Changes

Neoplastic processes are a complex group of disorders that develop as a result of the accumulation of genetic alterations including gene mutations, chromosomal rearrangements, gain and loss of genetic material, epigenetic changes, loss of heterozygosity (LOH), and various other genetic changes. Defining and understanding the genetic alterations of specific neoplastic disorders influences the diagnoses, prognoses, and therapeutic choices for patients with both malignant and benign neoplasms.<ref>Swerdlow SH, Campo E, Harris NL, et al. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues, 4th edn, International Agency for Research on Cancer: Lyon, France, 2008.</ref><ref>Astbury C. Clinical Cytogenetics in Clinics in Laboratory Medicine, vol. 31(4). Elsevier Saunders: Philadelphia, PA, 2011.</ref><ref>Byrd JC, Mrózek K, Dodge RK, et al.; Cancer and Leukemia Group B (CALGB 8461). Pretreatment cytogenetic abnormalities are predictive of induction success, cumulative incidence of relapse, and overall survival in adult patients with de novo acute myeloid leukemia: results from Cancer and Leukemia Group B (CALGB 8461). Blood 2002;100:4325–4336.</ref><ref>Döhner H, Stilgenbauer S, Benner A, et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med 2000;343:1910–1916.</ref><ref>Heim S, Mitelman F. Cancer Cytogenetics, Chromosomal and Molecular Genetic Aberrations of Tumor Cells, 3rd edn. Wiley: Hoboken, New Jersey, 2009.</ref><ref>Moorman AV, Harrison CJ, Buck GA, et al.; Adult Leukaemia Working Party, Medical Research Council/National Cancer Research Institute. Karyotype is an independent prognostic factor in adult acute lymphoblastic leukemia (ALL): analysis of cytogenetic data from patients treated on the Medical Research Council (MRC) UKALLXII/Eastern Cooperative Oncology Group (ECOG) 2993 trial. Blood 2007;109:3189–3197.</ref><ref>Mrózek K, Heerema NA, Bloomfield CD. Cytogenetics in acute leukemia. Blood Rev 2004;18:115–136.</ref>

Neoplastic processes are a complex group of disorders that develop as a result of the accumulation of genetic alterations including gene mutations, chromosomal rearrangements, gain and loss of genetic material, epigenetic changes, loss of heterozygosity (LOH), and various other genetic changes. Defining and understanding the genetic alterations of specific neoplastic disorders influences the diagnoses, prognoses, and therapeutic choices for patients with both malignant and benign neoplasms.<ref>Swerdlow SH, Campo E, Harris NL, et al. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues, 4th edn, International Agency for Research on Cancer: Lyon, France, 2008.</ref><ref>Astbury C. Clinical Cytogenetics in Clinics in Laboratory Medicine, vol. 31(4). Elsevier Saunders: Philadelphia, PA, 2011.</ref><ref>Byrd JC, Mrózek K, Dodge RK, et al.; Cancer and Leukemia Group B (CALGB 8461). Pretreatment cytogenetic abnormalities are predictive of induction success, cumulative incidence of relapse, and overall survival in adult patients with de novo acute myeloid leukemia: results from Cancer and Leukemia Group B (CALGB 8461). Blood 2002;100:4325–4336.</ref><ref>Döhner H, Stilgenbauer S, Benner A, et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med 2000;343:1910–1916.</ref><ref>Heim S, Mitelman F. Cancer Cytogenetics, Chromosomal and Molecular Genetic Aberrations of Tumor Cells, 3rd edn. Wiley: Hoboken, New Jersey, 2009.</ref><ref>Moorman AV, Harrison CJ, Buck GA, et al.; Adult Leukaemia Working Party, Medical Research Council/National Cancer Research Institute. Karyotype is an independent prognostic factor in adult acute lymphoblastic leukemia (ALL): analysis of cytogenetic data from patients treated on the Medical Research Council (MRC) UKALLXII/Eastern Cooperative Oncology Group (ECOG) 2993 trial. Blood 2007;109:3189–3197.</ref><ref>Mrózek K, Heerema NA, Bloomfield CD. Cytogenetics in acute leukemia. Blood Rev 2004;18:115–136.</ref>

