genetics

2022 Volume 13, Page(s) 1009430

Abstract: Retinitis pigmentosa (RP) is the most common cause of hereditary blindness, and may occur in isolation as a non-syndromic condition or alongside other features in a syndromic presentation. Biallelic or monoallelic mutations in one of eight genes encoding ...

Abstract	Retinitis pigmentosa (RP) is the most common cause of hereditary blindness, and may occur in isolation as a non-syndromic condition or alongside other features in a syndromic presentation. Biallelic or monoallelic mutations in one of eight genes encoding pre-mRNA splicing factors are associated with non-syndromic RP. The molecular mechanism of disease remains incompletely understood, limiting opportunities for targeted treatment. Here we use CRISPR and base edited
Language	English
Publishing date	2022-09-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.1009430
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Article ; Online: The epigenetic landscape of Alzheimer's disease.

Lord, Jenny / Cruchaga, Carlos

Nature neuroscience

2014 Volume 17, Issue 9, Page(s) 1138–1140

Abstract: Two independent epigenome-wide association studies of Alzheimer’s disease cohorts have identified overlapping methylation signals in four loci, ANK1, RPL13, RHBDF2 and CDH23, not previously associated with Alzheimer’s disease. These studies also suggest ... ...

Abstract	Two independent epigenome-wide association studies of Alzheimer’s disease cohorts have identified overlapping methylation signals in four loci, ANK1, RPL13, RHBDF2 and CDH23, not previously associated with Alzheimer’s disease. These studies also suggest that epigenetic changes contribute more to Alzheimer’s disease than expected.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Alzheimer Disease/genetics ; Alzheimer Disease/pathology ; Ankyrins/genetics ; Carrier Proteins/genetics ; Cerebral Cortex/physiology ; DNA Methylation/genetics ; Female ; Humans ; Intracellular Signaling Peptides and Proteins ; Male ; Nuclear Proteins/genetics ; Tumor Suppressor Proteins/genetics
Chemical Substances	ANK1 protein, human ; Adaptor Proteins, Signal Transducing ; Ankyrins ; BIN1 protein, human ; Carrier Proteins ; Intracellular Signaling Peptides and Proteins ; Nuclear Proteins ; RHBDF2 protein, human ; Tumor Suppressor Proteins
Language	English
Publishing date	2014-08-27
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1420596-8
ISSN	1546-1726 ; 1097-6256
ISSN (online)	1546-1726
ISSN	1097-6256
DOI	10.1038/nn.3792
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Zs.A 4891: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Markers of adipose tissue fibrogenesis associate with clinically significant liver fibrosis and are unchanged by synbiotic treatment in patients with NAFLD.

Bilson, Josh / Oquendo, Carolina J / Read, James / Scorletti, Eleonora / Afolabi, Paul R / Lord, Jenny / Bindels, Laure B / Targher, Giovanni / Mahajan, Sumeet / Baralle, Diana / Calder, Philip C / Byrne, Christopher D / Sethi, Jaswinder K

Metabolism: clinical and experimental

2023 Volume 151, Page(s) 155759

Abstract: Background and aims: Subcutaneous adipose tissue (SAT) dysfunction contributes to NAFLD pathogenesis and may be influenced by the gut microbiota. Whether transcript profiles of SAT are associated with liver fibrosis and are influenced by synbiotic ... ...

