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.


Who's afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data.
Epigenetics & chromatin
Inkster AM and Wong MT and Matthews AM and Brown CJ and Robinson WP
DOI: 10.1186/s13072-022-00477-0
PubMed: 36609459

Human germline heterozygous gain-of-function STAT6 variants cause severe allergic disease
Journal of Experimental Medicine
DOI: 10.1084/jem.20221755

Genome-wide sequencing and the clinical diagnosis of genetic disease: The CAUSES study.
HGG advances
Elliott AM and Adam S and du Souich C and Lehman A and Nelson TN and van Karnebeek C and Alderman E and Armstrong L and Aubertin G and Blood K and Boelman C and Boerkoel C and Bretherick K and Brown L and Chijiwa C and Clarke L and Couse M and Creighton S and Watts-Dickens A and Gibson WT and Gill H and Tarailo-Graovac M and Hamilton S and Heran H and Horvath G and Huang L and Hulait GK and Koehn D and Lee HK and Suzanne Lewis and Lopez E and Louie K and Niederhoffer K and Matthews A and Meagher K and Peng JJ and Patel MS and Race S and Richmond P and Rupps R and Salvarinova R and Seath K and Selby K and Steinraths M and Stockler S and Tang K and Tyson C and van Allen M and Wasserman W and Mwenifumbo J and Friedman JM
DOI: 10.1016/j.xhgg.2022.100108
PubMed: 35599849

Human Germline Heterozygous Gain-of-Function STAT6 Variants Cause Severe Allergic Disease
Sharma, M. and Lu, H.Y. and Vaseghi-Shanjani, M. and Del Bel, K.L. and Fornes, O. and van der Lee, R. and Richmond, P.A. and Lin, S. and Dalmann, J. and Lee, J.J. and Matthews, A. and Blanchard-Rohner, G. and van Karnebeek, C.D.M. and Bedford, H.M. and Wasserman, W.W. and Seear, M. and McKinnon, M.L. and Ahmed, H. and Turvey, S.E.
DOI: 10.1101/2022.04.25.22274265

Secondary biogenic amine deficiencies: genetic etiology, therapeutic interventions, and clinical effects.
van Karnebeek CD and Blydt-Hansen I and Allison Matthews and Vladimir Avramovic and Price M and Drogemoller B and Shyr C and Lee J and Mwenifumbo J and Ghani A and Stockler S and Jan M. Friedman and Lehman A and CAUSES Genomic Study and Ross CJ and Wasserman WW and Maja Tarailo-Graovac and Horvath GA
DOI: 10.1007/s10048-021-00652-7
PubMed: 34213677

A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta.
Biology of sex differences
Amy Inkster and Yuan V and Konwar C and Matthews AM and Brown CJ and Wendy Robinson
DOI: 10.1186/s13293-021-00381-4
PubMed: 34044884

A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta
Amy M. Inkster and Victor Yuan and Chaini Konwar and Allison M. Matthews and Carolyn J. Brown and Wendy P. Robinson
DOI: 10.1101/2021.03.08.434471

Is the diagnostic rate for the common subtypes of A1AT deficiency consistent across two Canadian Provinces?
Clinical Biochemistry
Estey, M.P. and Tahooni, T. and Nelson, T.N. and Parker, M.L. and Agbor, T.A. and Yang, H.-M. and Jen, R. and Barakauskas, V.E. and Lam, G.Y. and Matthews, A. and Mattman, A.
DOI: 10.1016/j.clinbiochem.2021.05.002

Atypical cerebral palsy: genomics analysis enables precision medicine
Genetics in Medicine
DOI: 10.1038/s41436-018-0376-y

Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review
Journal of Inherited Metabolic Disease
Emma Graham and Jessica Lee and Magda Price and Maja Tarailo-Graovac and Allison Matthews and Udo Engelke and Jeffrey Tang and Leo A. J. Kluijtmans and Ron A. Wevers and Wyeth W. Wasserman and Clara D. M. van Karnebeek and Sara Mostafavi
DOI: 10.1007/s10545-018-0139-6

Bone health and SATB2-associated syndrome
Clinical Genetics
Zarate, Y.A. and Steinraths, M. and Matthews, A. and Smith, W.E. and Sun, A. and Wilson, L.C. and Brain, C. and Allgove, J. and Jacobs, B. and Fish, J.L. and Powell, C.M. and Wasserman, W.W. and van Karnebeek, C.D. and Wakeling, E.L. and Ma, N.S.
DOI: 10.1111/cge.13121

