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Article ; Online: Identifying the best PCR enzyme for library amplification in NGS.

Quail, Michael A / Corton, Craig / Uphill, James / Keane, Jacqueline / Gu, Yong

2024 Volume 10, Issue 4

Abstract: Background. ...

Abstract	Background.
MeSH term(s)	Polymerase Chain Reaction/methods ; Saccharomyces cerevisiae ; Gene Library ; DNA ; High-Throughput Nucleotide Sequencing/methods
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2024-04-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2835258-0
ISSN	2057-5858 ; 2057-5858
ISSN (online)	2057-5858
ISSN	2057-5858
DOI	10.1099/mgen.0.001228
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Article ; Online: Variants of PLCXD3 are not associated with variant or sporadic Creutzfeldt-Jakob disease in a large international study.

Balendra, Rubika / Uphill, James / Collinson, Claire / Druyeh, Ronald / Adamson, Gary / Hummerich, Holger / Zerr, Inga / Gambetti, Pierluigi / Collinge, John / Mead, Simon

BMC medical genetics

2016 Volume 17, Page(s) 28

Abstract: Background: Human prion diseases are relentlessly progressive neurodegenerative disorders which include sporadic Creutzfeldt-Jakob disease (sCJD) and variant CJD (vCJD). Aside from variants of the prion protein gene (PRNP) replicated association at ... ...

Abstract	Background: Human prion diseases are relentlessly progressive neurodegenerative disorders which include sporadic Creutzfeldt-Jakob disease (sCJD) and variant CJD (vCJD). Aside from variants of the prion protein gene (PRNP) replicated association at genome-wide levels of significance has proven elusive. A recent association study identified variants in or near to the PLCXD3 gene locus as strong disease risk factors in multiple human prion diseases. This study claimed the first non-PRNP locus to be highly significantly associated with prion disease in genomic studies. Methods: A sub-study of a genome-wide association study with imputation aiming to replicate the finding at PLCXD3 including 129 vCJD and 2500 sCJD samples. Whole exome sequencing to identify rare coding variants of PLCXD3. Results: Imputation of relevant polymorphisms was accurate based on wet genotyping of a sample. We found no supportive evidence that PLCXD3 variants are associated with disease. Conclusion: The marked discordance in vCJD genotype frequencies between studies, despite extensive overlap in vCJD cases, and the finding of Hardy-Weinberg disequilibrium in the original study, suggests possible reasons for the discrepancies between studies.
MeSH term(s)	Creutzfeldt-Jakob Syndrome/diagnosis ; Creutzfeldt-Jakob Syndrome/genetics ; Exons ; Genetic Loci ; Genome-Wide Association Study ; Genotyping Techniques ; Germany ; Humans ; Linkage Disequilibrium ; Phosphoinositide Phospholipase C/genetics ; Polymorphism, Single Nucleotide ; Prion Proteins ; Prions/genetics ; Prions/metabolism ; Risk Factors ; United States
Chemical Substances	PRNP protein, human ; Prion Proteins ; Prions ; Phosphoinositide Phospholipase C (EC 3.1.4.11) ; phosphatidylinositol specific phospholipase C, human (EC 3.1.4.11)
Language	English
Publishing date	2016-04-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2041359-2
ISSN	1471-2350 ; 1471-2350
ISSN (online)	1471-2350
ISSN	1471-2350
DOI	10.1186/s12881-016-0278-2
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Article ; Online: Inherited mtDNA variations are not strong risk factors in human prion disease.

Hudson, Gavin / Uphill, James / Hummerich, Holger / Blevins, Janice / Gambetti, Pierluigi / Zerr, Inga / Collinge, John / Mead, Simon / Chinnery, Patrick F

Neurobiology of aging

2015 Volume 36, Issue 10, Page(s) 2908.e1–3

Abstract: Aside from variation in the prion protein gene, genetic risk factors for sporadic Creutzfeldt-Jakob disease remain elusive. Given emerging evidence implicating mitochondrial dysfunction in the pathogenesis of the disorders, we studied the role of ... ...