Published clinically applicable data now show the utility of DNA microarray analysis in the assessment of multiple neoplastic disorders.<ref>Armengol G, Canellas A, Alvarez Y, et al. Genetic changes including gene copy number alterations and their relation to prognosis in childhood acute myeloid leukemia. Leuk Lymphoma 2010;51:114–124.</ref><ref>Gunnarsson R, Staaf J, Jansson M, et al. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia–a comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes Cancer 2008;47:697–711.</ref><ref>Okamoto R, Ogawa S, Nowak D, et al. Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia. Haematologica 2010;95:1481–1488.</ref><ref>Slovak ML, Bedell V, Hsu YH, et al. Genomic alterations in Hodgkin and Reed/Sternberg (HRS) cells at disease onset reveals distinct signatures for chemo-sensitive and primary refractory Hodgkin lymphoma. Clin Cancer Res 2011;17:3443–3454.</ref><ref>Walter MJ, Payton JE, Ries RE, et al. Acquired copy number alterations in adult acute myeloid leukemia genomes. Proc Natl Acad Sci USA 2009;106:12950–12955.</ref><ref>Yu L, Slovak ML, Mannoor K, et al. Microarray detection of multiple recurring submicroscopic chromosomal aberrations in pediatric T-cell acute lymphoblastic leukemia. Leukemia 2011;25:1042–1046.</ref> Data indicate that microarray technologies provide information about gain and loss of genetic material in neoplastic disorders, including hematologic malignancies and solid tumors.<ref name=Bungaro>Bungaro S, Dell’Orto MC, Zangrando A, et al. Integration of genomic and gene expression data of childhood ALL without known aberrations identifies subgroups with specific genetic hallmarks. Genes Chromosomes Cancer 2009;48:22–38.</ref><ref name=Carrasco>Carrasco DR, Tonon G, Huang Y, et al. High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients. Cancer Cell 2006;9:313–325.</ref><ref name=Gunn>Gunn SR, Mohammed MS, Gorre ME, et al. Whole-genome scanning by array comparative genomic hybridization as a clinical tool for risk assessment in chronic lymphocytic leukemia. J Mol Diagn 2008;10:442–451.</ref><ref name=Hagenkord>Hagenkord JM, Gatalica Z, Jonasch E, Monzon FA. Clinical genomics of renal epithelial tumors. Cancer Genet 2011;204:285–297.</ref> These gains and losses, represented as an increase or decrease in the proportion of genetic material as compared with a reference genome, are collectively referred to as copy-number variants (CNVs). Microarray methodologies are appropriate complementary methods to standard methods of chromosome and fluorescence in situ hybridization (FISH) analyses for detection of genetic anomalies in neoplastic disorders.