Abstract	Background and aims: Subcutaneous adipose tissue (SAT) dysfunction contributes to NAFLD pathogenesis and may be influenced by the gut microbiota. Whether transcript profiles of SAT are associated with liver fibrosis and are influenced by synbiotic treatment (that changes the gut microbiome) is unknown. We investigated: (a) whether the presence of clinically significant, ≥F2 liver fibrosis associated with adipose tissue (AT) dysfunction, differential gene expression in SAT, and/or a marker of tissue fibrosis (Composite collagen gene expression (CCGE)); and (b) whether synbiotic treatment modified markers of AT dysfunction and the SAT transcriptome. Methods: Sixty-two patients with NAFLD (60 % men) were studied before and after 12 months of treatment with synbiotic or placebo and provided SAT samples. Vibration-controlled transient elastography (VCTE)-validated thresholds were used to assess liver fibrosis. RNA-sequencing and histological analysis of SAT were performed to determine differential gene expression, CCGE and the presence of collagen fibres. Regression modelling and receiver operator characteristic curve analysis were used to test associations with, and risk prediction for, ≥F2 liver fibrosis. Results: Patients with ≥F2 liver fibrosis (n = 24) had altered markers of AT dysfunction and a SAT gene expression signature characterised by enrichment of inflammatory and extracellular matrix-associated genes, compared to those with <F2 fibrosis (n = 38). Differences in transcript profiles between patients with vs without ≥F2 liver fibrosis were largely explained by adjusting for differences in HOMA-IR. Gut microbiome-modifying synbiotic treatment did not change SAT transcriptomic profiles or circulating inflammatory/adipokine markers. SAT CCGE values were independently associated with (8.38 (1.72-40.88), p = 0.009), and were a good predictor of, ≥F2 fibrosis (AUROC 0.79, 95 % CI 0.69-0.90). Associations between SAT transcriptomic profiles and ≥F2 fibrosis were reproduced using end-of-trial data.<br />Conclusion: A differential gene expression signature in SAT associates with ≥F2 liver fibrosis is explained by a measure of systemic insulin resistance and is not changed by synbiotic treatment. SAT CCGE values are a good predictor of ≥F2 liver fibrosis in NAFLD.
MeSH term(s)	Male ; Humans ; Female ; Non-alcoholic Fatty Liver Disease/genetics ; Non-alcoholic Fatty Liver Disease/therapy ; Non-alcoholic Fatty Liver Disease/complications ; Synbiotics ; Biomarkers ; Liver Cirrhosis/genetics ; Liver Cirrhosis/therapy ; Liver Cirrhosis/complications ; Fibrosis ; Adipose Tissue/pathology ; Collagen/genetics ; Liver/pathology
Chemical Substances	Biomarkers ; Collagen (9007-34-5)
Language	English
Publishing date	2023-12-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	80230-x
ISSN	1532-8600 ; 0026-0495
ISSN (online)	1532-8600
ISSN	0026-0495
DOI	10.1016/j.metabol.2023.155759
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Article ; Online: Fetal central nervous system anomalies: When should we offer exome sequencing?

Baptiste, Caitlin / Mellis, Rhiannon / Aggarwal, Vimla / Lord, Jenny / Eberhardt, Ruth / Kilby, Mark D / Maher, Eamonn R / Wapner, Ronald / Giordano, Jessica / Chitty, Lyn

Prenatal diagnosis

2022 Volume 42, Issue 6, Page(s) 736–743

Abstract: Objective: To investigate the detection of pathogenic variants using exome sequencing in an international cohort of fetuses with central nervous system (CNS) anomalies.: Methods: We reviewed trio exome sequencing (ES) results for two previously ... ...

