Human Genetics Laboratory 985440 Nebraska Medical Center Omaha, NE 68198-5440 Address Service Requested

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page 1 ACOG recommends Prenatal Microarray in this Recent recommendations have increased the use of microarray in the prenatal setting. page 4 FISH for Non-Small Cell Lung Carcinoma (NSCLC) Tiered FISH testing is recommended to detect abnormalities in ALK, ROS1, and RET. issue page 6 A new approach to comprehensive gene panel testing Next Generation Sequencing (NGS) combined with Deletion/Duplication Analysis allows detection of both sequenced-based variations and intragenic copy number changes.

Human Genetics Laboratory Newsletter | Summer 2014 UNMC Human Genetics Laboratory

for health care providers Prenatal Microarray ur laboratory offers a wide This opinion recommends the use Orange of prenatal genetic testing of microarray analysis when fetal services, which include chromosome ultrasound anomalies are detected or analysis (karyotyping), fluorescence when a patient is undergoing invasive in situ hybridization (FISH), and prenatal diagnostic testing and microarray analysis. Historically, emphasizes that this analysis should be chromosome analysis and FISH made available to patients regardless have been the predominant assays of maternal age.1 of choice for indications such as advanced maternal age; abnormal In the prenatal setting, our laboratory ultrasound findings; abnormal 1st, uses a microarray platform designed 2nd, or combined maternal serum specifically for the detection of screening result; and a family submicroscopic deletions and history of a genetic or chromosomal duplications in regions of known abnormality. These tests continue to clinical relevance. In addition, this provide practitioners and patients platform offers whole genome with valuable diagnostic information coverage for accurate copy number in the prenatal period. assessment and includes single nucleotide polymorphisms (SNPs) for More recently, the use of microarray enhanced detection of maternal cell analysis in the prenatal setting has contamination. Results for this testing steadily increased, at least partly as are typically available within 1-2 weeks a result of the joint opinion put forth of specimen receipt in the laboratory. by the American College of Obstetrics Please contact us for additional and Gynecology (ACOG) and the information about the benefits of Society of Maternal Fetal Medicine. Prenatal Microarray for your patients.

1 The use of chromosomal microarray analysis in prenatal diagnosis. Committee Opinion No. 581. American College of Obstetricians and Gynecologists. Obstet Gynecol, 122:1374-1377, 2013.

Genetic Counselors Essential to Laboratory Mission As part of our comprehensive services, the Human Genetics Laboratory team includes licensed and board-certified genetic counselors to assist providers and their patients. Our genetic counselors have current clinical experience as well as dedicated areas of expertise, ranging from prenatal and postnatal genetics to oncology. Serving as a liaison between providers and laboratory services, genetic counselors recommend indication-specific testing strategies, request additional clinical information for improved testing and interpretation, notify providers of STAT results, and discuss test results and pertinent management issues. Our counselors look forward to interacting with you.

Human Genetics Laboratory Newsletter | Summer 2014 From the director

Our laboratory continues to provide diagnostic genetic testing services to clinicians across a number of specialties, including pediatrics, obstetrics and gynecology, neurology, cardiology, genetic medicine, medical oncology, and pathology. In addition, clinical geneticists and genetic counselors continue to offer consultation in Omaha and across the state of Nebraska. Because genetic testing is constantly evolving, our team remains committed to provider outreach and education and has bolstered our ability to do so in a number of ways over the past year: • We now have a dedicated marketing specialist who serves as a resource for providers. • Our laboratory directors, genetic counselors, and marketing specialist routinely make personal visits to clinics and hospitals. • Our clinical genetics team has expanded their specialty clinics to include adult genetics, autism, complex craniofacial, hereditary cancer, metabolism, neurosensory, and prenatal development. • We have enhanced provider and patient educational materials, including prenatal and postnatal testing booklets, hereditary cancer testing and oncology flyers, and patient brochures.