Abstract	Aside from variation in the prion protein gene, genetic risk factors for sporadic Creutzfeldt-Jakob disease remain elusive. Given emerging evidence implicating mitochondrial dysfunction in the pathogenesis of the disorders, we studied the role of inherited mitochondrial DNA variation in a 2255 sporadic prion disease cases and 3768 controls. Our analysis indicates that inherited mitochondrial DNA variation does not have a major role in the risk of developing the disorder.
MeSH term(s)	Cohort Studies ; DNA, Mitochondrial/genetics ; Genetic Association Studies ; Genetic Variation/genetics ; Humans ; Prion Diseases/genetics ; Risk Factors
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2015-07-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2015.07.005
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Article ; Online: Rare structural genetic variation in human prion diseases.

Lukic, Ana / Uphill, James / Brown, Craig A / Beck, John / Poulter, Mark / Campbell, Tracy / Adamson, Gary / Hummerich, Holger / Whitfield, Jerome / Ponto, Claudia / Zerr, Inga / Lloyd, Sarah E / Collinge, John / Mead, Simon

Neurobiology of aging

2015 Volume 36, Issue 5, Page(s) 2004.e1–8

Abstract: Prion diseases are a diverse group of neurodegenerative conditions, caused by the templated misfolding of prion protein. Aside from the strong genetic risk conferred by multiple variants of the prion protein gene (PRNP), several other variants have been ... ...

Abstract	Prion diseases are a diverse group of neurodegenerative conditions, caused by the templated misfolding of prion protein. Aside from the strong genetic risk conferred by multiple variants of the prion protein gene (PRNP), several other variants have been suggested to confer risk in the most common type, sporadic Creutzfeldt-Jakob disease (sCJD) or in the acquired prion diseases. Large and rare copy number variants (CNVs) are known to confer risk in several related disorders including Alzheimer's disease (at APP), schizophrenia, epilepsy, mental retardation, and autism. Here, we report the first genome-wide analysis for CNV-associated risk using data derived from a recent international collaborative association study in sCJD (n = 1147 after quality control) and publicly available controls (n = 5427). We also investigated UK patients with variant Creutzfeldt-Jakob disease (n = 114) and elderly women from the Eastern Highlands of Papua New Guinea who proved highly resistant to the epidemic prion disease kuru, who were compared with healthy young Fore population controls (n = 395). There were no statistically significant alterations in the burden of CNVs >100, >500, or >1000 kb, duplications, or deletions in any disease group or geographic region. After correction for multiple testing, no statistically significant associations were found. A UK blood service control sample showed a duplication CNV that overlapped PRNP, but these were not found in prion disease. Heterozygous deletions of a 3' region of the PARK2 gene were found in 3 sCJD patients and no controls (p = 0.001, uncorrected). A cell-based prion infection assay did not provide supportive evidence for a role for PARK2 in prion disease susceptibility. These data are consistent with a modest impact of CNVs on risk of late-onset neurologic conditions and suggest that, unlike APP, PRNP duplication is not a causal high-risk mutation.
MeSH term(s)	3' Untranslated Regions/genetics ; Aged ; Cells, Cultured ; Creutzfeldt-Jakob Syndrome/genetics ; DNA Copy Number Variations/genetics ; Female ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study ; Humans ; Kuru/genetics ; Loss of Heterozygosity/genetics ; Male ; Prion Diseases/genetics ; Prion Proteins ; Prions/genetics ; Risk ; Ubiquitin-Protein Ligases/genetics
Chemical Substances	3' Untranslated Regions ; PRNP protein, human ; Prion Proteins ; Prions ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; parkin protein (EC 2.3.2.27)
Language	English
Publishing date	2015-01-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2015.01.011
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Article ; Online: A novel exon 2 I27V VCP variant is associated with dissimilar clinical syndromes.

Rohrer, Jonathan D / Warren, Jason D / Reiman, David / Uphill, James / Beck, Jonathan / Collinge, John / Rossor, Martin N / Isaacs, Adrian M / Mead, Simon

Journal of neurology

2011 Volume 258, Issue 8, Page(s) 1494–1496

Abstract: Mutations in valosin-containing protein (VCP) are associated with a syndromic constellation of inclusion body myositis, Paget's disease of bone and frontotemporal dementia. Here we describe the case reports of two patients with a novel variation (p.I27V) ...

