Cytogenetic Nomenclature: Changes in the ISCN 2013 Compared to the 2009 Edition

Simons, Annet; Shaffer, Lisa G.; Hastings, Ros

doi:10.1159/000353118

Cited by 215 publications

(170 citation statements)

References 3 publications

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“…Because of the disparity in techniques from which genetic data are obtained, all the curated genetic test result information was manually reviewed to extract the coordinates and genome assembly of the chromosomal abnormalities. Chromosomal coordinates for CGH were extracted from the relevant structured fields (chromosome, gain/loss, start, end), and from the International Society of Cytogenetics Nomenclature (ISCN 2013) standard (Simons, Shaffer, & Hastings, 2013) and comments where necessary. Chromosomal coordinates for FISH results were directly obtained in the GRCh38/hg38 genome assembly (Miga et al, 2014) from the National Center for Biotechnology Information (NCBI) Clone database (Schneider et al, 2013).…”

Section: Methodsmentioning

confidence: 99%

Phelan‐McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports

Kothari

Wack

Hassen‐Khodja

et al. 2017

American J of Med Genetics Pt B

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The heterogeneity of patient phenotype data are an impediment to the research into the origins and progression of neuropsychiatric disorders. This difficulty is compounded in the case of rare disorders such as Phelan‐McDermid Syndrome (PMS) by the paucity of patient clinical data. PMS is a rare syndromic genetic cause of autism and intellectual deficiency. In this paper, we describe the Phelan‐McDermid Syndrome Data Network (PMS_DN), a platform that facilitates research into phenotype–genotype correlation and progression of PMS by: a) integrating knowledge of patient phenotypes extracted from Patient Reported Outcomes (PRO) data and clinical notes—two heterogeneous, underutilized sources of knowledge about patient phenotypes—with curated genetic information from the same patient cohort and b) making this integrated knowledge, along with a suite of statistical tools, available free of charge to authorized investigators on a Web portal https://pmsdn.hms.harvard.edu. PMS_DN is a Patient Centric Outcomes Research Initiative (PCORI) where patients and their families are involved in all aspects of the management of patient data in driving research into PMS. To foster collaborative research, PMS_DN also makes patient aggregates from this knowledge available to authorized investigators using distributed research networks such as the PCORnet PopMedNet. PMS_DN is hosted on a scalable cloud based environment and complies with all patient data privacy regulations. As of October 31, 2016, PMS_DN integrates high‐quality knowledge extracted from the clinical notes of 112 patients and curated genetic reports of 176 patients with preprocessed PRO data from 415 patients.

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Section: Methodsmentioning

confidence: 99%

Phelan‐McDermid syndrome data network: Integrating patient reported outcomes with clinical notes and curated genetic reports

Kothari

Wack

Hassen‐Khodja

et al. 2017

American J of Med Genetics Pt B

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“…The slides were rinsed with water and air-dried. The karyotypes were expressed according to the International System for Human Cytogenetic Nomenclature 2013 (14).…”

Section: Patient Characteristicsmentioning

confidence: 99%

Myxoid liposarcoma with cartilaginous differentiation showing DDIT3 rearrangement

et al. 2017

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Abstract. Myxoid liposarcoma (MLPS) is the second most common histologic subtype of liposarcoma. However, cartilaginous differentiation within MLPS is an extremely rare phenomenon, with only 7 cases of MLPS with cartilaginous differentiation reported to date. The majority of MLPS cases show the t(12;16)(q13;p11) translocation, resulting in the fused in sarcoma-DNA damage-inducible transcript 3 (FUS-DDIT3) fusion gene. This fusion gene as a hallmark of MLPS is very useful for differential diagnosis from other soft tissue sarcomas, and the associated protein, FUS-DDIT3, performs an important role in the phenotypic selection of targeted multipotent mesenchymal cells during oncogenesis. In this report, a case of MLPS with cartilaginous differentiation that occurred in the thigh of a 44-year-old woman is described. Histopathologically, the tumor was composed of a typical myxoid liposarcoma area and a mature hyaline cartilaginous area. Using fluorescence in situ hybridization analysis, rearrangement of the DDIT3 gene was detected in not only the liposarcomatous area but also in the chondrocytes of the cartilaginous area. Based on these findings, the cartilaginous differentiation area appears to be partially associated with oncogenesis through the specific fusion gene FUS-DDIT3. IntroductionLiposarcoma is one of the most common soft tissue sarcomas in adults, representing an estimated 17-25% of all sarcomas (1,2). The tumor occurs at all ages, but is most commonly identified in individuals between 40 and 60 years of age. A total of four distinct histologic subtypes of liposarcoma are recognized by the World Health Organization: i) Atypical lipomatous tumor (ALT); ii) dedifferentiated liposarcoma (DLPS); iii) myxoid liposarcoma (MLPS); and iv) pleomorphic liposarcoma (PLPS). ALT and DLPS are genetically defined by a giant marker or ring chromosomes with an amplification on chromosome 12 affecting, among others, the genes mouse double minute 2 homolog and cyclin-dependent kinase 4 (3). MLPS denotes one such entity and is the second most common liposarcoma following ALT (4). A significant proportion of MLPS cases have the major cytogenetic hallmark of the t(12;16) (q13;p11) chromosomal translocation. This translocation leads to fusion of fused in liposarcoma (FUS; also termed translocated in liposarcoma) and DNA damage-inducible transcript 3 (DDIT3; also termed CCAAT/enhancer-binding protein homologous protein) genes, resulting in the production of the FUS-DDIT3 fusion protein (5). In another subset of MLPS, a minor chromosomal translocation, t(12;22)(q13;q12), results in fusion of the Ewing's sarcoma (EWSR1) and DDIT3 genes (6). PLPS is less frequent and harbors a complex genomic profile with numerous gains and losses similar to the genomic profile observed in poorly differentiated sarcoma (7).The histopathological findings of MLPS are typically composed of well-circumscribed lobulated tumors. These contain a mixture of uniform round to oval-shaped nonlipogenic mesenchymal cells and signet ring lipoblasts in a prominent ...

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“…исследованных членов ее семьи arr (1-22, X)×2, что соответствует нормальному женскому кариотипу [41]. Был выявлен ряд вариаций числа копий (CNVcopy number variation) сегментов ДНК размером от 1000 п.н., отличающихся от референсного генома (уменьшение -делеция или увеличение -дуплика-ция копийности) (рис.…”

Section: синдромunclassified