Carriers of balanced reciprocal translocation are usually phenotypically normal; however, they have an increased risk of producing gametes with chromosomal imbalance through different types of meiotic segregation of the translocation quadrivalent. The genetically imbalanced gametes when they survive can result in embryos with chromosomal abnormalities. Here we report a family with two siblings inheriting partial trisomy for 9p and 18p concurrently resulting from a 3:1 meiotic segregation of a maternal balanced translocation involving chromosome 9q and 18p, and the associated phenotype. The family was ascertained because of severe congenital anomalies in a newborn male (sibling 1). The karyotype of this patient was 47,XY,+del(9)(q13q34). Cytogenetic analysis revealed that the phenotypically normal mother harbored a balanced translocation 46,XX,t(9;18)(q13;p11.21). Chromosomal microarray analysis (CMA) of the abnormal child detected segmental trisomy for 9p and 18p. In conjunction with conventional cytogenetic results of the mother and CMA results of the affected child, the final karyotype of sibling one was 47,XY,+der(9)t(9;18) (q13;p11.22)dmat. arr[GRCh36] 9p24.3q13(199254_70163189)× 3, 18p11.32p11.22(131491_9640590)× 3; this resulted in segmental duplication of 69.96 Mb on 9pter->q13 and 9.51 Mb on 18p. There was a subsequent birth of a female sibling (sibling two) with multiple anomalies, including dysmorphic facial features, kidney aberration, cardiac defects, and abnormal brain MRI. The G-banded karyotype of this sibling was 47,XX,+del(9)(q13q34). The final karyotype of this sibling after CMA results was 47,XX,+der(9)t(9;18)(q13;p11.22)dmat. arr[GRCh37] 9p24.3p13.1(209020_38763958)× 3; 18p11.32p11.22(146484_9640912)× 3. The apparent discrepancy between the array results of the two siblings is attributed to difference in the design of array chips and genome builds used for these patients (NimbleGen/Roche v2.0 3-plex and GRCh36 for sibling one, and GGXChip + SNP array and GRCh37 of Agilent Technologies for sibling two). There are 182 OMIM genes in the duplicated region of 9p and 33 OMIM genes in the duplicated region of 18p which may have contributed to the clinical features of the affected siblings. To our knowledge, we report the first two cases of concurrent partial trisomy 9p and 18p in the same family. This report adds more information about phenotypic effects of these chromosomal copy number gains and supports chromosomal microarray analysis as the standard for precise identification or demarking regions of duplications, particularly when the translocation involves at least one subterminal segment. In view of the recurring infants with congenital anomalies the couple may benefit from prenatal chromosome analysis of future pregnancies or opting to assisted reproductive methods and transferring normal embryos for implantation.
Background: Fluorescence labeled DNA probes and in situ hybridization methods had shorter turn round time for results revolutionized their clinical application. Signals obtained from these probes are highly specific, yet they can produce fusion signals not necessarily representing fusion of actual genes due to other genes included in the probe design. In this study we evaluated discordance between cytogenetic, FISH and RNAseq results in 3 different patients with hematologic malignancies and illustrated the need to perform next generation sequencing (NGS) or RNASeq to accurately interpret FISH results. Methods: Bone marrow or peripheral blood karyotypes and FISH were performed to detect recurring translocations associated with hematologic malignancies in clinical samples routinely referred to our clinical cytogenetics laboratory. When required, NGS was performed on DNA and RNA libraries to detect somatic alterations and gene fusions in some of these specimens. Discordance in results between these methods is further evaluated. Results: For a patient with plasma cell leukemia standard FGFR3 / IGH dual fusion FISH assay detected fusion that was interpreted as FGFR3-positive leukemia, whereas NGS/RNASeq detected NSD2::IGH. For a pediatric acute lymphoblastic leukemia patient, a genetic diagnosis of PDGFRB-positive ALL was rendered because the PDGFRB break-apart probe detected clonal rearrangement, whereas NGS detected MEF2D::CSF1R. A MYC-positive B-prolymphocytic leukemia was rendered for another patient with a cytogenetically identified t(8;14) and MYC::IGH by FISH, whereas NGS detected a novel PVT1::RCOR1 not previously reported. Conclusions: These are 3 cases in a series of several other concordant results, nevertheless, elucidate limitations when interpreting FISH results in clinical applications, particularly when other genes are included in probe design. In addition, when the observed FISH signals are atypical, this study illustrates the necessity to perform complementary laboratory assays, such as NGS and/or RNASeq, to accurately identify fusion genes in tumorigenic translocations.
