Widespread clinical laboratory implementation of next-generation sequencingebased cancer testing has highlighted the importance and potential benefits of standardizing the interpretation and reporting of molecular results among laboratories. A multidisciplinary working group tasked to assess the current status of next-generation sequencingebased cancer testing and establish standardized consensus classification, annotation, interpretation, and reporting conventions for somatic sequence variants was

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Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by heterozygous point mutations or genomic deletion copy-number variants (CNVs) of FOXF1 or its upstream enhancer involving fetal lung-expressed long noncoding RNA genes LINC01081 and LINC01082. Using custom-designed array comparative genomic hybridization, Sanger sequencing, whole exome sequencing (WES), and bioinformatic analyses, we studied 22 new unrelated families (20 postnatal and two prenatal) with clinically diagnosed ACDMPV. We describe novel deletion CNVs at the FOXF1 locus in 13 unrelated ACDMPV patients. Together with the previously reported cases, all 31 genomic deletions in 16q24.1, pathogenic for ACDMPV, for which parental origin was determined, arose de novo with 30 of them occurring on the maternally inherited chromosome 16, strongly implicating genomic imprinting of the FOXF1 locus in human lungs. Surprisingly, we have also identified four ACDMPV families with the pathogenic variants in the FOXF1 locus that arose on paternal chromosome 16. Interestingly, a combination of the severe cardiac defects, including hypoplastic left heart, and single umbilical artery were observed only in children with deletion CNVs involving FOXF1 and its upstream enhancer. Our data demonstrate that genomic imprinting at 16q24.1 plays an important role in variable ACDMPV manifestation likely through long-range regulation of FOXF1 expression, and may be also responsible for key phenotypic features of maternal uniparental disomy 16. Moreover, in one family, WES revealed a de novo missense variant in ESRP1, potentially implicating FGF signaling in etiology of ACDMPV.

Genomic copy number microarrays have significantly increased the diagnostic yield over a karyotype for clinically significant imbalances in individuals with developmental delay, intellectual disability, multiple congenital anomalies, and autism, and they are now accepted as a first tier diagnostic test for these indications. As it is not feasible to validate microarray technology that targets the entire genome in the same manner as an assay that targets a specific gene or syndromic region, a new paradigm of validation and regulation is needed to regulate this important diagnostic technology. We suggest that these microarray platforms be evaluated and manufacturers regulated for the ability to accurately measure copy number gains or losses in DNA (analytical validation) and that the subsequent interpretation of the findings and assignment of clinical significance be determined by medical professionals with appropriate training and certification. To this end, the American College of Medical Genetics, as the professional organization of board-certified clinical laboratory geneticists, herein outlines recommendations for the design and performance expectations for clinical genomic copy number microarrays and associated software intended for use in the postnatal setting for detection of constitutional abnormalities.

X inactivation involves initiation, propagation, and maintenance of genetic inactivation. Studies of replication timing in X;autosome translocations have suggested that X inactivation may spread into adjacent autosomal DNA. To examine the inactivation of autosomal material at the molecular level, we assessed the transcriptional activity of X-linked and autosomal loci spanning an inactive translocation in a phenotypically normal female with a karyotype of 46,X,der(X)t(X;4)(q22;q24). Since 4q duplications usually manifest dysmorphic features and severe growth and mental retardation, the normal phenotype of this individual suggested the spreading of X inactivation throughout the autosomal material. Consistent with this model, reverse transcription-PCR analysis of 20 transcribed sequences spanning 4q24-qter revealed that three known genes and 11 expressed sequence tags (ESTs) were not expressed in a somatic-cell hybrid that carries the translocation chromosome. However, three ESTs and three known genes were expressed from the t(X;4) chromosome and thus "escaped" X inactivation. This direct assay of expression demonstrated that the spreading of inactivation from the adjoining X chromosome was incomplete and noncontiguous. These findings are broadly consistent with the existence of genes known to escape inactivation on normal inactive X chromosomes. However, the fact that a high proportion (30%) of tested autosomal genes escaped inactivation may indicate that autosomal material lacks X chromosome-specific features that are associated with the spreading and/or maintenance of inactivation.

Disclaimer: This guideline is designed primarily as an educational resource for health care providers to help them provide quality medical genetic services. Adherence to this guideline does not necessarily ensure a successful medical outcome. This guideline should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the geneticist should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen. It may be prudent, however, to document in the patient's record the rationale for any significant deviation from this guideline. Abstract:Turner syndrome is a disorder that has distinct clinical features and has karyotypic aberrations with loss of critical regions of the X chromosome. Several clinical guidelines on the diagnosis and management of patients with Turner syndrome have been published, but there is relatively little on the laboratory aspects associated with this disorder. This disease-specific laboratory guideline provides laboratory guidance for the diagnosis/study of patients with Turner syndrome and its variants. Because the diagnosis of Turner syndrome involves both a clinical and laboratory component, both sets of guidelines are required for the provision of optimal care for patients with Turner syndrome. Genet Med 2010:12(1):52-55.

Fluorescence in situ hybridization (FISH) provides an important adjunct to conventional cytogenetics and molecular studies in the evaluation of chromosome abnormalities associated with hematologic malignancies. FISH employs DNA probes and methods that are generally not Food and Drug Administration-approved, and therefore, their use as analyte-specific reagents involves unique pre-and postanalytical requirements. We provide an overview of the technical parameters influencing a reliable FISH result and encourage laboratories to adopt specific procedures and policies in implementing metaphase and interphase The World Health Organization recent classification of tumors of hematopoietic and lymphoid tissues emphasizes the importance of chromosome abnormalities for accurate diagnosis, appropriate treatment, and monitoring response to therapy.1 In certain scenarios, fluorescence in situ hybridization (FISH) analysis offers one of the most sensitive, specific, and reliable strategies for identifying acquired chromosomal changes associated with hematologic disorders. With the growth in the understanding of the importance of cytogenetic abnormalities associated with these diseases and the availability of commercial FISH probes, this area of clinical laboratory testing is rapidly expanding. Here, we offer guidance for initiating, validating, routinely performing, and reporting FISH studies for hematologic disorders. The recommendations in this article provide detailed assistance for implementing FISH testing and are meant to assist laboratories with complying with existing

Background Urine cytology has been used for screening of bladder cancer but has been limited by its low sensitivity. UroVysion is a FISH assay that detects common chromosome abnormalities in bladder cancers. The present study evaluates the effectiveness of UroVysion and urine cytology in detecting urothelial cell carcinoma (UCC) in same urine sample. Methods 1,835 cases with the following criteria were selected: valid results of both UroVysion and cytology from same urine sample; histological and/or cystoscopic follow up within 4 months of the original tests, or at least 3 year clinical follow up information. The results of the UroVysion and cytology were correlated with clinical outcome that was derived from combination of histological, cystoscopic and clinical follow up information. Results Of 1,835 cases, 1,045 cases were for surveillance of recurrent UCC, 790 cases were for hematuria. Overall sensitivity, specificity, PPV and NPV in detecting UCC were 61.9%, 89.7%, 53.9% and 92.4%, respectively for UroVysion, and 29.1%, 96.9%, 64.4% and 87.5%, respectively for cytology. The performance of both UroVysion and cytology was generally better in the surveillance population and in samples with high grade UCC. In 95 of 296 cases with atypical cytology that were proven to have UCC, 61 cases, mostly high grade UCC, were positive for UroVysion. Conclusions UroVysion was more sensitive than cytology in detecting UCC, but produced more false positive result. Our data suggest that the use of UroVysion as a reflex test following an equivocal cytological diagnosis may play an effective role for UCC detection.