Molecular Diagnostics—An Emerging Frontier in Dermatopathology

Advances made within the field of genomics and proteomics have facilitated the emergence of a new era of molecular diagnostics. However, ongoing rapid developments in molecular methodology ensure that this remains a complex field, accessible primarily to scientists who routinely utilize these techniques. For this reason, in this article we provide a concise overview of established and emerging molecular methods and discuss their role as diagnostic adjuncts in Dermatopathology. Important nonmolecular techniques that are used in conjunction with molecular methods are also highlighted.

[1]  Preface to Genomic Pathology – a New Frontier , 2001, The Journal of pathology.

[2]  Mariaelena Pierobon,et al.  Laser capture microdissection technology , 2007, Expert review of molecular diagnostics.

[3]  L. Liotta,et al.  Laser Capture Microdissection , 1996, Science.

[4]  H. Thiesen,et al.  DNA microarray technology and its applications in dermatology , 2004, Experimental dermatology.

[5]  C. Morrison,et al.  Assessment of TCR‐β clonality in a diverse group of cutaneous T‐Cell infiltrates , 2008 .

[6]  C. Lebbé,et al.  Value of cytogenetic analysis in the treatment of dermatofibrosarcoma protuberans. , 2008, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[7]  T. Belbin,et al.  DNA microarrays: from structural genomics to functional genomics. The applications of gene chips in dermatology and dermatopathology. , 2004, Journal of the American Academy of Dermatology.

[8]  T. McCalmont,et al.  Primary cicatricial alopecia: histopathologic findings do not distinguish clinical variants. , 2005, Journal of the American Academy of Dermatology.

[9]  D. Smeets,et al.  Historical prospective of human cytogenetics: from microscope to microarray. , 2004, Clinical biochemistry.

[10]  B. Ylstra,et al.  Microarray‐based comparative genomic hybridization and its applications in human genetics , 2004, Clinical genetics.

[11]  Jane Fridlyand,et al.  Improving Melanoma Classification by Integrating Genetic and Morphologic Features , 2008, PLoS medicine.

[12]  A. Ranki,et al.  Chromosomal abnormalities in cutaneous T-cell lymphoma and in its premalignant conditions as detected by G-banding and interphase cytogenetic methods. , 1997, The Journal of investigative dermatology.

[13]  S. Whittaker,et al.  Fine mapping of chromosome 10q deletions in mycosis fungoides and sezary syndrome: Identification of two discrete regions of deletion at 10q23.33–24.1 and 10q24.33–25.1 , 2005, Genes, chromosomes & cancer.

[14]  M. Smith,et al.  Fluorescence In Situ Hybridization (FISH) as an Ancillary Diagnostic Tool in the Diagnosis of Melanoma , 2011 .

[15]  D. Denhardt.  Osteopontin expression correlates with melanoma invasion. , 2005, The Journal of investigative dermatology.

[16]  Christos Hatzis,et al.  Commercialized multigene predictors of clinical outcome for breast cancer. , 2008, The oncologist.

[17]  J. Zehnder,et al.  T-cell clonality analysis in biopsy specimens from two different skin sites shows high specificity in the diagnosis of patients with suggested mycosis fungoides. , 2007, Journal of the American Academy of Dermatology.

[18]  L. French,et al.  T-cell clonality assays: how do they compare? , 2008, The Journal of investigative dermatology.

[19]  T. Ushiki,et al.  The structure of human metaphase chromosomes: its histological perspective and new horizons by atomic force microscopy. , 2002, Archives of histology and cytology.

[20]  M. Hameed,et al.  Pathology and genetics of adipocytic tumors , 2007, Cytogenetic and Genome Research.

[21]  R. Aebersold,et al.  Proteomics: the first decade and beyond , 2003, Nature Genetics.

[22]  J. Goldblum,et al.  Fluorescence in situ hybridization for MDM2 gene amplification as a diagnostic tool in lipomatous neoplasms , 2008, Modern Pathology.

[23]  Francesco Falciani,et al.  DNA Microarrays: a Powerful Genomic Tool for Biomedical and Clinical Research , 2007, Molecular medicine.

[24]  R. Elashoff,et al.  Prognostic significance of molecular upstaging of paraffin-embedded sentinel lymph nodes in melanoma patients. , 2004, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[25]  C. Antonescu.  Targeted therapy of cancer: new roles for pathologists in identifying GISTs and other sarcomas , 2008, Modern Pathology.

[26]  M. Mahalingam,et al.  Apolipoprotein D in CD34-positive and CD34-negative cutaneous neoplasms: a useful marker in differentiating superficial acral fibromyxoma from dermatofibrosarcoma protuberans , 2008, Modern Pathology.

