BCCHR Researchers Find a Researcher

Allison Matthews

BSc, PhD

Investigator and Genomic Specialist, BC Children's Hospital

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.

Academic Affiliations

Clinical Assistant Professor, , Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia
Research Theme: Childhood Diseases
Research Group(s): Rare Diseases

Contact Information

Location

4500 Oak St, Vancouver, BC, Canada, V6H 3N1

(604) 875-2000 ext. 7317

allison.matthews@cw.bc.ca

SCN3A -related neurodevelopmental disorder: Clinical case reports and biophysical characterization.

Channels (Austin, Tex.)

Ghovanloo MR and Gershome C and van der Lee R and Drogemoller B and Zhang L and Matthews A and Blydt-Hansen I and Nikkel SM and Demos M and Wasserman WW and Ross CJ and van Karnebeek CD and Ruben PC

DOI: 10.1080/19336950.2025.2580175 PubMed: 41165134

10 / 2025

Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta

Biology of Sex Differences

Inkster, A.M. and Matthews, A.M. and Phung, T.N. and Plaisier, S.B. and Wilson, M.A. and Brown, C.J. and Robinson, W.P.

DOI: 10.1186/s13293-025-00696-6

ASXL1 deficiency causes epigenetic dysfunction, combined immunodeficiency, and EBV-associated lymphoma

Journal of Experimental Medicine

Fu, M.P. and Sharma, M. and Yousefi, P. and Merrill, S.M. and Tan, R. and Samra, S. and Setiadi, A. and Golding, L. and Modi, B.P. and Del Bel, K.L. and Deyell, R.J. and Rozmus, J. and Rehmus, W. and Hildebrand, K.J. and James, E. and Blanchard-Rohner, G. and Lin, S. and Shopsowitz, K.E. and Terry, J. and Lee, A.F. and Dr{\"o}gem{\"o}ller, B.I. and Matthews, A. and Tarailo-Graovac, M. and Sauv{\'e}, L. and Mitchell, H. and Prendiville, J.S. and MacIsaac, J.L. and Dever, K. and Lin, D.T.S. and Meijer, M. and Ross, C.J.D. and Dobson, S.R.M. and Vercauteren, S.M. and Wasserman, W.W. and van Karnebeek, C.D.M. and McKinnon, M.L. and Kobor, M.S. and Turvey, S.E. and Biggs, C.M.

DOI: 10.1084/jem.20240945

Human ASXL1 Deficiency Causes Epigenetic Dysfunction, Combined Immunodeficiency and EBV"Associated Hodgkin Lymphoma

Medrxiv

Fu, M.P. and Sharma, M. and Merrill, S.M. and Yousefi, P. and Tan, R. and Modi, B.P. and Bel, K.D. and Deyell, R.J. and Rozmus, J. and Rehmus, W. and Hildebrand, K.J. and James, E. and Blanchard-Rohner, G. and Lin, S. and Shopsowitz, K.E. and Setiadi, A. and Terry, J. and Lee, A.F. and Dr{\"o}gem{\"o}ller, B.I. and Matthews, A. and Tarailo-Graovac, M. and Sauv{\'e}, L. and Mitchell, H. and Prendiville, J.S. and MacIsaac, J.L. and Dever, K. and Lin, D.T.S. and Meijer, M. and Ross, C.J.D. and Dobson, S.R.M. and Vercauteren, S.M. and Wasserman, W.W. and van Karnebeek, C.D.M. and McKinnon, M.L. and Kobor, M.S. and Turvey, S.E. and Biggs, C.M.

DOI: 10.1101/2023.12.20.23300096

Whos afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data

Epigenetics and Chromatin

Inkster, A.M. and Wong, M.T. and Matthews, A.M. and Brown, C.J. and Robinson, W.P.

DOI: 10.1186/s13072-022-00477-0

Genome-wide sequencing and the clinical diagnosis of genetic disease: The CAUSES study

Human Genetics and Genomics Advances

Elliott, A.M. and Adam, S. and du Souich, C. and Lehman, A. and Nelson, T.N. 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, W.T. and Gill, H. and Tarailo-Graovac, M. and Hamilton, S. and Heran, H. and Horvath, G. and Huang, L. and Hulait, G.K. and Koehn, D. and Lee, H.K. and Lewis, S. and Lopez, E. and Louie, K. and Niederhoffer, K. and Matthews, A. and Meagher, K. and Peng, J.J. and Patel, M.S. 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, J.M.

