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Atkinson C, McInerney-Leo AM, Proctor M, Lanagan C, Stevenson AJ, Dehkhoda F, Caole M, Maas E, Ainger S, Pritchard AL, Johansson PA, Leo P, Hayward NK, Sturm RA, Duncan EL, Gabrielli B. The ATM Ser49Cys Variant Effects ATM Function as a Regulator of Oncogene-Induced Senescence. Int J Mol Sci 2024; 25:1664. [PMID: 38338943 PMCID: PMC10855307 DOI: 10.3390/ijms25031664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/21/2024] [Indexed: 02/12/2024] Open
Abstract
An apical component of the cell cycle checkpoint and DNA damage repair response is the ataxia-telangiectasia mutated (ATM) Ser/Thr protein kinase. A variant of ATM, Ser49Cys (rs1800054; minor allele frequency = 0.011), has been associated with an elevated risk of melanoma development; however, the functional consequence of this variant is not defined. ATM-dependent signalling in response to DNA damage has been assessed in a panel of patient-derived lymphoblastoid lines and primary human melanocytic cell strains heterozygous for the ATM Ser49Cys variant allele. The ATM Ser49Cys allele appears functional for acute p53-dependent signalling in response to DNA damage. Expression of the variant allele did reduce the efficacy of oncogene expression in inducing senescence. These findings demonstrate that the ATM 146C>G Ser49Cys allele has little discernible effect on the acute response to DNA damage but has reduced function observed in the chronic response to oncogene over-expression. Analysis of melanoma, naevus and skin colour genomics and GWAS analyses have demonstrated no association of this variant with any of these outcomes. The modest loss of function detected suggest that the variant may act as a modifier of other variants of ATM/p53-dependent signalling.
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Affiliation(s)
- Caroline Atkinson
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Aideen M. McInerney-Leo
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Martina Proctor
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Catherine Lanagan
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | | | - Farhad Dehkhoda
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Mary Caole
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Ellie Maas
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Stephen Ainger
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Antonia L. Pritchard
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Peter A. Johansson
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Paul Leo
- Centre of Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Nicholas K. Hayward
- Queensland Institute for Medical Research Berghofer, Brisbane, QLD 4006, Australia
| | - Richard A. Sturm
- Dermatology Research Centre, Frazer Institute, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Emma L. Duncan
- Department of Twin Research and Genetic Epidemiology, School of Life Course & Population Sciences, Faculty of Life Sciences and Medicine, King’s College London, London SE1 1UL, UK
| | - Brian Gabrielli
- Mater Research Institute, The University of Queensland, Brisbane, QLD 4102, Australia
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Stark MS, Sturm RA, Pan Y, Smit DJ, Kommajosyula V, Lee KJ, Jagirdar K, McLean C, Duffy DL, Soyer HP, Mar VJ. Assessing the genetic risk of nodular melanoma using a candidate gene approach. Br J Dermatol 2024; 190:199-206. [PMID: 37766469 DOI: 10.1093/bjd/ljad365] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/28/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023]
Abstract
BACKGROUND Nodular melanoma (NM) is a challenge to diagnose early due to its rapid growth and more atypical clinical presentation, making it the largest contributor to melanoma mortality. OBJECTIVES Our study aim was to perform a rare-variant allele (RVA) analysis of whole-exome sequencing of patients with NM and non-NM (minor allele frequency ≤ 1% non-Finnish European) for a set of 500 candidate genes potentially implicated in melanoma. METHODS This study recruited 131 participants with NM and 194 with non-NM from South-east Queensland and patients with NM from Victoria to perform a comparative analysis of possible genetic differences or similarities between the two melanoma cohorts. RESULTS Phenotypic analysis revealed that a majority of patients diagnosed with NM were older males with a higher frequency of fair skin and red hair than is seen in the general population. The distribution of common melanoma polygenic risk scores was similar in patients with NM and non-NM, with over 28% in the highest quantile of scores. There was also a similar frequency of carriage of familial/high-penetrant melanoma gene and loss-of-function variants. We identified 39 genes by filtering 500 candidate genes based on the greatest frequency in NM compared with non-NM cases. The genes with RVAs of greatest frequency in NM included PTCH1, ARID2 and GHR. Rare variants in the SMO gene, which interacts with PTCH1 as ligand and receptor, were also identified, providing evidence that the Hedgehog pathway may contribute to NM risk. There was a cumulative effect in carrying multiple rare variants in the NM-associated genes. A 14.8-fold increased ratio for NM compared with non-NM was seen when two RVAs of the 39 genes were carried by a patient. CONCLUSIONS This study highlights the importance of considering frequency of RVA to identify those at risk of NM in addition to known high penetrance genes.
