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Hire Dr. Reuben P.
United Kingdom
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Expert in genomic data anlysis - making data biologically meaningful
Profile Summary
Subject Matter Expertise
Services
Writing
Technical Writing
Research
Feasibility Study
Consulting
Scientific and Technical Consulting
Data & AI
Statistical Analysis,
Data Visualization
Work Experience
Lecturer in Computational Genetics
University of Southampton
September 2017 - Present
Research Fellow
University of Southampton
January 2015 - September 2017
Postgraduate Researcher
University of Southampton
September 2012 - September 2015
Intern Biologist
Selcia Ltd
June 2010 - July 2011
Education
PhD Human Genetics (Faculty of Medicine)
University of Southampton
September 2012 - December 2015
MBiol (hons) Molecular and Cellular Biology (Department of Biology and Biochemistry)
University of Bath
September 2008 - July 2012
Certifications
- Certification details not provided.
Publications
JOURNAL ARTICLE
Norma Alejandra Vergara Lope Gracia, M.Reza Jabalameli, Clare Horscroft, Sarah Ennis, Andrew Collins, Reuben J. Pengelly(2019). Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data . Scientific Data. 6. p. 1--4. Nature Publishing Group
Norma, Alejandra Vergara Lope Gracia, Sarah Ennis, Igor Vorechovsky, Reuben J. Pengelly, Andrew Collins(2019). Heterogeneity in extent of linkage disequilibrium amongst exonic, intronic, non-coding RNA and intergenic chromosome regions . European Journal of Human Genetics. 27. (9). p. 1436--1444. Nature Publishing Group
Collins, A and Arias, L and Pengelly, R and Mart\'\\inez, J and Brice\~no, I and Ennis, S(2013). The potential for next-generation sequencing to characterise the genetic variation underlying non-syndromic cleft lip and palate phenotypes . OA Genetics.
The potential for next generation sequencing to characterise the genetic variation underlying nonsyndromic cleft lip and palate phenotypes @article{3b6f23301d854e68af90ae9eebed0c49,
title = "The potential for next generation sequencing to characterise the genetic variation underlying nonsyndromic cleft lip and palate phenotypes",
abstract = "Introduction: Next-generation sequencing is revolutionising the study of genetic variation and its role in disease. Individual DNA samples can now be sequenced cost-effectively enabling analysis of the complete spectrum of genetic variation. This technology has the potential to contribute significantly to the understanding of non-syndromic cleft lip and/or palate. This condition occurs with relatively high frequency and only a proportion of the underlying genetic causal factors have been identified. Many of the genes implicated have been found through genome-wide association studies but further progress is limited because these approaches consider only common genetic variants and neglect rarer variations. Because many of the causal genetic variants remain unknown, the role of gene-environment and gene-gene interaction is difficult to characterise. The identification of novel, low frequency, variants will provide new insights into the biological mechanisms and pathways involved in the condition. Sequence-based analysis will also be invaluable for fine mapping causal variants in the larger regions already identified by linkage and association studies for which positive identification of causal genetic variants has proven difficult. This review considers the available evidence for the genes involved and current understanding of how genetic variation interacts with environmental factors known to influence risk. Only by characterising the underlying genetic factors will the effort to understand gene-environment interaction and underlying functional processes be successful.Conclusion: Success with next-generation sequencing will lead to improvements in prediction, prevention, and treatment for cleft lip and palate patients.",
author = "A. Collins and L. Arias and R. Pengelly and I. Martinez and S. Ennis",
year = "2013",
month = sep,
day = "1",
language = "English",
volume = "1",
pages = "1--6",
journal = "OA Genetics",
issn = "2054-197X",
number = "1",
}. OA Genetics.
CONFERENCE POSTER
Analysis of loss of heterozygosity by whole-exome sequencing yields insights into pseudomyxoma peritonei @conference{c4a428b3843e4ab594bf87559b67e4d8,
title = "Analysis of loss of heterozygosity by whole-exome sequencing yields insights into pseudomyxoma peritonei",
author = "Reuben Pengelly",
year = "2019",
month = oct,
day = "4",
language = "English",
note = "International Workshop on Pseudomyxoma Peritonei ; Conference date: 04-10-2019 Through 04-10-2019",
}. International Workshop on Pseudomyxoma Peritonei, Spain, 4/10/19.
Reuben J. Pengelly(2016). Linkage disequilibrium patterns for the identification of functional regions of the non-coding genome. Functional genetic variation in the non-coding genome, London, United Kingdom, 10/11/16.
Reuben J. Pengelly(2015). Primary immunodeficiency caused by a novel compound heterozygote mutation in MTHFD1. Stratified, personalised or P4 medicine: a new direction, Southampton, United Kingdom, 12/05/15.