Published clinically applicable data now show the utility of DNA microarray analysis in the assessment of multiple neoplastic disorders.<ref>Armengol G, Canellas A, Alvarez Y, et al. Genetic changes including gene copy number alterations and their relation to prognosis in childhood acute myeloid leukemia. Leuk Lymphoma 2010;51:114–124.</ref><ref name=Gunnarsson>Gunnarsson R, Staaf J, Jansson M, et al. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia–a comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes Cancer 2008;47:697–711.</ref><ref>Okamoto R, Ogawa S, Nowak D, et al. Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia. Haematologica 2010;95:1481–1488.</ref><ref>Slovak ML, Bedell V, Hsu YH, et al. Genomic alterations in Hodgkin and Reed/Sternberg (HRS) cells at disease onset reveals distinct signatures for chemo-sensitive and primary refractory Hodgkin lymphoma. Clin Cancer Res 2011;17:3443–3454.</ref><ref>Walter MJ, Payton JE, Ries RE, et al. Acquired copy number alterations in adult acute myeloid leukemia genomes. Proc Natl Acad Sci USA 2009;106:12950–12955.</ref><ref>Yu L, Slovak ML, Mannoor K, et al. Microarray detection of multiple recurring submicroscopic chromosomal aberrations in pediatric T-cell acute lymphoblastic leukemia. Leukemia 2011;25:1042–1046.</ref> Data indicate that microarray technologies provide information about gain and loss of genetic material in neoplastic disorders, including hematologic malignancies and solid tumors.<ref name=Bungaro>Bungaro S, Dell’Orto MC, Zangrando A, et al. Integration of genomic and gene expression data of childhood ALL without known aberrations identifies subgroups with specific genetic hallmarks. Genes Chromosomes Cancer 2009;48:22–38.</ref><ref name=Carrasco>Carrasco DR, Tonon G, Huang Y, et al. High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients. Cancer Cell 2006;9:313–325.</ref><ref name=Gunn>Gunn SR, Mohammed MS, Gorre ME, et al. Whole-genome scanning by array comparative genomic hybridization as a clinical tool for risk assessment in chronic lymphocytic leukemia. J Mol Diagn 2008;10:442–451.</ref><ref name=Hagenkord>Hagenkord JM, Gatalica Z, Jonasch E, Monzon FA. Clinical genomics of renal epithelial tumors. Cancer Genet 2011;204:285–297.</ref> These gains and losses, represented as an increase or decrease in the proportion of genetic material as compared with a reference genome, are collectively referred to as copy-number variants (CNVs). Microarray methodologies are appropriate complementary methods to standard methods of chromosome and fluorescence in situ hybridization (FISH) analyses for detection of genetic anomalies in neoplastic disorders.

DNA microarray technologies should confirm genetic imbalances identified by conventional and molecular cytogenetic or FISH analyses and provide further detail of the aberrations.<ref name=Carrasco></ref><ref name=Gunn></ref><ref name=Hagenkord></ref> However, additional important information about the genetics of specific disorders may be revealed, e.g., leukemia with normal cytogenetic and FISH analyses.<ref>Paulsson K, Forestier E, Lilljebjörn H, et al. Genetic landscape of high hyperdiploid childhood acute lymphoblastic leukemia. Proc Natl Acad Sci USA 2010;107:21719–21724.</ref><ref>Rücker FG, Bullinger L, Schwaenen C, et al. Disclosure of candidate genes in acute myeloid leukemia with complex karyotypes using microarray-based molecular characterization. J Clin Oncol 2006;24:3887–3894.</ref><ref>Usvasalo A, Elonen E, Saarinen-Pihkala UM, et al. Prognostic classification of patients with acute lymphoblastic leukemia by using gene copy number profiles identified from array-based comparative genomic hybridization data. Leuk Res 2010;34:1476–1482.</ref><ref>Gorletta TA, Gasparini P, D’Elios MM, Trubia M, Pelicci PG, Di Fiore PP. Frequent loss of heterozygosity without loss of genetic material in acute myeloid leukemia with a normal karyotype. Genes Chromosomes Cancer 2005;44:334–337.</ref><ref>O’Keefe C, McDevitt MA, Maciejewski JP. Copy neutral loss of heterozygosity: a novel chromosomal lesion in myeloid malignancies. Blood 2010;115:2731–2739.</ref><ref>Kawamata N, Ogawa S, Zimmermann M, et al. Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray. Blood 2008;111:776–784.</ref>