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Affiliation(s)
- Mitchell S Stark
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Richard A Sturm
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Yan Pan
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences
| | - Darren J Smit
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Varsha Kommajosyula
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Katie J Lee
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Kasturee Jagirdar
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
| | - Catriona McLean
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences
| | - David L Duffy
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - H Peter Soyer
- Frazer Institute, The University of Queensland, Dermatology Research Centre, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Victoria J Mar
- Victorian Melanoma Service, The Alfred Hospital, Melbourne, Vic, Australia
- School of Public Health and Preventive Medicine; Monash University, Melbourne, Vic, Australia
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3
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Wallingford CK, Demeshko A, Krishnakripa AK, Smit D, Duffy DL, Betz-Stablein B, Pflugfelder A, Jagirdar K, Holland E, Mann GJ, Primiero CA, Yanes T, Malvehy J, Badenas C, Carrera C, Aguilera P, Olsen C, Ward SV, Haass NK, Sturm RA, Puig S, Whiteman D, Law MH, Cust AE, Potrony M, Soyer H P, McInerney-Leo AM. The MC1R r allele does not increase melanoma risk in MITF E318K carriers. Br J Dermatol 2023; 188:770-776. [PMID: 36879448 PMCID: PMC10230961 DOI: 10.1093/bjd/ljad041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/18/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Population-wide screening for melanoma is not cost-effective, but genetic characterization could facilitate risk stratification and targeted screening. Common Melanocortin-1 receptor (MC1R) red hair colour (RHC) variants and Microphthalmia-associated transcription factor (MITF) E318K separately confer moderate melanoma susceptibility, but their interactive effects are relatively unexplored. OBJECTIVES To evaluate whether MC1R genotypes differentially affect melanoma risk in MITF E318K+ vs. E318K- individuals. MATERIALS AND METHODS Melanoma status (affected or unaffected) and genotype data (MC1R and MITF E318K) were collated from research cohorts (five Australian and two European). In addition, RHC genotypes from E318K+ individuals with and without melanoma were extracted from databases (The Cancer Genome Atlas and Medical Genome Research Bank, respectively). χ2 and logistic regression were used to evaluate RHC allele and genotype frequencies within E318K+/- cohorts depending on melanoma status. Replication analysis was conducted on 200 000 general-population exomes (UK Biobank). RESULTS The cohort comprised 1165 MITF E318K- and 322 E318K+ individuals. In E318K- cases MC1R R and r alleles increased melanoma risk relative to wild type (wt), P < 0.001 for both. Similarly, each MC1R RHC genotype (R/R, R/r, R/wt, r/r and r/wt) increased melanoma risk relative to wt/wt (P < 0.001 for all). In E318K+ cases, R alleles increased melanoma risk relative to the wt allele [odds ratio (OR) 2.04 (95% confidence interval 1.67-2.49); P = 0.01], while the r allele risk was comparable with the wt allele [OR 0.78 (0.54-1.14) vs. 1.00, respectively]. E318K+ cases with the r/r genotype had a lower but not significant melanoma risk relative to wt/wt [OR 0.52 (0.20-1.38)]. Within the E318K+ cohort, R genotypes (R/R, R/r and R/wt) conferred a significantly higher risk compared with non-R genotypes (r/r, r/wt and wt/wt) (P < 0.001). UK Biobank data supported our findings that r did not increase melanoma risk in E318K+ individuals. CONCLUSIONS RHC alleles/genotypes modify melanoma risk differently in MITF E318K- and E318K+ individuals. Specifically, although all RHC alleles increase risk relative to wt in E318K- individuals, only MC1R R increases melanoma risk in E318K+ individuals. Importantly, in the E318K+ cohort the MC1R r allele risk is comparable with wt. These findings could inform counselling and management for MITF E318K+ individuals.