DOI: 10.1016/j.xhgg.2022.100108

Human Germline Heterozygous Gain-of-Function STAT6 Variants Cause Severe Allergic Disease

medRxiv

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.

Neurogenetics

DOI: 10.1007/s10048-021-00652-7 PubMed: 34213677

07 / 2021

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

05 / 2021

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

03 / 2021

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

Matthews, A.M. and Blydt-Hansen, I. and Al-Jabri, B. and Andersen, J. and Tarailo-Graovac, M. and Price, M. and Selby, K. and Demos, M. and Connolly, M. and Drgemoller, B. and Shyr, C. and Mwenifumbo, J. and Elliott, A.M. and Lee, J. and Ghani, A. and Stckler, S. and Salvarinova, R. and Vallance, H. and Sinclair, G. and Ross, C.J. and Wasserman, W.W. and McKinnon, M.L. and Horvath, G.A. and Goez, H. and van Karnebeek, C.D.

DOI: 10.1038/s41436-018-0376-y

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

Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review

Journal of Inherited Metabolic Disease

Graham, E. and Lee, J. and Price, M. and Tarailo-Graovac, M. and Matthews, A. and Engelke, U. and Tang, J. and Kluijtmans, L.A.J. and Wevers, R.A. and Wasserman, W.W. and van Karnebeek, C.D.M. and Mostafavi, S.

DOI: 10.1007/s10545-018-0139-6

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

Matthews, A.M. and Tarailo-Graovac, M. and Price, E.M. and Blydt-Hansen, I. and Ghani, A. and Drgemller, B.I. and Robinson, W.P. and Ross, C.J. and Wasserman, W.W. and Siden, H. and van Karnebeek, C.D.

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

Genetics in medicine : official journal of the American College of Medical Genetics

Tarailo-Graovac, M. and Zhu, J.Y.A. and Matthews, A. and van Karnebeek, C.D.M. and Wasserman, W.W.

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

Vieira, P. and Cameron, J. and Rahikkala, E. and Keski-Filppula, R. and Zhang, L.-H. and Santra, S. and Matthews, A. and Myllynen, P. and Nuutinen, M. and Moilanen, J.S. and Rodenburg, R.J. and Rolfs, A. and Uusimaa, J. and van Karnebeek, C.D.M.

DOI: 10.1016/j.ymgme.2017.02.003

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

10 / 2016

Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target?

Molecular Genetics and Metabolism

Horvath, G.A. and Demos, M. and Shyr, C. and Matthews, A. and Zhang, L. and Race, S. and Stockler-Ipsiroglu, S. and Van Allen, M.I. and Mancarci, O. and Toker, L. and Pavlidis, P. and Ross, C.J. and Wasserman, W.W. and Trump, N. and Heales, S. and Pope, S. and Helen Cross, J. and van Karnebeek, C.D.M.

DOI: 10.1016/j.ymgme.2015.11.008

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

Scientific Reports

Chen, C.-Y. and Shi, W. and Balaton, B.P. and Matthews, A.M. and Li, Y. and Arenillas, D.J. and Mathelier, A. and Itoh, M. and Kawaji, H. and Lassmann, T. and Hayashizaki, Y. and Carninci, P. and Forrest, A.R.R. and Brown, C.J. and Wasserman, W.W.

DOI: 10.1038/srep37324

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

11 / 2014

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

09 / 2014

Variable escape from X-chromosome inactivation: Identifying factors that tip the scales towards expression

BioEssays

Samantha B. Peeters and Allison M. Cotton and Carolyn J. Brown

DOI: 10.1002/bies.201400032

06 / 2014

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

05 / 2014

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

10 / 2013

Translating dosage compensation to trisomy 21

Nature

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

07 / 2013

X-Chromosome Inactivation

Epigenetics and Complex Traits

Wendy P. Robinson and Allison M. Cotton and Maria S. Pe{\~{n}}aherrera 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 Farr 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

