scholarly journals Inherited unbalanced translocation (4p16.3p15.32 duplication/8p23.3p23.2deletion) in the four generation pedigree with intellectual disability/developmental delay

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Dongmei Hao ◽  
Yajuan Li ◽  
Lisha Chen ◽  
Xiliang Wang ◽  
Mengxing Wang ◽  
...  
Keyword(s):  
Mental Retardation ◽  
Intellectual Disability ◽  
Developmental Delay ◽  
Copy Number Variants ◽  
Snp Array ◽  
Normal Karyotype ◽  
Clinical Syndrome ◽  
Chromosome 8 ◽  
Fish Analysis ◽  
Balanced Translocation

AbstractChromosomal copy number variants (CNVs) are an important cause of congenital malformations and mental retardation. This study reported a large Chinese pedigree (4-generation, 76 members) with mental retardation caused by chromosome microduplication/microdeletion. There were 10 affected individuals with intellectual disability (ID), developmental delay (DD), and language delay phenotypes. SNP array analysis was performed in the proband and eight patients and found all of them had a microduplication of chromosome 4p16.3p15.2 and a microdeletion of chromosome 8p23.3p23.2. The high-resolution karyotyping analysis of the proband had unbalanced karyotype [46, XY, der(8)t(4;8)(p15.2;p23.1)mat], his mother had balanced karyotype [46, XX, t(4;8) (p15.2;p23.1)], whereas his father had normal karyotype [46,XY]. Fluorescence in situ hybridization (FISH) analysis further confirmed that the proband’s mother had a balanced translocation between the short arm terminal segment of chromosome 4 and the short arm end segment of chromosome 8, ish t(4;8)(8p + ,4q + ;4p + ,8q +). In conclusion, all the patients inherited chromosomes 8 with 4p16.3p15.2 duplication and 8p23.3p23.2 deletion from their parental balanced translocation, which might be the cause of the prevalence of intellectual disability. Meanwhile, 8p23.3p23.2 deletion, rather than 4p16.3p15.2 duplication might cause a more severe clinical syndrome.

Genomic Syndromes in Schizophrenia

2013 ◽  
pp. 247-255
Author(s):  
George Kirov ◽  
Michael C. O’Donovan ◽  
Michael J. Owen
Keyword(s):  
Intellectual Disability ◽  
Developmental Delay ◽  
Neurodevelopmental Disorders ◽  
Copy Number ◽  
De Novo ◽  
Copy Number Variants ◽  
Individual Risk ◽  
Genomic Deletions ◽  
Pathogenic Cnvs ◽  
Cognition And Learning

Several submicroscopic genomic deletions and duplications known as copy number variants (CNVs) have been reported to increase susceptibility to schizophrenia. Those for which the evidence is particularly strong include deletions at chromosomal segments 1q21.1, 3q29, 15q11.2, 15q13.3, 17q12 and 22q11.2, duplications at 15q11.2-q13.1, 16p13.1, and 16p11.2, and deletions atthe gene NRXN1. The effect of each on individual risk is relatively large, but it does not appear that any of them is alone sufficient to cause disorder in carriers. These CNVs often arise as new mutations(de novo). Analyses of genes enriched among schizophrenia implicated CNVs highlight the involvement in the disorder of post-synaptic processes relevant to glutamatergicsignalling, cognition and learning. CNVs that contribute to schizophrenia risk also contribute to other neurodevelopmental disorders, including intellectual disability, developmental delay and autism. As a result of selection, all known pathogenic CNVs are rare, and none makes a sizeable contribution to overall population risk of schizophrenia, although the study of these mutations is nevertheless providing important insights into the origins of the disorder.

High-Resolution SNP-Array Profiling of Chronic Lymphocytic Leukemia

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 50-50 ◽  
Author(s):  
Jennifer Edelmann ◽  
Karlheinz Holzmann ◽  
W.M. Michael Kühn ◽  
Lars Bullinger ◽  
Ina Radtke ◽  
...  
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Copy Number ◽  
Research Funding ◽  
Snp Array ◽  
Normal Karyotype ◽  
Lymphocytic Leukemia ◽  
Fish Analysis ◽  
Paired Data ◽  
New Genes ◽  
Genomic Aberrations

