Frequency, variations, and prognostic implications of chromosome 14q32 deletions in chronic lymphocytic leukemia.

The clinical implications of deletions within chromosome 14q32 in CLL pathogenesis remain unclear. We examined the frequency of 14q32 deletions among CLL cases by karyotype and FISH, categorized the variation using genomic microarray, and assessed the prognostic impact by time-to-first-treatment (TTFT) analysis. A 14q32 abnormality was detected in 35 % (245/698) of cases, with the majority containing a 5' partial telomeric 14q32 deletion. These deletions within the IGH variable region (35/40) ranged from 236 kb to 1.4 Mb involving FAM30A, ADAM6, LINC00226, and LINC00221. The 214 kb minimum deleted region implicated in CLL pathogenesis encompassed LINC00221. Cases with a 14q32 deletion had a shorter median TTFT compared to cases with a sole deletion/nullisomy 13q, a good prognostic indicator, and longer than cases with a sole deletion of 11q or 17p, conferring an unfavorable prognosis. This investigation underscores the importance of comprehensive testing to apprehend the implications of 14q32 deletions in CLL.

Breast Cancer and Non-Hodgkin Lymphoma in a Young Male with Cowden Syndrome.

Male breast cancer (MBC) is unusual, especially in young adults. Most cases of MBC as a secondary malignancy relate to the previous treatment with ionizing radiation. MBC can be associated with mutations in hereditary cancer predisposition syndrome genes (i.e., BRCA2); however, no such association has been reported in patients with Cowden syndrome (involving the phosphatase and tensin homolog [PTEN] gene). We describe a patient with Cowden syndrome who was initially diagnosed with B-cell lymphoblastic lymphoma at the age of 7 years, then MBC at the age of 31 years, and never received radiation therapy.

Assessing the utility of confirmatory studies following identification of large-scale genomic imbalances by microarray.

PURPOSE: The identification of clinically relevant genomic dosage anomalies assists in accurate diagnosis, prognosis, and medical management of affected individuals. Technological advancements within the field, such as the advent of microarray, have markedly increased the resolution of detection; however, clinical laboratories have maintained conventional techniques for confirmation of genomic imbalances identified by microarray to ensure diagnostic accuracy. In recent years the utility of this confirmatory testing of large-scale aberrations has been questioned but has not been scientifically addressed. METHODS: We retrospectively reviewed 519 laboratory cases with genomic imbalances meeting reportable criteria by microarray and subsequently confirmed with a second technology, primarily fluorescence in situ hybridization. RESULTS: All genomic imbalances meeting reportable criteria detected by microarray were confirmed with a second technology. Microarray analysis generated no false-positive results. CONCLUSION: Confirmatory testing of large-scale genomic imbalances (deletion of ≥150 kb, duplication of ≥500 kb) solely for the purpose of microarray verification may be unwarranted. In some cases, however, adjunct testing is necessary to overcome limitations inherent to microarray. A recommended clinical strategy for adjunct testing following identified genomic imbalances using microarray is detailed.

Duplication of 20qter and deletion of 20pter due to paternal pericentric inversion: patient report and review of 20qter duplications.

Duplications of the terminal long arm of chromosome 20 are rare chromosomal anomalies. We report a male infant found on array comparative genomic hybridization analysis to have a 19.5 Mb duplication of chromosome 20q13.12-13.33, as well as an 886 kb deletion of 20p13 at 18,580-904,299 bp. This anomaly occurred as the recombinant product of a paternal pericentric inversion. There have been 23 reported clinical cases involving 20qter duplications; however, to our knowledge this is only the second reported patient with a paternal pericentric inversion resulting in 46,XY,rec(20)dup(20q). This patient shares many characteristics with previously described patients with 20qter duplications, including microphthalmia, anteverted nares, long ears, cleft palate, small chin, dimpled chin, cardiac malformations, and normal intrauterine growth. While there is variable morbidity in patients with terminal duplications of 20q, a review of previously reported patients and comparison to our patient's findings shows significant phenotypic similarity.