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 and M. Tarailo-Graovac and E.M. Price and I. Blydt-Hansen and A. Ghani and B.I. Drögemöller and W.P. Robinson and C.J. Ross and W.W. Wasserman and H. Siden and C.D. van Karnebeek
DOI: 10.1016/j.ejmg.2017.07.015

Assessment of the ExAC data set for the presence of individuals with pathogenic genotypes implicated in severe Mendelian pediatric disorders
Maja Tarailo-Graovac and Jing Yun Alice Zhu and Allison Matthews and Clara D M van Karnebeek and 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 and Jessie Cameron and Elisa Rahikkala and Riikka Keski-Filppula and Lin-Hua Zhang and Saikat Santra and Allison Matthews and Päivi Myllynen and Matti Nuutinen and Jukka S. Moilanen and Richard J. Rodenburg and Arndt Rolfs and Johanna Uusimaa and 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 and Wenqiang Shi and Bradley P. Balaton and Allison M. Matthews and Yifeng Li and David J. Arenillas and Anthony Mathelier and Masayoshi Itoh and Hideya Kawaji and Timo Lassmann and Yoshihide Hayashizaki and Piero Carninci and Alistair R. R. Forrest and Carolyn J. Brown and Wyeth W. Wasserman
DOI: 10.1038/srep37324

Optic atrophy, cataracts, lipodystrophy/lipoatrophy, and peripheral neuropathy caused by a de novoOPA3mutation
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 and Michelle Demos and Casper Shyr and Allison Matthews and Linhua Zhang and Simone Race and Sylvia Stockler-Ipsiroglu and Margot I. Van Allen and Ogan Mancarci and Lilah Toker and Paul Pavlidis and Colin J. Ross and Wyeth W. Wasserman and Natalie Trump and Simon Heales and Simon Pope and J. Helen Cross and 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 and Allison M. Cotton and 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 and E. Magda Price and Meaghan J. Jones and Bradley P. Balaton and Michael S. Kobor and 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 and Allison M Cotton and Angela D Kelsey and Carolyn J Brown
DOI: 10.1186/s12863-014-0089-4

Variable escape from X-chromosome inactivation: Identifying factors that tip the scales towards expression
Samantha B. Peeters and Allison M. Cotton and 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 and Raj Chari and Kelsie L. Thu and Ian M. Wilson and Allison M. Cotton and Jennifer Y. Kennett and May Zhang and Kim M. Lonergan and Katrina Steiling and Carolyn J. Brown and Annette McWilliams and Keishi Ohtani and Marc E. Lenburg and Don D. Sin and Avrum Spira and Calum E. MacAulay and Stephen Lam and 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 and Chih-Yu Chen and Lucia L. Lam and Wyeth W. Wasserman and Michael S. Kobor and Carolyn J. Brown
DOI: 10.1093/hmg/ddt513

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

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

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

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

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

Targeting of >1.5 Mb of Human DNA into the Mouse X Chromosome Reveals Presence of cis -Acting Regulators of Epigenetic Silencing
Christine Yang and Andrea J. McLeod and Allison M. Cotton and Charles N. de Leeuw and Stéphanie Laprise and Kathleen G. Banks and Elizabeth M. Simpson and 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 and Allison M. Cotton and Maria S. Peñaherrera and Deborah E. McFadden and Michael S. Kobor and Wendy Robinson
DOI: 10.4161/epi.20221

X-chromosome inactivation: molecular mechanisms from the human perspective
Human Genetics
Christine Yang and Andrew G. Chapman and Angela D. Kelsey and Jakub Minks and Allison M. Cotton and 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 and Lucia Lam and Joslynn G. Affleck and Ian M. Wilson and Maria S. Peñaherrera and Deborah E. McFadden and Michael S. Kobor and Wan L. Lam and Wendy P. Robinson and 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 and Luana Avila and Maria S. Penaherrera and Joslynn G. Affleck and Wendy P. Robinson and Carolyn J. Brown
DOI: 10.1093/hmg/ddp299

X chromosome inactivation: heterogeneity of heterochromatin
Biochemistry and Cell Biology
Sharan K. Sidhu and Jakub Minks and Samuel C. Chang and Allison M. Cotton and 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