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Affiliation(s)
- Courtney K Wallingford
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Anastassia Demeshko
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | | | - Darren J Smit
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - David L Duffy
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, Australia
| | - Brigid Betz-Stablein
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, Australia
| | - Annette Pflugfelder
- Center of Dermato-Oncology, Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Kasturee Jagirdar
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- Biochemistry and Molecular Biology Department, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Elizabeth Holland
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, Australia
| | - Graham J Mann
- The Melanoma Institute Australia, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Clare A Primiero
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Tatiane Yanes
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Josep Malvehy
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Cèlia Badenas
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, Barcelona, Spain
| | - Cristina Carrera
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Paula Aguilera
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Catherine M Olsen
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, Australia
| | - Sarah V Ward
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
| | - Nikolas K Haass
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Richard A Sturm
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
| | - Susana Puig
- Dermatology Department, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - David C Whiteman
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Queensland, Australia
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD, 4006, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, Australia
| | - Anne E Cust
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council NSW, Sydney, Australia
- The Melanoma Institute Australia, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Miriam Potrony
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, IDIBAPS, Barcelona, Spain
| | - H Peter Soyer
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Australia
| | - Aideen M McInerney-Leo
- Frazer Institute, University of Queensland, Dermatology Research Centre, Brisbane, Australia
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4
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Lambertini M, Zengarini C, Ravaioli GM, Veronesi G, Mussi M, Ferrari T, Braschi G, Campione E, Dika E. Multiple primary melanomas: Is there a correlation between dermoscopic features and germline mutations? Australas J Dermatol 2023; 64:e182-e185. [PMID: 36774630 DOI: 10.1111/ajd.14007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Accepted: 01/24/2023] [Indexed: 02/13/2023]
Affiliation(s)
- Martina Lambertini
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Corrado Zengarini
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Giulia Maria Ravaioli
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Giulia Veronesi
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Martina Mussi
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Tiziano Ferrari
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum University of Bologna, Bologna, Italy
| | | | - Elena Campione
- Dermatology Unit, Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Emi Dika
- Dermatology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum University of Bologna, Bologna, Italy
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5
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Kataria S, Dabas P, Saraswathy KN, Sachdeva MP, Jain S. Investigating the morphology and genetics of scalp and facial hair characteristics for phenotype prediction. Sci Justice 2023; 63:135-148. [PMID: 36631178 DOI: 10.1016/j.scijus.2022.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Microscopic traits and ultrastructure of hair such as cross-sectional shape, pigmentation, curvature, and internal structure help determine the level of variations between and across human populations. Apart from cosmetics and anthropological applications, such as determining species, somatic origin (body area), and biogeographic ancestry, the evidential value of hair has increased with rapid progression in the area of forensic DNA phenotyping (FDP). Individuals differ in the features of their scalp hair (greying, shape, colour, balding, thickness, and density) and facial hair (eyebrow thickness, monobrow, and beard thickness) features. Scalp and facial hair characteristics are genetically controlled and lead to visible inter-individual variations within and among populations of various ethnic origins. Hence, these characteristics can be exploited and made more inclusive in FDP, thereby leading to more comprehensive, accurate, and robust prediction models for forensic purposes. The present article focuses on understanding the genetics of scalp and facial hair characteristics with the goal to develop a more inclusive approach to better understand hair biology by integrating hair microscopy with genetics for genotype-phenotype correlation research.
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Affiliation(s)
- Suraj Kataria
- Department of Anthropology, University of Delhi, India.
| | - Prashita Dabas
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India.
| | | | - M P Sachdeva
- Department of Anthropology, University of Delhi, India.
| | - Sonal Jain
- Department of Anthropology, University of Delhi, India.
