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Population Genomics and Genetics of Complex Traits

Published in "Nature Genetics 2008", Vol. 40, pp 492-193

We have a strong interest in population genomics and genetics of complex traits. We are using various methodologies to understand the role of genetic variation in phenotypic variation. We also aim to understand what fraction of genetic variation is harbored within functional elements of the human genome, and develop methodologies for their efficient identification. Our main focus is on genome-wide analysis of gene expression variation and cellular phenotypes and association with nucleotide variation with a focus on disease susceptibility: We attempt to detect functional genetic variation in regulatory elements and subsequently use regulatory variation and accurately measured gene expression variation to bridge the genotype with disease phenotypes in association studies. Gene expression variation is interrogated either by deep mRNA sequencing using 2nd generation sequencing technologies or expression arrays.
br> We are also participating in the analysis of sequence and phenotype data of various disease samples and prospective cohorts with deep phenotyping at the cellular and organismal level. Our group also has a leading role in the HapMap3 projects and the 1000 Genome project.

Group's publications

Genetic variation of regulatory systems.
CURRENT OPINION IN GENETICS AND DEVELOPMENT
2009 vol. 19(6) pp. 586-590
DIMAS AS, DERMITZAKIS ET

The resolution of the genetics of gene expression.
HUMAN MOLECULAR GENETICS
2009 vol. 18(R2) pp. 211-215
MONTGOMERY S, DERMITZAKIS ET

Gene expression levels are a target of recent natural selection in the human genome.
MOLECULAR BIOLOGY AND EVOLUTION
2009 vol. 26(3) pp. 649-658
KUDARAVALLI S, VEYRIERAS JB, STRANGER BE, DERMITZAKIS ET, PRITCHARD JK

A genome-wide association study of testicular germ cell tumor.
NATURE GENETICS
2009 vol. 41(7) pp. 807-810
RAPLEY EA AND AL.

Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size.
PLOS GENETICS
2009 vol. 5(4) pp. 1000445-1000445
SORANZO N AND AL.

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner
SCIENCE
2009 vol. 325(5945) pp. 1246-1250
DIMAS AS AND AL.

Genetics. Life after GWA studies.
SCIENCE
2009 vol. 326(5950) pp. 239-240
DERMITZAKIS ET, CLARK AG

Regulatory variation and evolution: implications for disease.
ADVANCES IN GENETICS
2008 vol. 61 pp. 295-306
DERMITZAKIS ET

Williams-Beuren syndrome TRIM50 encodes an E3 ubiquitin ligase.
EUROPEAN JOURNAL OF HUMAN GENETICS
2008 vol. 16(9) pp. 1038-1049
MICALE L, FUSCO C, AUGELLO B, NAPOLITANO LM, DERMITZAKIS ET, MERONI G, MERLA G, REYMOND A

Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells.
GENOME BIOLOGY
2008 vol. 9(12) pp. 168-168
ATTANASIO C AND AL

Using gene expression to investigate the genetic basis of complex disorders.
HUMAN MOLECULAR GENETICS
2008 vol. 17(R2) pp. 129-134
NICA A, DERMITZAKIS ET

From gene expression to disease risk.
NATURE GENETICS
2008 vol. 40(5) pp. 492-493
DERMITZAKIS ET

Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines.
PLOS GENETICS
2008 vol. 4(11) pp. 1000287-1000287
CHOY E AND AL.