Abstract	Mutations in valosin-containing protein (VCP) are associated with a syndromic constellation of inclusion body myositis, Paget's disease of bone and frontotemporal dementia. Here we describe the case reports of two patients with a novel variation (p.I27V) in the VCP gene that was not identified in a healthy control population. One patient presented with a frontotemporal dementia syndrome associated with raised serum alkaline phosphatase and a family history of progressive muscle disease and behavioural decline, while the second patient presented with isolated progressive dysarthria. Together these cases suggest a potential for the same VCP mutation to produce distinct patterns of brain damage, underlining the clinical heterogeneity of VCP-associated disease.
MeSH term(s)	Adenosine Triphosphatases/genetics ; Aged ; Cell Cycle Proteins/genetics ; Dysarthria/genetics ; Dysarthria/physiopathology ; Exons/genetics ; Female ; Frontotemporal Dementia/genetics ; Frontotemporal Dementia/physiopathology ; Humans ; Male ; Middle Aged ; Phenotype ; Valosin Containing Protein
Chemical Substances	Cell Cycle Proteins ; Adenosine Triphosphatases (EC 3.6.1.-) ; VCP protein, human (EC 3.6.4.6) ; Valosin Containing Protein (EC 3.6.4.6)
Language	English
Publishing date	2011-03-09
Publishing country	Germany
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187050-6
ISSN	1432-1459 ; 0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
ISSN (online)	1432-1459
ISSN	0340-5354 ; 0012-1037 ; 0939-1517 ; 1619-800X
DOI	10.1007/s00415-011-5966-4
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Article: Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms

Mead, Simon / Poulter, Mark / Beck, John / Uphill, James / Jones, Chris / Ang, Cheng Eng / Mein, Charles A / Collinge, John

Human mutation. 2008 Dec., v. 29, no. 12

2008

Abstract: Highly accurate and high-throughput SNP genotyping platforms are increasingly popular but the performance of suboptimal DNA samples remains unclear. The aim of our study was to determine the best platform, amplification technique, and loading ... ...

Abstract	Highly accurate and high-throughput SNP genotyping platforms are increasingly popular but the performance of suboptimal DNA samples remains unclear. The aim of our study was to determine the best platform, amplification technique, and loading concentration to maximize genotype accuracy and call rate using degraded samples. We amplified high-molecular weight genomic DNA samples recently extracted from whole blood and degraded DNA samples extracted from 50-year-old patient sera. Two whole-genome amplification (WGA) methodologies were used: an isothermal multiple displacement amplification method (MDA) and a fragmentation-PCR-based method (GenomePlex® [GPLEX]; Sigma-Aldrich, St. Louis, MO). Duplicate runs were performed on genome-wide dense SNP arrays (Nsp-Mendel; Affymetrix) and custom SNP platforms based on molecular inversion probes (Targeted Genotyping [TG]; Affymetrix) and BeadArray technology (Golden Gate [GG]; Illumina). Miscalls and no-calls on Mendel arrays were correlated with each other, with confidence scores from the Bayesian calling algorithm, and with average probe intensity. Degraded DNA amplified with MDA gave low call rates and concordance across all platforms at standard loading concentrations. The call rate with MDA on GG was improved when a 5 x concentration of amplified DNA was used. The GPLEX amplification gave high call rate and concordance for degraded DNA at standard and higher loading concentrations on both TG and GG platforms. Based on these analyses, after standard filtering for SNP and sample performance, we were able to achieve a mean call rate of 99.7% and concordance 99.7% using degraded samples amplified by GPLEX on GG technology at 2 x loading concentration. These findings may be useful for investigators planning case-control association studies with patient samples of suboptimal quality. Hum Mutat 0, 1-7, 2008.
Language	English
Dates of publication	2008-12
Size	p. 1452-1458.
Publishing place	Wiley Subscription Services, Inc., A Wiley Company
Document type	Article
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.20782
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Successful amplification of degraded DNA for use with high-throughput SNP genotyping platforms.

