Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways

David M. Evans | A. Uitterlinden | T. Spector | D. Schadendorf | E. Gillanders | J. Barrett | D. Bishop | M. Iles | M. Brown | S. Novaković | S. Chanock | D. Hunter | D. Duffy | N. Martin | D. Easton | P. Kraft | G. Mann | F. Song | C. Amos | Jiali Han | G. Montgomery | N. Hayward | S. MacGregor | W. Chen | A. Goldstein | D. Nyholt | K. Pooley | A. Dunning | J. Beesley | L. Akslen | A. Heath | D. Mackey | Rajiv Kumar | M. Wright | J. Lubiński | M. Ikram | A. Molven | D. Evans | E. Friedman | P. Madden | G. Smith | C. Ingvar | S. Fang | M. Kayser | M. Hočevar | L. Simms | M. Falchi | D. Glass | V. Bataille | E. Moses | E. Nelson | D. Whiteman | A. Henders | A. Hewitt | G. Zhu | R. Sturm | J. Hansson | R. MacKie | S. Yazar | J. Craig | K. Burdon | A. Green | T. Nijsten | J. N. Newton Bishop | M. Harland | N. Gruis | A. Visconti | M. Landi | F. Liu | L. Jacobs | P. Kanetsky | F. Demenais | M. Avril | R. van Doorn | G. Lathrop | A. Stratigos | A. Ikram | T. Dębniak | H. Schulze | V. Höiom | J. Puig-Butillé | A. Cust | John C. Taylor | M. Law | P. Ghiorzo | J. N. Bishop | J. Randerson-Moor | E. Azizi | J. Lang | P. A. Andresen | N. van der Stoep | P. Helsing | L. Bowdler | M. Brossard | Hampus Olsson | K. Kypreou | G. B. Scarrà | S. Ward | Xin Li | Marianna Sanna | S. Macgregor | Fan Liu | Jeffrey E. Lee | S. Puig | Paul D. P. Pharoah | N. Orr | Pilar Galan | D. E. Elder | K. Brown | N. Martin | M. Wright | A. Uitterlinden | David M. Evans | Wei V. Chen | Anthony J. Swerdlow | M. Wright | N. Martin | Fan Lui | Graham L. Radford-Smith | N. Martin | N. Martin | D. Hunter | A. Green | E. Friedman | David M. Evans | Rajiv Kumar

[1]  A. Uitterlinden,et al.  Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure , 2018, Nature Communications.

[2]  Nicola J. Rinaldi,et al.  Genetic effects on gene expression across human tissues , 2017, Nature.

[3]  T. Chatila,et al.  DOCK8 deficiency: Insights into pathophysiology, clinical features and management. , 2017, Clinical immunology.

[4]  S. Jarrett,et al.  Divergence of cAMP signalling pathways mediating augmented nucleotide excision repair and pigment induction in melanocytes , 2017, Experimental dermatology.

[5]  Xiawei Wei,et al.  FTO is required for myogenesis by positively regulating mTOR-PGC-1α pathway-mediated mitochondria biogenesis , 2017, Cell Death & Disease.

[6]  N. Haass,et al.  NFIB Mediates BRN2 Driven Melanoma Cell Migration and Invasion Through Regulation of EZH2 and MITF , 2017, EBioMedicine.

[7]  J. Witte,et al.  Telomere structure and maintenance gene variants and risk of five cancer types , 2016, International journal of cancer.

[8]  S. Levy,et al.  The mammalian LINC complex regulates genome transcriptional responses to substrate rigidity , 2016, Scientific Reports.

[9]  Jeffrey E. Lee,et al.  A comprehensive genome‐wide analysis of melanoma Breslow thickness identifies interaction between CDC42 and SCIN genetic variants , 2016, International journal of cancer.

[10]  L. Liang,et al.  A comprehensive survey of genetic variation in 20 , 691 subjects from four large cohorts 1 , 2016 .

[11]  P. Puigserver,et al.  A PGC1α-mediated transcriptional axis suppresses melanoma metastasis , 2016, Nature.

[12]  S. Rosso,et al.  Association of Interferon Regulatory Factor-4 Polymorphism rs12203592 With Divergent Melanoma Pathways. , 2016, Journal of the National Cancer Institute.