In addition, clinical and laboratory faculty and genetic counselors are always willing to provide formal educational lectures for your staff. Please contact our marketing specialist, Nicole Hackendahl (see left sidebar), if you would like more information about the educational materials available or if you would like to schedule a formal meeting with one of our faculty. Newsletter | Summer 2014 Our dedicated and experienced technical staff is continually researching and developing new, This Newsletter is produced by the Human Genetics Laboratory, clinically-relevant genetic testing in order to improve the diagnostic yield for your patients. We have part of Munroe-Meyer Institute expanded our test menu to include high resolution deletion/duplication analysis of clinically-relevant at the University of Nebraska genes to complement our sequencing panels. Over the past year, we also developed and validated Medical Center. a hereditary breast cancer panel designed to detect abnormalities in six high-risk genes associated with breast cancer, and I am pleased to announce that we are expanding this service to other For additional printed copies, hereditary cancers (including colorectal, ovarian, uterine, endocrine, neuroendocrine, neurologic, or other information, please contact: pancreatic, and renal) early this fall. We have also validated additional oncology fluorescence in situ hybridization (FISH) probes for clinically relevant loci, such as IGK, IGL, ROS1, and RET. Please Nicole (Nikki) Hackendahl Marketing Specialist continue to check our website for the most up-to-date test offerings and continue to communicate 402-559-6935 your genetic testing needs to our laboratory team, as your requests serve as the basis for our future [email protected] assay developments.

Human Genetics Laboratory Thank you for your ongoing loyalty and trust in our genetic services. We are honored to partner with 985440 Nebraska Medical Center you in service to patients and remain committed to doing so with unparalleled accuracy, efficiency, Omaha, NE 68498-5440 and compassion. [email protected] www.unmc.edu/geneticslab

Warren G. Sanger, Ph.D. Director, Human Genetics Laboratory Interim Director, Genetic Medicine Munroe-Meyer Institute University of Nebraska Medical Center

Newsletter | 2 FACULTY HIGHLIGHTS

R. Tanner Hagelstrom, PhD, MBA, FACMG Jennifer N. Sanmann, PhD, MB(ASCP)CMCGCM Dr. Tanner Hagelstrom is an Associate Director of the Following completion of a two year clinical cytogenetics Human Genetics Laboratory at the Munroe-Meyer Institute. fellowship this June, Dr. Jennifer Sanmann joined the Human He is a Fellow of the American College of Genetics Laboratory as an Associate Director. She is board and Genomics (ACMG) and eligible in the subspecialty of is board certified in Clinical Clinical Cytogenetics through Cytogenetics and Clinical the American Board of Medical Molecular Genetics through Genetics and Genomics. the American Board of Medical Although her roles and Genetics and Genomics. responsibilities in the laboratory Dr. Hagelstrom received his have changed over time, Dr. PhD and MBA from Colorado Sanmann has been a member of State University in 2007 and the Human Genetics Laboratory 2010, respectively. Following team since 2005. She completed a postdoctoral training at the both her doctoral and clinical Translational Genomics Research postdoctoral training under the Institute in Scottsdale, Arizona, Dr. Hagelstrom completed direction of Dr. Warren Sanger in 2012 and 2014, respectively. his Clinical Cytogenetics and Molecular Genetics fellowships Dr. Sanmann began her academic appointment at UNMC at the University of Colorado Anschutz Medical Center. as an Assistant Professor of the Munroe-Meyer Institute on Dr. Hagelstrom joined the laboratory in July 2013 and July 1. She currently serves as a board member for the Great is currently an Assistant Professor of the Munroe-Meyer Plains Chapter of the Clinical Laboratory Management Institute at UNMC. He serves on the ACMG Program Association. Dr. Sanmann’s research focuses on understanding Committee, and his research interests focus primarily on the relationship between genotype and phenotype in both identifying unique genetic changes that can be utilized for the constitutional and oncology settings using a variety of diagnostic purposes or treatment decisions in malignancies. cytogenetic and molecular genetic techniques.

Tips & Tools: Preauthorization of Genetic Testing Due to the rapid advancements in genetics, a growing number of practitioners are utilizing genetic testing for the diagnosis and medical management of their patients. Consequently, preauthorization for genetic testing has become increasingly prominent in clinics and hospitals across the country. In order to aid practitioners in this preauthorization process, our laboratory has developed specimen- and diagnosis-specific forms that query the information required for the determination of coverage and preauthorization. The following preauthorization forms are available on the Human Genetics Laboratory website: • prenatal • pregnancy loss • postnatal (peripheral blood) • hematology / oncology Upon request, our laboratory will obtain preauthorization for your patient’s genetic studies. Please contact our billing team with any questions or concerns related to this process. 402.559.5070 FIND US ONLINE www.unmc.edu/geneticslab

