Chercheur

    Philip Awadalla , Ph.D.

    philip.awadalla@umontreal.ca
    Philip Awadalla
    Axe de recherche
    Maladies virales, immunitaires et cancers
    Thème de recherche
    Maladies inflammatoires et de l'immunité: étude des mécanismes physiopathologiques et de l'approche
    Adresse
    CHUSJ - Centre de Recherche

    Téléphone
    514 345-4931 #3393

    Fax
    514 345-4731

    Sur le Web

    Titres

    • Professeur agrégé, Département de pédiatrie, Université de Montréal, 2007
    • Conseiller scientifique, CARTaGENE, 2015
    • Directeur scientifique, CARTaGENE, 2010-2015

    Formation

    • Postdoctorat, Université de Californie, Davis, É.-U., 2001-2004.
    • Postdoctorat, Université de la Colombie-Britannique, Vancouver, 2000-2001.
    • PhD, Université d'Édimbourg, 1997-2000.
    • MSc, Université de Toronto, 1994-1996.

    Intérêts de recherche

    • Génomique médicale, génomique des populations et autres systèmes modèles
      • L’intégration de diverses applications de nouvelle génération pour le séquençage à l’échelle du génome entier des données génétiques sur les populations humaines ainsi que sur des agents pathogènes pertinents à l’aide de méthodes statistiques. Les objectifs sont notamment d’identifier certaines régions génomiques clés associées à la maladie, à l’adaptation et/ou à la spéciation et reliées à l’immunité ainsi que de comprendre des processus déterministes et stochastiques associés à la variation chez les humains et dans les cohortes de maladies pédiatriques ou neurologiques.
    • Épidémiologie génomique médicale des maladies chroniques
      • Études de cohortes à grande échelle portant sur des traits quantitatifs cliniquement pertinents.
      • Projet CARTaGENE : approche de biologie des systèmes visant l’identification des réseaux génomiques critiques associés aux maladies chroniques.
    • Génomique computationnelle
      • Élaboration de modèles statistiques et d’approches computationnelles pour calculer des inférences génomiques des populations et des données comparatives.Accent mis sur les méthodes probabilistes pour l’inférence des valeurs adaptives, les conséquences des mutations, les inférences démographiques et la cartographie génétique.
    • Génomique fonctionnelle et évolutionnaire des humains et des maladies
      • Reséquençage à l’échelle du génome entier, génotypage et études d’expression d’échantillons humains (provenant de sujets sains et de patients atteints de paludisme) et d’échantillons de paludisme provenant de partout dans le monde avec un accent mis sur les populations africaines et asiatiques. Une approche biologique des systèmes des populations visant l’identification de certains gènes clés et de réseaux de gènes associés à l’infection et à la résistance chez le hôte et le pathogène.

    Prix et distinctions

    • Prix de soutien Joe Doupe à un chercheur débutant 2012 de la Société canadienne de recherche clinique (SCRC)
    • Prix de Génome Québec, Génomique médicale et génomique des populations, 2010-2015.
    • Chercheur-boursier Junior 1, FRSQ, 2008-2011.
    • Bourse de recherche, Faculté Sigma Xi, Université de la Caroline du Nord, É.-U., 2007.
    • Bourse de voyage, Wellcome Trust, 2001-2004.
    • Bourse postdoctorale, Conseil de recherches en sciences naturelles et en génie du Canada, 2001.
    • Bourse postdoctorale, Killam Trust, 2000.

Nouvelles associées

Publications

Genomic architecture of sickle cell disease in West African children - Quinlan J, Idaghdour Y, Goulet P, Gbeha E, de Malliard T, Bruat V, Grenier JC, Gomez S, Sanni A, Rahimy MC, Awadalla P. Genomic architecture of sickle cell disease in West African children. Front Genet 2014; 5: 26. doi: 10.3389/fgene.2014.00026. eCollection 2014.

High-resolution genomic analysis of human mitochondrial RNA sequence variation - Hodgkinson A, Idaghdour Y, Gbeha E, Grenier JC, Hip-Ki E, Bruat V, Goulet JP, de Malliard T, Awadalla P. High-resolution genomic analysis of human mitochondrial RNA sequence variation. Science 2014; 344(6182): 413-415.

Prevalence, awareness, and management of CKD and cardiovascular risk factors in publicly funded health care - Verhave JC, Troyanov S, Mongeau F, Fradette L, Bouchard J, Awadalla P, Madore F. Prevalence, awareness, and management of CKD and cardiovascular risk factors in publicly funded health care. Clin J Am Soc Nephrol 2014; (sous presse).