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6
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Ekanayake Weeramange C, Shu D, Tang KD, Batra J, Ladwa R, Kenny L, Vasani S, Frazer IH, Dolcetti R, Ellis JJ, Sturm RA, Leo P, Punyadeera C. Analysis of human leukocyte antigen associations in human papillomavirus-positive and -negative head and neck cancer: Comparison with cervical cancer. Cancer 2022; 128:1937-1947. [PMID: 35176174 PMCID: PMC9306518 DOI: 10.1002/cncr.34148] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 11/08/2022]
Abstract
Background Although the majority of human papillomavirus (HPV) infections are cleared by the immune system, a small percentage of them progress to develop HPV‐driven cancers. Cervical cancer studies highlight that HPV persistence and cancer risk are associated with genetic factors, especially at the human leukocyte antigen (HLA) genes. This study was conducted to investigate such associations in head and neck cancer (HNC). Methods In all, 192 patients with HNC and 384 controls were genotyped with the Infinium Global Screening Array (Illumina, Inc). HLA variants were imputed with SNP2HLA, and an association analysis was performed by logistic regression. Results HPV‐positive HNCs were significantly associated with single‐nucleotide polymorphisms (SNPs) at DRB1_32660090 (P = 1.728 × 10–6) and DRB1_32660116 (P = 1.728 × 10–6) and with the amino acid variant DRB1_11_32660115 (P = 1.728 × 10–6). None of these associations were observed in the HPV‐negative cohort, and this suggested their specificity to convey risk for HPV‐associated HNCs. In general, associations observed for HPV‐negative HNC were relatively weak, and variants in the HLA‐DPA1 region were the strongest among them (P = 4.531 × 10–4). Several lead signals reported by previous HNC genome‐wide association studies, including SNPs rs3135001 (P = .012), rs1049055 (P = .012), and rs34518860 (P = .029) and allele HLA‐DQB1*06 (P = .009), were replicated in the current study. However, these associations were limited to the HPV‐positive HNC group. Several cervical cancer–associated HLA variants, including SNPs rs9272143 (P = .002) and rs9271858 (P = .002) and alleles HLA‐B‐1501 (P = .009) and HLA‐B‐15 (P = .015), were also exclusively associated with HPV‐positive HNC. Conclusions HPV‐positive HNC risk is associated with distinct HLA variants, and some of them are shared by both cervical cancer and HPV‐positive HNC. Human papillomavirus (HPV)–positive head and neck cancer (HNC) risk is associated with distinct human leukocyte antigen variants, and some of them are shared by both cervical cancer and HPV‐positive HNC. Lay Summary Cervical cancer studies highlight that human papillomavirus (HPV)–driven cancer risk is linked with human leukocyte antigen (HLA) polymorphism. Hence, the current study was designed to investigate the HLA associations in HPV‐positive and HPV‐negative head and neck cancer (HNC) and compare these associations with cervical cancer. Several lead signals reported by previous HNC and cervical genome‐wide association studies were replicated in the current study. However, these associations were limited to the HPV‐positive HNC group, and this suggests that HPV‐positive HNC risk is associated with distinct HLA variants, and some of them are shared by both cervical cancer and HPV‐positive HNC.