Abstract Abstract 50 Genomic aberrations are important prognostic factors in chronic lymphocytic leukemia (CLL) [Döhner et al., 2000]. However, known genomic aberrations fail to fully explain the biologic and clinical heterogeneity of the disease. We sought to precisely map copy number alterations (CNA) and copy number neutral losses of heterozygocity (LOH) to better characterize known recurrent aberrations and to identify new genetic lesions. We used Affymetrix 6.0 single nucleotide polymorphism (SNP) array analyses on CD19 sorted CLL cells. Data were analyzed using dChipSNP, a modified array normalization algorithm guided by cytogenetic abnormalities and a circular binary segmentation. We studied samples from 346 patients enrolled on the CLL8 trial of the German CLL Study Group. Data of 145 samples were analyzed against intraindividual reference DNA (paired), data of 201 samples against a pool of reference DNA (unpaired). FISH data were available for all samples, the distribution of genomic aberrations was as follows: del(13q14) in 59.8%, del(11q23) in 26.3%, trisomy 12 in 11.6%, and del(17p13) in 8.4%. IGHV was mutated in 32.9%, unmutated in 63.3%, and unknown in 3.8%. In total, 261 tumor-specific CNA could be discovered among the 145 paired samples. Genomic aberrations were found in 85.5% of these cases. The average number of aberrations per case was 1.8; according to the hierarchical model of genomic aberrations, it was 3.5 in del(17p), 2.4 in del(11q23), 1.7 in del(13q14) single, and 0.5 in normal karyotype CLL. The minimally deleted region (MDR) on 13q14 was 277.25 kb in size and contained mir15a and mir16, DLEU1 and DLEU2; RFP2 was not part of the MDR. Deletions on 13q were highly heterogeneous in size, ranging from 294 kb to 68 Mb. On 11q23 the MDR only contained ATM, the smallest lesion of 78.5 kb being intragenic; in two of theses cases, the deletion size was too small to be detected by FISH analysis. TP53 was affected in all del(17p13) cases except two; one tumor-specific deletion of 635.7 kb was detected in cytoband 17p13.2 harboring 30 genes and a second deletion of 780 kb in 17p13.3 containing – among 15 other genes – MNT, a tumor suppressor acting as an antagonist of MYC. A partial trisomy on chromosome 12 was not detected. Of the 261 CNA, 95 were located in genomic regions that are not evaluated by our routine FISH probe panel; 17 regions were affected recurrently: del(1p35.3) [2/145], del(1q23.3) [2/145], del(1q42.12) [2/145], +2p [5/145], del(3p21.31) [2/145], del(6p25.3) [3/145], +(6p25.3) [2/145], del(6q) [11/145], del(7q23.1) [2/145], +(8q24.21) [3/145], del(9q13-q21.13) [2/145], del(10q24) [2/145], del(14q24.3) [2/145], del(14q12.3) [2/145], del(15q15.1) [2/145], +18 [3/145] and +19 [7/145]. The frequency of these CNA was subsequently evaluated within the cohort of 201 (unpaired) samples. Five of 17 regions were affected in more than 2% in the whole cohort: +2p, del(6q), +8q24.21, del(15q15.1), and +19. Gain of 2p was found in 6.9% of cases, the minimally amplified region was 1.9 Mb in size and contained e.g. BCL11A and REL. Del(6q) was detected in 6,4%, the deletions were heterogeneous, an MDR could not be identified. 16 cases had 8q24.21 gains, the minimally amplified region was delineated by three intragenic gains in MYC. 14 cases had loss in 15q15.1 focussing on MGA, a potential suppressor of transcriptional activation by MYC. 8 cases had total or partial gains of chromosome 19, among those two overlapping partial gains with a minimally amplified region of 2.17 Mb in 19p13.2. Tumor-specific LOH were identified in 6.0% (9/145) located on 13q in three cases and in one case each on 17p, 12q, 11p, 1p, 3 and 22q. The LOH on chromosomes one and three overlapped with recurrent losses in 1p35.3 and 3p21.31. Essential members of the ATR-pathway were located in these regions: ATRIP and RPA2. However, mutational analyses of the two candidate genes in 48 cases revealed no mutations. SNP array analysis is a reliable tool to identify and further characterize genomic aberrations in CLL. MDR on 13q14 was delineated to a 277.25 kb segment affecting mir15a, mir16, DLEU1 and DLEU2 but not RFP2; the MDR on 11q23 to a segment only containing ATM. Cases with del(11q23) and del(17p) showed a higher genomic complexity than those with normal karyotype or del(13q14) as single abnormality. Relatively few novel genetic lesions were identified. Although occurring at low frequency, they may lead to the discovery of new genes involved in CLL pathogenesis. Disclosures: Stilgenbauer: Amgen: Research Funding; Bayer: Consultancy, Honoraria, Research Funding; Boehringer-Ingelheim: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Genzyme: Consultancy, Honoraria, Research Funding; GSK: Consultancy, Honoraria, Research Funding; Mundipharma: Consultancy, Honoraria, Research Funding; Roche: Consultancy, Honoraria, Research Funding; Sanofi Aventis: Research Funding.