Characterization of six novel patients with MECP2 duplications due to unbalanced rearrangements of the X chromosome.

Males with duplication of the Xq28 region, including methyl CpG-binding protein 2 (MECP2), exhibit a characteristic phenotype, including developmental delay, intellectual disability, limited or absent speech, limited or absent ambulation, and recurrent respiratory infections. We report six males with MECP2 duplications identified using array comparative genomic hybridization. The minimal sizes of these duplications range from ∼0.08 to 14.13 Mb, which, to the best of our knowledge, are respectively the smallest and largest minimal size duplications molecularly characterized to date. Adjunct metaphase fluorescence in situ hybridization analysis further classified these duplications as tandem or as products of complex chromosomal rearrangements. Specifically, one complex rearrangement was described as a der(12)t(X;12)(q28;q24.33), which is the first report of a translocation involving MECP2 on Xq and chromosome 12. The other complex rearrangement was described as a rec(X)dup(Xq)inv(X)(p22.32q28)mat. Synthesis of the dysmorphic features identified in individuals with rec(X) chromosomes, including deletions in the pseudoautosomal region 1 (PAR1) at Xp22.33/Yp11.3 and duplications of the distal Xq region including MECP2, revealed a high prevalence of undescended testes (7/8) and micropenis (3/8) in this cohort. Given that micropenis is rare in the general population, but present in 38% of individuals in this cohort, a dosage anomaly at one or both loci may be a significant risk factor for this condition. Therefore, we recommend microarray testing for patients with unexplained micropenis, particularly when accompanied by other phenotypic anomalies.

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

PURPOSE: Copy number variants have emerged as a major cause of human disease such as autism and intellectual disabilities. Because copy number variants are common in normal individuals, determining the functional and clinical significance of rare copy number variants in patients remains challenging. The adoption of whole-genome chromosomal microarray analysis as a first-tier diagnostic test for individuals with unexplained developmental disabilities provides a unique opportunity to obtain large copy number variant datasets generated through routine patient care. METHODS: A consortium of diagnostic laboratories was established (the International Standards for Cytogenomic Arrays consortium) to share copy number variant and phenotypic data in a central, public database. We present the largest copy number variant case-control study to date comprising 15,749 International Standards for Cytogenomic Arrays cases and 10,118 published controls, focusing our initial analysis on recurrent deletions and duplications involving 14 copy number variant regions. RESULTS: Compared with controls, 14 deletions and seven duplications were significantly overrepresented in cases, providing a clinical diagnosis as pathogenic. CONCLUSION: Given the rapid expansion of clinical chromosomal microarray analysis testing, very large datasets will be available to determine the functional significance of increasingly rare copy number variants. This data will provide an evidence-based guide to clinicians across many disciplines involved in the diagnosis, management, and care of these patients and their families.

Deletion 17q12 is a recurrent copy number variant that confers high risk of autism and schizophrenia.

Autism spectrum disorders (ASD) and schizophrenia are neurodevelopmental disorders for which recent evidence indicates an important etiologic role for rare copy number variants (CNVs) and suggests common genetic mechanisms. We performed cytogenomic array analysis in a discovery sample of patients with neurodevelopmental disorders referred for clinical testing. We detected a recurrent 1.4 Mb deletion at 17q12, which harbors HNF1B, the gene responsible for renal cysts and diabetes syndrome (RCAD), in 18/15,749 patients, including several with ASD, but 0/4,519 controls. We identified additional shared phenotypic features among nine patients available for clinical assessment, including macrocephaly, characteristic facial features, renal anomalies, and neurocognitive impairments. In a large follow-up sample, the same deletion was identified in 2/1,182 ASD/neurocognitive impairment and in 4/6,340 schizophrenia patients, but in 0/47,929 controls (corrected p = 7.37 × 10⁻5). These data demonstrate that deletion 17q12 is a recurrent, pathogenic CNV that confers a very high risk for ASD and schizophrenia and show that one or more of the 15 genes in the deleted interval is dosage sensitive and essential for normal brain development and function. In addition, the phenotypic features of patients with this CNV are consistent with a contiguous gene syndrome that extends beyond RCAD, which is caused by HNF1B mutations only.