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Affiliation(s)
- Chameera Ekanayake Weeramange
- Centre for Biomedical Technologies, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery and Menzies Health Institute Queensland, Southport, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia.,Department of Medical Laboratory Sciences, Faculty of Health Sciences, Open University of Sri Lanka, Nugegoda, Sri Lanka
| | - Danhua Shu
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia.,Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kai Dun Tang
- Centre for Biomedical Technologies, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Jyotsna Batra
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Rahul Ladwa
- Department of Cancer Care Services, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.,Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Lizbeth Kenny
- Faculty of Medicine, University of Queensland, Herston, Queensland, Australia.,Department of Cancer Care Services, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Sarju Vasani
- Faculty of Medicine, University of Queensland, Herston, Queensland, Australia.,Department of Otolaryngology, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Ian H Frazer
- Translational Research Institute, Woolloongabba, Queensland, Australia.,Faculty of Medicine, University of Queensland, Herston, Queensland, Australia
| | - Riccardo Dolcetti
- Faculty of Medicine, University of Queensland, Herston, Queensland, Australia.,Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan J Ellis
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia.,Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Richard A Sturm
- Diamantina Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Paul Leo
- School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia.,Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Chamindie Punyadeera
- Centre for Biomedical Technologies, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia.,Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery and Menzies Health Institute Queensland, Southport, Queensland, Australia.,Translational Research Institute, Woolloongabba, Queensland, Australia
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7
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Predictive value of global dermoscopic pattern in patients diagnosed with cutaneous melanoma. Postepy Dermatol Alergol 2021; 38:572-577. [PMID: 34658696 PMCID: PMC8501438 DOI: 10.5114/ada.2020.94593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 02/21/2020] [Indexed: 12/04/2022] Open
Abstract
Introduction Dermoscopy is one of the most commonly used methods in early diagnosis of melanoma. It is conducted to differentiate between benign and malignant patterns in melanocytic lesions. Aim To determine if there is a predominance of one dermoscopic pattern in patients with melanoma and if there is a significant difference in dominant global dermoscopic pattern in patients with cutaneous melanomas correlated with patients’ sex and the location of the primary tumor. Material and methods The study included 162 patients with prior diagnosis of cutaneous melanoma. Dermoscopic and videodermoscopic pictures and patient data were analyzed with regard to the pattern: reticular, globular, homogeneous and mixed pattern (two-component pattern; reticular-globular pattern) with central or peripheral globules and multicomponent (mixed – at least 3 types of structures in one nevus). Results The reticular pattern was significantly more prevalent in male patients (38.57%, 27 patients) in comparison to female patients (18.45%, 17 patients). We also found a statistically significant lower prevalence of reticular pattern in patients diagnosed with melanomas located on upper limbs. The homogeneous pattern was statistically significantly more prevalent in patients in whom primary tumors were located on the head and upper limbs. Conclusions Our study suggests that predominant complex patterns are more commonly observed in patients diagnosed with cutaneous melanoma, although there is a significant number of patients with predominant reticular and homogeneous patterns, which are not often associated with an increased risk of development of melanoma.
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8
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Lee KJ, Janda M, Stark MS, Sturm RA, Soyer HP. On Naevi and Melanomas: Two Sides of the Same Coin? Front Med (Lausanne) 2021; 8:635316. [PMID: 33681261 PMCID: PMC7933521 DOI: 10.3389/fmed.2021.635316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/13/2022] Open
Abstract
Benign naevi are closely linked to melanoma, as risk factors, simulators, or sites of melanoma formation. There is a heavy genetic overlap between the two lesions, a shared environmental influence of ultraviolet radiation, and many similar cellular features, yet naevi remain locally situated while melanomas spread from their primary site and may progress systemically to distal organs. Untangling the overlapping contributors and predictors of naevi and melanoma is an ongoing area of research and should eventually lead to more personalized prevention and treatment strategies, through the development of melanoma risk stratification tools and early detection of evolving melanomas. This will be achieved through a range of complementary strategies: risk-adjusted primary prevention counseling; the use of lesion imaging technologies such as sequential 3D total body photography and consumer-performed lesion imaging; artificial intelligence deep phenotyping and clinical assistance; a better understanding of genetic drivers of malignancy, risk variants, clinical genetics, and polygenic effects; and the interplay between genetics, phenotype and the environment.
