The business of genomic testing: a survey of early adopters.

PURPOSE: The practice of "genomic" (or "personalized") medicine requires the availability of appropriate diagnostic testing. Our study objective was to identify the reasons for health systems to bring next-generation sequencing into their clinical laboratories and to understand the process by which such decisions were made. Such information may be of value to other health systems seeking to provide next-generation sequencing testing to their patient populations. METHODS: A standardized open-ended interview was conducted with the laboratory medical directors and/or department of pathology chairs of 13 different academic institutions in 10 different states. RESULTS: Genomic testing for cancer dominated the institutional decision making, with three primary reasons: more effective delivery of cancer care, the perceived need for institutional leadership in the field of genomics, and the premise that genomics will eventually be cost-effective. Barriers to implementation included implementation cost; the time and effort needed to maintain this newer testing; challenges in interpreting genetic variants; establishing the bioinformatics infrastructure; and curating data from medical, ethical, and legal standpoints. Ultimate success depended on alignment with institutional strengths and priorities and working closely with institutional clinical programs. CONCLUSION: These early adopters uniformly viewed genomic analysis as an imperative for developing their expertise in the implementation and practice of genomic medicine.

Challenges in Pathology Specimen Processing in the New Era of Precision Medicine.

CONTEXT.­: Precision therapies for patients with driver mutations can offer deep and durable responses that correlate with diagnosis, metastasis prognosis, and improvement in survival. The use of such targeted therapies will continue to increase, pushing us to change our traditional approaches. We needed to search for new tools to effectively integrate technological advancements into our practices because of their capability to improve the efficiency and accuracy of our diagnostic and treatment approaches. Perhaps nothing is as relevant as identifying and implementing new workflows for processing pathologic specimens and for improving communication of critical laboratory information to and from clinicians for appropriate care of patients in an efficient and timely manner. OBJECTIVES.­: To define the gold standard in delivering the best care for patients, to identify gaps in the process, and to identify potential solutions that would improve our process, including gaps related to knowledge, skills, attitudes, and practices. DESIGN.­: We assembled a multidisciplinary team to systematically perform a gap analysis study to clarify the discrepancy between the current reality in pathology specimen processing and the desired optimal situation to deliver the results intended for patient care. RESULTS.­: A practical collaborative workflow for specimen management that seeks the cooperation of stakeholders in each medical discipline to provide guidelines in specimen collection, delivery, processing, and reporting of results with the ultimate goal of improving patient outcomes is provided. CONCLUSIONS.­: New tools are required to effectively integrate data-driven approaches in specimen processing to meet the new demands.

Cutaneous myelofibrosis with JAK2 V617F mutation: metastasis, not merely extramedullary hematopoiesis!

Primary myelofibrosis (PMF) is a myeloproliferative neoplasm. There are 31 reported cases of cutaneous involvement by PMF, most of which have been described as "extramedullary hematopoiesis." We report a new case of cutaneous involvement by PMF and demonstrate mutation of the Janus kinase 2 gene in the cutaneous lesions. Extramedullary myelofibrosis is best considered a metastatic phenomenon. Reporting such cases as extramedullary hematopoiesis may cause confusion with reactive forms of extramedullary hematopoiesis.

Molecular Pathology Economics 101: An Overview of Molecular Diagnostics Coding, Coverage, and Reimbursement: A Report of the Association for Molecular Pathology.

Widespread indications for use of molecular diagnostics in various aspects of clinical medicine have driven proliferation of testing. The rapid adoption and continuous technological evolution of molecular diagnostics have often strained the development and maintenance of a functional underlying framework of coding, coverage, and reimbursement policies, thereby presenting challenges to various stakeholders, including molecular professionals, payers, and patients. A multidisciplinary working group convened by the Association for Molecular Pathology Economic Affairs Committee was tasked to describe the complex landscape of molecular pathology economics and highlight opportunities for member engagement. In this article, on the basis of review and synthesis of government regulations and procedures, published payer policy documents, peer-reviewed literature, and expert consensus, the Working Group navigates the ecosystem of molecular pathology economics in terms of stakeholders, coding systems and processes, coverage policy determination, and pricing mechanisms. The composition and interrelatedness of various working groups and committees are emphasized to highlight the functional underpinnings of the system. Molecular professionals must be conversant in the language and complex inner workings of molecular pathology economics to lead successful, viable laboratories and advocate effectively for policy development on their behalf. This overview is provided to be a resource to molecular professionals as they navigate the reimbursement landscape.