Human Genetics Laboratory Newsletter | Summer 2014 Any FISH Necessary to Clarify Diagnosis, Clarified FISH Analysis: Non-Small Cell Lung Carcinoma (NSCLC) We recently modified our Oncology Test Request Form to simplify the ordering process for clinicians and their staff. There is an option on the form within Test Selection that, when checked, authorizes our laboratory to perform any FISH necessary to clarify the patient’s Lung cancer is the most common diagnosis. For ease, this option is now located directly below Chromosome Analysis. cancer worldwide and is the leading p Chromosome Analysis p Perform any FISH necessary to clarify diagnosis cause of cancer death in the United p FISH [specify]: States.1-2 By selecting the “any FISH necessary to clarify diagnosis” option on the test request form, ordering providers eliminate any delay in testing that may occur while authorization is obtained and fulfill the laboratory’s regulatory requirement for written orders without disruption of your clinic or hospital for authorization. Our laboratory staff will only add adjunct FISH when indicated by diagnosis or when needed to clarify an abnormality observed by Chromosome Analysis (karyotyping). In addition, we will always provide a fax notification when tests are added to keep the ordering physician abreast of the pending studies. Please note that this option does not replace the specified FISH test selection, which should still be used in cases where the physician wants to order a specific FISH test at the time of specimen collection. A current list of all of our available hematology, lymphoma, and solid tumor FISH probes is available on our laboratory website. p Chromosome Analysis p Perform any FISH necessary to clarify diagnosis ALK (2p23) Dual Color Breakapart Probe, positive p FISH [specify]: CLL Panel for rearrangement in a polyploidy population Optimized microarray for subotimal specimens, including solid tissue tumors Our laboratory has recently obtained the OncoScanTM microarray platform, which has been designed to circumvent the obstacles typically encountered with these degraded specimens.

This whole genome assay will detect genomic dosage anomalies (deletions and duplications) and copy-neutral loss of heterozygosity at a resolution of 50-100kb in approximately 900 cancer- related genes and at a resolution of The Human Genetics Laboratory has performed 300kb throughout the remaining genomic chromosomal microarray studies on a variety of sample backbone. Thus, this platform is ideal types since the technology’s infancy. However, historical for the identification of diagnosis-specific platforms have long been challenged to analyze genetic profiles in solid tissue tumors. DNA of suboptimal quality, such as that from formalin fixed paraffin-embedded (FFPE) tissues, which has Currently, the platform is being restricted genomic analysis on certain specimens. utilized for research aimed at

Newsletter | 4 FISH Analysis: Non-Small Cell Lung Carcinoma (NSCLC)

Lung cancer is divided into two histologic subgroups: (1) non-small cell lung cancer (NSCLC), which accounts for more than 85% of cases and can be subdivided into non-squamous carcinoma (including adenocarcinoma, large cell carcinoma, other cell types) and 2 squamous cell carcinoma and (2) small cell lung cancer, which accounts for the remaining ~15% of lung cancer cases. In recent years, the understanding and knowledge of the pathogenesis of NSCLC, particularly adenocarcinoma, has grown exponentially and has led to the discovery of novel acquired genetic abnormalities that allow for targeted therapies.

Several biomarkers have been identified in NSCLC that help drive therapy and predict treatment efficacy. These predictive biomarkers include EGFR, HER2 (ERBB2), and BRAF mutations; ALK, ROS1, and RET rearrangements; and MET amplification.2 The NCCN Guidelines for NSCLC recommend EGFR mutation testing and ALK gene rearrangement analysis for patients with adenocarcinoma; large cell carcinoma; NSCLC not otherwise specified (NOS); or squamous cell carcinoma in never smokers, a small biopsy specimen, or a specimen with mixed histology.2 The NCCN guidelines recommend subsequent consideration should be given to the other genetic biomarker testing following EGFR and ALK as appropriate.

To meet clinical testing needs, our laboratory offers assessment of the ALK, ROS1, and RET loci using fluorescence in situ hybridization (FISH). The FISH assay for each of these three loci is designed to detect rearrangement of the gene that, if present, is known to be susceptible to targeted therapies. The ALK, ROS1, and RET FISH testing is typically performed on 4-6 µm sections prepared from paraffin-embedded tumor tissue, and results are available within 3-5 days of specimen receipt. Please contact the laboratory for any questions regarding this testing.

