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Zhang S, Cui Q, Yang S, Zhang F, Li C, Wang X, Lei B, Sheng X. Exome and genome sequencing to unravel the precise breakpoints of partial trisomy 6q and partial Monosomy 2q. BMC Pediatr 2023; 23:586. [PMID: 37993819 PMCID: PMC10664609 DOI: 10.1186/s12887-023-04368-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/15/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND Patients with complex phenotypes and a chromosomal translocation are particularly challenging, since several potentially pathogenic mechanisms need to be investigated. CASE PRESENTATION Here, we combined exome and genome sequencing techniques to identify the precise breakpoints of heterozygous microduplications in the 6q25.3-q27 region and microdeletions in the 2q37.1-q37.3 region in a proband. The 5-year-old girl exhibited a severe form of congenital cranial dysinnervation disorder (CCDD) in addition to skeletal dysmorphism anomalies and severe intellectual disability. This is the second case affecting chromosomes 2q and 6q. The individual's karyotype showed an unbalanced translocation 46,XX,del(2)t(2;6)(q37.1;q25.3), which was inherited from her unaffected father [46,XY,t(2;6)(q37.1;q25.3)]. We also obtained the precise breakpoints of a de novo heterozygous copy number deletion [del(2)(q37.1q37.3)chr2:g.232963568_24305260del] and a copy number duplication [dup(6)(q25.3q27)chr6:g.158730978_170930050dup]. The parental origin of the observed balanced translocation was not clear because the parents declined genetic testing. CONCLUSION Patients with a 2q37 deletion and 6q25.3 duplication may exhibit severe significant neurological and skeletal dysmorphisms, and the utilization of exome and genome sequencing techniques has the potential to unveil the entire translocation of the CNV and the precise breakpoint.
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Affiliation(s)
- Shuang Zhang
- People's Hospital of Ningxia Hui Autonomous Region (Ningxia Medical University), Ningxia Eye Hospital, Yinchuan, 750001, China
| | - Qianwei Cui
- People's Hospital of Ningxia Hui Autonomous Region (Ningxia Medical University), Ningxia Eye Hospital, Yinchuan, 750001, China
| | - Shangying Yang
- People's Hospital of Ningxia Hui Autonomous Region (Ningxia Medical University), Ningxia Eye Hospital, Yinchuan, 750001, China
| | - Fangxia Zhang
- People's Hospital of Ningxia Hui Autonomous Region (Ningxia Medical University), Ningxia Eye Hospital, Yinchuan, 750001, China
| | - Chunxia Li
- People's Hospital of Ningxia Hui Autonomous Region (Ningxia Medical University), Ningxia Eye Hospital, Yinchuan, 750001, China
| | - Xiaoguang Wang
- People's Hospital of Ningxia Hui Autonomous Region (Ningxia Medical University), Ningxia Eye Hospital, Yinchuan, 750001, China
| | - Bo Lei
- Henan Eye Institute, Henan Eye Hospital, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan, 450003, China.
| | - Xunlun Sheng
- Gansu Aier Ophthalmology & Optometry Hospital, Lanzhou, 730030, China.
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Kluth M, Jung S, Habib O, Eshagzaiy M, Heinl A, Amschler N, Masser S, Mader M, Runte F, Barow P, Frogh S, Omari J, Möller-Koop C, Hube-Magg C, Weischenfeldt J, Korbel J, Steurer S, Krech T, Huland H, Graefen M, Minner S, Sauter G, Schlomm T, Simon R. Deletion lengthening at chromosomes 6q and 16q targets multiple tumor suppressor genes and is associated with an increasingly poor prognosis in prostate cancer. Oncotarget 2017; 8:108923-108935. [PMID: 29312579 PMCID: PMC5752492 DOI: 10.18632/oncotarget.22408] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/16/2017] [Indexed: 12/21/2022] Open
Abstract
Prostate cancer is characterized by recurrent deletions that can considerably vary in size. We hypothesized that large deletions develop from small deletions and that this “deletion lengthening” might have a “per se” carcinogenic role through a combinatorial effect of multiple down regulated genes. In vitro knockdown of 37 genes located inside the 6q12-q22 deletion region identified 4 genes with additive tumor suppressive effects, further supporting a role of the deletion size for cancer aggressiveness. Employing fluorescence in-situ hybridization analysis on prostate cancer tissue microarrays, we determined the deletion size at 6q and 16q in more than 3,000 tumors. 16q and 6q deletion length was strongly linked to poor clinical outcome and this effect was even stronger if the length of both deletions was combined. To study deletion lengthening in cancer progression we eventually analyzed the entire cancers from 317 patients for 6q and 16q deletion length heterogeneity and found that the deletion expanded within 50-60% of 6q and 16q deleted cancers. Taken together, these data suggest continuous “deletion lengthening” as a key mechanism for prostate cancer progression leading to parallel down regulation of genes with tumor suppressive properties, some of which act cooperatively.