Mead, Simon / Poulter, Mark / Beck, John / Uphill, James / Jones, Chris / Ang, Cheng Eng / Mein, Charles A / Collinge, John

Human mutation

2008 Volume 29, Issue 12, Page(s) 1452–1458

Abstract	Highly accurate and high-throughput SNP genotyping platforms are increasingly popular but the performance of suboptimal DNA samples remains unclear. The aim of our study was to determine the best platform, amplification technique, and loading concentration to maximize genotype accuracy and call rate using degraded samples. We amplified high-molecular weight genomic DNA samples recently extracted from whole blood and degraded DNA samples extracted from 50-year-old patient sera. Two whole-genome amplification (WGA) methodologies were used: an isothermal multiple displacement amplification method (MDA) and a fragmentation-PCR-based method (GenomePlex [GPLEX]; Sigma-Aldrich, St. Louis, MO). Duplicate runs were performed on genome-wide dense SNP arrays (Nsp-Mendel; Affymetrix) and custom SNP platforms based on molecular inversion probes (Targeted Genotyping [TG]; Affymetrix) and BeadArray technology (Golden Gate [GG]; Illumina). Miscalls and no-calls on Mendel arrays were correlated with each other, with confidence scores from the Bayesian calling algorithm, and with average probe intensity. Degraded DNA amplified with MDA gave low call rates and concordance across all platforms at standard loading concentrations. The call rate with MDA on GG was improved when a 5 x concentration of amplified DNA was used. The GPLEX amplification gave high call rate and concordance for degraded DNA at standard and higher loading concentrations on both TG and GG platforms. Based on these analyses, after standard filtering for SNP and sample performance, we were able to achieve a mean call rate of 99.7% and concordance 99.7% using degraded samples amplified by GPLEX on GG technology at 2 x loading concentration. These findings may be useful for investigators planning case-control association studies with patient samples of suboptimal quality.
MeSH term(s)	DNA/metabolism ; Genetic Techniques ; Genome, Human ; Humans ; Kuru/genetics ; Middle Aged ; Nucleic Acid Amplification Techniques/methods ; Polymorphism, Single Nucleotide
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2008-04-15
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.20782
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Article: Identification of genetic loci affecting mouse-adapted bovine spongiform encephalopathy incubation time in mice.

Lloyd, Sarah E / Uphill, James B / Targonski, Paul V / Fisher, Elizabeth M C / Collinge, John

Neurogenetics

2002 Volume 4, Issue 2, Page(s) 77–81

Abstract: Prion diseases are fatal neurodegenerative disorders of humans and animals, which include bovine spongiform encephalopathy (BSE) and its human form, variant Creutzfeldt-Jakob disease (vCJD). They are characterized by a prolonged incubation period, which ... ...

Abstract	Prion diseases are fatal neurodegenerative disorders of humans and animals, which include bovine spongiform encephalopathy (BSE) and its human form, variant Creutzfeldt-Jakob disease (vCJD). They are characterized by a prolonged incubation period, which is known to be influenced by polymorphisms in the prion protein gene. Previous studies of inbred mice have demonstrated that additional genetic loci also contribute to the observed variation in incubation period. However, a substantial transmission barrier between cow and mouse complicates studies using BSE. As a result, primary transmissions display large variations in incubation period and not all animals develop clinical signs of disease. To identify quantitative trait loci for BSE without the presence of a transmission barrier, we analysed 124 animals from an F2 intercross between CAST/Ei and NZW/OlaHsd mice and challenged them intracerebrally with a strain of BSE that was passaged twice through C57BL/6OlaHsd mice. Interval mapping identified two highly significant linked regions on chromosomes 2 and 11 with peak lod scores of 6.34 and 4.77, respectively. Composite interval mapping suggests that chromosome 2 includes three linked quantitative trait loci. Loci in the same position on chromosomes 2 and 11 were also identified in a previous study using the same mouse cross but infected with Chandler/RML scrapie prions. If these are the same loci, it suggests that these loci may be influencing incubation time independently of prion strain. This provides hope that it may be possible to identify human quantitative trait loci for prion incubation time using mouse models that may allow identification of at-risk individuals and the discovery of novel therapeutic targets.
MeSH term(s)	Animals ; Cattle ; Chromosomes, Mammalian ; Encephalopathy, Bovine Spongiform/genetics ; Encephalopathy, Bovine Spongiform/transmission ; Female ; Genetic Linkage ; Male ; Mice ; Mice, Inbred C57BL ; Prions/genetics ; Quantitative Trait Loci ; Species Specificity
Chemical Substances	Prions
Language	English
Publishing date	2002-12-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1339887-8
ISSN	1364-6753 ; 1364-6745
ISSN (online)	1364-6753
ISSN	1364-6745
DOI	10.1007/s10048-002-0133-9
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Article: Apolipoprotein e genotype modifies the phenotype of Alzheimer disease.