Bone Marrow Failure with 13q Deletion: A Distinct Clinicopathological Entity with Immune Pathophysiology,

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 3420-3420
Author(s):  
Kohei Hosokawa ◽  
Takamasa Katagiri ◽  
Naomi Sugimori ◽  
Ken Ishiyama ◽  
Yumi Sasaki ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Conflicts Of Interest ◽  
Bone Marrow Failure ◽  
Survival Rates ◽  
Snp Array ◽  
Normal Karyotype ◽  
Genetic Alterations ◽  
Fish Analysis ◽  
Hematopoietic Stem ◽  
Who 2008

Abstract Abstract 3420 Background: Numerical karyotypic abnormalities such as −7/del(7q) and del(13q) are occasionally seen in patients with bone marrow (BM) failure who do not have typical signs of myelodysplasia. The WHO 2008 defined this subset of BM failure as MDS-U because of its likely association with a risk of evolving into leukemia, while the presence of isolated abnormalities including +8, del(20q), and -Y was not considered to be presumptive evidence of MDS. Previous studies showed that BM failure patients with del(13q) responded to immunosuppressive therapy (IST) and had a favorable prognosis (Ishiyama K et al, Br J Haematol; 117: 747. 2002; Sloand, JCO 2010). However, the clinical features of del(13q) BM failure remain unclear due to its low incidence as well as the frequently associated karyotypic abnormalities. Objectives/Methods: To characterize the clinicopathological features of patients with BM failure with del(13q), this study reviewed the clinical data of 1705 BM failure patients (733 with AA, 286 with MDS-RCUD, 149 with RCMD, 60 with MDS-U) whose blood was examined for the presence of glycosylphosphatidyl-inositol anchored protein (GPI-AP)-deficient granulocytes and erythrocytes from May 1999 through July 2010. Genomic DNA was isolated from the peripheral blood cells of 7 patients with 13q- and was subjected to SNP array-based genome-wide analysis for genetic alterations using GeneChip® 250K arrays to identify the gene locus that is commonly deleted as a result of 13q-. Results: The 13q- clone was found in 25 (1.5%) of the 1705 patients. All the 13q- patients were classified as MDS-U, due to the absence of significant dysplasia to fulfill the criteria for MDS defined by the WHO 2008 classification. BM was hypocellular in 17 patients and normocellular in 6. Seventeen patients had a clone with 13q- alone, while the remaining 8 patients had a clone with 13q- and other numerical abnormalities including –Y, +mar in 2, and −20, del(7q), +8, der(1;7) in 1. A significant increase in the percentage of GPI-AP- granulocytes was detected in 366 (50%) of 733 patients with AA and 115 (23%) of 495 patients with MDS. GPI-AP- cells were detected in all (100%) of the 17 patients with 13q- alone. On the other hand, the prevalence of increased GPI-AP− cells in patients with 13q- plus other abnormalities and in those with the normal karyotype was 38% (3/8) and 43% (405/937), respectively. Fifteen patients with 13q- alone were treated with IST (ATG + cyclosporine in 6 and cyclosporine ± anabolic steroid in 9) and all of them achieved either a PR or a CR, while in the patients with 13q- plus other abnormalities, the response rate to IST was 40%. A total of 106 patients with the normal karyotype were treated with ATG+CsA (48) or CsA±AS (58) and the response rates were 73% and 85%, respectively. None of the 17 13q- patients progressed to advanced MDS or AML during the follow-up period of 3 to 108 months (median: 52 months) while 2 of 8 patients with 13q- plus other abnormalities developed AML. The 5-year overall survival rates of the patients with 13q-, those with 13q- plus other abnormalities, and patients with a normal karyotype were 84%, 45%, and 91%, respectively. The percentage of 13q- clones increased in 5 patients, and decreased in 3 patients after successful IST. When GPI-AP- and GPI-AP+ granulocytes were subjected to a FISH analysis using a 13q probe (13q14.3), the 13q- clones were detected only in of GPI-AP+ granulocytes, suggesting that 13q- cells are derived from non-PIG-A mutant HSCs. SNP arrays identified 13q13.3 to 13q14.3 regions in all cases. Conclusions: MDS-U with 13q- is a benign BM failure syndrome characterized by a good response to IST and a markedly high prevalence of GPI-AP cells. Patients with this type of BM failure may be inappropriately treated with hypomethylating agents or hematopoietic stem cell transplantation from unrelated donors, which is associated with high therapy-related mortality. Therefore, del(13q) should be eliminated from the intermediate prognosis group defined by the IPSS, and BM failure with del(13q) should be managed as idiopathic AA. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Detection of pathogenic copy number variants in children with idiopathic intellectual disability using 500 K SNP array genomic hybridization