[13]  Ji-Ying Song,et al.  Transcription Factor NFIB Is a Driver of Small Cell Lung Cancer Progression in Mice and Marks Metastatic Disease in Patients , 2016, Cell reports.

[14]  Joseph K. Pickrell,et al.  Detection and interpretation of shared genetic influences on 42 human traits , 2015, Nature Genetics.

[15]  B. Bastian,et al.  From melanocytes to melanomas , 2016, Nature Reviews Cancer.

[16]  K. Jalink,et al.  Rapid Remodeling of Invadosomes by Gi-coupled Receptors , 2016, The Journal of Biological Chemistry.

[17]  Daniel Marbach,et al.  Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics , 2016, PLoS Comput. Biol..

[18]  Manolis Kellis,et al.  HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease , 2015, Nucleic Acids Res..

[19]  T. Lange,et al.  53BP1 and the LINC Complex Promote Microtubule-Dependent DSB Mobility and DNA Repair , 2015, Cell.

[20]  N. Martin,et al.  The association between childhood maltreatment, psychopathology, and adult sexual victimization in men and women: results from three independent samples , 2015, Psychological Medicine.

[21]  Manolis Kellis,et al.  FTO Obesity Variant Circuitry and Adipocyte Browning in Humans. , 2015, The New England journal of medicine.

[22]  Marko Hočevar,et al.  Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma , 2015, Nature Genetics.

[23]  Steven J. M. Jones,et al.  Genomic Classification of Cutaneous Melanoma , 2015, Cell.

[24]  Donghyung Lee,et al.  DISTMIX: direct imputation of summary statistics for unmeasured SNPs from mixed ethnicity cohorts , 2015, Bioinform..

[25]  M. Parra.  Class IIa HDACs – new insights into their functions in physiology and pathology , 2015, The FEBS journal.

[26]  A. Heck,et al.  Proteomic Analyses Uncover a New Function and Mode of Action for Mouse Homolog of Diaphanous 2 (mDia2)* , 2015, Molecular & Cellular Proteomics.

[27]  S. Aerts,et al.  Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells , 2015, eLife.

[28]  G. Giles,et al.  Accuracy of Self-Reported Nevus and Pigmentation Phenotype Compared with Clinical Assessment in a Population-Based Study of Young Australian Adults , 2015, Cancer Epidemiology, Biomarkers & Prevention.

[29]  Y. Zhan,et al.  RE: The Effect on Melanoma Risk of Genes Previously Associated With Telomere Length. , 2014, Journal of the National Cancer Institute.

[30]  J. Orange,et al.  DOCK8 Deficiency: Clinical and Immunological Phenotype and Treatment Options - a Review of 136 Patients , 2015, Journal of Clinical Immunology.

[31]  S. Kõks,et al.  Melanocytes in the Skin – Comparative Whole Transcriptome Analysis of Main Skin Cell Types , 2014, PloS one.

[32]  I. Rigoutsos,et al.  The emerging roles of GPRC5A in diseases , 2014, Oncoscience.

[33]  E. Oancea,et al.  Data set for the genome-wide transcriptome analysis of human epidermal melanocytes , 2014, Data in brief.

[34]  Jeffrey E. Lee,et al.  The Effect on Melanoma Risk of Genes Previously Associated With Telomere Length , 2014, Journal of the National Cancer Institute.

[35]  Andrew D. Johnson,et al.  Parent-of-origin specific allelic associations among 106 genomic loci for age at menarche , 2014, Nature.

[36]  Liqun Luo,et al.  A molecular basis for classic blond hair color in Europeans , 2014, Nature Genetics.

[37]  A. Sokolenko,et al.  High prevalence of GPRC5A germline mutations in BRCA1‐mutant breast cancer patients , 2014, International journal of cancer.

[38]  Ashley M. Zehnder,et al.  Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition , 2014, Genome research.

[39]  M. Stephens,et al.  Efficient multivariate linear mixed model algorithms for genome-wide association studies. , 2014, Nature methods.

[40]  C. Wallace,et al.  Bayesian Test for Colocalisation between Pairs of Genetic Association Studies Using Summary Statistics , 2013, PLoS genetics.