Abstract	Objective: To investigate the detection of pathogenic variants using exome sequencing in an international cohort of fetuses with central nervous system (CNS) anomalies. Methods: We reviewed trio exome sequencing (ES) results for two previously reported unselected cohorts (Prenatal Assessment of Genomes and Exomes (PAGE) and CUIMC) to identify fetuses with CNS anomalies with unremarkable karyotypes and chromosomal microarrays. Variants were classified according to ACMG guidelines and association of pathogenic variants with specific types of CNS anomalies explored. Results: ES was performed in 268 pregnancies with a CNS anomaly identified using prenatal ultrasound. Of those with an isolated, single, CNS anomaly, 7/97 (7.2%) had a likely pathogenic/pathogenic (LP/P) variant. This includes 3/23 (13%) fetuses with isolated mild ventriculomegaly and 3/10 (30%) fetuses with isolated agenesis of the corpus callosum. Where there were multiple anomalies within the CNS, 12/63 (19%) had LP/P variants. Of the 108 cases with CNS and other organ system anomalies, 18 (16.7%) had LP/P findings. Conclusion: ES is an important tool in the prenatal evaluation of fetuses with any CNS anomaly. The rate of LP/P variants tends to be highest in fetuses with multiple CNS anomalies and multisystem anomalies, however, ES may also be of benefit for isolated CNS anomalies.
MeSH term(s)	Exome ; Female ; Fetus/abnormalities ; Fetus/diagnostic imaging ; Humans ; Nervous System Malformations/diagnostic imaging ; Nervous System Malformations/genetics ; Pregnancy ; Prenatal Diagnosis/methods ; Ultrasonography, Prenatal/methods ; Whole Exome Sequencing/methods
Language	English
Publishing date	2022-04-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	82031-3
ISSN	1097-0223 ; 0197-3851
ISSN (online)	1097-0223
ISSN	0197-3851
DOI	10.1002/pd.6145
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Article ; Online: A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies.

Nazlamova, Liliya / Thomas, N Simon / Cheung, Man-Kim / Legebeke, Jelmer / Lord, Jenny / Pengelly, Reuben J / Tapper, William J / Wheway, Gabrielle

Human genetics

2020 Volume 140, Issue 4, Page(s) 593–607

Abstract: Ciliopathies are a broad range of inherited developmental and degenerative diseases associated with structural or functional defects in motile or primary non-motile cilia. There are around 200 known ciliopathy disease genes and whilst genetic testing can ...

Abstract	Ciliopathies are a broad range of inherited developmental and degenerative diseases associated with structural or functional defects in motile or primary non-motile cilia. There are around 200 known ciliopathy disease genes and whilst genetic testing can provide an accurate diagnosis, 24-60% of ciliopathy patients who undergo genetic testing do not receive a genetic diagnosis. This is partly because following current guidelines from the American College of Medical Genetics and the Association for Molecular Pathology, it is difficult to provide a confident clinical diagnosis of disease caused by missense or non-coding variants, which account for more than one-third of cases of disease. Mutations in PRPF31 are the second most common cause of the degenerative retinal ciliopathy autosomal dominant retinitis pigmentosa. Here, we present a high-throughput high-content imaging assay providing quantitative measure of effect of missense variants in PRPF31 which meets the recently published criteria for a baseline standard in vitro test for clinical variant interpretation. This assay utilizes a new PRPF31
MeSH term(s)	CRISPR-Cas Systems ; Cell Line ; Cells, Cultured ; Ciliopathies/diagnostic imaging ; Ciliopathies/genetics ; Diagnostic Imaging/methods ; Eye Proteins/genetics ; Gene Editing ; Gene Knockout Techniques ; Guidelines as Topic ; Image Processing, Computer-Assisted ; Mutation, Missense ; Retina/diagnostic imaging ; Retinal Degeneration/diagnostic imaging ; Retinal Degeneration/genetics ; Retinitis Pigmentosa/diagnostic imaging ; Retinitis Pigmentosa/genetics
Chemical Substances	Eye Proteins ; PRPF31 protein, human
Language	English
Publishing date	2020-10-23
Publishing country	Germany
Document type	Journal Article
ZDB-ID	223009-4
ISSN	1432-1203 ; 0340-6717
ISSN (online)	1432-1203
ISSN	0340-6717
DOI	10.1007/s00439-020-02228-1
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Article: Identification of rare variants in Alzheimer's disease.

Lord, Jenny / Lu, Alexander J / Cruchaga, Carlos

Frontiers in genetics

2014 Volume 5, Page(s) 369

Abstract: Much progress has been made in recent years in identifying genes involved in the risk of developing Alzheimer's disease (AD), the most common form of dementia. Yet despite the identification of over 20 disease associated loci, mainly through genome wide ... ...