REFERENCES 1 World Health Organization. Cancer. Fact Sheet No 297. January 2013. 2 National Comprehensive Cancer Network (NCCN). Non-Small Cell Lung Cancer (Version 4.2014) Optimized microarray for subotimal specimens, Education and Outreach The Human Genetics Laboratory was represented at the national American including solid tissue tumors College of Medical Genetics and Genomics (ACMG) meeting in Nashville in March. The meeting provided a great opportunity for several of our improving our understanding faculty and staff to learn about the of the genetic hallmarks of latest advancements in the field various pediatric brain tumors. and to reconnect with colleagues. In addition, the ACMG meeting Additionally, this platform is being afforded our team the opportunity to validated for use in the clinical setting share our newest clinical test offerings (FFPE or otherwise suboptimal with attendees and to present our specimens) and is projected to be latest research efforts in the postnatal available for order in the fall of 2014. realm, which included the following: 2014 Human Genectics Laboratory ACMG booth.

If you would like more information • Clinical and Laboratory Collaboration: Team Approach to Next Generation about how this assay may assist Sequencing Variant Interpretation (D.L. Bishay, et al.) with your research goals, or if you • Genetic Testing for Dilated Cardiomyopathy: Ethical Dilemmas Including PSEN1 and PSEN2 (A.C. Carter, et al.) would like additional information • Hajdu-Cheney syndrome: patient with rare complex heart defect (L.J. Starr, et al.) as this assay transitions to a • Psychiatric Disease is Common and Undertreated in Ehlers-Danlos Syndrome clinical test offering, please Hypermobile Type (E.T. Rush, et al.) contact Dr. Sanmann for details. • Utility of Fluorescence In Situ Hybridization (FISH) to Confirm Copy Number [email protected] Changes Identified by Microarray (J.N. Sanmann, et al.)

Abstracts above available upon request.

Human Genetics Laboratory Newsletter | Summer 2014 A COMPREHENSIVE APPROACH TO GENE PANEL TESTING Gene Panel enetic changes that result in disease come in several different forms, Gincluding sequence-based mutations (changes in the DNA at the base- The Human Genetics Laboratory offers pair level) and intragenic deletions/duplications (copy number changes a panel designed to detect aberrations within the target gene). Regardless of the type of disease-causing change in four genes known to be associated observed, these genetic aberrations often result in a similarly aberrant with craniosynostosis, the premature protein product. Current technology does not allow for both sequence-based closure of one or more sutures in an variations and intragenic copy number changes to be detected reliably in individual’s . With an incidence of a single assay. Thus, comprehensive analysis of genes for disease-causing 1 in every 2,000-2,500 births, many aberrations typically requires a multi-assay approach. craniosynostosis syndromes exist and often have additional clinical features, In order to ensure comprehensive analysis of clinically-relevant genes of making a single panel for the evaluation interest, our laboratory recently added high resolution deletion/duplication of these various syndromes ideal for both analysis for all of the genes that we have traditionally sequenced using the clinician and the patient.1 Additionally, our next generation sequencing (NGS) technology. Therefore, we are able aberrations in these genes can inhibit to evaluate a panel of indication-specific genes for both sequence-based or alter growth; therefore, several mutations and small-scale deletions or duplications in a time- and cost- skeletal dysplasias are also covered by efficient manner. This combination of testing can be easily ordered on this panel. our test request form by selecting the “comprehensive testing” box for any of our panel tests. When comprehensive testing is selected, testing is SUSPECTED SYNDROMES: performed in a tiered manner to eliminate unnecessary costs to the patient. The tiered approach for each indication-specific panel is outlined next to the • comprehensive testing selection on the test request form for easy reference. • Antley-Bixler syndrome COMPREHENSIVE TESTING EXAMPLE • Connective Tissue Disorders Panel • Beare-Stevenson syndrome p Comprehensive testing [includes: seq, reflex to del/dup] • CATSHL (tall stature, ) p Sequencing only • p Del/dup only •

Alternatively, individual tests, such as sequencing only or high resolution • Jackson-Weiss syndrome deletion/duplication analysis only, can be selected easily on the test • request form, as indicated below. • LADD SINGLE TESTING EXAMPLE • Connective Tissue Disorders Panel • p Comprehensive testing [includes: seq, reflex to del/dup] • Radioulnar synostosis p Sequencing only • Rhizomelic limb shortening p Del/dup only • Robinow-Sorauf syndrome • Saethre-Chotzen syndrome Please contact the laboratory if you have any questions about this new test offering or the updated postnatal test request form.