Inherited 14q duplication and 21q deletion: a rare adjacent-2 segregation in multiple family members.

We present a family with multiple carriers of a subtle balanced translocation t(14;21)(q21.2;q21.2) and three patients with a resultant adjacent-2 malsegregation containing a +der(14)t(14;21)(q21.2;q21.2),-21 in their chromosome complement. The initial study was performed when a 2-month-old female was referred to genetics clinic for evaluation of developmental delay, growth retardation, and failure to thrive. Physical findings included prominent eyes, micrognathia, prominent and simple external ears, camptodactyly, contractures of the wrists, ankles, and hips, hypoplasia of the corpus callosum, prominent atria and occipital horns, cerebellopontine hypoplasia; and small atrial septal defect. High resolution chromosomes showed an extra band on the proximal 21q and fluorescence in situ hybridization (FISH) demonstrated only one signal for the centromere of 21. Karyotypes of the parents and grandparents revealed that the mother and maternal grandfather were carriers of a balanced translocation, and the propositus contained an unbalanced chromosome complement with partial duplication of proximal 14q and partial deletion of proximal 21q. Investigations performed on an institutionalized maternal aunt revealed identical karyotypic abnormalities as in the propositus. More recently, array comparative genomic hybridization (aCGH) on a subsequent child with multiple congenital anomalies further out in the extended family allowed for more accurate identification of the breakpoints. Our investigation includes analysis on a total of 11 family members spanning three generations. Among those investigated, there were no living members with other possible consequential unbalanced translocations or with adjacent-2 segregation resulting in -14,+der(21). Chromosome rearrangements require FISH and aCGH studies for accurate identification and elucidation of the abnormality and breakpoints.

Array-based comparative genomic hybridization analysis of 1176 consecutive clinical genetics investigations.

PURPOSE: Cytogenetic investigations are useful for etiologic determinations of mental retardation, developmental delay, multiple congenital anomalies, and pregnancy complications; however, the causes remain elusive in a majority of cases despite high-resolution cytogenetic studies and multiple fluorescence in situ hybridization examinations. Array-based comparative genomic hybridization has the ability to examine the genome at a higher resolution and may yield an increased detection of genetic abnormalities. The purpose of this study was to assess the use of array-based comparative genomic hybridization in a clinical genetics setting. METHODS: DNA from 1176 patients was analyzed using a bacterial artificial chromosome array-based comparative genomic hybridization platform. All abnormal cases were confirmed by fluorescence in situ hybridization and parental studies were completed when possible. RESULTS: Of the 1176 patients included in this survey, 163 showed a genomic imbalance identified by array-based comparative genomic hybridization. Of these 163 cases, 116 had a clinically relevant genetic abnormality. A total of 9.8% (116 of 1176 cases) were determined to exhibit a causative genomic imbalance. Twenty-five of the 116 abnormal cases had a previously identified cytogenetic abnormality yielding an increased detection rate of 7.9% (91 of 1146) in cases with normal or no cytogenetics. CONCLUSION: Array-based comparative genomic hybridization increases the overall abnormality detection rate, thus improving the diagnostic potential of clinical cytogenetics investigations.

9q34 rearrangements in BCR/ABL fusion-negative acute lymphoblastic leukemia.

