ARTICLE Impact of genotype-first diagnosis: the detection of microdeletion and microduplication syndromes with cancer predisposition by aCGH Sara Anne Adams, MS1, Justine Coppinger, MS1, Sulagna C. Saitta, MD, PhD2, Tracy Stroud, MD3, Manikum Kandamurugu, MD4, Zheng Fan, PhD4, Blake C. Ballif, PhD1, Lisa G. Shaffer, PhD1,5, and Bassem A. Bejjani, MD1,6,7 1–4 Background: The use of microarray-based comparative genomic hy- syndromes, expanded phenotypic spectrums of previously 5 bridization has allowed the genetic diagnosis of some conditions before identified syndromes, elucidated the genomic basis of well- 6 their full clinical presentation. This “genotype-first” diagnosis has the defined clinical syndromes, and refined molecular mechanisms 7 most clinical implications for genomic alterations that confer an ele- of chromosomal aberrations identified by routine karyotyping. vated risk of cancer. In these cases, diagnosis before the manifestation This technology is frequently used to assist in diagnosing of the patient’s full phenotype dramatically impacts genetic counseling, patients without clinical findings suggestive of a specific struc- 8 clinical management, and eventual prognosis and survivability. Meth- tural chromosome disorder. Before the adoption of aCGH in ods: Using microarray-based comparative genomic hybridization, we diagnostic testing, the recommended cytogenetic evaluations for tested 18,437 individuals with indications such as developmental dis- individuals with intellectual disability, developmental delay, abilities and congenital anomalies. Results: We identified 34 (0.18%) birth defects, abnormalities in growth, seizures, or behavior individuals with DNA copy number gains or losses that encompassed differences such as autism consisted of karyotyping followed by gene regions associated with recognized genetic conditions with an subtelomeric fluorescence in situ hybridization (FISH). If clin- increased risk for cancer. Three of the 34 individuals (8.8%) had a ical features increased suspicion for a specific microdeletion or previously abnormal cytogenetic study which microarray-based com- microduplication syndrome, single-locus FISH could be pur- parative genomic hybridization confirmed and/or further characterized. sued, but success in diagnosis depended on classic phenotypic Seven of the 34 individuals (20.6%) either had the correct disease presentation and the clinician’s ability to recognize character- specified in the clinical indication for study or had clinical features istic clinical features. In contrast to the “phenotype-first” ap- highly indicative of that syndrome. The remaining 24 patients (70.6%) proach of the past, aCGH expands upon the “genotype-first” had indications for study that were not specific to the diagnosed syn- approach of routine chromosome analysis and, more recently, drome, such as “developmental delay” or “dysmorphic features.” Con- subtelomeric FISH studies, by allowing a comprehensive ob- clusions: The ability of microarray-based comparative genomic hybrid- jective interrogation of chromosome structure for microscopic ization to rapidly and objectively interrogate the genome for and submicroscopic imbalances throughout the genome in in- chromosomal imbalances has led to the opportunity to optimize medical dividuals who may not exhibit recognizable phenotypic features management and outcome. This has an even more profound impact and of a specific disorder.9 This genotype-first approach allows for clinical utility in conditions associated with cancer predisposition the diagnosis of genetic conditions in infants and children syndromes. Genet Med 2009:11(5):314–322. before the full manifestation of classic or recognizable clinical Key Words: array CGH, comparative genomic hybridization, cancer, features to a greater extent than has ever been available in the predisposition testing, mental retardation past. Early diagnosis provides opportunities to refine medical management to optimize patient health and medical outcome. One of the most dramatic examples of the clinical utility icroarray-based comparative genomic hybridization of aCGH and how this technology optimizes medical man- M(aCGH) has become an important cytogenetic diagnostic agement is the diagnosis of genetic conditions that confer an tool in the evaluation of patients with intellectual disabilities, increased risk of cancer. Many cancer syndromes have asso- developmental delays, birth defects, seizures, behavior distur- ciated congenital anomalies that bring the child to clinical bances, or aberrant growth patterns. aCGH has identified new attention before the onset or suspicion of neoplasia.10,11 Although most mutations that cause cancer predisposition are From the 1Signature Genomic Laboratories, LLC, Spokane, Washington; sequence