BMC Genomics ◽  
2009 ◽  
Vol 10 (1) ◽  
pp. 526 ◽  
Author(s):  
JM Friedman ◽  
Shelin Adam ◽  
Laura Arbour ◽  
Linlea Armstrong ◽  
Agnes Baross ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Copy Number ◽  
Copy Number Variants ◽  
Snp Array ◽  
Genomic Hybridization

scholarly journals Clinical, genetic, and molecular characterization of hyperphosphatasia with mental retardation: a case report and literature review

2019 ◽  
Vol 14 (1) ◽  
Author(s):  
Layal Abi Farraj ◽  
Wassim Daoud Khatoun ◽  
Naji Abou Chebel ◽  
Victor Wakim ◽  
Katia Dawali ◽  
...  
Keyword(s):  
Alkaline Phosphatase ◽  
Mental Retardation ◽  
Intellectual Disability ◽  
Developmental Delay ◽  
Novel Mutation ◽  
Blood Levels ◽  
Facial Dysmorphism ◽  
Loss Of Function ◽  
Clinical Genetic ◽  
Severe Intellectual Disability

Abstract Background Hyperphosphatasia with mental retardation syndrome (HPMRS) is a recessive disorder characterized by high blood levels of alkaline phosphatase together with typical dysmorphic signs such as cleft palate, intellectual disability, cardiac abnormalities, and developmental delay. Genes involved in the glycosylphosphatidylinositol pathway and known to be mutated in HPMRS have never been characterized in the Lebanese population. Case presentation Herein, we describe a pair of monozygotic twins presenting with severe intellectual disability, distinct facial dysmorphism, developmental delay, and increased alkaline phosphatase level. Two individuals underwent whole exome sequencing followed by Sanger sequencing to confirm the co-segregation of the mutation in the consanguineous family. A biallelic loss of function mutation in PGAP3 was detected. Both patients were homozygous for the c.203delC (p.C68LfsX88) mutation and the parents were carriers confirming the founder effect of the mutation. High ALP serum levels confirmed the molecular diagnosis. Conclusion Our findings have illustrated the genomic profile of PGAP3-related HPMRS which is essential for targeted molecular and genetic testing. Moreover, we found previously unreported clinical findings such as hypodontia and skin hyperpigmentation. These features, together with the novel mutation expand the phenotypic and genotypic spectrum of this rare recessive disorder.

Use of SNP-array-based karyotyping for cytogenetic prognostication in unclassified cases of myelodysplasia and associated overlap disorders

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. 7016-7016 ◽  
Author(s):  
B. Bhatnagar ◽  
R. V. Tiu ◽  
L. P. Gondek ◽  
C. O'Keefe ◽  
J. Huh ◽  
...  
Keyword(s):  
Chromosomal Abnormalities ◽  
Neutral Loss ◽  
Copy Number Variants ◽  
Snp Array ◽  
Normal Karyotype ◽  
Myeloproliferative Disorders ◽  
Categorical Variables ◽  
International Prognostic Scoring System ◽  
Exact Test ◽  
Chromosomal Defects