The t(9;22)(q11.2;q34) translocation is found in a subset of acute lymphoblastic leukemia (ALL). The presence of this translocation involving the fusion of BCR/ABL genes represents a poor prognostic group. Because of the importance in detecting t(9;22) in ALL patients and because occasionally a cytogenetically cryptic BCR/ABL fusion is detected with fluorescence in situ hybridization (FISH), our laboratory routinely performs BCR/ABL FISH tests on all newly diagnosed ALL patients. In the past year, 25 consecutive, newly diagnosed, untreated ALL cases were analyzed. We report the cytogenetics and FISH findings of three cases containing a rearranged 9q34 region with an intact BCR (22q11.2) region and an absence of the BCR/ABL fusion. A split ABL signal representing a translocation of the 9q34 region with chromosome segments other than 22q11.2 (BCR) was observed in 3 cases. Two of these patients were 3 years old; one was 21 at the time of diagnosis. A split ABL FISH signal without the involvement of BCR does not represent a t(9;22) translocation, and prognostic implications of this apparent subgroup of ALL cases have not been determined. Cytogenetic, pathologic, and clinical aspects of these three cases are presented.

Cytogenetics and fluorescence in situ hybridization studies of diffuse large B-cell lymphoma in children and young adults.

Diffuse large B-cell lymphoma (DLBCL), the most common subtype of adult non-Hodgkin lymphoma (NHL), is infrequently seen in adolescents and is rare in children. Due to the infrequency of the disease, single institution-based cytogenetic and fluorescence in situ hybridization (FISH) studies of pediatric DLBCL have not been reported so far and, hence, the possible differences in pediatric and adult DLBCL have not been evaluated. We performed cytogenetic and FISH analyses of 7 pediatric and 5 young adult DLBCL cases referred to the University of Nebraska Medical Center. Karyotypic studies revealed numeric and structural chromosome abnormalities in all cases. Loss of chromosomes 2, 3, 4, 6, 12, 15, 16, and 17, and gain of 12, 18, and X were observed in more than 20% of the cases (#10878;3 cases). Sex chromosome abnormalities and cytogenetically unidentifiable chromosomes and/or segments were observed in 80% (10/12) of the cases. Recurrent breakpoints (observed in 3 or more cases) included 14q32 (IGH) and 17p13 (TP53), which clustered in the young adult group. The breakpoints 7q36, 9p24, 13q34, and 16q24 were noted in two cases each. We performed interphase FISH studies to verify the possible rearrangements of the breakpoints that are frequently implicated in adult DLBCL. Our results confirmed that the pediatric cases did not show rearrangements of 3q27 (BCL6), 14q32 (IGH), 18q21 (BCL2), 8q24 (CMYC), and 17p13 (TP53), except for one case with IGH;BCL2 dual fusion [t(14;18)(q32;q21)] and one with a 17p13 (TP53) deletion. Although 3q27 was noted to be rearranged by conventional cytogenetics in two young adult DLBCL cases, FISH investigations verified that BCL6 was not disrupted. The t(8;14)(q24;q32) with rearranged CMYC ascertained by FISH, was observed in a single young adult DLBCL case. These results highlight a distinctly different representation of cytogenetic abnormalities in pediatric versus adult DLBCL.

BCL2 translocation defines a unique tumor subset within the germinal center B-cell-like diffuse large B-cell lymphoma.

Gene expression profiling of diffuse large B-cell lymphoma (DLBCL) has revealed prognostically important subgroups: germinal center B-cell-like (GCB) DLBCL, activated B cell-like (ABC) DLBCL, and primary mediastinal large B-cell lymphoma. The t(14;18)(q32;q21) has been reported previously to define a unique subset within the GCB-DLBCL. We evaluated for the translocation in 141 cases of DLBCL that were successfully gene expression profiled. Using a dual-probe fluorescence in situ hybridization assay, we detected the t(14;18) in 17% of DLBCLs and in 34% of the GCB subgroup which contained the vast majority of positive cases. In addition, 12 t(14;18)-positive cases detected by polymerase chain reaction assays on additional samples were added to the fluorescence in situ hybridization-positive cases for subsequent analysis. Immunohistochemical data indicated that BCL2, BCL6, and CD10 protein were preferentially expressed in the t(14;18)-positive cases as compared to t(14;18)-negative cases. Within the GCB subgroup, the expression of BCL2 and CD10, but not BCL6, differed significantly between cases with or without the t(14;18): 88% versus 24% for BCL2 and 72% versus 32% for CD10, respectively. In the GCB-DLBCL subgroup, a heterogeneous group of genes is overexpressed in the t(14;18)-positive subset, among which BCL2 is a significant discriminator. Interestingly, the t(14;18)-negative subset is dominated by overexpression of cell cycle-associated genes, indicating that these tumors are significantly more proliferative, suggesting distinctive pathogenetic mechanisms. However, despite this higher proliferative activity, there was no significant difference in overall or failure-free survival between the t(14;18)-positive and -negative subsets within the GCB subgroup.