mutations within critical genes that would not be 2Division of Human Genetics, Children’s Hospital of Philadelphia, Phila- detectable by aCGH, many deletions have been reported of delphia, Pennsylvania; 3Thompson Center for Autism and Neurodevelop- various cancer predisposition genes, such as PTEN, WT1, ment Disorders, University of Missouri, Columbia, Missouri; 4Division of RB1, and APC.12,13 In addition, patients with deletions often Pediatrics, Genetics and Metabolism, University of North Carolina, Chapel have larger regions deleted than just the immediate gene, Hill, North Carolina; 5School of Molecular Biosciences, Washington State University; 6WWAMI Medical Education Program, Washington State Uni- which can cause features more typical of chromosomal ab- versity; and 7Sacred Heart Medical Center, Spokane, Washington. normalities, such as mental retardation, birth defects, and 14,15 Bassem A. Bejjani, MD, Signature Genomic Laboratories, LLC, 2820 N. behavioral anomalies. Because of its utility in diagnosing Astor Street, Spokane, WA 99207. E-mail: [email protected]. individuals with nonspecific clinical findings, aCGH may detect DNA copy gains or losses that can predispose to Disclosure: L.G. Shaffer and B. A. Bejjani have ownership and sit on the Members’ Board of Signature Genomic Laboratories, LLC. neoplasm (Table 1). We report our experience with diagnosis of cancer syndromes using aCGH and present case examples Submitted for publication November 18, 2008. to demonstrate how this genotype-first approach to diagnos- Accepted for publication February 9, 2009. tic testing refines and guides medical management and im- DOI: 10.1097/GIM.0b013e3181a028a5 proves clinical outcome. 314 Genetics IN Medicine • Volume 11, Number 5, May 2009 Genetics Genetics Table 1 Summary of disorders predisposing to childhood neoplasia detectable by aCGH IN IN Medicine Proportion caused Medicine Critical by cytogenetic Condition OMIM gene(s) Associated tumors with risk onset in childhood Associated tumors with risk onset in adulthood abnormality, % • Volume 11, Number 5, May 2009 Alagille 118450 JAG1 Hepatocellular carcinoma 3–7 • Volume 11, Number 5, May 2009 Basal cell nevus/ 109400 PTCH1 Basal cell carcinoma, cysts (epidermoid, lymphomesenteric, pleural), fibroma Fibroma (ovarian), fibrosarcoma Rare Gorlin-Goltz (cardiac), medulloblastoma, meningioma, neuroblastoma, odontogenic keratocysts, rhabdomyoma Beckwith- 130650 IGF2 Adrenocortical carcinoma, adenoma, fibroadenoma, ganglioneuroma, Rare Wiedemann gonadoblastoma, hamartoma, hepatoblastoma, myxoma, neuroblastoma, rhabdomyosarcoma, Wilms tumor Down 190685 NA Acute leukemia ϳ99 FAP/MR 175100 APC Adenomatous digestive tract polyps, colorectal cancer, desmoid, fibroma, Duodenal cancer, gastric cancer, pancreatic Rare gastric fundic gland polyps cancer, thyroid cancer (papillary) Gardnera 175100 APC Cysts (dentigerous, epidermal, sebaceous), lipoma, hepatoblastoma, Rare osteoma, osteosarcoma Turcotb 276300 APC Glioblastoma, medulloblastoma Rare Juvenile polyposis 174900 BMPR1A, Hamartomatous digestive tract polyps Colon cancer, small intestinal cancer, gastric 7 MADH4 cancer, pancreatic adenocarcinoma, rectal cancer Klinefelter NA NA Ependymoma, germinoma (cranial, mediastinal), teratoma (mediastinal) Breast cancer, leukemia, lung cancer, ϳ99 lymphoma (non-Hodgkin), seminoma Li Fraumenib 151623 TP53 Adrenocortical carcinoma, brain cancer (multiple types), laryngeal cancer, Breast cancer, leukemia (acute), lung cancer, Rare neuroblastoma, sarcoma (chondro-, fibro-, osteo-, rhabdomyo-, other lymphoma (non-Hodgkin), testicular cancer soft-tissue) Neurofibromatosis 1 162200 NF1 Brain (m), hamartoma (iris), leukemia (juvenile myeolomonocytic), malignant Breast cancer, carcinoid (duodenal & other), 5–20 peripheral nerve sheath tumor (MPNST), neuroblastoma, neurofibroma gastrointestinal stromal tumor (GIST) (plexiform, simple), optic pathway astrocytoma/glioma, pheochromocytoma, rhabdomyosarcoma, Wilms tumor Neurofibromatosis 2 101000 NF2 Hamartoma (retinal), neurofibroma (plexiform, simple) Brain cancer (m), meningioma (cranial, 15–21 spinal), schwannoma (spinal, vestibular) Peutz-Jeghers 175200 STK11 Esophageal cancer, gastric cancer, nasal polyps, reproductive tract cancer (m), Breast cancer, colon cancer, lung cancer, small intestinal cancer pancreatic adenocarcinoma Pheochromocytoma- 115310 SDHD Paraganglioma, pheochromocytoma Gastrointestinal stromal tumor (GIST), paraganglioma 4 parathyroid adenoma, renal cell carcinoma, thyroid cancer (papillary) Adams et al. Potocki-Shaffer 601224 EXT2/WT1 Chondrosarcoma, Wilms tumor ϳ99 (Continued) 315 316 Detection of cancer predisposition by aCGH Table 1 Continued Proportion caused Critical by cytogenetic Condition OMIM gene(s) Associated