[41]  Matthew Stephens,et al.  BAYESIAN METHODS FOR GENETIC ASSOCIATION ANALYSIS WITH HETEROGENEOUS SUBGROUPS: FROM META-ANALYSES TO GENE-ENVIRONMENT INTERACTIONS. , 2011, The annals of applied statistics.

[42]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[43]  D. Mackey,et al.  Raine Eye Health Study: Design, Methodology and Baseline Prevalence of Ophthalmic Disease in a Birth-cohort Study of Young Adults , 2013, Ophthalmic genetics.

[44]  A. Kornberg,et al.  GPRC5D is a promising marker for monitoring the tumor load and to target multiple myeloma cells , 2013, Hematology.

[45]  Michelle R. Campbell,et al.  A Polymorphic p53 Response Element in KIT Ligand Influences Cancer Risk and Has Undergone Natural Selection , 2013, Cell.

[46]  M. Peters,et al.  Systematic identification of trans eQTLs as putative drivers of known disease associations , 2013, Nature Genetics.

[47]  Stephen R. Piccolo,et al.  Genomic pathway analysis reveals that EZH2 and HDAC4 represent mutually exclusive epigenetic pathways across human cancers , 2013, BMC Medical Genomics.

[48]  Pedro G. Ferreira,et al.  Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.

[49]  Hua Zhou,et al.  Mendel: the Swiss army knife of genetic analysis programs , 2013, Bioinform..

[50]  J. Szustakowski,et al.  LMX1B mutations cause hereditary FSGS without extrarenal involvement. , 2013, Journal of the American Society of Nephrology : JASN.

[51]  Nazneen Rahman,et al.  Meta-analysis identifies four new loci associated with testicular germ cell tumor , 2013, Nature Genetics.

[52]  P. O’Reilly,et al.  Identification of seven loci affecting mean telomere length and their association with disease , 2013, Nature Genetics.

[53]  Eugenia G. Giannopoulou,et al.  NFIB is a governor of epithelial–melanocyte stem cell behaviour in a shared niche , 2013, Nature.

[54]  David M. Evans,et al.  Using Genetic Proxies for Lifecourse Sun Exposure to Assess the Causal Relationship of Sun Exposure with Circulating Vitamin D and Prostate Cancer Risk , 2013, Cancer Epidemiology, Biomarkers & Prevention.

[55]  Jonathan E. Shoag,et al.  PGC-1 coactivators regulate MITF and the tanning response. , 2013, Molecular cell.

[56]  D. Lawlor,et al.  Cohort Profile: The ‘Children of the 90s’—the index offspring of the Avon Longitudinal Study of Parents and Children , 2012, International journal of epidemiology.

[57]  D. Lawlor,et al.  Cohort Profile: The Avon Longitudinal Study of Parents and Children: ALSPAC mothers cohort , 2012, International journal of epidemiology.

[58]  Meike W. Vernooij,et al.  The Rotterdam Study: 2014 objectives and design update , 2013, European Journal of Epidemiology.

[59]  Doug Speed,et al.  Improved heritability estimation from genome-wide SNPs. , 2012, American journal of human genetics.

[60]  D. Whiteman,et al.  Good test-retest reproducibility for an instrument to capture self-reported melanoma risk factors. , 2012, Journal of clinical epidemiology.

[61]  Joseph Beyene,et al.  Meta-analysis of genetic association studies under heterogeneity , 2012, European Journal of Human Genetics.

[62]  U. Jaeger,et al.  Overexpression of G protein‐coupled receptor 5D in the bone marrow is associated with poor prognosis in patients with multiple myeloma , 2012, European journal of clinical investigation.

[63]  A. McRae,et al.  Genetic Influences on Life Span and Its Relationship to Personality: A 16-Year Follow-Up Study of a Sample of Aging Twins , 2012, Psychosomatic medicine.

[64]  J. Barrett,et al.  Pathway-Based Analysis of a Melanoma Genome-Wide Association Study: Analysis of Genes Related to Tumour-Immunosuppression , 2011, PloS one.

[65]  Sarah E. Medland,et al.  A Quantitative-Trait Genome-Wide Association Study of Alcoholism Risk in the Community: Findings and Implications , 2011, Biological Psychiatry.

[66]  Mark I McCarthy,et al.  Genomic inflation factors under polygenic inheritance , 2011, European Journal of Human Genetics.