Cohort profile of the CARTaGENE study: Quebec's population-based biobank for public health and personalized genomics - Awadalla P, Boileau C, Payette Y, Idaghdour Y, Goulet J, Knoppers B, Hamet P, Laberge C, on behalf of the CARTaGENE Project. Cohort profile of the CARTaGENE study: Quebec's population-based biobank for public health and personalized genomics. Int J Epidemiol 2013; 42(5): 1285-1299.

Rare allelic forms of PRDM9 associated with childhood leukemogenesis - Hussin J, Sinnett D, Casals F, Idaghdour Y, Bruat V, Saillour V, Healy J, Grenier JC, de Malliard T, Busche S, Spinella JF, Larivière M, Gibson G, Andersson A, Holmfeldt L, Ma J, Wei L, Zhang J, Andelfinger G, Downing JR, Mullighan CG, Awadalla P. Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Genome Res 2013; 23(3): 419-430.

Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans - Casals F, Hodgkinson A, Hussin J, Idaghdour Y, Bruat V, de Malliard T, Grenier JC, Gbeha E, Hamdan F, Girard S, Spinella JF, Larivière M, Saillour V, Healy J, Fernandes I, Sinnett D, Michaud JL, Rouleau GA, Haddad E, Le Deist F, Awadalla P. Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. PLoS Genet 2013; 9(9): e1003815.

Selective constraint, background selection, and mutation accumulation variability within and between human populations - Hodgkinson A, Casals F, Idaghdour Y, Grenier JC, Hernandez R, Awadalla P. Selective constraint, background selection, and mutation accumulation variability within and between human populations. BMC Evol Biol 2013; 14: 495. doi: 10.1186/1471-2164-14-495.

Exploiting gene expression variation to capture gene-environment interactions for disease - Idaghdour Y, Awadalla P. Exploiting gene expression variation to capture gene-environment interactions for disease. Front Genet 2013; 31: 3:228. doi: 10.3389/fgene.2012.00228. eCollection 2012.

Integrative annotation of variants from 1092 humans: application to cancer genomics - Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüs ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth GT, Muzny D, Pers TH, Ritchie GR, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F, 1000 Genomes Project Consortium, including, Awadalla P. Integrative annotation of variants from 1092 humans: application to cancer genomics. Science 2013; 342(6154): 1235587. doi: 10.1126/science.1235587.

Hypervariable antigen genes in malaria have ancient roots - Zilversmit M, Chase EK, Chen DS, Awadalla P, Day KP, McVean G. Hypervariable antigen genes in malaria have ancient roots. BMC Evol Biol 2013; 13: 110. doi: 10.1186/1471-2148-13-110.

Exome sequencing identifies mutations in the gene TTC7A in French-Canadian cases with hereditary multiple intestinal atresia - Samuels ME, Majewski J, Aljazaeri A, Fernandez I, Casals F, Patey N, Decaluwé H, Gosselin I, Haddad E, Hodgkinson A, Idaghdour Y, Marchand V, Michaud JL, Rodrigue MA, Desjardins S, Dubois S, Le Deist F, Awadalla P, Raymond V, Maranda B. Exome sequencing identifies mutations in the gene TTC7A in French-Canadian cases with hereditary multiple intestinal atresia. J Med Genet 2013; 50(5): 324-329.

Harnessing genomics to identify environmental determinants of heritable disease - Yauk CL, Lucas Argueso J, Auerbach SS, Awadalla P, Davis SR, Demarini DM, Douglas GR, Dubrova YE, Elespuru RK, Glover TW, Hales BF, Hurles ME, Klein CB, Lupski JR, Manchester DK, Marchetti F, Montpetit A, Mulvihill JJ, Robaire B, Robbins WA, Rouleau GA, Shaughnessy DT, Somers CM, Taylor JG 6th, Trasler J, Waters MD, Wilson TE, Witt KL, Bishop JB. Harnessing genomics to identify environmental determinants of heritable disease. Mutat Res 2013; 752(1): 6-9.

An integrated map of genetic variation from 1,092 human genomes - 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean G, Awadalla P. An integrated map of genetic variation from 1,092 human genomes. Nature 2012; 491(7422): 56-65.

Evidence for additive and interaction effects of host genotype and infection in malaria - Idaghdour Y, Quinlan J, Goulet J, Berghout J, Gbeha E, Bruat V, de Malliard T, Grenier JC, Gomez S, Gros P, Rahimy MC, Sanni A, Awadalla P. Evidence for additive and interaction effects of host genotype and infection in malaria. Proc Natl Acad Sci USA 2012; 109(42): 16786-16793.

Next-generation sequencing approaches for genetic mapping of complex diseases - Casals F, Idaghdour Y, Hussin J, Awadalla P. Next-generation sequencing approaches for genetic mapping of complex diseases. J Neuroimmunol 2012; 248(1-2): 10-22.