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Affiliation(s)
- Katie J Lee
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Monika Janda
- Centre for Health Services Research, The University of Queensland, Brisbane, QLD, Australia
| | - Mitchell S Stark
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - H Peter Soyer
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia.,Department of Dermatology, Princess Alexandra Hospital, Brisbane, QLD, Australia
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9
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Pozzobon FC, Tell-Marti G, Calbet-Llopart N, Barreiro A, Espinosa N, Potrony M, Alejo B, Podlipnik S, Combalia M, Puig-Butillé JA, Carrera C, Malvehy J, Puig S. Influence of germline genetic variants on dermoscopic features of melanoma. Pigment Cell Melanoma Res 2021; 34:618-628. [PMID: 33342058 DOI: 10.1111/pcmr.12954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 12/02/2020] [Accepted: 12/11/2020] [Indexed: 01/12/2023]
Abstract
Nevus count is highly determined by inherited variants and has been associated with the origin of melanoma. De novo melanomas (DNMMs) are more prevalent in patients with a low nevus count and have distinctive dermoscopic features than nevus-associated melanomas. We evaluated the impact of nine single nucleotide polymorphisms (SNPs) of MTAP (rs10811629, rs2218220, rs7023329 and rs751173), PLA2G6 (rs132985 and rs2284063), IRF4 (rs12203592), and PAX3 (rs10180903 and rs7600206) genes associated with nevus count and melanoma susceptibility, and the MC1R variants on dermoscopic features of 371 melanomas from 310 patients. All MTAP variants associated with a low nevus count were associated with regression structures (peppering and mixed regression), blue-whitish veil, shiny white structures, and pigment network. SNPs of PLA2G6 (rs132985), PAX3 (rs7600206), and IRF4 (rs12203592) genes were also associated with either shiny white structures or mixed regression (all corrected p-values ≤ .06). Melanomas from red hair color MC1R variants carriers showed lower total dermoscopy score (p-value = .015) and less blotches than melanomas from non-carriers (p-value = .048). Our results provide evidence that germline variants protective for melanoma risk and/or associated with a low nevus count are associated with certain dermoscopic features, more characteristic of de novo and worse prognosis melanomas.
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Affiliation(s)
- Flavia Carolina Pozzobon
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain.,Universidad Nacional de Colombia, Bogotá, Colombia
| | - Gemma Tell-Marti
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain.,Biomedical Research Networking Center on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain
| | - Neus Calbet-Llopart
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain.,Biomedical Research Networking Center on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain
| | - Alicia Barreiro
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain
| | - Natalia Espinosa
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain
| | - Míriam Potrony
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain.,Biomedical Research Networking Center on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain
| | - Beatriz Alejo
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain
| | - Sebastian Podlipnik
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain
| | - Marc Combalia
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain
| | - Joan Anton Puig-Butillé
- Biomedical Research Networking Center on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain.,Biochemical and Molecular Genetics Service, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain
| | - Cristina Carrera
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain.,Biomedical Research Networking Center on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain
| | - Josep Malvehy
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain.,Biomedical Research Networking Center on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain.,Medicine Department, Universitat de Barcelona, Barcelona, Spain
| | - Susana Puig
- Melanoma Unit, Dermatology Department, Hospital Clínic & IDIBAPS (Institut d'Investigacions Biomèdiques August Pi i Sunyer), Barcelona, Spain.,Biomedical Research Networking Center on Rare Diseases (CIBERER), ISCIII, Barcelona, Spain.,Medicine Department, Universitat de Barcelona, Barcelona, Spain
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10
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Rayner JE, Duffy DL, Smit DJ, Jagirdar K, Lee KJ, De’Ambrosis B, Smithers BM, McMeniman EK, McInerney-Leo AM, Schaider H, Stark MS, Soyer HP, Sturm RA. Germline and somatic albinism variants in amelanotic/hypomelanotic melanoma: Increased carriage of TYR and OCA2 variants. PLoS One 2020; 15:e0238529. [PMID: 32966289 PMCID: PMC7510969 DOI: 10.1371/journal.pone.0238529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