[67]  Eleazar Eskin,et al.  Random-effects model aimed at discovering associations in meta-analysis of genome-wide association studies. , 2011, American journal of human genetics.

[68]  Jeffrey E. Lee,et al.  Genome-wide association study identifies nidogen 1 ( NID1 ) as a susceptibility locus to cutaneous nevi and melanoma risk , 2022 .

[69]  D. Hunter,et al.  A germline variant in the interferon regulatory factor 4 gene as a novel skin cancer risk locus. , 2011, Cancer research.

[70]  G. Abecasis,et al.  MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes , 2010, Genetic epidemiology.

[71]  Wolfgang Viechtbauer,et al.  Conducting Meta-Analyses in R with the metafor Package , 2010 .

[72]  J. Barrett,et al.  Melanocytic Nevi, Nevus Genes, and Melanoma Risk in a Large Case-Control Study in the United Kingdom , 2010, Cancer Epidemiology, Biomarkers & Prevention.

[73]  Nicole Soranzo,et al.  IRF4 variants have age-specific effects on nevus count and predispose to melanoma. , 2010, American journal of human genetics.

[74]  P. Visscher,et al.  A versatile gene-based test for genome-wide association studies. , 2010, American journal of human genetics.

[75]  Yun Li,et al.  METAL: fast and efficient meta-analysis of genomewide association scans , 2010, Bioinform..

[76]  P. Visscher,et al.  Common SNPs explain a large proportion of heritability for human height , 2011 .

[77]  A. Dobrovic,et al.  Mutations in KIT occur at low frequency in melanomas arising from anatomical sites associated with chronic and intermittent sun exposure , 2010, Pigment cell & melanoma research.

[78]  R. Lotan,et al.  Knockout of the Tumor Suppressor Gene Gprc5a in Mice Leads to NF-κB Activation in Airway Epithelium and Promotes Lung Inflammation and Tumorigenesis , 2010, Cancer Prevention Research.

[79]  D. Duffy,et al.  Multiple pigmentation gene polymorphisms account for a substantial proportion of risk of cutaneous malignant melanoma. , 2010, The Journal of investigative dermatology.

[80]  D. Whiteman,et al.  Estimating the Attributable Fraction for Cancer: A Meta-analysis of Nevi and Melanoma , 2010, Cancer Prevention Research.

[81]  Theo Stijnen,et al.  Dealing with Heterogeneity between Cohorts in Genomewide SNP Association Studies , 2010, Statistical applications in genetics and molecular biology.

[82]  C. Shanahan,et al.  Novel Nuclear Nesprin-2 Variants Tether Active Extracellular Signal-regulated MAPK1 and MAPK2 at Promyelocytic Leukemia Protein Nuclear Bodies and Act to Regulate Smooth Muscle Cell Proliferation* , 2009, The Journal of Biological Chemistry.

[83]  Cong Sun,et al.  Twins Eye Study in Tasmania (TEST): Rationale and Methodology to Recruit and Examine Twins , 2009, Twin Research and Human Genetics.

[84]  Peter Kraft,et al.  Genome-wide association study of tanning phenotype in a population of European ancestry. , 2009, The Journal of investigative dermatology.

[85]  T. Spector,et al.  Genome-wide association study identifies variants at 9p21 and 22q13 associated with development of cutaneous nevi , 2009, Nature Genetics.

[86]  Nandita Mitra,et al.  Common variation in KITLG and at 5q31.3 predisposes to testicular germ cell cancer , 2009, Nature Genetics.

[87]  Monique M. B. Breteler,et al.  The Rotterdam Study: 2016 objectives and design update , 2015, European Journal of Epidemiology.

[88]  Margaret A Tucker.  Melanoma epidemiology. , 2009, Hematology/oncology clinics of North America.

[89]  G. Walker,et al.  Ribosomal stress, p53 activation and the tanning response. , 2008, Expert review of dermatology.

[90]  D. Duffy,et al.  The Queensland Study of Melanoma: Environmental and Genetic Associations (Q-MEGA); Study Design, Baseline Characteristics, and Repeatability of Phenotype and Sun Exposure Measures , 2008, Twin Research and Human Genetics.

[91]  R. Lotan,et al.  Identification of the Retinoic Acid – Inducible Gprc5a as a New Lung Tumor Suppressor Gene , 2022 .