DNA microarray technologies should confirm genetic imbalances identified by conventional and molecular cytogenetic or FISH analyses and provide further detail of the aberrations.<ref name=Carrasco></ref><ref name=Gunn></ref><ref name=Hagenkord></ref> However, additional important information about the genetics of specific disorders may be revealed, e.g., leukemia with normal cytogenetic and FISH analyses.<ref>Paulsson K, Forestier E, Lilljebjörn H, et al. Genetic landscape of high hyperdiploid childhood acute lymphoblastic leukemia. Proc Natl Acad Sci USA 2010;107:21719–21724.</ref><ref>Rücker FG, Bullinger L, Schwaenen C, et al. Disclosure of candidate genes in acute myeloid leukemia with complex karyotypes using microarray-based molecular characterization. J Clin Oncol 2006;24:3887–3894.</ref><ref>Usvasalo A, Elonen E, Saarinen-Pihkala UM, et al. Prognostic classification of patients with acute lymphoblastic leukemia by using gene copy number profiles identified from array-based comparative genomic hybridization data. Leuk Res 2010;34:1476–1482.</ref><ref>Gorletta TA, Gasparini P, D’Elios MM, Trubia M, Pelicci PG, Di Fiore PP. Frequent loss of heterozygosity without loss of genetic material in acute myeloid leukemia with a normal karyotype. Genes Chromosomes Cancer 2005;44:334–337.</ref><ref>O’Keefe C, McDevitt MA, Maciejewski JP. Copy neutral loss of heterozygosity: a novel chromosomal lesion in myeloid malignancies. Blood 2010;115:2731–2739.</ref><ref>Kawamata N, Ogawa S, Zimmermann M, et al. Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray. Blood 2008;111:776–784.</ref>

== DNA Microarray Platforms ==

== DNA Microarray Platforms ==

Different types of DNA microarray platforms currently available for clinical testing include bacterial artificial chromosome–based array comparative genomic hybridization, oligonucleotide-based array comparative genomic hybridization, oligonucleotide plus single-nucleotide polymorphism (SNP)-based arrays that contain both copy-number (intensity-only) and SNP (allele-differentiating) probes, as well as SNP-only–based arrays [9,24,25,26].

Different types of DNA microarray platforms currently available for clinical testing include bacterial artificial chromosome–based array comparative genomic hybridization, oligonucleotide-based array comparative genomic hybridization, oligonucleotide plus single-nucleotide polymorphism (SNP)-based arrays that contain both copy-number (intensity-only) and SNP (allele-differentiating) probes, as well as SNP-only–based arrays [9,24,25,26].<ref name=Gunnarsson></ref><ref>Hagenkord JM, Monzon FA, Kash SF, Lilleberg S, Xie Q, Kant JA. Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: performance comparison of Affymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays. J Mol Diagn 2010;12:184–196.</ref><ref>Kallioniemi A. CGH microarrays and cancer. Curr Opin Biotechnol 2008;19:36–40.</ref><ref>Maciejewski JP, Tiu RV, O’Keefe C. Application of array-based whole genome scanning technologies as a cytogenetic tool in haematological malignancies. Br J Haematol 2009;146:479–488.</ref>

For comparative genomic hybridization–based microarrays, patient DNA and reference DNA are labeled with different fluorochromes and hybridized to probes on the microarray. SNP-based arrays use a single color dye compared with an in silico reference. A scanner measures differences in the intensities of the fluorochromes, and the data are expressed as having more or less signal as compared with the reference. For genomic regions with two copies of the DNA sequence, copy-number data are graphed as a log2 ratio with the expected normal copy number equaling “0.” Duplications will have signals of greater intensity (log2 > 0) and deletions less intensity (log2 < 0). Microarrays that incorporate SNP probes allow simultaneous detection of DNA copy-number changes and absence of heterozygosity (AOH) by providing information about the intensity of the signals at the loci. AOH may be due to LOH, hemizygosity, or homozygosity.

For comparative genomic hybridization–based microarrays, patient DNA and reference DNA are labeled with different fluorochromes and hybridized to probes on the microarray. SNP-based arrays use a single color dye compared with an in silico reference. A scanner measures differences in the intensities of the fluorochromes, and the data are expressed as having more or less signal as compared with the reference. For genomic regions with two copies of the DNA sequence, copy-number data are graphed as a log2 ratio with the expected normal copy number equaling “0.” Duplications will have signals of greater intensity (log2 > 0) and deletions less intensity (log2 < 0). Microarrays that incorporate SNP probes allow simultaneous detection of DNA copy-number changes and absence of heterozygosity (AOH) by providing information about the intensity of the signals at the loci. AOH may be due to LOH, hemizygosity, or homozygosity.