[27]  W. Schempp,et al.  Molecular diagnosis in dermatopathology: What makes sense, and what doesn’t , 2009, Experimental dermatology.

[28]  M. Gulley,et al.  Clinical laboratory reports in molecular pathology. , 2007, Archives of pathology & laboratory medicine.

[29]  B. Kumar,et al.  Development of a polymerase chain reaction dot‐blotting system for detecting cutaneous tuberculosis , 2000, The British journal of dermatology.

[30]  A. Beaudet,et al.  Array-based DNA diagnostics: let the revolution begin. , 2008, Annual review of medicine.

[31]  S. Tyring,et al.  Molecular diagnosis of infectious diseases in dermatology. , 2004, Journal of the American Academy of Dermatology.

[32]  N. Kiviat,et al.  Merkel cell polyomavirus is more frequently present in North American than Australian Merkel cell carcinoma tumors. , 2009, The Journal of investigative dermatology.

[33]  Henry A. Erlich,et al.  The polymerase chain reaction. , 1989, Trends in genetics : TIG.

[34]  G. Esposito.  Complementary techniques: laser capture microdissection--increasing specificity of gene expression profiling of cancer specimens. , 2007, Advances in experimental medicine and biology.

[35]  Beena Kumar,et al.  Tissue microarrays: a practical guide. , 2004, Pathology.

[36]  Graeme I Murray,et al.  An overview of laser microdissection technologies. , 2007, Acta histochemica.

[37]  Dermatological applications of DNA array technology , 2002, Clinical and experimental dermatology.

[38]  M. Mahalingam,et al.  Involvement of the bulge region in primary scarring alopecia , 2008, Journal of cutaneous pathology.

[39]  R. Happle,et al.  Molecular genetics of the hair follicle: the state of the art. , 2000, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[40]  I. Eltoum,et al.  Microdissection of Histologic Sections: Past, Present, and Future , 2002, Advances in anatomic pathology.

[41]  Stephen M Hewitt,et al.  Perspectives in tissue microarrays. , 2004, Combinatorial chemistry & high throughput screening.

[42]  C. Antonescu.  The role of genetic testing in soft tissue sarcoma , 2006, Histopathology.

[43]  M. Raffeld,et al.  Laser capture microdissection in pathology. , 2000, Journal of clinical pathology.

[44]  J. Guitart,et al.  Fluorescence in situ hybridization as a tool for microstaging in malignant melanoma , 2009, Modern Pathology.

[45]  P. Quaglino,et al.  TCRgamma-chain gene rearrangement by PCR-based GeneScan: diagnostic accuracy improvement and clonal heterogeneity analysis in multiple cutaneous T-cell lymphoma samples. , 2008, The Journal of investigative dermatology.

[46]  D. Pinkel,et al.  Chromosomal gains and losses in primary cutaneous melanomas detected by comparative genomic hybridization. , 1998, Cancer research.

[47]  Michael R. Speicher,et al.  The new cytogenetics: blurring the boundaries with molecular biology , 2005, Nature Reviews Genetics.

[48]  D L Rimm,et al.  Amplification of tissue by construction of tissue microarrays. , 2001, Experimental and molecular pathology.

[49]  R. Elashoff,et al.  Sentinel-node biopsy or nodal observation in melanoma. , 2006, The New England journal of medicine.

[50]  J. Becker,et al.  MC polyomavirus is frequently present in Merkel cell carcinoma of European patients. , 2009, The Journal of investigative dermatology.

[51]  J. Q. Rosso,et al.  Merkel cell polyomavirus DNA detection in lesional and nonlesional skin from patients with Merkel cell carcinoma or other skin diseases , 2011 .

[52]  C. Featherstone.  Epidermolysis bullosa: from fundamental molecular biology to clinical therapies. , 2007, Journal of Investigative Dermatology.

[53]  H. Fei,et al.  Identification of proteins involved in aggregation of human dermal papilla cells by proteomics. , 2007, Journal of dermatological science.

[54]  Daniel Pinkel,et al.  Classifying melanocytic tumors based on DNA copy number changes. , 2003, The American journal of pathology.

[55]  Manfred Dietel,et al.  Personalized medicine and development of targeted therapies: the upcoming challenge for diagnostic molecular pathology. A review , 2006, Virchows Archiv.

[56]  Jag Bhawan,et al.  Incidental Microscopic Foci of Nevic Aggregates in Skin , 2008, The American Journal of dermatopathology.

[57]  H. Joensuu,et al.  Clinical factors associated with Merkel cell polyomavirus infection in Merkel cell carcinoma. , 2009, Journal of the National Cancer Institute.

[58]  L. Laghi,et al.  Differences and evolution of the methods for the assessment of microsatellite instability , 2008, Oncogene.

[59]  M. Nosrati,et al.  Novel Role for RGS1 in Melanoma Progression , 2008, The American journal of surgical pathology.

[60]  A. Emley,et al.  RAS and RAF mutations in banal melanocytic aggregates contiguous with primary cutaneous melanoma: clues to melanomagenesis , 2009, The British journal of dermatology.

[61]  C. Giacomantonio,et al.  Detection of tyrosinase mRNA in the sentinel lymph nodes of melanoma patients is not a predictor of short-term disease recurrence , 2007, Modern Pathology.

[62]  Ally‐Khan Somani,et al.  Toponomics: visualizing cellular protein networks in health and disease –‘A single picture is worth more than a thousand words!’ , 2008, Journal of cutaneous pathology.

[63]  Ronald Simon,et al.  Tissue Microarrays , 2010, Methods in Molecular Biology.

[64]  G. Mann,et al.  Diagnosis of cutaneous melanocytic tumours by four‐colour fluorescence in situ hybridisation , 2009, Pathology.

[65]  O. Dadzie,et al.  What can primary cutaneous neuroendocrine carcinomas with squamoid and neuroendocrine differentiation teach us about the origin of Merkel cells? , 2009, International journal of dermatology.

[66]  C. Kirkpatrick,et al.  PCR testing for Treponema pallidum in paraffin-embedded skin biopsy specimens: test design and impact on the diagnosis of syphilis , 2007, Journal of Clinical Pathology.

[67]  M. Teixeira,et al.  Combined classical and molecular cytogenetic analysis of cancer. , 2002, European journal of cancer.

[68]  G. Makrigiorgos,et al.  PCR-based methods for the enrichment of minority alleles and mutations. , 2009, Clinical chemistry.

[69]  M. Mahalingam,et al.  MSH-6: extending the reliability of immunohistochemistry as a screening tool in Muir–Torre syndrome , 2008, Modern Pathology.

[70]  G. Saldanha,et al.  Understanding spitzoid tumours: new insights from molecular pathology , 2007, The British journal of dermatology.

[71]  Nancy Wang.  Methodologies in cancer cytogenetics and molecular cytogenetics. , 2002, American journal of medical genetics.

[72]  L. Jin,et al.  In situ hybridization: Methods and applications , 1997, Journal of clinical laboratory analysis.

[73]  E. Lander.  Array of hope , 1999, Nature Genetics.

[74]  M. Mahalingam,et al.  Cutaneous sebaceous neoplasms as markers of Muir‐Torre syndrome: a diagnostic algorithm , 2009, Journal of cutaneous pathology.

[75]  H. Moch,et al.  Tissue microarray (TMA) technology: miniaturized pathology archives for high‐throughput in situ studies , 2001, The Journal of pathology.

[76]  B. Thiers,et al.  Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma , 2009 .

[77]  M. Flaig,et al.  Laser‐capture microdissection: Applications in routine molecular dermatopathology , 2004, Journal of cutaneous pathology.

[78]  Ronald Simon,et al.  Tissue microarrays for miniaturized high-throughput molecular profiling of tumors. , 2002, Experimental hematology.

[79]  C. Bodemer,et al.  Early skin biopsy is helpful for the diagnosis and management of neonatal and infantile erythrodermas , 2010, Journal of cutaneous pathology.

[80]  B. Bastian,et al.  Dose‐dependent, complete response to imatinib of a metastatic mucosal melanoma with a K642E KIT mutation , 2008, Pigment cell & melanoma research.

[81]  K K Jain,et al.  Current status of fluorescent in-situ hybridisation. , 2004, Medical device technology.

[82]  B. Bastian,et al.  Distinguishing melanocytic nevi from melanoma by DNA copy number changes: comparative genomic hybridization as a research and diagnostic tool , 2006, Dermatologic therapy.

[83]  V. Speirs,et al.  Tissue microarrays--big potential from small samples (review). , 2004, International journal of oncology.

[84]  R. Burgemeister.  New Aspects of Laser Microdissection in Research and Routine , 2005, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[85]  L. Medeiros,et al.  Clonal heterogeneity in mycosis fungoides and its relationship to clinical course. , 2002, Blood.

[86]  M. Cid,et al.  Stimulatory autoantibodies to the PDGF receptor in scleroderma. , 2006, The New England journal of medicine.

[87]  G. Richard.  Molecular genetics of the ichthyoses , 2004, American journal of medical genetics. Part C, Seminars in medical genetics.

[88]  I. Tomlinson,et al.  Loss of heterozygosity analysis: Practically and conceptually flawed? , 2002, Genes, chromosomes & cancer.

[89]  H. Tsao,et al.  Genetics of melanoma tumorigenesis , 2007, The British journal of dermatology.

[90]  E. Campo,et al.  Tissue macroarrays ("microchops") for gene expression analysis , 2001, Virchows Archiv.

[91]  M. Morley,et al.  Making and reading microarrays , 1999, Nature Genetics.

[92]  S. Whittaker,et al.  Molecular cytogenetic characterization of Sézary syndrome , 2003, Genes, Chromosomes and Cancer.

[93]  E. Reed,et al.  Clinical Utility of Microarrays: Current Status, Existing Challenges and Future Outlook , 2008, Current genomics.

[94]  C. Goh,et al.  Clinical utility of polymerase chain reaction in the detection of Mycobacterium tuberculosis in different types of cutaneous tuberculosis and tuberculids. , 2001, Annals of the Academy of Medicine, Singapore.

[95]  S. Lodha,et al.  Discordance in the histopathologic diagnosis of difficult melanocytic neoplasms in the clinical setting , 2008, Journal of cutaneous pathology.

[96]  T. Liehr,et al.  Current developments in human molecular cytogenetic techniques. , 2002, Current molecular medicine.

[97]  M. Werner,et al.  Frequent detection of Merkel cell polyomavirus in human Merkel cell carcinomas and identification of a unique deletion in the VP1 gene. , 2008, Cancer research.

[98]  C. Urban,et al.  Successful treatment of progressive cutaneous mastocytosis with imatinib in a 2-year-old boy carrying a somatic KIT mutation. , 2008, Blood.

[99]  L. Bolund,et al.  Are keratoacanthomas variants of squamous cell carcinomas? A comparison of chromosomal aberrations by comparative genomic hybridization. , 2006, The Journal of investigative dermatology.

[100]  M. Poljak,et al.  Detection of Human Papillomaviruses in Tissue Specimens , 1998, Advances in anatomic pathology.

[101]  A. Lazar,et al.  Sebaceous neoplasia and Torre-Muir syndrome. , 2007, Current diagnostic pathology.

[102]  M. Becich,et al.  Practical aspects of planning, building, and interpreting tissue microarrays: The Cooperative Prostate Cancer Tissue Resource experience , 2007, Journal of Molecular Histology.

[103]  K. Halling,et al.  Fluorescence in situ hybridization in diagnostic cytology. , 2007, Human pathology.

[104]  C. Maercker.  Protein Arrays in Functional Genome Research , 2005, Bioscience reports.

[105]  J. Hunt.  Molecular pathology in anatomic pathology practice: a review of basic principles. , 2008, Archives of pathology & laboratory medicine.

[106]  K. Mullis,et al.  Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. , 1985, Science.

[107]  D. Mason,et al.  Immunofluorescent and FISH Analysis of Skin Biopsies , 2004, The American Journal of dermatopathology.

[108]  P. Gerami,et al.  Chromosomal copy number changes supporting the classification of lentiginous junctional melanoma of the elderly as a subtype of melanoma , 2009, Modern Pathology.

[109]  A. Cochran,et al.  Molecular classification of melanomas and nevi using gene expression microarray signatures and formalin-fixed and paraffin-embedded tissue , 2009, Modern Pathology.

[110]  E. Petricoin,et al.  Laser Capture Microdissection , 1996, Science.

[111]  A. Gottlieb,et al.  A potential role for imatinib and other small molecule tyrosine kinase inhibitors in the treatment of systemic and localized sclerosis. , 2008, Journal of the American Academy of Dermatology.

[112]  M. Murphy,et al.  Molecular diagnosis of a benign proliferative nodule developing in a congenital melanocytic nevus in a 3-month-old infant. , 2008, Journal of the American Academy of Dermatology.

[113]  G. Shipley,et al.  Molecular diagnosis of cutaneous diseases. , 2005, Archives of dermatology.

[114]  A. Ranki,et al.  Molecular cytogenetics in the study of cutaneous T-cell lymphomas (CTCL) , 2007, Cytogenetic and Genome Research.

[115]  R. Davis,et al.  Biomarkers of human cutaneous squamous cell carcinoma from tissues and cell lines identified by DNA microarrays and qRT-PCR. , 2003, Biochemical and biophysical research communications.

[116]  Supratim Choudhuri,et al.  Microarrays in biology and medicine , 2004, Journal of biochemical and molecular toxicology.

[117]  M. van de Rijn,et al.  Applications of microarrays to histopathology , 2004, Histopathology.

[118]  J. Uitto.  Progress in heritable skin diseases: translational implications of mutation analysis and prospects of molecular therapies*. , 2009, Acta dermato-venereologica.

[119]  Bassem A Bejjani,et al.  Application of array-based comparative genomic hybridization to clinical diagnostics. , 2006, The Journal of molecular diagnostics : JMD.

[120]  J. Carlson,et al.  New techniques in dermatopathology that help to diagnose and prognosticate melanoma. , 2009, Clinics in dermatology.