D. Perez-Gil
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The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas Open
Background Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological vari…
View article: The impact of a secondary, rare, non-pathogenic PKD1 variant on disease progression in autosomal dominant polycystic kidney disease
The impact of a secondary, rare, non-pathogenic PKD1 variant on disease progression in autosomal dominant polycystic kidney disease Open
Background Autosomal dominant polycystic kidney disease (ADPKD) is caused primarily by pathogenic variants in the PKD1 and PKD2 genes. Although the type of ADPKD variant can influence disease severity, rare, hypomorphic PKD1 variants have …
View article: Normal and pathogenic variation of <i>RFC1</i> repeat expansions: implications for clinical diagnosis
Normal and pathogenic variation of <i>RFC1</i> repeat expansions: implications for clinical diagnosis Open
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) is an autosomal recessive neurodegenerative disease, usually caused by biallelic AAGGG repeat expansions in RFC1. In this study, we leveraged whole genome sequencing …
Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping Open
Background Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as …
View article: The genomic landscape of familial glioma
The genomic landscape of familial glioma Open
Glioma is a rare brain tumor with a poor prognosis. Familial glioma is a subset of glioma with a strong genetic predisposition that accounts for approximately 5% of glioma cases. We performed whole-genome sequencing on an exploratory cohor…
View article: Widespread genomic influences on phenotype in Dravet syndrome, a ‘monogenic’ condition
Widespread genomic influences on phenotype in Dravet syndrome, a ‘monogenic’ condition Open
Dravet syndrome is an archetypal rare severe epilepsy, considered ‘monogenic’, typically caused by loss-of-function SCN1A variants. Despite a recognizable core phenotype, its marked phenotypic heterogeneity is incompletely explained by dif…
View article: Unexpected frequency of the pathogenic <i>AR</i> CAG repeat expansion in the general population
Unexpected frequency of the pathogenic <i>AR</i> CAG repeat expansion in the general population Open
CAG repeat expansions in exon 1 of the AR gene on the X chromosome cause spinal and bulbar muscular atrophy, a male-specific progressive neuromuscular disorder associated with a variety of extra-neurological symptoms. The disease has a rep…
View article: Functional genomics provide key insights to improve the diagnostic yield of hereditary ataxia
Functional genomics provide key insights to improve the diagnostic yield of hereditary ataxia Open
Improvements in functional genomic annotation have led to a critical mass of neurogenetic discoveries. This is exemplified in hereditary ataxia, a heterogeneous group of disorders characterised by incoordination from cerebellar dysfunction…
View article: Repeat expansions in <i>NOP56</i> are a cause of spinocerebellar ataxia Type 36 in the British population
Repeat expansions in <i>NOP56</i> are a cause of spinocerebellar ataxia Type 36 in the British population Open
Spinocerebellar ataxias form a clinically and genetically heterogeneous group of neurodegenerative disorders characterized by progressive cerebellar ataxia. Their prevalence varies among populations and ethnicities. Spinocerebellar ataxia …
View article: Expanding SPTAN1 monoallelic variant associated disorders: From epileptic encephalopathy to pure spastic paraplegia and ataxia
Expanding SPTAN1 monoallelic variant associated disorders: From epileptic encephalopathy to pure spastic paraplegia and ataxia Open
We found that SPTAN1 is a genetic cause of neurodevelopmental disorder, which we classified into 3 distinct subgroups. The first comprises developmental epileptic encephalopathy. The second group exhibits milder phenotypes of developmental…
View article: An intermediate-effect size variant in <i>UMOD</i> confers risk for chronic kidney disease
An intermediate-effect size variant in <i>UMOD</i> confers risk for chronic kidney disease Open
The kidney-specific gene UMOD encodes for uromodulin, the most abundant protein excreted in normal urine. Rare large-effect variants in UMOD cause autosomal dominant tubulointerstitial kidney disease (ADTKD), while common low-impact varian…
Late-Onset Autosomal Dominant Macular Degeneration Caused by Deletion of the CRX Gene Open
Previous studies had found that carriers for a single defective CRX allele that was predicted to produce no functional CRX protein had a normal ocular phenotype. Here, we show that CRX whole-gene deletion in fact does cause a dominant late…