B-cell acute lymphoblastic leukemia (B-ALL) is the most common malignancy in pediatric patients and the leading cause of cancer-related death in children and young adults. Translocations of 9p24 involving JAK2 (9p24) and gain-of-function mutations of JAK2 with subsequent activation of the JAK2 kinase have been described in several hematological malignancies including B-ALL. However, rearrangements involving JAK2 are rare in B-ALL as only few cases have been described in the literature.Herein, we present a case of pediatric B-ALL whose conventional cytogenetics revealed an abnormal karyotype with a reciprocal translocation involving 9p24 (JAK2) and 12p11.2. Fluorescence in situ hybridization (FISH) studies using the RP11-927H16 Spectrum Green JAK2 probe on previously G-banded metaphases confirmed the involvement of JAK2 in this rearrangement. Further FISH studies on the same previously G-banded metaphases using the LSI MLL probe helped to characterize an insertion of MLL into 6q27 as an additional abnormality in this karyotype. FISH studies performed on interphase nuclei also revealed an abnormal clone with MLL rearrangements in 23.6% of the nuclei examined as well as an abnormal clonal population with a deletion of the 5'IGH@ region in 88.3% of the nuclei examined.Rearrangements of 9p24 can result in constitutive activation of JAK2, and have been observed in B-ALL. Rearrangements of the MLL gene have also been described extensively in B-ALL. However, rearrangements of MLL with a partner at 6q27 and in conjunction with a translocation involving JAK2 have not been previously described. This case pinpoints the importance of FISH and conventional cytogenetics to characterize complex rearrangements in which JAK2 and MLL are involved. The therapeutic targeting of JAK2 and MLL in cases like this may be prognostically beneficial.
Gene alterations in TP53 are observed in a wide array of tumor samples. Approximately 75% of abnormalities of TP53 are manifested as sequence variations, impacting mainly the DNA binding domain located in exons 4-9. These variations lead to amino acid changes that could potentially have adverse effects on the protein's structure and function. The classification and clinical interpretation of germline and somatic non-synonymous sequence variants in TP53 poses challenges in the clinical context. Presently, numerous bioinformatic tools, including PolyPhen-2 and SIFT, play a role in predicting pathogenicity.
JAK2 is a cytoplasmic tyrosine kinase whose gene is located on chromosome 9p24. It is involved in the regulation of different cytokines and growth factors and plays an important role in the diagnosis and treatment of myeloproliferative neoplasms (Smith et al., 2008). Translocations involving the JAK2 locus are uncommon with just a few cases described in the literature, and they usually lead to a fusion protein with JAK2 (Patnaik et al., 2010). Chromosome 9p24 abnormalities have been described in myeloid and lymphoid neoplasms including chronic myelogenous leukemia (CML), acute megakaryoblastic leukemia, CD10+ B-cell acute lymphoblastic leukemia, T-cell ALL and chronic myeloproliferative disorders (CMD) (Smith et al., 2008; Lacronique et al., 1997). Although the breakpoints of each translocation are known, characterization of the partner gene has not been done in many of the cases reported due to insufficient sample or other factors. In the present study we review all translocations involving JAK2 that have been reported in the literature.
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin Lymphoma comprising of greater than 30% of adult non-Hodgkin Lymphomas. DLBCL represents a diverse set of lymphomas, defined as diffuse proliferation of large B lymphoid cells. Numerous cytogenetic studies including karyotypes and fluorescent in situ hybridization (FISH), as well as morphological, biological, clinical, microarray and sequencing technologies have attempted to categorize DLBCL into morphological variants, molecular and immunophenotypic subgroups, as well as distinct disease entities. Despite such efforts, most lymphoma remains undistinguishable and falls into DLBCL, not otherwise specified (DLBCL-NOS). The advent of microarray-based studies (chromosome, RNA, gene expression, etc) has provided a plethora of high-resolution data that could potentially facilitate the finer classification of DLBCL. This review covers the microarray data currently published for DLBCL. We will focus on these types of data; 1) array based CGH; 2) classical CGH; and 3) gene expression profiling studies. The aims of this review were three-fold: (1) to catalog chromosome loci that are present in at least 20% or more of distinct DLBCL subtypes; a detailed list of gains and losses for different subtypes was generated in a table form to illustrate specific chromosome loci affected in selected subtypes; (2) to determine common and distinct copy number alterations among the different subtypes and based on this information, characteristic and similar chromosome loci for the different subtypes were depicted in two separate chromosome ideograms; and, (3) to list re-classified subtypes and those that remained indistinguishable after review of the microarray data. To the best of our knowledge, this is the first effort to compile and review available literatures on microarray analysis data and their practical utility in classifying DLBCL subtypes. Although conventional cytogenetic methods such as Karyotypes and FISH have played a major role in classification schemes of lymphomas, better classification models are clearly needed to further understanding the biology, disease outcome and therapeutic management of DLBCL. In summary, microarray data reviewed here can provide better subtype specific classifications models for DLBCL.