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Affiliation(s)
- Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon Jung
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Omar Habib
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mina Eshagzaiy
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Heinl
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Amschler
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sawinee Masser
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Mader
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Frederic Runte
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philipp Barow
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sohall Frogh
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jazan Omari
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christina Möller-Koop
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joachim Weischenfeldt
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jan Korbel
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Krech
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Urology, Section for Translational Prostate Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Steurer S, Mayer PS, Adam M, Krohn A, Koop C, Ospina-Klinck D, Tehrani AA, Simon R, Tennstedt P, Graefen M, Wittmer C, Brors B, Plass C, Korbel J, Weischenfeldt J, Sauter G, Huland H, Tsourlakis MC, Minner S, Schlomm T. TMPRSS2-ERG fusions are strongly linked to young patient age in low-grade prostate cancer. Eur Urol 2014; 66:978-81. [PMID: 25015038 DOI: 10.1016/j.eururo.2014.06.027] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 06/17/2014] [Indexed: 11/18/2022]
Abstract
Based on next-generation sequencing of early-onset prostate cancer (PCa), we earlier demonstrated that PCa in young patients is prone to rearrangements involving androgen-regulated genes-such as transmembrane protease, serine 2 (TMPRSS2)-v-ets avian erythroblastosis virus E26 oncogene homolog (ERG) fusion-and provided data suggesting that this situation might be caused by increased androgen signaling in younger men. In the same study, an accumulation of chromosomal deletions was found in cancers of elderly patients. To determine how age-dependent molecular features relate to cancer phenotype, an existing data set of 11,152 PCas was expanded by additional fluorescence in situ hybridization analyses of phosphatase and tensin homolog (PTEN), 6q15 and 5q21. The results demonstrate that the decrease in TMPRSS2-ERG fusions with increasing patient age is limited to low-grade cancers (Gleason ≤3+4) and that the significant increase in the deletion frequency with age was strictly limited to ERG-negative cancers for 6q15 and 5q21 but to ERG-positive cancers for PTEN. These data suggest that the accumulation of non-androgen-linked genomic alterations with advanced patient age may require an appropriate microenvironment, such as a positive or negative ERG status. The strong link of ERG activation to young patient age and low-grade cancers may help to explain a slight predominance of low-grade cancers in young patients.