Hamartomas, teratomas and teratocarcinosarcomas of the head and neck: Report of 3 new cases with clinico-pathologic correlation, cytogenetic analysis, and review of the literature.

BACKGROUND: Germ-cell tumors (GCT) are a histologically and biologically diverse group of neoplasms which primarily occur in the gonads but also develop at different extragonadal sites in the midline of the body. The head and neck region including the upper respiratory tract is a very rare location for such tumors in both children and adults, which can cause diagnostic and therapeutic difficulties. METHODS: We describe here two new cases of multilineage tumors including sinonasal teratocarcinosarcoma [SNTCS], and congenital oronasopharyngeal teratoma (epignathus) and compare their features with those of a new case of a rare salivary gland anlage tumor [SGAT], an entity for which the pathogenesis is unclear (i.e. hamartoma versus neoplasm). We correlate their presenting clinico-pathological features and compare histologic and cytogenetic features in an attempt to elucidate their pathogenesis and biologic potentials. RESULTS AND DISCUSSION: Cytogenetic analysis revealed chromosomal abnormalities only in the case of SNTCS that showed trisomy 12 and 1p deletion. Both cytogenetic abnormalities are characteristically present in malignant germ cell tumors providing for the first time evidence that this rare tumor type indeed might represent a variant of a germ cell neoplasm. The SGAT and epignathus carried no such cytogenetic abnormalities, in keeping with their limited and benign biologic potential. CONCLUSION: The comparison of these three cases should serve to emphasize the diversity of multilineage tumors (hamartomas and GCT) of the upper respiratory tract in regards to their biology, age of presentation and clinical outcomes. Malignant tumors of germ cell origins are more likely to affect adults with insidious symptom development, while benign tumors can nevertheless cause dramatic clinical symptoms which, under certain circumstances, can be fatal.

The Spectrum of Clinical Utilities in Molecular Pathology Testing Procedures for Inherited Conditions and Cancer: A Report of the Association for Molecular Pathology.

Clinical utility describes the benefits of each laboratory test for that patient. Many stakeholders have adopted narrow definitions for the clinical utility of molecular testing as applied to targeted pharmacotherapy in oncology, regardless of the population tested or the purpose of the testing. This definition does not address all of the important applications of molecular diagnostic testing. Definitions consistent with a patient-centered approach emphasize and recognize that a clinical test result's utility depends on the context in which it is used and are particularly relevant to molecular diagnostic testing because of the nature of the information they provide. Debates surrounding levels and types of evidence needed to properly evaluate the clinical value of molecular diagnostics are increasingly important because the growing body of knowledge, stemming from the increase of genomic medicine, provides many new opportunities for molecular testing to improve health care. We address the challenges in defining the clinical utility of molecular diagnostics for inherited diseases or cancer and provide assessment recommendations. Starting with a modified analytic validity, clinical validity, clinical utility, and ethical, legal, and social implications model for addressing clinical utility of molecular diagnostics with a variety of testing purposes, we recommend promotion of patient-centered definitions of clinical utility that appropriately recognize the valuable contribution of molecular diagnostic testing to improve patient care.

Monosomy 22 as a diagnostic aid in a case of late recurrence of adult granulosa cell tumor of the ovary.

Cytogenetic analysis of a case of metastatic granulosa cell tumor recurring 21 years after oophorectomy revealed monosomy 22. This anomaly, typical of granulosa cell tumor, coupled with the pathologic and immunophenotypic findings assisted in establishing the proper diagnosis of this lesion in the absence of the original histopathologic slides.

Standards for Clinical Grade Genomic Databases.

