A Review of the Genomic Analysis of Children Presenting with Developmental Delay/Intellectual Disability and Associated Dysmorphic Features.

This review describes the clinical criteria of developmental delay (DD)/intellectual disability (ID) as well as the various techniques that are currently implemented to diagnose neurodevelopmental disorders that typically present with associated dysmorphic features such as Angelman syndrome, Prader-Willi syndrome, and DiGeorge syndrome. These analyses include various forms of chromosomal microarray (CMA), which have proven to be superior to previously implemented techniques such as G-banded karyotyping and fluorescent in situ hybridization (FISH) analysis, as well as whole exome sequencing (WES), which is implemented as a secondary examination when CMA analysis is unrevealing. The clinical significance of identified variants and how it relates to facilitating the management of specific genetic disorders such as the above mentioned is also discussed. In addition, the importance of genomic databases and bioinformatics technologies as they relate to variant classification is also considered. Essentially, the discovery of pathogenic variants allows for enhanced management of a patient's clinical phenotype, whereas the identification of variants of uncertain significance (VUS) has proven to have an increase in the number of associated conflicts as they typically generate more ambiguity in regard to the clinical manifestations present within the child. As a result, additional procedures need to be implemented to mitigate the issues that surround their identification. The concluding remarks are in regard to both the ethical and legal considerations of genetic testing as they relate to informed consent, testing of minors, how to handle secondary findings, as well as the anticipated future direction of genomic analysis.

The Evolving Role of the Laboratory Professional in the Age of Genome Sequencing: A Vision of the Association for Molecular Pathology.

In conclusion, to maximize the benefit of the genomic era, the molecular laboratory director will continue to be essential in the generation, analysis, and interpretation of patient results, which now include genomic data obtained through NGS approaches. That includes integrating this information as part of the complete care of the patient and communicating and interacting with professionals across disciplines. In addition, the molecular laboratory director must continue to provide training and education to current and future colleagues, within and outside of molecular pathology and molecular genetics. Professionalism includes volunteerism in professional organizations and education and advocacy to policy makers, health administrators, payers, and the public. It also includes efforts to increase visibility of the profession to our colleagues from other medical disciplines and the public at large. Thus, the role of the molecular laboratory professional is multifaceted, but, above all, it is to ensure the access to and quality of molecular pathology testing, the responsible implementation of expanded test modalities such as genome sequencing, and the interpretation thereof to aid the clinician in the medical management of the patient and ultimately to benefit the society by providing precision patient care.

College of American Pathologists' laboratory standards for next-generation sequencing clinical tests.

CONTEXT: The higher throughput and lower per-base cost of next-generation sequencing (NGS) as compared to Sanger sequencing has led to its rapid adoption in clinical testing. The number of laboratories offering NGS-based tests has also grown considerably in the past few years, despite the fact that specific Clinical Laboratory Improvement Amendments of 1988/College of American Pathologists (CAP) laboratory standards had not yet been developed to regulate this technology. OBJECTIVE: To develop a checklist for clinical testing using NGS technology that sets standards for the analytic wet bench process and for bioinformatics or "dry bench" analyses. As NGS-based clinical tests are new to diagnostic testing and are of much greater complexity than traditional Sanger sequencing-based tests, there is an urgent need to develop new regulatory standards for laboratories offering these tests. DESIGN: To develop the necessary regulatory framework for NGS and to facilitate appropriate adoption of this technology for clinical testing, CAP formed a committee in 2011, the NGS Work Group, to deliberate upon the contents to be included in the checklist. Results . -A total of 18 laboratory accreditation checklist requirements for the analytic wet bench process and bioinformatics analysis processes have been included within CAP's molecular pathology checklist (MOL). CONCLUSIONS: This report describes the important issues considered by the CAP committee during the development of the new checklist requirements, which address documentation, validation, quality assurance, confirmatory testing, exception logs, monitoring of upgrades, variant interpretation and reporting, incidental findings, data storage, version traceability, and data transfer confidentiality.

Nucleic acid-based assays for the detection of high-risk human papillomavirus: a technical review.

Nucleic acid-based high-risk human papillomavirus (hrHPV) testing is essential to contemporary cervical cancer screening. The numbers of commercially available assays approved by the US Food and Drug Administration for HPV nucleic acid detection have increased, each offering various approaches to analysis. An understanding of the methodologies associated with HPV testing is important to the practice of laboratory medicine. An overview of instruments, chemistries, laboratory workflows, and test limitations associated with current US Food and Drug Administration-approved assays is provided.

Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology.

This report of the Whole Genome Analysis group of the Association for Molecular Pathology illuminates the opportunities and challenges associated with clinical diagnostic genome sequencing. With the reality of clinical application of next-generation sequencing, technical aspects of molecular testing can be accomplished at greater speed and with higher volume, while much information is obtained. Although this testing is a next logical step for molecular pathology laboratories, the potential impact on the diagnostic process and clinical correlations is extraordinary and clinical interpretation will be challenging. We review the rapidly evolving technologies; provide application examples; discuss aspects of clinical utility, ethics, and consent; and address the analytic, postanalytic, and professional implications.

Use of a multitarget fluorescence in situ hybridization assay to diagnose bladder cancer in patients with hematuria.

PURPOSE: We evaluated the multitarget UroVysion fluorescence in situ hybridization assay for the diagnosis of bladder cancer in patients with hematuria and no history of bladder cancer. MATERIALS AND METHODS: A multicenter, blinded trial was performed to compare the sensitivity of the fluorescence in situ hybridization assay to that of voided cytology in patients with gross or microscopic hematuria. Confirmation of hematuria was required. Voided urine was sent to a central laboratory for each study before cystoscopy. Suspicious lesions on cystoscopy were biopsied or resected. A centrally reviewed histopathological interpretation was used to confirm cancer and assign grade and stage. RESULTS: A total of 497 patients were enrolled at 23 centers and in 473 (95.2%) fluorescence in situ hybridization and cytology results were interpretable. Bladder cancer was diagnosed histologically in 50 patients (10.1%) and ureteral cancer was diagnosed in 1. Fluorescence in situ hybridization assay detected 69% of cases and cytology detected 38% (95% CI 25 to 52). When low grade, low stage (TaG1) tumors were excluded, fluorescence in situ hybridization detected 25 of 30 cancers (84%), while cytology detected only 15 (50%). Of 265 current or past smokers with hematuria and positive fluorescence in situ hybridization assay findings bladder cancer was detected in 65% with a history of greater than 40 pack-years compared to 13.6% to 24.2% in those with no, less than a 20 or a 20 to 40-pack-year smoking history. CONCLUSIONS: The UroVysion fluorescence in situ hybridization assay is significantly more sensitive than voided cytology for detecting bladder cancer in patients evaluated for gross or microscopic hematuria for all grades and stages. Based on these data UroVysion was approved by the Food and Drug Administration for use in patients with hematuria.