7016 Background: Myeloproliferative disorders (MPD) and myelodysplastic syndromes (MDS) often have overlapping features resulting in unclassifiable cases (MDS-U and MDS/MPD-U). Chromosomal abnormalities impact prognosis, but 50% of cases show normal karyotype by metaphase cytogenetics (MC). Single nucleotide polymorphism arrays (SNP-A) are novel karyotyping tools with superior resolution and ability to detect copy neutral loss of heterozygosity, a defect not detected by MC. Methods: MDS-U (N = 17) and MDS/MPD-U (N = 61) patients were selected from an MDS database (N = 720, median age = 76, median follow-up = 42 mos). SNP-A was performed on 67 patients and 751 controls. An algorithm for identification of somatic lesions was designed: 1) Lesions detected by MC and SNP-A required no further analysis; 2) Micro-duplications/ deletions overlapping with copy number variants (CNV) were excluded. Lesions not in CNV databases were confirmed by CD3 lymphocytes; 3) UPD <25 Mb were unlikely somatic and excluded. Telomeric and interstitial (≥ 25 Mb) UPD were considered somatic. International Prognostic Scoring System (IPSS) was used to assess routine risk. Fisher's exact test was used for categorical variables. Overall (OS) and event-free (EFS) survival defined by the MDS working group criteria were analyzed by Kaplan Meier analysis (log-rank or Wilcoxon and 2-sided significance). Results: SNP-A yielded superior detection rate for chromosomal defects compared to MC (71% vs 47%, p = 0.008). UPD was seen in 17 patients and frequently involved chromosomes 1, 3, 6, 8, 11, 17. MDS/MPD-U and MDS-U patients had similar OS and EFS (OS = 42 vs. 45 mos, p = 0.13; EFS = 42 vs. 45 mos p = 0.63). SNP-A revealed a more complex karyotype in patients with advanced MDS. Furthermore, SNP-A karyotyping resulted in prognostic refinement of previously assigned IPSS: Unclassified cases = 6% versus 0%, int-1 = 45% versus 53%, int-2 = 6% versus 19%, high = 5% versus 8%. Overall, patients with new SNP-A lesions had worse OS and EFS (OS = 41 mos vs NR, p = 0.07; EFS = 32 vs 112 mos, p = 0.07). Conclusions: SNP-A karyotyping complements MC in detecting chromosomal defects in MDS-U and MDS/MPD-U. This technology will be helpful in refining diagnosis based on characteristic recurrent chromosomal lesions including UPD. No significant financial relationships to disclose.

Chromosomal Abnormalities in the Early Stem Cell Population of CML Patients in Complete Cytogenetic Remission.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 36-36 ◽  
Author(s):  
Thomas G.P. Bumm ◽  
Amy Hanlon Newell ◽  
Jay Oost ◽  
Jonathan VanDyke ◽  
Susan B. Olson ◽  
...  
Keyword(s):  
Cell Population ◽  
Mononuclear Cells ◽  
Normal Karyotype ◽  
Cytogenetic Response ◽  
Chromosome 8 ◽  
Chromosome 7 ◽  
Stem Cell Population ◽  
Fish Analysis ◽  
Trisomy 8 ◽  
Cd 34

Abstract Clonal cytogenetic abnormalities, most commonly involving chromosomes 7 and 8, are detectable by conventional karyotyping in Ph-negative metaphases of some chronic myeloid leukemia (CML) patients with a major cytogenetic response (MCyR) to imatinib. It is unknown whether these abnormalities involve the primitive progenitor cell compartment, and whether their frequency in this compartment may exceed the frequency detected by karyotyping. To answer these questions we analyzed lineage-negative CD34+/CD38− and CD34+/CD38+ cells from CML patients in complete cytogenetic response (CCyR), using by fluorescent in situ hybridization (FISH) for chromosome 7 and 8 abnormalities and BCR-ABL. Methods: Mononuclear cells (MNC) were selected from the bone marrow of patients with CCR by Ficoll-Hypaque density gradient centrifugation and enriched for lineage-negative cells using an immunomagnetic column. Lineage-negative cells were further sorted into CD34+/38− and CD34+/38+ cells by multicolor FACS. Interphase FISH analysis was performed using 7 LSI D7S522 Spectrum Orange / CEP7 Spectrum Green (chromosome 7), CEP8 Spectrum Aqua (chromosome 8) and LSI BCR/ABL +9q34 TriColor Dual Fusion Probe. Thus far, 5 CML patients with CCR (3 with a normal karyotype and 2 with trisomy 8) and 1 normal control have been analyzed. Results: Of the three CML patients in CCR with normal karyotype, one had 9% deletion 7q (internal cut off of 0.5%) and the second 1.2% trisomy 8 (just over the internal cut off of 1%) cells in the CD-34+/38− population, while the CD-34+/38+ cell population did not show abnormalities. The third CCR patient had no abnormalities in the CD-34+/38− and CD-34+/38+ cell populations. Two CML patients in CCR with 45% trisomy 8 abnormal cells by conventional cytogenetics had 44% and 60% trisomy 8 positive cells in the CD34+/38+ population (two few CD34+/CD38− cells were available for analysis). No BCR-ABL signal was detected in any cell. In the healthy control, the CD34+/38+ cells were normal, but 4.1% of CD34+/38− showed a deletion of 7q. Conclusion: Clonal chromosomal of chromosomes 7 and 8 in Ph-negative primitive hematopoietic progenitor cells may be more common than suggested by conventional karyotyping. A larger cohort of CML patients in CCR and healthy individuals is under study to determine if this phenomenon is indeed related to CML or occurs also in normals. Results will have implications for the interpretation of karyotypes in patients with hematologic malignancies.

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