Genetics

Christine Yang and Andrea J. McLeod and Allison M. Cotton and Charles N. de Leeuw and Stphanie Laprise and Kathleen G. Banks and Elizabeth M. Simpson and Carolyn J. Brown

DOI: 10.1534/genetics.112.143743

09 / 2012

Different measures of genome-wide DNA methylation exhibit unique properties in placental and somatic tissues

Epigenetics

E. Magda Price and Allison M. Cotton and Maria S. Peaherrera and Deborah E. McFadden and Michael S. Kobor and Wendy Robinson

DOI: 10.4161/epi.20221

06 / 2012

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. Peaherrera 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

05 / 2011

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

05 / 2011

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

07 / 2009

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

10 / 2008

Grants

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

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Every day, our researchers work towards breakthroughs to transform the lives of kids in BC and around the world. Learn about our latest innovations and advancements in child health.

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Genetic sequencing can find answers and improve care for atypical cerebral palsy
For children and families, a diagnosis of atypical cerebral palsy (CP) comes with as many questions as it does answers. CP is a broad category of disorders that affect a child’s movement and ability to communicate. Around two in every 1,000 children will develop the condition.
Read more

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At BC Children’s, we are making discoveries that save lives and transform health care for children in our province and around the world. Our research portfolio includes basic, clinical, population, and public health research.

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Allison Matthews

BSc, PhD

Investigator and Genomic Specialist, BC Children's Hospital

Academic Affiliations

Contact Information

Location

Publications

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SCN3A -related neurodevelopmental disorder: Clinical case reports and biophysical characterization.

Breaking rules: the complex relationship between DNA methylation and X-chromosome inactivation in the human placenta

ASXL1 deficiency causes epigenetic dysfunction, combined immunodeficiency, and EBV-associated lymphoma

Human ASXL1 Deficiency Causes Epigenetic Dysfunction, Combined Immunodeficiency and EBV"Associated Hodgkin Lymphoma

Whos afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data

Genome-wide sequencing and the clinical diagnosis of genetic disease: The CAUSES study

Human Germline Heterozygous Gain-of-Function STAT6 Variants Cause Severe Allergic Disease

Secondary biogenic amine deficiencies: genetic etiology, therapeutic interventions, and clinical effects.

A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta.

A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta

Is the diagnostic rate for the common subtypes of A1AT deficiency consistent across two Canadian Provinces?

Atypical cerebral palsy: genomics analysis enables precision medicine

Bone health and SATB2-associated syndrome

Integration of genomics and metabolomics for prioritization of rare disease variants: a 2018 literature review

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

Assessment of the ExAC data set for the presence of individuals with pathogenic genotypes implicated in severe Mendelian pediatric disorders

Novel homozygous PCK1 mutation causing cytosolic phosphoenolpyruvate carboxykinase deficiency presenting as childhood hypoglycemia, an abnormal pattern of urine metabolites and liver dysfunction

Optic atrophy, cataracts, lipodystrophy/lipoatrophy, and peripheral neuropathy caused by a de novo OPA3 mutation

Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target?

YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

Derivation of consensus inactivation status for X-linked genes from genome-wide studies

Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation

Differentially methylated CpG island within human XIST mediates alternative P2 transcription and YY1 binding

Variable escape from X-chromosome inactivation: Identifying factors that tip the scales towards expression

DNA Methylation Is Globally Disrupted and Associated with Expression Changes in Chronic Obstructive Pulmonary Disease Small Airways

Spread of X-chromosome inactivation into autosomal sequences: role for DNA elements, chromatin features and chromosomal domains

Translating dosage compensation to trisomy 21

X-Chromosome Inactivation

Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array

XIST-induced silencing of flanking genes is achieved by additive action of repeat a monomers in human somatic cells

Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome

Targeting of >1.5 Mb of Human DNA into the Mouse X Chromosome Reveals Presence of cis -Acting Regulators of Epigenetic Silencing

Different measures of genome-wide DNA methylation exhibit unique properties in placental and somatic tissues

Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation

X-chromosome inactivation: molecular mechanisms from the human perspective

Inactive X chromosome-specific reduction in placental DNA methylation

X chromosome inactivation: heterogeneity of heterochromatin

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Genetic sequencing can find answers and improve care for atypical cerebral palsy

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