High-resolution mapping of expression-QTLs yields insight into human gene regulation.
PLOS GENETICS
2008 vol. 4(10) pp. 1000214-1000214
VEYRIERAS JB, KUDARAVALLI S, KIM SY, DERMITZAKIS ET, GILAD Y, STEPHENS M, PRITCHARD JK

Large-scale population study of human cell lines indicates that dosage compensation is virtually complete.
PLOS GENETICS
2008 vol. 4(1) pp. 9-9
JOHNSTON CM, LOVELL FL, LEONGAMORNLERT DA, STRANGER BE, DERMITZAKIS ET, ROSS MT

Modifier effects between regulatory and protein-coding variation.
PLOS GENETICS
2008 vol. 4(10) pp. 1000244-1000244
DIMAS A, STRANGER BE, BEAZLEY C, FINN RD, INGLE CE, FORREST MS, RITCHIE ME, DELOUKAS P, TAVARE S, DERMITZAKIS ET

The functional impact of structural variation in humans.
TRENDS IN GENETICS
2008 vol. 24(5) pp. 238-245
HURLES ME, DERMITZAKIS ET, TYLER-SMITH C

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.
GENOME BIOLOGY
2007 vol. 8(10) pp. 228-228
MARIONI JC AND AL.

Fast-evolving noncoding sequences in the human genome.
GENOME BIOLOGY
2007 vol. 8(6) pp. 118-118
BIRD CP, STRANGER BE, LIU M, THOMAS DJ, INGLE CE, BEAZLEY C, MILLER W, HURLES ME, DERMITZAKIS ET

A second generation human haplotype map of over 3.1 million SNPs.
NATURE
2007 vol. 449(7164) pp. 851-861
FRAZER KA AND AL.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
NATURE
2007 vol. 447 pp. 799-816
ENCODE PROJECT CONS. ET AL

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
NATURE
2007 vol. 447(7146) pp. 799-816
BIRNEY E AND AL.

Genome variation and evolution of the malaria parasite Plasmodium falciparum.
NATURE GENETICS
2007 vol. 39(1) pp. 120-125
JEFFARES DC AND AL

Genome variation and evolution of the malaria parasite Plasmodium falciparum.
NATURE GENETICS
2007 vol. 39(1) pp. 120-125
JEFFARES DC AND AL.

Population genomics of human gene expression.
NATURE GENETICS
2007 vol. 39(10) pp. 1217-1224
STRANGER BE, NICA AC, FORREST MS, DIMAS A, BIRD CP, BEAZLEY C, INGLE CE, DUNNING M, FLICEK P, KOLLER D, MONTGOMERY S, TAVARE S, DELOUKAS P, DERMITZAKIS ET

Population genomics of human gene expression.
NATURE GENETICS
2007 vol. 39(10) pp. 1217-1224
STRANGER BE AND AL.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.
SCIENCE
2007 vol. 315(5813) pp. 848-853
STRANGER BE AND AL

Functional variation and evolution of non-coding DNA.
CURRENT OPINION IN GENETICS AND DEVELOPMENT
2006 vol. 16(6) pp. 559-564
BIRD CP, STRANGER BE, DERMITZAKIS ET

Tandem chimerism as a means to increase protein complexity in the human genome
GENOME RESEARCH
2006 vol. 16 pp. 37-44
PARRA G, REYMOND A, DABBOUSEH N, DERMITZAKIS ET, CASTELO R, THOMSON TM, ANTONARAKIS SE, GUIGO R

Genetic variation in human gene expression.
MAMMALIAN GENOME
2006 vol. 17(6) pp. 503-508
DERMITZAKIS ET, STRANGER BE

Conserved noncoding sequences are selectively constrained and not mutation cold spots
NATURE GENETICS
2006 vol. 38(2) pp. 223-227
DRAKE JARED A. ET AL.

Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes
HUMAN MOLECULAR GENETICS
2005 vol. 14(23) pp. 3741-3749
DEUTSCH SAMUEL ET AL.

