Christos Proukakis
YOU?
Author Swipe
View article: VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements
VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements Open
Inversions, duplications, and other critical medically challenging variations are often ignored by routine genetic analyses. This is due to the complexity of these alleles but also because of the inability to accurately align them with sta…
View article: The novel p.<scp>A30G <i>SNCA</i></scp> pathogenic variant in Greek patients with familial and sporadic Parkinson's disease
The novel p.<span>A30G <i>SNCA</i></span> pathogenic variant in Greek patients with familial and sporadic Parkinson's disease Open
Background The p.A53T variant in the SNCA gene was considered, until recently, to be the only SNCA variant causing familial Parkinson's disease (PD) in the Greek population. We identified a novel heterozygous p.A30G (c.89 C>G) SNCA pathoge…
View article: Single cell long read whole genome sequencing reveals somatic transposon activity in human brain
Single cell long read whole genome sequencing reveals somatic transposon activity in human brain Open
The advent of single cell DNA sequencing revealed astonishing dynamics of genomic variability, but failed at characterizing smaller to mid size variants that on the germline level have a profound impact. In this work we discover novel dyna…
View article: Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes Open
The presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. Here we co…
View article: Sequencing dMDA Products on the MinION using Oxford Nanopore&#39;s Rapid Barcoding Kit v1
Sequencing dMDA Products on the MinION using Oxford Nanopore's Rapid Barcoding Kit v1 Open
Using Oxford Nanopore MinION and the Rapid Barcoding library preparation kit, we perform long read sequencing on droplet multiple displacement amplification (dMDA) products generated from single nuclei. Single nuclei contain around 6.6pg o…
View article: Detection of mosaic and population-level structural variants with Sniffles2
Detection of mosaic and population-level structural variants with Sniffles2 Open
Calling structural variations (SVs) is technically challenging, but using long reads remains the most accurate way to identify complex genomic alterations. Here we present Sniffles2, which improves over current methods by implementing a re…
View article: Phenotypic effect of GBA1 variants in individuals with and without Parkinson's disease: The RAPSODI study
Phenotypic effect of GBA1 variants in individuals with and without Parkinson's disease: The RAPSODI study Open
Our results support previous evidence that GBA1-positive PD has a specific phenotype with more severe non-motor symptoms. However, we did not reproduce previous findings of more frequent prodromal PD signs in non-affected GBA1 carriers.
View article: Sex Distribution of <scp>GBA1</scp> Variants Carriers with Dementia with Lewy Bodies and Parkinson's Disease
Sex Distribution of <span>GBA1</span> Variants Carriers with Dementia with Lewy Bodies and Parkinson's Disease Open
A recent article by Ortega et al1 reported sex-specific differences in GBA1-related Parkinson's disease (PD), with an excess of females in carriers of severe variants and of males in carriers of mild variants, although these differences we…
View article: Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes Open
The presence of somatic mutations, including copy number variants (CNVs), in the brain is well recognized. Comprehensive study requires single-cell whole genome amplification, with several methods available, prior to sequencing. We compare…
View article: Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes Open
Variable and constant sized bins for GRCh38 and T2T-Chm13 were generated using the buildGenome scripts provided with Ginkgo (https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts).
View article: Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes Open
Variable and constant sized bins for GRCh38 and T2T-Chm13 were generated using the buildGenome scripts provided with Ginkgo (https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts).
View article: VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements
VACmap: An Accurate Long-Read Aligner for Unraveling Complex Genomic Rearrangements Open
Inversions, duplications, and other critical medically challenging variations are often ignored by routine genetic analyses. This is due to the complexity of these alleles but also because of the inability to accurately align them with sta…
View article: Phenotypic effect of<i>GBA1</i>variants in individuals with and without Parkinson disease: the RAPSODI study
Phenotypic effect of<i>GBA1</i>variants in individuals with and without Parkinson disease: the RAPSODI study Open
Background Variants in the GBA1 gene cause the lysosomal storage disorder Gaucher disease (GD). They are also risk factors for Parkinson disease (PD), and modify the expression of the PD phenotype. The penetrance of GBA1 variants in PD is …
View article: Somatic <scp><i>SNCA</i></scp> Copy Number Variants in Multiple System Atrophy are Related to Pathology and Inclusions
Somatic <span><i>SNCA</i></span> Copy Number Variants in Multiple System Atrophy are Related to Pathology and Inclusions Open
Background Somatic α‐synuclein ( SNCA ) copy number variants (CNVs, specifically gains) occur in multiple system atrophy (MSA) and Parkinson's disease brains. Objective The aim was to compare somatic SNCA CNVs in MSA subtypes (striatonigra…
View article: <scp>CAG</scp> Somatic Instability in a Huntington Disease Expansion Carrier Presenting with a Progressive Supranuclear Palsy‐like Phenotype
<span>CAG</span> Somatic Instability in a Huntington Disease Expansion Carrier Presenting with a Progressive Supranuclear Palsy‐like Phenotype Open
Pathogenic expansions in huntingtin (HTT) may present as progressive supranuclear palsy (PSP)/frontotemporal degeneration, or amyotrophic lateral sclerosis (ALS), without chorea.1 We present the first autopsy report of a PSP-like presentat…
View article: Comprehensive Structural Variant Detection: From Mosaic to Population-Level
Comprehensive Structural Variant Detection: From Mosaic to Population-Level Open
Long-read Structural Variation (SV) calling remains a challenging but highly accurate way to identify complex genomic alterations. Here, we present Sniffles2, which is faster and more accurate than state-of-the-art SV caller across differe…
View article: Comprehensive analysis of <i>GBA</i> using a novel algorithm for Illumina whole-genome sequence data or targeted Nanopore sequencing
Comprehensive analysis of <i>GBA</i> using a novel algorithm for Illumina whole-genome sequence data or targeted Nanopore sequencing Open
GBA variants cause the autosomal recessive Gaucher disease, and carriers are at increased risk of Parkinson’s disease (PD) and Lewy body dementia (LBD). The presence of a highly homologous nearby pseudogene ( GBAP1 ) predisposes to a range…
View article: Intronic Haplotypes in the <scp><i>GBA</i></scp> Gene Do Not Predict Age at Diagnosis of Parkinson's Disease
Intronic Haplotypes in the <span><i>GBA</i></span> Gene Do Not Predict Age at Diagnosis of Parkinson's Disease Open
Background GBA mutations are a common risk factor for Parkinson's disease (PD). A recent study has suggested that GBA haplotypes, identified by intronic variants, can affect age at diagnosis of PD. Objectives In this study, we assess this …
View article: Complex mosaic structural variations in human fetal brains
Complex mosaic structural variations in human fetal brains Open
Somatic mosaicism, manifesting as single nucleotide variants (SNVs), mobile element insertions, and structural changes in the DNA, is a common phenomenon in human brain cells, with potential functional consequences. Using a clonal approach…
View article: Investigation of Somatic Mutations in Human Brains Targeting Genes Associated With Parkinson's Disease
Investigation of Somatic Mutations in Human Brains Targeting Genes Associated With Parkinson's Disease Open
Background: Somatic single nucleotide variant (SNV) mutations occur in neurons but their role in synucleinopathies is unknown. Aim: We aimed to identify disease-relevant low-level somatic SNVs in brains from sporadic patients with synuclei…
View article: A crowdsourced set of curated structural variants for the human genome
A crowdsourced set of curated structural variants for the human genome Open
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs…