Arupa Ganguly

Prognosis of Uveal Melanoma in 500 Cases Using Genetic Testing of Fine-Needle Aspiration Biopsy Specimens

PURPOSEnTo determine the relationship between monosomy 3 and incidence of metastasis after genetic testing of uveal melanoma using fine-needle aspiration biopsy (FNAB).nnnDESIGNnNoncomparative retrospective case series.nnnPARTICIPANTSnFive hundred patients.nnnMETHODSnFine-needle aspiration biopsy was performed intraoperatively immediately before plaque radiotherapy. The specimen underwent genetic analysis using DNA amplification and microsatellite assay. Systemic follow-up was obtained regarding melanoma-related metastasis.nnnMAIN OUTCOME MEASURESnPresence of chromosome 3 monosomy (loss of heterozygosity) and occurrence of melanoma metastasis.nnnRESULTSnDisomy 3 was found in 241 melanomas (48%), partial monosomy 3 was found in 133 melanomas (27%), and complete monosomy 3 was found in 126 melanomas (25%). The cumulative probability for metastasis by 3 years was 2.6% for disomy 3, 5.3% for partial monosomy 3 (equivocal monosomy 3), and 24.0% for complete monosomy 3. At 3 years, for tumors with disomy 3, the cumulative probability of metastasis was 0% for small (0-3 mm thickness), 1.4% for medium (3.1-8 mm thickness), and 23.1% for large (>8 mm thickness) melanomas. At 3 years, for tumors with partial monosomy 3, the cumulative probability of metastasis was 4.5% for small, 6.9% for medium, and [insufficient numbers] for large melanomas. At 3 years, for tumors with complete monosomy 3, the cumulative probability of metastasis was 0% for small, 24.4% for medium, and 57.5% for large melanomas. The most important factors predictive of partial or complete monosomy 3 included increasing tumor thickness (P = 0.001) and increasing distance to optic disc (P = 0.002).nnnCONCLUSIONSnAccording to FNAB results, patients with uveal melanoma demonstrating complete monosomy 3 have substantially poorer prognosis at 3 years than those with partial monosomy 3 or disomy 3. Patients with partial monosomy 3 do not significantly differ in outcome from those with disomy 3.

Early Diagnosis of Fibrodysplasia Ossificans Progressiva

BACKGROUND. Fibrodysplasia ossificans progressiva is a rare and disabling genetic condition characterized by congenital malformation of the great toes and by progressive heterotopic ossification in specific anatomic patterns. Most patients with fibrodysplasia ossificans progressiva are misdiagnosed early in life before the appearance of heterotopic ossification and undergo diagnostic procedures that can cause lifelong disability. Recently, the genetic cause of fibrodysplasia ossificans progressiva was identified, and definitive genetic testing for fibrodysplasia ossificans progressiva is now available before the appearance of heterotopic ossification. METHODS. We recently evaluated 7 children for diagnosis of fibrodysplasia ossificans progressiva before the onset of heterotopic ossification. A medical history, physical examination, and skeletal survey were obtained on all of the patients, as well as clinical genetic testing for the canonical fibrodysplasia ossificans progressiva mutation. RESULTS. All 7 of the children (4 girls and 3 boys; ages 3 months to 6 years) had congenital malformations of the great toes, but none had radiographic evidence of heterotopic ossification at the time of evaluation. Five of the 7 children had soft tissue lesions of the neck and back, suggestive of early fibrodysplasia ossificans progressiva flare-ups, 3 of whom had undergone invasive diagnostic procedures that exacerbated their condition. Two children had no history or signs of soft tissue swelling or flare-ups. DNA sequence analysis found that all 7 of the children had the recurrent fibrodysplasia ossificans progressiva missense mutation, a single nucleotide substitution (c.617G>A) at codon 206 in the glycine-serine activation domain of activin receptor IA, a bone morphogenetic protein type 1 receptor. CONCLUSION. Clinical suspicion of fibrodysplasia ossificans progressiva early in life on the basis of malformed great toes can lead to early clinical diagnosis, confirmatory diagnostic genetic testing, and the avoidance of additional harmful diagnostic and treatment procedures. This is the first report of genetic confirmation of fibrodysplasia ossificans progressiva before the appearance of heterotopic ossification. Pediatricians should be aware of the early diagnostic features of fibrodysplasia ossificans progressiva, even before the appearance of heterotopic ossification. This awareness should prompt early genetic consultation and testing and the institution of assiduous precautions to prevent iatrogenic harm.

Genotype and Phenotype Correlations in 417 Children With Congenital Hyperinsulinism

CONTEXTnHypoglycemia due to congenital hyperinsulinism (HI) is caused by mutations in 9 genes.nnnOBJECTIVEnOur objective was to correlate genotype with phenotype in 417 children with HI.nnnMETHODSnMutation analysis was carried out for the ATP-sensitive potassium (KATP) channel genes (ABCC8 and KCNJ11), GLUD1, and GCK with supplemental screening of rarer genes, HADH, UCP2, HNF4A, HNF1A, and SLC16A1.nnnRESULTSnMutations were identified in 91% (272 of 298) of diazoxide-unresponsive probands (ABCC8, KCNJ11, and GCK), and in 47% (56 of 118) of diazoxide-responsive probands (ABCC8, KCNJ11, GLUD1, HADH, UCP2, HNF4A, and HNF1A). In diazoxide-unresponsive diffuse probands, 89% (109 of 122) carried KATP mutations; 2% (2 of 122) had GCK mutations. In mutation-positive diazoxide-responsive probands, 42% were GLUD1, 41% were dominant KATP mutations, and 16% were in rare genes (HADH, UCP2, HNF4A, and HNF1A). Of the 183 unique KATP mutations, 70% were novel at the time of identification. Focal HI accounted for 53% (149 of 282) of diazoxide-unresponsive probands; monoallelic recessive KATP mutations were detectable in 97% (145 of 149) of these cases (maternal transmission excluded in all cases tested). The presence of a monoallelic recessive KATP mutation predicted focal HI with 97% sensitivity and 90% specificity.nnnCONCLUSIONSnGenotype to phenotype correlations were most successful in children with GLUD1, GCK, and recessive KATP mutations. Correlations were complicated by the high frequency of novel missense KATP mutations that were uncharacterized, because such defects might be either recessive or dominant and, if dominant, be either responsive or unresponsive to diazoxide. Accurate and timely prediction of phenotype based on genotype is critical to limit exposure to persistent hypoglycemia in infants and children with congenital HI.

Congenital Hyperinsulinism–Associated ABCC8 Mutations That Cause Defective Trafficking of ATP-Sensitive K+ Channels: Identification and Rescue

Congenital hyperinsulinism (CHI) is a disease characterized by persistent insulin secretion despite severe hypoglycemia. Mutations in the pancreatic ATP-sensitive K+ (KATP) channel proteins sulfonylurea receptor 1 (SUR1) and Kir6.2, encoded by ABCC8 and KCNJ11, respectively, is the most common cause of the disease. Many mutations in SUR1 render the channel unable to traffic to the cell surface, thereby reducing channel function. Previous studies have shown that for some SUR1 trafficking mutants, the defects could be corrected by treating cells with sulfonylureas or diazoxide. The purpose of this study is to identify additional mutations that cause channel biogenesis/trafficking defects and those that are amenable to rescue by pharmacological chaperones. Fifteen previously uncharacterized CHI-associated missense SUR1 mutations were examined for their biogenesis/trafficking defects and responses to pharmacological chaperones, using a combination of immunological and functional assays. Twelve of the 15 mutations analyzed cause reduction in cell surface expression of KATP channels by >50%. Sulfonylureas rescued a subset of the trafficking mutants. By contrast, diazoxide failed to rescue any of the mutants. Strikingly, the mutations rescued by sulfonylureas are all located in the first transmembrane domain of SUR1, designated as TMD0. All TMD0 mutants rescued to the cell surface by the sulfonylurea tolbutamide could be subsequently activated by metabolic inhibition on tolbutamide removal. Our study identifies a group of CHI-causing SUR1 mutations for which the resulting KATP channel trafficking and expression defects may be corrected pharmacologically to restore channel function.

Update on molecular diagnosis of hereditary hemorrhagic telangiectasia

Hereditary hemorrhagic telangiectasia (HHT) is an autosomal dominant, vascular disease hallmarked by the development of arteriovenous malformations (AVMs). Germline mutations in two genes, endoglin (ENG) and activin receptor like kinase 1 (ACVRL1), have been implicated in this disease. This report describes molecular diagnosis in a consecutive series of 600 individuals with clinical features of HHT disease. Each coding exon and flanking intronic regions of ENG and ACVRL1 genes was sequenced. Exonic copy number was quantified in probands without a coding sequence mutation. Novel nonsynonymous variants were further analyzed to predict functional consequences. In addition, common single nucleotide polymorphisms genotypes and haplotypes for the two genes were compared between individuals with and without mutations. The highest mutation detection rate (87% [95% CI 80.2–91.5]) was observed in probands who met all four Curacao criteria (epistaxis, telangiectases, AVMs and family history). More than 30% of identified mutations were novel; however, only 6% were variants of unknown significance. Determining the significance of novel mutations as related to disease presents additional challenges. Detection of multiple alterations in the same proband also requires careful evaluation for disease association. In conclusion, the sensitivity of molecular diagnosis is highest in probands with a clinically confirmed diagnosis of HHT. However, a substantial fraction of probands in this group do not carry an identifiable mutation in the coding exons of these two genes. This suggests alternate mechanisms of gene inactivation or involvement of alternate loci, and it requires further investigation.

Genomic profile of 320 uveal melanoma cases: chromosome 8p-loss and metastatic outcome.

PURPOSEnUveal melanoma (UM) was a fatal malignancy in 40% to 50% of cases. The aim of this study is to evaluate the independent contributions of chromosome 1, 3, 6, and 8 abnormalities for prognostication of metastasis, and to define multichromosome copy number aberration (CNA) signatures that can be used to evaluate risk.nnnMETHODSnA series of 320 UM were analyzed for chromosome 1, 3, 6, and 8 abnormalities using whole genome single-nucleotide polymorphism arrays. Results for changes in six chromosomal regions were analyzed using univariate and multivariate Cox proportional hazard modeling to identify significant predictors of metastasis and CNA signatures.nnnRESULTSnUnivariate Cox analysis indicated that losses of chromosome 3, 1p, 6q, and 8p and gain of 8q, as well as sex, source of tumor tissue (fine-needle aspiration biopsy [FNAB] compared with tumor from an enucleated eye), tumor basal diameter and height, and ciliary body involvement were all significant predictors of poor metastatic outcome. In the multivariate analysis, loss of chromosome 3 and 8p remained significant after adjusting for the effects of all other variables, as did sex, tissue source, and basal diameter. Multivariate analysis of the joint effects of changes in the six chromosomal regions showed that six signatures, including chromosome 3-loss, 1p-loss, 8p-loss, and/or 8q-gain had hazard ratios (HR) ranging from 7.90 to 37.25.nnnCONCLUSIONSnIn UM, tumor size and location, tissue source, and sex were all significantly associated with increased metastasis. In addition, chromosome 3-loss and 8p-loss were found to be independent predictors of poor metastatic outcome and CNA signatures were identified that can add a specific HR value for classification of risk categories.

Recent advances in retinoblastoma genetic research.

Purpose of review Retinoblastoma is a pediatric eye tumor that serves as a paradigm for understanding the genetic basis of cancer. This review will highlight recent advances in retinoblastoma genetic research and discuss how these new findings influence our knowledge of retinoblastoma tumorigenesis and management. Recent findings Current data demonstrate that retinomas, benign retinal tumors found in some retinoblastoma patients, exhibit bi-allelic mutations in RB1, the retinoblastoma gene, and lack of expression of the retinoblastoma protein. Interestingly, retinomas demonstrate a low level of genomic instability that becomes progressively more severe in retinoblastoma tumors. Additionally, a subset of retinomas share genomic alterations with retinoblastoma. Collectively, these data suggest that retinomas represent true premalignant lesions and not regressed retinoblastoma tumors, as previously thought. Translational advances in retinoblastoma genetic research include development of an allele-specific assay that now enables the identification of mutational mosaicism, thereby increasing the rate of RB1 mutation detection in bilaterally affected patients to as high as 95%. Summary These and related research efforts reveal novel data that enhance our understanding of the biology of retinoblastoma. These observations may facilitate new therapeutic approaches to further decrease the morbidity and mortality associated with retinoblastoma and other more common forms of cancer.

Regression of uveal melanoma after plaque radiotherapy and thermotherapy based on chromosome 3 status.

Purpose: To evaluate regression rates after plaque radiotherapy and thermotherapy of uveal melanoma with chromosome 3 monosomy versus disomy. Design: Noncomparative case series. Participants: Two hundred and seventy patients with uveal melanoma. Methods: Fine needle aspiration biopsy was used at the time of plaque radiotherapy to sample tumor cells for genetic testing. Main outcome measures: Tumor thickness regression based on chromosome 3 status. Results: At the time of plaque radiotherapy, the median tumor thickness was 4.0 mm for melanomas with chromosome 3 monosomy and 3.5 mm for those with disomy 3. The median tumor thickness (% original thickness) at 4, 8, 12, 15, and 18 months after radiotherapy for melanoma with monosomy 3 was 77%, 67%, 58%, 55%, and 50% and for those with disomy 3 was 82%, 70%, 69%, 67%, and 61%. The median monthly regression rate was 3.1% for tumors with monosomy 3 and 2.7% for those with disomy 3. The overall regression and monthly rate of regression was statistically greater at 12 months (P < 0.001) and 15 months (P = 0.003) for melanomas with monosomy 3 compared with disomy 3. Conclusions: Uveal melanomas with chromosome 3 monosomy showed faster and greater tumor thickness regression at 12 and 15 months after plaque radiotherapy and thermotherapy than melanomas with disomy 3.

Molecular karyotype of sporadic unilateral retinoblastoma tumors.

Background: Retinoblastoma (RB) is a childhood ocular malignancy associated with mutations in RB1, a tumor susceptibility gene. Inactivation of both copies of the RB1 gene in a retinal cell is followed by the sequential acquisition of additional genetic changes that define the course to tumor formation. Methods: To identify the genetic events that cooperate with loss of the RB1 gene function, we performed a whole genome sampling assay based on single nucleotide polymorphism genotyping. We used DNA isolated from 25 sporadic, unilateral RB tumors and matched blood samples. Results: Genomic profiles were analyzed to identify regions of loss of heterozygosity or amplification. Two major subclasses of RB tumors were defined by the presence (n = 18) or absence (n = 7) of loss of heterozygosity of chromosome 13. Loss of heterozygosity in most cases was the result of copy-neutral events caused by mitotic recombination and mitotic nondisjunction. Tumors harbored novel regions of amplification at 1q44, 3p25, 11q14, 11q25, 14q23, 15q21, 16p13, 17p11.2, 19q13, and 20q13, whereas regions of loss included 6q22, 7q21, and 21q2. Conclusion: Whole genome sampling assay-based analysis of unilateral RB tumors revealed novel regions as significant. These minimum critical regions that are lost or amplified are expected to harbor genes that aid the process of tumorigenesis.

Medical radiation exposure and risk of retinoblastoma resulting from new germline RB1 mutation

Although ionizing radiation induces germline mutations in animals, human studies of radiation‐exposed populations have not detected an effect. We conducted a case‐control study of sporadic bilateral retinoblastoma, which results from a new germline RB1 mutation, to investigate gonadal radiation exposure of parents from medical sources before their childs conception. Parents of 206 cases from nine North American institutions and 269 controls participated; fathers of 184 cases and 223 friend and relative controls and mothers of 204 cases and 260 controls provided information in telephone interviews on their medical radiation exposure. Cases provided DNA for RB1 mutation testing. Of common procedures, lower gastrointestinal (GI) series conferred the highest estimated dose to testes and ovaries. Paternal history of lower GI series was associated with increased risk of retinoblastoma in the child [matched odds ratio (OR) = 3.6, 95% confidence interval (CI) = 1.2–11.2, two‐sided p = 0.02], as was estimated total testicular dose from all procedures combined (OR for highest dose=3.9, 95% CI = 1.2–14.4, p = 0.02). Maternal history of lower GI series was also associated with increased risk (OR = 7.6, 95% CI = 2.8–20.7, p < 0.001) as was the estimated total dose (OR for highest dose = 3.0, 95% CI = 1.4–7.0, p = 0.005). The RB1 mutation spectrum in cases of exposed parents did not differ from that of other cases. Some animal and human data support our findings of an association of gonadal radiation exposure in men and women with new germline RB1 mutation detectable in their children, although bias, confounding, and/or chance may also explain the results.