Abstract	Much progress has been made in recent years in identifying genes involved in the risk of developing Alzheimer's disease (AD), the most common form of dementia. Yet despite the identification of over 20 disease associated loci, mainly through genome wide association studies (GWAS), a large proportion of the genetic component of the disorder remains unexplained. Recent evidence from the AD field, as with other complex diseases, suggests a large proportion of this "missing heritability" may be due to rare variants of moderate to large effect size, but the methodologies to detect such variants are still in their infancy. The latest studies in the field have been focused on the identification of coding variation associated with AD risk, through whole-exome or whole-genome sequencing. Such variants are expected to have larger effect sizes than GWAS loci, and are easier to functionally characterize, and develop cellular and animal models for. This review explores the issues involved in detecting rare variant associations in the context of AD, highlighting some successful approaches utilized to date.
Language	English
Publishing date	2014-10-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2014.00369
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Article ; Online: Uncovering the burden of hidden ciliopathies in the 100 000 Genomes Project: a reverse phenotyping approach.

Best, Sunayna / Yu, Jing / Lord, Jenny / Roche, Matthew / Watson, Christopher Mark / Bevers, Roel P J / Stuckey, Alex / Madhusudhan, Savita / Jewell, Rosalyn / Sisodiya, Sanjay M / Lin, Siying / Turner, Stephen / Robinson, Hannah / Leslie, Joseph S / Baple, Emma / Toomes, Carmel / Inglehearn, Chris / Wheway, Gabrielle / Johnson, Colin A

Journal of medical genetics

2022 Volume 59, Issue 12, Page(s) 1151–1164

Abstract: Background: The 100 000 Genomes Project (100K) recruited National Health Service patients with eligible rare diseases and cancer between 2016 and 2018. PanelApp virtual gene panels were applied to whole genome sequencing data according to Human ... ...

Abstract	Background: The 100 000 Genomes Project (100K) recruited National Health Service patients with eligible rare diseases and cancer between 2016 and 2018. PanelApp virtual gene panels were applied to whole genome sequencing data according to Human Phenotyping Ontology (HPO) terms entered by recruiting clinicians to guide focused analysis. Methods: We developed a reverse phenotyping strategy to identify 100K participants with pathogenic variants in nine prioritised disease genes ( Results: We identified 62 reportable molecular diagnoses with variants in these nine ciliopathy genes. Forty-four have been reported by 100K, 5 were previously unreported and 13 are new diagnoses. We identified 11 participants with unreportable, novel molecular diagnoses, who lacked key clinical features to justify reporting to recruiting clinicians. Two participants had likely pathogenic structural variants and one a deep intronic predicted splice variant. These variants would not be prioritised for review by standard 100K diagnostic pipelines. Conclusion: Reverse phenotyping improves the rate of successful molecular diagnosis for unsolved 100K participants with primary ciliopathies. Previous analyses likely missed these diagnoses because incomplete HPO term entry led to incorrect gene panel choice, meaning that pathogenic variants were not prioritised. Better phenotyping data are therefore essential for accurate variant interpretation and improved patient benefit.
MeSH term(s)	Humans ; Antigens, Neoplasm ; Bardet-Biedl Syndrome/genetics ; Carrier Proteins/genetics ; Cell Cycle Proteins/genetics ; Ciliopathies/diagnosis ; Ciliopathies/genetics ; Cytoskeletal Proteins/genetics ; Genotype ; Microtubule-Associated Proteins/genetics ; Phenotype ; State Medicine ; Genome, Human
Chemical Substances	Antigens, Neoplasm ; Bbs1 protein, human ; Carrier Proteins ; Cell Cycle Proteins ; Cep290 protein, human ; Cytoskeletal Proteins ; Microtubule-Associated Proteins ; WDR34 protein, human
Language	English
Publishing date	2022-06-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	220881-7
ISSN	1468-6244 ; 0022-2593
ISSN (online)	1468-6244
ISSN	0022-2593
DOI	10.1136/jmedgenet-2022-108476
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