A haplotype map of the human genome.
NATURE
2005 vol. 437(7063) pp. 1299-1320
INTERNA. HAPMAP CONSO. AND AL

Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains.
NATURE GENETICS
2005 vol. 37(5) pp. 532-536
ADAMS DJ, DERMITZAKIS ET, COX T, SMITH J, DAVIES R, BANERJEE R, BONFIELD J, MULLIKIN JC, CHUNG YJ, ROGERS J, BRADLEY A

Conserved non-genic sequences - an unexpected feature of mammalian genomes.
NATURE REVIEWS GENETICS
2005 vol. 6(2) pp. 151-157
DERMITZAKIS ET, REYMOND A, ANTONARAKIS SE

Evolutionary comparison provides evidence for pathogenicity of RMRP mutations
PLOS GENETICS
2005 vol. 1(4) pp. 47-47
BONAFÉ LUISA ET AL.

Genome-wide associations of gene expression variation in humans
PLOS GENETICS
2005 vol. 1(6) pp. 78-78
STRANGER BARBARA E. ET AL.

Polymorphisms in the low-density lipoprotein receptor-related protein 5 (LRP5) gene are associated with variation in vertebral bone mass, vertebral bone size, and stature in whites
AMERICAN JOURNAL OF HUMAN GENETICS
2004 vol. 74 pp. 866-875
FERRARI SL, DEUTSCH S, CHOUDHURY U, CHEVALLEY T, BONJOUR JP, DERMITZAKIS ET, RIZZOLI R, ANTONARAKIS SE

Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment.
GENOME RESEARCH
2004 vol. pp. 852-859
DERMITZAKIS ET, KIRKNESS E, SCHWARZ S, BIRNEY E, REYMOND ALEXANDRE, ANTONARAKIS STYLIANOS

Chromosome 21 and down syndrome: from genomics to pathophysiology.
NATURE REVIEWS. GENETICS
2004 vol. pp. 725-738
ANTONARAKIS STYLIANOS, LYLE ROBERT, DERMITZAKIS ET, REYMOND ALEXANDRE, DEUTSCH S

The ENCODE project Consortium
SCIENCE
2004 vol. pp. 636-640
FEINGOLD EA ET AL.