Newsletter | 6 Connective Tissue Disorders Gene Panel Individuals with inherited connective tissue disorders frequently harbor an aberration in a gene involved in the structure or function of connective tissue. Such disorders typically include medical issues with the joints, eyes, skin, and cardiovascular system, though other body systems are commonly affected. Often, genetic testing is useful for the establishment of an appropriate diagnosis and medical management plan for an affected individual or family. To aid in the diagnosis of patients with connective tissue disorders, the Human Genetics Laboratory launched an indication-specific gene panel in the fall of 2013. Our laboratory is pleased to announce that as of June 1, 2014, the connective tissue disorders panel has been expanded to CLINICAL INDICATIONS FOR TESTING: include a total of 33 clinically useful genes.  Craniosynostosis CLINICAL INDICATIONS FOR TESTING:  Facial features such as proptosis (bulging eyes), , widely spaced eyes, flattened midface,  Joint issues: hypermobility, dislocations, chronic pain temporal bossing  Skin findings: cutis laxa, abnormal or atrophic scars, poor wound healing, spontaneous bruising  Syndactyly, clinodactyly, broad toes, broad thumbs  Ocular findings: ectopia lentis, myopia, retinal detachment  Short stature or shortened long  Pneumothorax  Cardiac findings: congenital heart defect, mitral valve prolapse, aortic  Palatal abnormalities (cleft or high palate) root enlargement, thoracic aneurysm, aortic dissection, other aneurysms/ dissections  Bone fusions, especially carpal, tarsal, and  Skeletal variants: Tall or short stature, pectus excavatum, pectus radioulnar synostosis carinatum, arachnodactyly, brachydactyly, pes planus, long wingspan  Personal or family history of sudden cardiac death, aneurysm/dissection,  Developmental delay, hearing loss, or vision rupture of internal organ, rectal or uterine prolapse concerns in a person suspected to have craniosynostosis or skeletal dysplasia  Craniofacial anomalies or dysmorphic features SUSPECTED SYNDROMES: GENE LIST: GENES COVERED2: • Arterial tortuosity syndrome ABCC6 FBN1 • Congenital contractural arachnodactyly FGFR1 5% Pfeiffer syndrome type 1 (Beals syndrome) ACTA2 FBN2 ATP7A FKBP14 100% Apert syndrome • Ehlers-Danlos syndrome (all subtypes) CBS FLNA <100% Beare-Stevenson syndrome • ELN-related conditions: 100% Crouzon syndrome --Autosomal dominant supravalvular aortic stenosis CHST14 MYH11 --Cutis laxa FGFR2 100% Jackson-Weiss syndrome COL1A1 MYLK 95% Pfeiffer syndrome type 1 • Familial thoracic aneurysms and aortic dissections (TAAD) COL1A2 PLOD1 100% Pfeiffer syndrome types 2 and 3 • FBN1-related disorders COL2A1 SKI 100% FGFR2-related isolated coronal synostosis --Marfan syndrome COL3A1 SLC2A10 --MASS phenotype 100% Crouzon syndrome with acanthosis nigricans COL5A1 SLC39A13 FGFR3 --Weill-Marchesani syndrome 100% Muenke syndrome --Isolated ectopia lentis COL5A2 SMAD3 COL9A1 SMAD4 TWIST >50% Saethre-Chotzen syndrome • FLNA-related cardiac valvular disease • Homocystinuria COL9A2 TGFB2 COL9A3 TGFBR1 1 Greenwood, Jaclyn, Pamela Flodman, Kathryn Osann, Simeon A. Boyadjiev, and Virginia Kimonis. • Loeys-Dietz syndrome, types I, II, III, IV “Familial Incidence and Associated Symptoms in a Population of Individuals with Nonsyndromic Craniosynostosis.” Genetics in Medicine (September 26, 2013). doi:10.1038/gim.2013.134. • Myhre syndrome COL11A1 TGFBR2 2 Robin, Nathaniel H, Falk, Marni J, and Haldeman-Englert, Chad R. "FGFR-Related • Shprintzen-Goldberg syndrome COL11A2 TNXB Craniosynostosis Syndromes". In GeneReviewsTM, edited by Roberta A Pagon, Margaret P Adam, Thomas D Bird, Cynthia R Dolan, Chin-To Fong, and Karen Stephens. Seattle (WA): University of • Stickler syndrome, types I, II, III, IV, V ELN Washington, Seattle, 1993. http://www.ncbi.nlm.nih.gov/books/NBK1455/.

Human Genetics Laboratory Newsletter | Summer 2014