CONTEXT: Next-generation sequencing performed in a clinical environment must meet clinical standards, which requires reproducibility of all aspects of the testing. Clinical-grade genomic databases (CGGDs) are required to classify a variant and to assist in the professional interpretation of clinical next-generation sequencing. Applying quality laboratory standards to the reference databases used for sequence-variant interpretation presents a new challenge for validation and curation. OBJECTIVES: To define CGGD and the categories of information contained in CGGDs and to frame recommendations for the structure and use of these databases in clinical patient care. DESIGN: Members of the College of American Pathologists Personalized Health Care Committee reviewed the literature and existing state of genomic databases and developed a framework for guiding CGGD development in the future. RESULTS: Clinical-grade genomic databases may provide different types of information. This work group defined 3 layers of information in CGGDs: clinical genomic variant repositories, genomic medical data repositories, and genomic medicine evidence databases. The layers are differentiated by the types of genomic and medical information contained and the utility in assisting with clinical interpretation of genomic variants. Clinical-grade genomic databases must meet specific standards regarding submission, curation, and retrieval of data, as well as the maintenance of privacy and security. CONCLUSION: These organizing principles for CGGDs should serve as a foundation for future development of specific standards that support the use of such databases for patient care.

Detection of high-risk HPV in head and neck squamous cell carcinomas: comparison of chromogenic in situ hybridization and a reverse line blot method.

Human papillomaviruses (HPVs) have been etiologically linked to a subset of head and neck squamous cell carcinomas (HNSCCs), generally arising in young patients without a history of tobacco smoking or alcohol use. These tumors typically lack mutations in TP53 and may show enhanced sensitivity to chemoradiation therapy with a correspondingly better overall prognosis. The determination of the HPV status in HNSCC therefore has therapeutic implications. We compared the Ventana ISH iView Blue Plus Detection Kit in situ hybridization (ISH) system and the Roche Linear Array HPV Genotyping Test for the detection of HPV in 98 formalin-fixed, paraffin-embedded HNSCC samples. A moderate concordance rate (70.4%) was observed between ISH and the Linear Array assays. ISH detected HPV in 39.8% of cases, whereas Linear Array detected HPV in 57.1% of cases. Sensitivity and specificity of ISH for detecting HPV in HNSCC specimens were determined to be 58.9% and 85.7%, respectively, using the Linear Array as the method of comparison (McNemar test, P=0.003). ISH offers the advantage of visual cell-type localization of viral infection but overall it is less sensitive than the polymerase chain reaction-based detection of HPV in HNSCC.

Comparison of 2 line blot assays for defining HPV genotypes in oral and oropharyngeal squamous cell carcinomas.

Patients with invasive oral and oropharyngeal squamous cell carcinomas infected with human papillomaviruses (HPV) demonstrate improved survival. HPV detection in tumors may assist in risk stratification of patients and in guiding optimum treatment. Two reverse line blot assays [Linear Array (LA) and INNO-LiPA (LiPA)] were evaluated for detection of HPV genotypes in paraffin-embedded biopsies. Overall, 82.4% of 131 biopsies were HPV+ by LiPA versus 61.1% by LA (κ = 0.32). Completely concordant results were observed in 52.7% of cases: 18 negative and 51 with exactly the same genotype(s). An additional 13 cases had partial agreement. These 82 completely or partially concordant cases revealed a high rate of HPV positivity (78.0%), primarily involving HPV16 (90.6%). HPV+ tumors occurred preferentially in the oropharynx, especially tonsils, with trends for male patients and poor differentiation. Significant differences in these associations were found when LA and LiPA results were analyzed independently. No relationships were found between tumor HPV status and tobacco or alcohol use.

HPV genotype distribution in oral and oropharyngeal squamous cell carcinoma using seven in vitro amplification assays.

