Dr. Matthews is part of a larger, highly collaborative team which combines the expertise of clinicians, bioinformaticians and basic science researchers to help diagnose patients with rare genetics diseases. When conventional analysis is unable to find the cause of a patient's disease, the team uses whole genome and exome sequencing to search for what could be a mistake as small as one letter in the 3 billion letters that make up the genome. As a bioinformation, Dr. Matthews's role is to use computers to help sort through the data and then to apply genetics to prioritize potential causes for each patients. Dr. Matthews has a focus on disease on the X chromosome as well as patients with intellectual disability, metabolic disorders and atypical cerebral palsy.


A de novo mosaic mutation in SPAST with two novel alternative alleles and chromosomal copy number variant in a boy with spastic paraplegia and autism spectrum disorder
European Journal of Medical Genetics
A.M. Matthews, M. Tarailo-Graovac, E.M. Price, I. Blydt-Hansen, A. Ghani, B.I. Drögemöller, W.P. Robinson, C.J. Ross, W.W. Wasserman, H. Siden, C.D. van Karnebeek
DOI: 10.1016/j.ejmg.2017.07.015

Bone health and SATB2-associated syndrome
Clinical Genetics
Yuri A. Zarate, Michelle Steinraths, Allison Matthews, Wendy Smith, Angela Sun, Louise C. Wilson, Caroline Brain, Jeremy Allgove, Benjamin Jacobs, Jennifer L. Fish, Cynthia M. Powell, Wyeth Wasserman, Clara Van Karnebeek, Emma L. Wakeling, Nina S. Ma
DOI: 10.1111/cge.13121

Assessment of the ExAC data set for the presence of individuals with pathogenic genotypes implicated in severe Mendelian pediatric disorders
Maja Tarailo-Graovac, Jing Yun Alice Zhu, Allison Matthews, Clara D M van Karnebeek, Wyeth W Wasserman
DOI: 10.1038/gim.2017.50

Novel homozygous PCK1 mutation causing cytosolic phosphoenolpyruvate carboxykinase deficiency presenting as childhood hypoglycemia, an abnormal pattern of urine metabolites and liver dysfunction
Molecular Genetics and Metabolism
Päivi Vieira, Jessie Cameron, Elisa Rahikkala, Riikka Keski-Filppula, Lin-Hua Zhang, Saikat Santra, Allison Matthews, Päivi Myllynen, Matti Nuutinen, Jukka S. Moilanen, Richard J. Rodenburg, Arndt Rolfs, Johanna Uusimaa, Clara D.M. van Karnebeek
DOI: 10.1016/j.ymgme.2017.02.003

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses
Scientific Reports
Chih-yu Chen, Wenqiang Shi, Bradley P. Balaton, Allison M. Matthews, Yifeng Li, David J. Arenillas, Anthony Mathelier, Masayoshi Itoh, Hideya Kawaji, Timo Lassmann, Yoshihide Hayashizaki, Piero Carninci, Alistair R. R. Forrest, Carolyn J. Brown, Wyeth W. Wasserman
DOI: 10.1038/srep37324

Optic atrophy, cataracts, lipodystrophy/lipoatrophy, and peripheral neuropathy caused by a de novo OPA3 mutation
Molecular Case Studies
Stephanie C. Bourne and Katelin N. Townsend and Casper Shyr and Allison Matthews and Scott A. Lear and Raj Attariwala and Anna Lehman and Wyeth W. Wasserman and Clara van Karnebeek and Graham Sinclair and Hilary Vallance and William T. Gibson
DOI: 10.1101/mcs.a001156

Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target?
Molecular Genetics and Metabolism
Gabriella A. Horvath, Michelle Demos, Casper Shyr, Allison Matthews, Linhua Zhang, Simone Race, Sylvia Stockler-Ipsiroglu, Margot I. Van Allen, Ogan Mancarci, Lilah Toker, Paul Pavlidis, Colin J. Ross, Wyeth W. Wasserman, Natalie Trump, Simon Heales, Simon Pope, J. Helen Cross, Clara D.M. van Karnebeek
DOI: 10.1016/j.ymgme.2015.11.008

Derivation of consensus inactivation status for X-linked genes from genome-wide studies
Biology of Sex Differences
Bradley P. Balaton, Allison M. Cotton, Carolyn J. Brown
DOI: 10.1186/s13293-015-0053-7

Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation
Human Molecular Genetics
Allison M. Cotton, E. Magda Price, Meaghan J. Jones, Bradley P. Balaton, Michael S. Kobor, Carolyn J. Brown
DOI: 10.1093/hmg/ddu564

Differentially methylated CpG island within human XIST mediates alternative P2 transcription and YY1 binding
BMC Genetics
Andrew G Chapman, Allison M Cotton, Angela D Kelsey, Carolyn J Brown
DOI: 10.1186/s12863-014-0089-4