A family-based probabilistic method for capturing de novo mutations from high-throughput short-read sequencing data - Cartwright R, Hussin J, Keebler J, Stone EA, Awadalla P. A family-based probabilistic method for capturing de novo mutations from high-throughput short-read sequencing data. Stat Appl Genet Mol Biol 2012; 11(2): (sous presse).

Rare copy number variants contribute to congenital left-sided heart disease - Hitz MP, Lemieux-Perreault LP, Marshall C, Feroz-Zada Y, Davies R, Yang SW, Lionel AC, D'Amours G, Lemyre E, Cullum R, Bigras JL, Thibeault M, Chetaille P, Montpetit A, Khairy P, Overduin B, Klaassen R, Hoodless P, Awadalla P, Hussin J, Idaghdour Y, Nemer M, Stewart A, Boerkoel CF, Scherer SW, Richter A, Dubé MP, Andelfinger G. Rare copy number variants contribute to congenital left-sided heart disease. PLoS Genet 2012; 8(9): e1002903.

The 1000 Genomes Project: data management and community access - Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P, Awadalla P, 1000 Genomes Project Consortium. The 1000 Genomes Project: data management and community access. Nature Methods 2012; 9(5): 459-462.

Variation in genome-wide mutation rates within and between human families - Conrad DF, Keebler J, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV, Zilversmit M, Cartwright R, Rouleau GA, Daly M, Stone EA, Hurles ME, Awadalla P, 1000 Genomes Project. Variation in genome-wide mutation rates within and between human families. Nat Genet 2011; 43(7): 712-714.

A population genetic approach to mapping neurological disorder genes using deep resequencing - Myers RA, Casals F, Gauthier J, Hamdan F, Keebler J, Boyko A, Bustamante C, Piton A, Spiegelman D, Zilversmit M, Hussin J, Quinlan J, Yang Y, Lafrenière RG, Griffing AR, Stone EA, Rouleau GA, Awadalla P. A population genetic approach to mapping neurological disorder genes using deep resequencing. PLoS Genet 2011; 7(2): e1001318.

Age-dependent recombination rates in human pedigrees - Hussin J, Roy-Gagnon M-H, Gendron R, Andelfinger G, Awadalla P. Age-dependent recombination rates in human pedigrees. PLoS Genet 2011; 7(9): e1002251.

The functional spectrum of low-frequency coding variation - Marth GT, Yu F, Indap AR, Garimella KV, Gravel S, Leong WF, Tyler-Smith C, Bainbridge M, Blackwell T, Zheng-Bradley X, Chen Y, Challis D, Clarke L, Ball EV, Cibulskis K, Cooper DN, Fulton B, Hartl CL, Koboldt D, Muzny D, Smith R, Sougnez C, Stewart C, Ward A, Yu J, Xue Y, Altshuler DL, Bustamante C, Clark AG, Daly M, DePristo MA, Flicek P, Gabriel S, Mardis E, Palotie A, Gibbs R, 1000 Genomes Project, including, Awadalla P. The functional spectrum of low-frequency coding variation. Genome Biol 2011; 12(9): R84. doi: 10.1186/gb-2011-12-9-r84.

Mapping copy number variation by population-scale genome sequencing - Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal O, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO, Awadalla P, 1000 Genomes Project. Mapping copy number variation by population-scale genome sequencing. Nature 2011; 470(7332): 59-65.

Demographic history and rare allele sharing among human populations - Gravel S, Henn BM, Gutenkunst RN, Indap AR, Marth GT, Clark AG, Yu F, Gibbs RA, Awadalla P, 1000 Genomes Project, Bustamante C. Demographic history and rare allele sharing among human populations. Proc Natl Acad Sci USA 2011; 108(29): 11983-11988.

The variant call format and VCFtools - Danecek P, Auton A, Abecasis GR, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, Awadalla P, 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics 2011; 27(15): 2156-2158.

Similarity in recombination rate estimates highly correlates with genetic differentiation in humans - Laayouni H, Montanucci L, Sikora M, Melé M, Dall'Olio GM, Lorente-Galdos B, McGee KM, Graffelman J, Awadalla P, Bosch E, Comas D, Navarro A, Calafell F, Casals F, Bertranpetit J. Similarity in recombination rate estimates highly correlates with genetic differentiation in humans. PLoS ONE 2011; 6(3): e17913.

High recombination rates and hotspots in a Plasmodium falciparum genetic cross - Jiang H, Li N, Gopalan V, Zilversmit M, Varma S, Nagarajan V, Li J, Mu J, Hayton K, Henschen B, Yi M, Stephens R, McVean G, Awadalla P, Wellems TE, Su XZ. High recombination rates and hotspots in a Plasmodium falciparum genetic cross. Genome 2011; 12(4): R33 (on line).