BACKGROUND: Molecular and epidemiologic evidence indicates that human papillomavirus (HPV) is involved in the etiology of oral and oropharyngeal squamous cell carcinomas (SCCs). HPV(+) tumors appear to be clinically distinct from HPV(-) tumors, conferring improved survival outcomes for patients. Determination of the HPV status of tumors may assist in patient risk-stratification and ultimately guide optimum treatment. The primary aim of this study was to examine the distribution of HPV in oral and oropharyngeal SCCs as assessed using seven different in vitro amplification assays. The secondary aim was to correlate the distribution of HPV in tumors with clinical and demographic patient data. MATERIALS AND METHODS: Sixty-eight invasive oral/oropharyngeal SCCs were tested for HPV using four laboratory-developed PCR assays for HPV16 or 18 and three commercial tests, INNO-LiPA® HPV Genotyping Extra (Innogenetics), Linear Array® HPV Genotyping Test (Roche Diagnostics), and Invader® HPV16/18 ASRs (Hologic Corp.). RESULTS: Consensus results between tests revealed that 71.9% of tumors were HPV(+), primarily with HPV16 (63.2%). Other genotypes were uncommon and generally occurred coincidently with HPV16. HPV-positivity was significantly higher in oropharyngeal tumors (76.9%), particularly of the tonsils (91.7%), versus oral cavity tumors (20.0%). HPV(+) tumors occurred in younger patients (average 54.4 years versus 61.1 years) and were significantly associated with lower histological differentiation (poorly, 100.0%; moderately, 65.6%; well-differentiated, 42.9%). CONCLUSION: A high rate of HPV-positivity, especially involving HPV16, occurred in oropharyngeal tumors, with a lower rate in oral cavity SCCs; however, solitary infections with HPV18, 33 or 45 in a minority of cases signified the potential oncogenicity of these additional genotypes and the likely need to screen for these less common genotypes in clinical specimens.

Comparison of molecular methods for detection of HPV in oral and oropharyngeal squamous cell carcinoma.

Substantial molecular evidence exists to implicate human papillomavirus (HPV) in the pathogenesis of a subset of oral and oropharyngeal squamous cell carcinomas. Several studies have shown that HPV-associated oral/oropharyngeal tumors differ etiologically, biologically, and clinically from those that lack the virus. HPV infection confers a significant survival benefit; therefore, HPV detection in tumors could be used to risk-stratify patients and drive optimum treatment strategies. We explored the clinical utility of 6 polymerase chain reaction (PCR)-based or signal amplification-based methods in the detection of HPV in 68 invasive oral/oropharyngeal SSCs and 10 reactive tonsil specimens. Agreement for HPV16 results among the 5 different assays capable of detecting this genotype was substantial (multirater κ=0.72). Only moderate agreement was noted for the 3 assays capable of detecting HPV18 (multirater κ=0.43). HPV results for each assay were evaluated relative to a "majority" HPV result derived from the results of all the detection methods. An HPV16 E6 PCR assay showed the highest concordance with adjudicated consensus HPV16 results (98.7%; κ=0.97), followed by the TaqMan (93.4%; κ=0.87), Linear Array (92.1%; κ=0.84), and E7 PCR (92.1%; κ=0.84) assays, all of which had agreements exceeding 90%, whereas the HPV16/18 Invader assay was lower (85.5%; κ=0.71). The presence of high-risk HPV in a minority of "normal" tonsillar tissues may confound assessment of the virus in oral/oropharyngeal squamous cell carcinoma biopsies using in vitro amplification methods.

Chronic idiopathic myelofibrosis (CIMF) resulting from a unique 3;9 translocation disrupting the janus kinase 2 (JAK2) gene.

We report a case of t(3;9)(q21;p24) in a patient with chronic idiopathic myelofibrosis (CIMF), a chronic myeloproliferative disorder (CMPD), initially detected by G-banding and fluorescent in situ hybridization (FISH) in an unstimulated culture of peripheral blood. Subsequent cytogenetic studies of bone marrow aspirates showed the presence and persistence of the same translocation. No additional cytogenetic abnormalities were found. This appears to be a unique translocation that has not been previously reported in the English literature, although both breakpoints, 3q21 and 9p24, are well known cancer-related breakpoints. The former is the mapped location of the ribophorin 1 (RPN1) gene, whereas the latter is the mapped location of the janus kinase 2 (JAK2) gene. This raises the possibility that disruption of one or both loci at the breakpoints of the presently described structural chromosomal rearrangement may be the primary event leading to the initiation and development of the hematopoietic disorder in this patient. It is not unreasonable to hypothesize that the juxtaposition of the RPN1 gene on 3q21 with the JAK2 gene on 9p24 leads to enhanced JAK2 activity. Additional studies will be needed to provide further support for or to disprove this hypothesis. To the best of our knowledge, this is the first reported case of CIMF associated with a reciprocal 3;9 translocation with the 3q21 and 9p24 breakpoints. The elucidation of the mechanism of leukemogenesis in CIMF may one day lead to successful targeted therapy in this hematopoietic disorder. It may also shed additional light on the diagnosis, prognosis and treatment of certain other cancers with similar genetic etiologies.