Schott, Jonathan M / Ridha, Basil H / Crutch, Sebastian J / Healy, Daniel G / Uphill, James B / Warrington, Elizabeth K / Rossor, Martin N / Fox, Nick C

Archives of neurology

2006 Volume 63, Issue 1, Page(s) 155–156

MeSH term(s)	Alzheimer Disease/genetics ; Alzheimer Disease/physiopathology ; Apolipoproteins E/genetics ; Female ; Genotype ; Humans ; Male ; Mental Status Schedule ; Middle Aged ; Neuropsychological Tests ; Phenotype
Chemical Substances	Apolipoproteins E
Language	English
Publishing date	2006-01-09
Publishing country	United States
Document type	Comparative Study ; Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	80049-1
ISSN	1538-3687 ; 0003-9942
ISSN (online)	1538-3687
ISSN	0003-9942
DOI	10.1001/archneur.63.1.155
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Article ; Online: PRNP allelic series from 19 years of prion protein gene sequencing at the MRC Prion Unit.

Beck, Jon A / Poulter, Mark / Campbell, Tracy A / Adamson, Gary / Uphill, James B / Guerreiro, Rita / Jackson, Graham S / Stevens, James C / Manji, Hadi / Collinge, John / Mead, Simon

Human mutation

2010 Volume 31, Issue 7, Page(s) E1551–63

Abstract: Mutation of the human prion protein gene (PRNP) open reading frame (ORF) accounts for almost all reported familial concurrence of prion disease. The more common mutations globally: octapeptide repeat insertions, P102L, D178N, E200K, and V210I have ... ...

Abstract	Mutation of the human prion protein gene (PRNP) open reading frame (ORF) accounts for almost all reported familial concurrence of prion disease. The more common mutations globally: octapeptide repeat insertions, P102L, D178N, E200K, and V210I have occurred in large multigenerational pedigrees and display autosomal dominant inheritance, however, many rare genetic changes have been reported that are of uncertain pathogenicity. Based on 19 years of PRNP sequencing at the MRC Prion Unit, London, and analysis of 3664 samples from patients referred with suspected prion disease and healthy populations, we present novel allele combinations, healthy control population data, results of screening the PRNP ORF in DNA from the entire referral series and the CEPH human genome diversity cell line panel. Of the 10 alleles detected in patients for which detailed cases histories are presented, 4 are unreported (G54S, D167N, V209M, Q212PP), two changes are thought to be pathogenic but have not been described in our regions (P105L from the UK, G114V from India and Turkey), and the remainder reported in healthy control populations or in trans to known pathogenic mutations suggesting non- or low pathogenicity (G54S, 1-OPRI, G142S, N171S, V209M, E219K). New genotype-phenotype correlations and population frequencies presented will help the diagnosis and genetic counselling of those with suspected inherited prion disease.
MeSH term(s)	Alleles ; DNA Mutational Analysis/methods ; Gene Frequency ; Genetic Association Studies ; Genotype ; Humans ; London ; Mutation, Missense ; Prion Diseases/diagnosis ; Prion Diseases/genetics ; Prions/genetics
Chemical Substances	Prions
Language	English
Publishing date	2010-06-25
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.21281
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