Reuben J. Pengelly(2015). Linkage disequilibrium maps highlight differential selection pressures between three breeds of Gallus gallus. Breeding for Bacon, Beer and Biofuels, Edinburgh, United Kingdom, 16/04/15.
Reuben J. Pengelly(2014). High resolution linkage disequilibrium maps derived from whole-genome sequencing data. 1000 Genomes Project and Beyond, Cambridge, United Kingdom, 24/06/14.
OTHER
The contribution of common population variants to hypomorphic oculocutaneous albinism phenotypes: a novel tri-allelic TYR genotype @article{3aa3179ed9ae4385ac72ea81be25f960,
title = "The contribution of common population variants to hypomorphic oculocutaneous albinism phenotypes: a novel tri-allelic TYR genotype",
abstract = "Purpose : Oculocutaneous albinism type 1 (OCA1) is the most common cause of albinism in European populations and is inherited through autosomal recessive mutations in the Tyrosinase (TYR) gene. The high level of reported missing heritability in OCA1 can obstruct confident diagnoses. We have used next generation sequencing techniques to interrogate the genotype for a cohort of patients with hypomorphic albinism and examined the hypothesis that common population variants can contribute to the hypomorphic albinism phenotype.Methods : We have interrogated the genetic cause of albinism in a well phenotyped, hypomorphic albinism cohort of 18 patients. Hypomorphic phenotypes were diagnosed as those with at least two, but not all features of albinism. DNA was sequenced on the TruSight One {\textquoteleft}clinical exome{\textquoteright} panel to search for causal variants in all OCA genes, as well as being analysed through multiple ligation dependent probe amplification (MLPA) to determine the presence of any large deletions in the TYR or OCA2 gene. Further analysis of OCA1 genotypes was carried out through segregation studies in phenotyped family members. Probands and family members were sequenced for TYR rare variants as well as the common variants S192Y and R402Q, both of which have a population frequency greater than 20%.Results : Of eighteen probands we confidently diagnose one with ocular albinism, two with OCA type 2, and one with a PAX6 mutation. Of six probands with only a single heterozygous mutation in TYR, all were found to have the two common variants S192Y and R402Q, figure 1. The predicted frequency of p.[S192Y;R402Q] in cis is 1.1%, however a cis versus trans distinction cannot be made in all cases.Conclusions : Our segregation results suggest that a combination of R402Q and S192Y with a deleterious mutation in a {\textquoteleft}tri-allelic genotype{\textquoteright} can account for missing heritability in a substantial number of hypomorphic OCA1B albinism phenotypes. The work also describes subtle phenotypic features that could be missed when a patient presents with nystagmus, thus leading to improvements in the overall diagnosis of congenital nystagmus.",
author = "Norman, {Chelsea Sarah} and Luke O'Gorman and Jane Gibson and Pengelly, {Reuben J.} and Diana Baralle and Ratnayaka, {J. Arjuna} and Sarah Ennis and Self, {James E.}",
year = "2018",
month = jul,
day = "1",
language = "English",
volume = "59",
pages = "5784",
journal = "Investigative Ophthamology & Visual Science",
number = "9",
}. Investigative Ophthamology & Visual Science.
DISSERTATION THESIS
Genomic data analysis: populations, patients and pipelines @phdthesis{25216740e62e4c7386981eb7075c0a8b,
title = "Genomic data analysis: populations, patients and pipelines",
abstract = "Methods for the ascertainment of genotype data have become more cost efficient by orders of magnitude with the use of high-density genotyping arrays and the advent of next generation sequencing (NGS). The resulting deluge of data has required ever advancing analytical approaches in order for the maximal information to be gleaned from these extensive data.In this work, many application of NGS to clinical research are discussed. This includes the application of targeted gene sequencing to a cohort of 83 patients with chronic kidney disease, whole-exome investigations of eight families with cleft lip/palate phenotypes, as well as five cases where analytical lessons can be learned from exome sequenced cases harbouring pathogenic variants refractory to identification. Additionally, a novel QC tool for the unambiguous tracking of samples undergoing exome sequencing is presented.Furthermore, work is presented investigating the linkage disequilibrium (LD) patterns in populations applying the Malecot-Morton model. We demonstrate that array genotyping is insufficient for the accurate determination of ne LD patterns in the human genome, with whole-genome sequencing providing more representative LD maps. Finally, we apply similar methods to Gallus gallus, generating the highest resolution maps of LD presented to date, showing that the patterns are highly discordant between commercial lines, and define features associated with recombination.Overall, we highlight the diversity of ways in which genetic data can be utilised effectively in the age of genomic `big data', and present tools which may be of benefit to other researchers utilising these technologies",
author = "Reuben Pengelly",
year = "2015",
month = oct,
language = "English",
school = "University of Southampton",
}.