Research's domains




DATABASE-RESEARCH	GROUP OF BASIC RESEARCH

E. Dermitzakis	Head of group CV	Research subject	Members of the group


	Links about the group Prof. E. Dermitzakis CMU / Med.Génét. et développement Rue Michel Servet 1 1211 Genève 4 Suisse Emmanouil.Dermitzakis@unige.ch Tel.: + 41 22 37 95 483 Fax: + 41 22 37 95 706 Group's web site / department Comments Pages updated the 07.05.2013		Reseach's subject \| Group's publications \| Research's domains Population Genomics and Genetics of Complex Traits Published in "Nature Genetics 2008", Vol. 40, pp 492-193 We have a strong interest in population genomics and genetics of complex traits. We are using various methodologies to understand the role of genetic variation in phenotypic variation. We also aim to understand what fraction of genetic variation is harbored within functional elements of the human genome, and develop methodologies for their efficient identification. Our main focus is on genome-wide analysis of gene expression variation and cellular phenotypes and association with nucleotide variation with a focus on disease susceptibility: We attempt to detect functional genetic variation in regulatory elements and subsequently use regulatory variation and accurately measured gene expression variation to bridge the genotype with disease phenotypes in association studies. Gene expression variation is interrogated either by deep mRNA sequencing using 2nd generation sequencing technologies or expression arrays. br> We are also participating in the analysis of sequence and phenotype data of various disease samples and prospective cohorts with deep phenotyping at the cellular and organismal level. Our group also has a leading role in the HapMap3 projects and the 1000 Genome project. Group's publications Genetic variation of regulatory systems. CURRENT OPINION IN GENETICS AND DEVELOPMENT 2009 vol. 19(6) pp. 586-590 DIMAS AS, DERMITZAKIS ET The resolution of the genetics of gene expression. HUMAN MOLECULAR GENETICS 2009 vol. 18(R2) pp. 211-215 MONTGOMERY S, DERMITZAKIS ET Gene expression levels are a target of recent natural selection in the human genome. MOLECULAR BIOLOGY AND EVOLUTION 2009 vol. 26(3) pp. 649-658 KUDARAVALLI S, VEYRIERAS JB, STRANGER BE, DERMITZAKIS ET, PRITCHARD JK A genome-wide association study of testicular germ cell tumor. NATURE GENETICS 2009 vol. 41(7) pp. 807-810 RAPLEY EA AND AL. Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. PLOS GENETICS 2009 vol. 5(4) pp. 1000445-1000445 SORANZO N AND AL. Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner SCIENCE 2009 vol. 325(5945) pp. 1246-1250 DIMAS AS AND AL. Genetics. Life after GWA studies. SCIENCE 2009 vol. 326(5950) pp. 239-240 DERMITZAKIS ET, CLARK AG Regulatory variation and evolution: implications for disease. ADVANCES IN GENETICS 2008 vol. 61 pp. 295-306 DERMITZAKIS ET Williams-Beuren syndrome TRIM50 encodes an E3 ubiquitin ligase. EUROPEAN JOURNAL OF HUMAN GENETICS 2008 vol. 16(9) pp. 1038-1049 MICALE L, FUSCO C, AUGELLO B, NAPOLITANO LM, DERMITZAKIS ET, MERONI G, MERLA G, REYMOND A Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. GENOME BIOLOGY 2008 vol. 9(12) pp. 168-168 ATTANASIO C AND AL Using gene expression to investigate the genetic basis of complex disorders. HUMAN MOLECULAR GENETICS 2008 vol. 17(R2) pp. 129-134 NICA A, DERMITZAKIS ET From gene expression to disease risk. NATURE GENETICS 2008 vol. 40(5) pp. 492-493 DERMITZAKIS ET Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLOS GENETICS 2008 vol. 4(11) pp. 1000287-1000287 CHOY E AND AL. High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLOS GENETICS 2008 vol. 4(10) pp. 1000214-1000214 VEYRIERAS JB, KUDARAVALLI S, KIM SY, DERMITZAKIS ET, GILAD Y, STEPHENS M, PRITCHARD JK Large-scale population study of human cell lines indicates that dosage compensation is virtually complete. PLOS GENETICS 2008 vol. 4(1) pp. 9-9 JOHNSTON CM, LOVELL FL, LEONGAMORNLERT DA, STRANGER BE, DERMITZAKIS ET, ROSS MT Modifier effects between regulatory and protein-coding variation. PLOS GENETICS 2008 vol. 4(10) pp. 