Amelanotic/hypomelanotic melanoma is a clinicopathologic subtype with absent or minimal melanin. This study assessed previously reported coding variants in albinism genes (TYR, OCA2, TYRP1, SLC45A2, SLC24A5, LRMDA) and common intronic, regulatory variants of OCA2 in individuals with amelanotic/hypomelanotic melanoma, pigmented melanoma cases and controls. Exome sequencing was available for 28 individuals with amelanotic/hypomelanotic melanoma and 303 individuals with pigmented melanoma, which were compared to whole exome data from 1144 Australian controls. Microarray genotyping was available for a further 17 amelanotic/hypomelanotic melanoma, 86 pigmented melanoma, 147 melanoma cases (pigmentation unknown) and 652 unaffected controls. Rare deleterious variants in TYR/OCA1 were more common in amelanotic/hypomelanotic melanoma cases than pigmented melanoma cases (set mixed model association tests P = 0.0088). The OCA2 hypomorphic allele p.V443I was more common in melanoma cases (1.8%) than controls (1.0%, X2 P = 0.02), and more so in amelanotic/hypomelanotic melanoma (4.4%, X2 P = 0.007). No amelanotic/hypomelanotic melanoma cases carried an eye and skin darkening haplotype of OCA2 (including rs7174027), present in 7.1% of pigmented melanoma cases (P = 0.0005) and 9.4% controls. Variants in TYR and OCA2 may play a role in amelanotic/hypomelanotic melanoma susceptibility. We suggest that somatic loss of function at these loci could contribute to the loss of tumor pigmentation, consistent with this we found a higher rate of somatic mutation in TYR/OCA2 in amelanotic/hypomelanotic melanoma vs pigmented melanoma samples (28.6% vs 3.0%; P = 0.021) from The Cancer Genome Atlas Skin Cutaneous Melanoma collection.
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Affiliation(s)
- Jenna E. Rayner
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - David L. Duffy
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- QIMR Berghofer Medical Research Institute, Brisbane, Qld, Australia
| | - Darren J. Smit
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Kasturee Jagirdar
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Katie J. Lee
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Brian De’Ambrosis
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, Qld, Australia
- South East Dermatology, Annerley, Brisbane, Qld, Australia
| | - B. Mark Smithers
- Queensland Melanoma Project, School of Medicine, The University of Queensland, Brisbane, Qld, Australia
| | - Erin K. McMeniman
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Aideen M. McInerney-Leo
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Helmut Schaider
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Mitchell S. Stark
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
| | - H. Peter Soyer
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- Dermatology Department, Princess Alexandra Hospital, Brisbane, Qld, Australia
| | - Richard A. Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Qld, Australia
- * E-mail:
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11
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McMeniman EK, Peach E, Lee KJ, Yanes T, Jagirdar K, Stark MS, Soyer HP, Duffy DL, McInerney-Leo AM, Sturm RA. CDKN2A testing threshold in a high-risk Australian melanoma cohort: number of primaries, family history and young age of onset impact risk. J Eur Acad Dermatol Venereol 2020; 34:e797-e798. [PMID: 32386439 DOI: 10.1111/jdv.16627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E K McMeniman
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia.,Dermatology Department, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - E Peach
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - K J Lee
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - T Yanes
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - K Jagirdar
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - M S Stark
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - H P Soyer
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia.,Dermatology Department, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - D L Duffy
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - A M McInerney-Leo
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - R A Sturm
- Dermatology Research Centre, The University of Queensland, The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
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12
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Abstract
Human skin and hair color are visible traits that can vary dramatically within and across ethnic populations. The genetic makeup of these traits-including polymorphisms in the enzymes and signaling proteins involved in melanogenesis, and the vital role of ion transport mechanisms operating during the maturation and distribution of the melanosome-has provided new insights into the regulation of pigmentation. A large number of novel loci involved in the process have been recently discovered through four large-scale genome-wide association studies in Europeans, two large genetic studies of skin color in Africans, one study in Latin Americans, and functional testing in animal models. The responsible polymorphisms within these pigmentation genes appear at different population frequencies, can be used as ancestry-informative markers, and provide insight into the evolutionary selective forces that have acted to create this human diversity.
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Affiliation(s)
- William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA;
| | - Richard A Sturm
- Dermatology Research Centre, The University of Queensland Diamantina Institute, The University of Queensland, Brisbane, Queensland 4102, Australia;
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