The t(14;18) defines a unique subset of diffuse large B-cell lymphoma with a germinal center B-cell gene expression profile.

Recently we have identified subgroups of de novo primary diffuse large B-cell lymphoma (DLBCL) based on complementary DNA microarray-generated gene expression profiles. To correlate the gene expression profiles with cytogenetic abnormalities in these DLBCLs, we examined the occurrence of the t(14;18)(q32;q21) in the 2 distinctive subgroups of DLBCL: one with the germinal center B-cell gene expression signature and the other with the activated B cell-like gene expression signature. The t(14;18) was detected in 7 of 35 cases (20%). All 7 t(14;18)-positive cases had a germinal center B-cell gene expression profile, representing 35% of the cases in this subgroup, and 6 of these 7 cases had very similar gene expression profiles. The expression of bcl-2 and bcl-6 proteins was not significantly different between the t(14;18)-positive and -negative cases, whereas CD10 was detected only in the group with the germinal center B-cell expression profile, and CD10 was most frequently expressed in the t(14;18)-positive cases. This study supports the validity of subdividing DLBCL into 2 major subgroups by gene expression profiling, with the t(14;18) being an important event in the pathogenesis of a subset of DLBCL arising from germinal center B cells. CD10 protein expression is useful in identifying cases of DLBCL with a germinal center B-cell gene expression profile and is often expressed in cases with the t(14;18).

Cytogenetic characterization of diffuse large cell lymphoma using multi-color fluorescence in situ hybridization.

We have employed multi-color fluorescence in situ hybridization (M-FISH) to characterize the cytogenetic changes in 20 diffuse large B-cell lymphomas (DLBCL), that contained complex and partially characterized karyotypes. The M-FISH analysis helped to delineate 94% of the unidentified abnormalities and assisted in redefining some unidentified/misidentified karyotypic changes. Recurrent breakpoints observed in approximately 20% cases included 14q32, 3p21, 3q27, 22q12, 1q25, and 18q21 (in decreasing order), and 1p22, 1q21, 4q31, 6q21, and 8q24 (in four cases each). Numerical gain of chromosomes 7, 9, 12, and X and loss of chromosomes 1, 4, 6, 17, and Y, were noted in approximately 20% of cases. The minimum deleted regions encompassed 6q21-q25, 1p22-p36, 1q32-q44, 2p23-p25, 4q31-q35, 13p13-q14, and 17p11-p13. Two cases presented with a sole structural abnormality, and one contained a der(17)t(9;17)(p21;p13), which has not been reported earlier as a sole abnormality in DLBCL. Upon completely characterizing the karyotypes, we observed with interesting that in 55% of the cases, more than one BCL gene bearing regions was involved in translocations. In the remaining 45%, where only one or none of the BCL gene regions was involved in a rearrangement, we observed the loss of chromosomes 6 and/or 17 or partial deletions of 6q and/or 17p or gain of 7 and/or 12. Our findings suggest that, although BCL2 and BCL6 are most often implicated in DLBCL, the possibility of the disruptions of BCL3, BCL8, BCL9, and BCL10 as a "primary event" in DLBCL cannot be ruled out. Most often, a combination of events may be necessary for the genesis of DLBCL or progression of follicular lymphoma to DLBCL. Overall, M-FISH has enhanced our ability to provide a comprehensive karyotypic analysis, and has helped in defining the importance of BCL3, BCL8, BCL9, and BCL10 carrying breakpoints in DLBCL.