1000244-1000244 DIMAS A, STRANGER BE, BEAZLEY C, FINN RD, INGLE CE, FORREST MS, RITCHIE ME, DELOUKAS P, TAVARE S, DERMITZAKIS ET The functional impact of structural variation in humans. TRENDS IN GENETICS 2008 vol. 24(5) pp. 238-245 HURLES ME, DERMITZAKIS ET, TYLER-SMITH C Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. GENOME BIOLOGY 2007 vol. 8(10) pp. 228-228 MARIONI JC AND AL. Fast-evolving noncoding sequences in the human genome. GENOME BIOLOGY 2007 vol. 8(6) pp. 118-118 BIRD CP, STRANGER BE, LIU M, THOMAS DJ, INGLE CE, BEAZLEY C, MILLER W, HURLES ME, DERMITZAKIS ET A second generation human haplotype map of over 3.1 million SNPs. NATURE 2007 vol. 449(7164) pp. 851-861 FRAZER KA AND AL. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project NATURE 2007 vol. 447 pp. 799-816 ENCODE PROJECT CONS. ET AL Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. NATURE 2007 vol. 447(7146) pp. 799-816 BIRNEY E AND AL. Genome variation and evolution of the malaria parasite Plasmodium falciparum. NATURE GENETICS 2007 vol. 39(1) pp. 120-125 JEFFARES DC AND AL Genome variation and evolution of the malaria parasite Plasmodium falciparum. NATURE GENETICS 2007 vol. 39(1) pp. 120-125 JEFFARES DC AND AL. Population genomics of human gene expression. NATURE GENETICS 2007 vol. 39(10) pp. 1217-1224 STRANGER BE, NICA AC, FORREST MS, DIMAS A, BIRD CP, BEAZLEY C, INGLE CE, DUNNING M, FLICEK P, KOLLER D, MONTGOMERY S, TAVARE S, DELOUKAS P, DERMITZAKIS ET Population genomics of human gene expression. NATURE GENETICS 2007 vol. 39(10) pp. 1217-1224 STRANGER BE AND AL. Relative impact of nucleotide and copy number variation on gene expression phenotypes. SCIENCE 2007 vol. 315(5813) pp. 848-853 STRANGER BE AND AL Functional variation and evolution of non-coding DNA. CURRENT OPINION IN GENETICS AND DEVELOPMENT 2006 vol. 16(6) pp. 559-564 BIRD CP, STRANGER BE, DERMITZAKIS ET Tandem chimerism as a means to increase protein complexity in the human genome GENOME RESEARCH 2006 vol. 16 pp. 37-44 PARRA G, REYMOND A, DABBOUSEH N, DERMITZAKIS ET, CASTELO R, THOMSON TM, ANTONARAKIS SE, GUIGO R Genetic variation in human gene expression. MAMMALIAN GENOME 2006 vol. 17(6) pp. 503-508 DERMITZAKIS ET, STRANGER BE Conserved noncoding sequences are selectively constrained and not mutation cold spots NATURE GENETICS 2006 vol. 38(2) pp. 223-227 DRAKE JARED A. ET AL. Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes HUMAN MOLECULAR GENETICS 2005 vol. 14(23) pp. 3741-3749 DEUTSCH SAMUEL ET AL. A haplotype map of the human genome. NATURE 2005 vol. 437(7063) pp. 1299-1320 INTERNA. HAPMAP CONSO. AND AL Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains. NATURE GENETICS 2005 vol. 37(5) pp. 532-536 ADAMS DJ, DERMITZAKIS ET, COX T, SMITH J, DAVIES R, BANERJEE R, BONFIELD J, MULLIKIN JC, CHUNG YJ, ROGERS J, BRADLEY A Conserved non-genic sequences - an unexpected feature of mammalian genomes. NATURE REVIEWS GENETICS 2005 vol. 6(2) pp. 151-157 DERMITZAKIS ET, REYMOND A, ANTONARAKIS SE Evolutionary comparison provides evidence for pathogenicity of RMRP mutations PLOS GENETICS 2005 vol. 1(4) pp. 47-47 BONAFÉ LUISA ET AL. Genome-wide associations of gene expression variation in humans PLOS GENETICS 2005 vol. 1(6) pp. 78-78 STRANGER BARBARA E. ET AL. Polymorphisms in the low-density lipoprotein receptor-related protein 5 (LRP5) gene are associated with variation in vertebral bone mass, vertebral bone size, and stature in whites AMERICAN JOURNAL OF HUMAN GENETICS 2004 vol. 74 pp. 866-875 FERRARI SL, DEUTSCH S, CHOUDHURY U, CHEVALLEY T, BONJOUR JP, DERMITZAKIS ET, RIZZOLI R, ANTONARAKIS SE Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. GENOME RESEARCH 2004 vol. pp. 852-859 DERMITZAKIS ET, KIRKNESS E, SCHWARZ S, BIRNEY E, REYMOND ALEXANDRE, ANTONARAKIS STYLIANOS Chromosome 21 and down syndrome: from genomics to pathophysiology. NATURE REVIEWS. GENETICS 2004 vol. pp. 725-738 ANTONARAKIS STYLIANOS, LYLE ROBERT, DERMITZAKIS ET, REYMOND ALEXANDRE, DEUTSCH S The ENCODE project Consortium SCIENCE 2004 vol. pp. 636-640 FEINGOLD EA ET AL. Research's domains