[92]  Karin Meyer,et al.  WOMBAT—A tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML) , 2007, Journal of Zhejiang University SCIENCE B.

[93]  T. Spector,et al.  Nevus Size and Number Are Associated with Telomere Length and Represent Potential Markers of a Decreased Senescence In vivo , 2007, Cancer Epidemiology Biomarkers & Prevention.

[94]  N. Hayward,et al.  Genome-wide loss of heterozygosity and copy number analysis in melanoma using high-density single-nucleotide polymorphism arrays. , 2007, Cancer research.

[95]  J. Trent,et al.  A genome-wide scan for naevus count: linkage to CDKN2A and to other chromosome regions , 2007, European Journal of Human Genetics.

[96]  Y. Nishimura,et al.  Novel reciprocal regulation of cAMP signaling and apoptosis by orphan G-protein-coupled receptor GPRC5A gene expression. , 2006, Biochemical and biophysical research communications.

[97]  T. Spector,et al.  Genome-wide search for nevus density shows linkage to two melanoma loci on chromosome 9 and identifies a new QTL on 5q31 in an adult twin cohort. , 2006, Human molecular genetics.

[98]  D. Pinkel,et al.  Somatic activation of KIT in distinct subtypes of melanoma. , 2006, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[99]  D. Fisher,et al.  MITF: master regulator of melanocyte development and melanoma oncogene. , 2006, Trends in molecular medicine.

[100]  R. Hofmann-Wellenhof,et al.  Age‐related prevalence of dermoscopy patterns in acquired melanocytic naevi , 2006, The British journal of dermatology.

[101]  K. Lange,et al.  Fishing for Pleiotropic QTLs in a Polygenic Sea , 2005, Annals of human genetics.

[102]  Graham A Colditz,et al.  Risk factors and individual probabilities of melanoma for whites. , 2005, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[103]  Margaret J. Wright,et al.  Brisbane Adolescent Twin Study: Outline of study methods and research projects , 2004 .

[104]  T. Shimomura,et al.  The RAIG family member, GPRC5D, is associated with hard-keratinized structures. , 2004, The Journal of investigative dermatology.

[105]  John D. Storey,et al.  Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach , 2004 .

[106]  John D. Storey.  The positive false discovery rate: a Bayesian interpretation and the q-value , 2003 .

[107]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[108]  N. Hayward,et al.  Melanocytic nevi, solar keratoses, and divergent pathways to cutaneous melanoma. , 2003, Journal of the National Cancer Institute.

[109]  John D. Storey.  A direct approach to false discovery rates , 2002 .

[110]  H. Hameister,et al.  Demethylation, reactivation, and destabilization of human fragile X full-mutation alleles in mouse embryocarcinoma cells. , 2001, American journal of human genetics.

[111]  J. Barrett,et al.  Heritability and gene-environment interactions for melanocytic nevus density examined in a U.K. adolescent twin study. , 2001, The Journal of investigative dermatology.

[112]  I. Marenholz,et al.  Identification of human epidermal differentiation complex (EDC)-encoded genes by subtractive hybridization of entire YACs to a gridded keratinocyte cDNA library. , 2001, Genome research.

[113]  M. Pembrey,et al.  ALSPAC--the Avon Longitudinal Study of Parents and Children. I. Study methodology. , 2001, Paediatric and perinatal epidemiology.

[114]  C. Garbe,et al.  Agreement between self-assessment of melanocytic nevi by patients and dermatologic examination. , 2000, American journal of epidemiology.

[115]  J F Aitken,et al.  A major quantitative-trait locus for mole density is linked to the familial melanoma gene CDKN2A: a maximum-likelihood combined linkage and association analysis in twins and their sibs. , 1999, American journal of human genetics.

[116]  A. Baldini,et al.  Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome , 1998, Nature Genetics.

[117]  J. Cuzick,et al.  The association between naevi and melanoma in populations with different levels of sun exposure: a joint case-control study of melanoma in the UK and Australia. , 1998, British Journal of Cancer.

[118]  M Berwick,et al.  Melanoma epidemiology. , 1997, Current opinion in oncology.

[119]  S. Harrison,et al.  Sunlight: a major factor associated with the development of melanocytic nevi in Australian schoolchildren. , 1994, Journal of the American Academy of Dermatology.