Genetic adaptation of the antibacterial human innate immunity network - Casals F, Sikora M, Laayouni H, Montanucci L, Muntasell A, Lazarus HM, Calafell F, Awadalla P, Netea MG, Bertranpetit J. Genetic adaptation of the antibacterial human innate immunity network. BMC Evol Biol 2011; 11: 202 (on line).

Plasmodium falciparum genetic diversity maintained and amplified over 5 years of a low transmission endemic in the Peruvian Amazon - Branch OH, Sutton PL, Barnes C, Castro JC, Hussin J, Awadalla P, Hijar G. Plasmodium falciparum genetic diversity maintained and amplified over 5 years of a low transmission endemic in the Peruvian Amazon. Mol Biol Evol 2011; 28(7): 1973-1986.

Direct measure of the de novo mutation rate in autism and schizophrenia cohorts - Awadalla P, Gauthier J, Myers RA, Casals F, Hamdan F, Griffing AR, Côté M, Henrion E, Spiegelman D, Tarabeux J, Piton A, Yang Y, Boyko A, Bustamante C, Xiong L, Rapoport JL, Addington AM, Delisi JL, Krebs MO, Joober R, Millet B, Fombonne E, Mottron L, Zilversmit M, Keebler J, Daoud H, Marineau C, Roy-Gagnon M-H, Dubé MP, Eyre-Walker A, Drapeau P, Stone EA, Lafrenière RG, Rouleau GA. Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Am J Hum Genet 2010; 87(3): 316-324.

Diversity of human copy number variation and multicopy genes - Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure J, 1000 Genomes Project Consortium, Eichler EE, Awadalla P. Diversity of human copy number variation and multicopy genes. Science 2010; 330(6004): 641-646.

A map of human genome variation from population-scale sequencing - 1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean G, Awadalla P. A map of human genome variation from population-scale sequencing. Nature 2010; 467(7319): 1061-1073.

Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4 - Guernsey DL, Jiang H, Hussin J, Arnold M, Bouyakdan K, Perry S, Babineau-Sturk T, Beis J, Dumas N, Evans S, Ferguson M, Matsuoka M, Macgillivray C, Nightingale M, Patry L, Rideout A, Thomas A, Orr A, Hoffmann I, Michaud JL, Awadalla P, Meek DC, Ludman M, Samuels ME. Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4. Am J Hum Genet 2010; 87(1): 40-51.

Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs - Mu J, Myers RA, Jiang H, Liu S, Ricklefs S, Waisberg M, Chotivanich K, Wilairatana P, Krudsood S, White NJ, Udomsangpetch R, Cui L, Ho M, Ou F, Li H, Song J, Li G, Wang X, Seila S, Sokunthea S, Socheat D, Sturdevant DE, Porcella SF, Fairhurst RM, Wellems TE, Awadalla P, Su XZ. Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nat Genet 2010; 42(3): 268-271.

De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia - Gauthier J, Champagne N, Lafrenière RG, Xiong L, Spiegelman D, Brustein E, Lapointe M, Peng H, Côté M, Noreau A, Hamdan F, Addington AM, Rapoport JL, Delisi LE, Krebs MO, Joober R, Fathalli F, Mouaffak F, Haghighi P, Néri C, Dubé MP, Samuels ME, Marineau C, Stone EA, Awadalla P, Barker PA, Carbonetto S, Drapeau P, Rouleau GA, S2D team. De novo mutations in the gene encoding the synaptic scaffolding protein SHANK3 in patients ascertained for schizophrenia. Proc Natl Acad Sci USA 2010; 107(17): 7863-7868.

Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome - Zilversmit M, Volkman SK, DePristo MA, Wirth DF, Awadalla P, Hartl DL. Low-complexity regions in Plasmodium falciparum: missing links in the evolution of an extreme genome. Mol Biol Evol 2010; 27(9): 2198-2209.

Genomewide association studies: history, rationale, and prospects for psychiatric disorders - Psychiatric GWAS Consortium Coordinating Committee, Awadalla P, Cichon S, Craddock N, Daly M, Faraone SV, Gejman PV, Kelsoe J, Lehner R, Levinson DF, Moran A, Sklar P, Sullivan PF. Genomewide association studies: history, rationale, and prospects for psychiatric disorders. Am J Psychiatry 2009; 166(5): 540-556.

Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents - Prugnolle F, McGee K, Keebler J, Awadalla P. Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents. BMC Evol Biol 2008; 8: 223.

Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome - Mu J, Awadalla P, Duan J, McGee K, Joy D, McVean G, Su X. Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome. Nat Genet 2007; 39(1): 126-130.

Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA - Bockhorst J, Lu F, Janes JH, Keebler J, Gamain B, Awadalla P, Su X, Samudrala R, Jojic N, Smith J. Structural polymorphism and diversifying selection on the pregnancy malaria vaccine candidate VAR2CSA. Mol Biochem Parasitol 2007; 155(2): 103-112.

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