Variable escape from X-chromosome inactivation: Identifying factors that tip the scales towards expressionProspects & Overviews
Samantha B. Peeters, Allison M. Cotton, Carolyn J. Brown
DOI: 10.1002/bies.201400032

DNA Methylation Is Globally Disrupted and Associated with Expression Changes in Chronic Obstructive Pulmonary Disease Small Airways
American Journal of Respiratory Cell and Molecular Biology
Emily A. Vucic, Raj Chari, Kelsie L. Thu, Ian M. Wilson, Allison M. Cotton, Jennifer Y. Kennett, May Zhang, Kim M. Lonergan, Katrina Steiling, Carolyn J. Brown, Annette McWilliams, Keishi Ohtani, Marc E. Lenburg, Don D. Sin, Avrum Spira, Calum E. MacAulay, Stephen Lam, Wan L. Lam
DOI: 10.1165/rcmb.2013-0304oc

Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains
Human Molecular Genetics
Allison M. Cotton, Chih-Yu Chen, Lucia L. Lam, Wyeth W. Wasserman, Michael S. Kobor, Carolyn J. Brown
DOI: 10.1093/hmg/ddt513

Translating dosage compensation to trisomy 21
Jun Jiang, Yuanchun Jing, Gregory J. Cost, Jen-Chieh Chiang, Heather J. Kolpa, Allison M. Cotton, Dawn M. Carone, Benjamin R. Carone, David A. Shivak, Dmitry Y. Guschin, Jocelynn R. Pearl, Edward J. Rebar, Meg Byron, Philip D. Gregory, Carolyn J. Brown, Fyodor D. Urnov, Lisa L. Hall, Jeanne B. Lawrence
DOI: 10.1038/nature12394

X-Chromosome Inactivation
Epigenetics and Complex Traits
Wendy P. Robinson, Allison M. Cotton, Maria S. Peñaherrera, Samantha B. Peeters, Carolyn J. Brown
DOI: 10.1007/978-1-4614-8078-5_3

Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome
Genome Biology
Allison M Cotton, Bing Ge, Nicholas Light, Veronique Adoue, Tomi Pastinen, Carolyn J Brown
DOI: 10.1186/gb-2013-14-11-r122

XIST-induced silencing of flanking genes is achieved by additive action of repeat a monomers in human somatic cells
Epigenetics & Chromatin
Jakub Minks, Sarah EL Baldry, Christine Yang, Allison M Cotton, Carolyn J Brown
DOI: 10.1186/1756-8935-6-23

Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array
Epigenetics & Chromatin
Magda E Price, Allison M Cotton, Lucia L Lam, Pau Farré, Eldon Emberly, Carolyn J Brown, Wendy P Robinson, Michael S Kobor
DOI: 10.1186/1756-8935-6-4

Targeting of >1.5 Mb of Human DNA into the Mouse X Chromosome Reveals Presence of cis -Acting Regulators of Epigenetic Silencing
Christine Yang, Andrea J. McLeod, Allison M. Cotton, Charles N. de Leeuw, Stéphanie Laprise, Kathleen G. Banks, Elizabeth M. Simpson, Carolyn J. Brown
DOI: 10.1534/genetics.112.143743

Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues
E. Magda Price, Allison M. Cotton, Maria S. Peñaherrera, Deborah E. McFadden, Michael S. Kobor, Wendy Robinson
DOI: 10.4161/epi.20221

X-chromosome inactivation: molecular mechanisms from the human perspective
Human Genetics
Christine Yang, Andrew G. Chapman, Angela D. Kelsey, Jakub Minks, Allison M. Cotton, Carolyn J. Brown
DOI: 10.1007/s00439-011-0994-9

Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation
Human Genetics
Allison M. Cotton, Lucia Lam, Joslynn G. Affleck, Ian M. Wilson, Maria S. Peñaherrera, Deborah E. McFadden, Michael S. Kobor, Wan L. Lam, Wendy P. Robinson, Carolyn J. Brown
DOI: 10.1007/s00439-011-1007-8

Inactive X chromosome-specific reduction in placental DNA methylation
Human Molecular Genetics
Allison M. Cotton, Luana Avila, Maria S. Penaherrera, Joslynn G. Affleck, Wendy P. Robinson, Carolyn J. Brown
DOI: 10.1093/hmg/ddp299

X chromosome inactivation: heterogeneity of heterochromatin
Biochemistry and Cell Biology
Sharan K. Sidhu, Jakub Minks, Samuel C. Chang, Allison M. Cotton, Carolyn J. Brown
DOI: 10.1139/o08-100


National Ataxia Foundation Research Seed Money Grant, Co-investigator

GenomeBC, GBC-Genomics England Rare Disease partnership, Co-investigator

Honours & Awards

Child & Family Research Institute Postdoctoral Fellowship

University of Guelph President’s Scholarship

Interdisciplinary Women’s Research Scholarship