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Affiliation(s)
- Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pascale Sophia Mayer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Meike Adam
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Antje Krohn
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christina Koop
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel Ospina-Klinck
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ali Attarchi Tehrani
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pierre Tennstedt
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Graefen
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Corinna Wittmer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benedikt Brors
- Division of Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg, Germany
| | - Jan Korbel
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartwig Huland
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Sarah Minner
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Bigdeli TB, Maher BS, Zhao Z, Sun J, Medeiros H, Akula N, McMahon FJ, Carvalho C, Ferreira SR, Azevedo MH, Knowles JA, Pato MT, Pato CN, Fanous AH. Association study of 83 candidate genes for bipolar disorder in chromosome 6q selected using an evidence-based prioritization algorithm. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:898-906. [PMID: 24123842 DOI: 10.1002/ajmg.b.32200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 08/13/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Prior genome-scans of bipolar disorder have revealed chromosome 6q22 as a promising candidate region. However, linkage disequilibrium (LD) mapping studies have yet to identify replicated susceptibility loci. METHODS We analyzed 1,422 LD-tagging single nucleotide polymorphisms (SNPs) in 83 genes to test single-marker and locus-wide evidence of association with bipolar disorder in the NIMH Genetics Initiative bipolar pedigrees and the Portuguese Island Collection (PIC) (N = 1,093 in 528 informative pairs). Both studies previously demonstrated significant evidence of linkage to 6q. SNPs were genotyped using an Illumina iSelect genotyping array which employs the Infinium assay. Evidence of single-marker association was assessed using the generalized disequilibrium test (GDT). Empirical estimates of gene-wide significance were obtained by permutation (via 100,000 gene-dropping simulations) of Fisher's combined test of P-values for each locus. RESULTS No single variant yielded significant experiment-wide evidence of association, for either the combined sample or in each subsample. Our gene-dropping simulations identified nominally significant gene-wide associations with multiple loci, of which NT5DC1 in the NIMH subsample and CCNC in the PIC were the strongest candidates. However, no one gene consistently exceeded empirical significance criteria in both independent samples or survived Bonferroni correction for the number of genes tested. CONCLUSIONS Using a gene-based approach to family-based association, we identified gene-wide associations with several genes, though no single locus was significantly associated with bipolar disorder in both cohorts. This suggests that chromosome 6q may harbor multiple susceptibility loci or that complex patterns of LD in this region may confound approaches based on common SNPs. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- T Bernard Bigdeli
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, Virginia
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5
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Fan J, Ionita-Laza I, McQueen MB, Devlin B, Purcell S, Faraone SV, Allen MH, Bowden CL, Calabrese JR, Fossey MD, Friedman ES, Gyulai L, Hauser P, Ketter TB, Marangell LB, Miklowitz DJ, Nierenberg AA, Patel JK, Sachs GS, Thase ME, Molay FB, Escamilla MA, Nimgaonkar VL, Sklar P, Laird NM, Smoller JW. Linkage disequilibrium mapping of the chromosome 6q21-22.31 bipolar I disorder susceptibility locus. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:29-37. [PMID: 19308960 PMCID: PMC4067321 DOI: 10.1002/ajmg.b.30942] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We previously reported genome-wide significant evidence for linkage between chromosome 6q and bipolar I disorder (BPI) by performing a meta-analysis of original genotype data from 11 genome scan linkage studies. We now present follow-up linkage disequilibrium mapping of the linked region utilizing 3,047 single nucleotide polymorphism (SNP) markers in a case-control sample (N = 530 cases, 534 controls) and family-based sample (N = 256 nuclear families, 1,301 individuals). The strongest single SNP result (rs6938431, P = 6.72 x 10(-5)) was observed in the case-control sample, near the solute carrier family 22, member 16 gene (SLC22A16). In a replication study, we genotyped 151 SNPs in an independent sample (N = 622 cases, 1,181 controls) and observed further evidence of association between variants at SLC22A16 and BPI. Although consistent evidence of association with any single variant was not seen across samples, SNP-wise and gene-based test results in the three samples provided convergent evidence for association with SLC22A16, a carnitine transporter, implicating this gene as a novel candidate for BPI risk. Further studies in larger samples are warranted to clarify which, if any, genes in the 6q region confer risk for bipolar disorder.
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Affiliation(s)
- Jinbo Fan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Boston, Massachusetts
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Matthew B. McQueen
- Department of Psychology, Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, Colorado
| | - Bernie Devlin
- Department of Psychiatry and Human Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Shaun Purcell
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Boston, Massachusetts,Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts,Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts
| | - Stephen V. Faraone
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, New York
| | - Michael H. Allen
- Department of Psychiatry, University of Colorado Denver, Denver, Colorado
| | - Charles L. Bowden
- Department of Psychiatry, University of Texas Health Science Center, San Antonio, Texas
| | - Joseph R. Calabrese
- Department of Psychiatry, University Hospitals Case Medical Center, Case Western Reserve University, Cleveland, Ohio
| | - Mark D. Fossey
- Department of Psychiatry, University of Oklahoma College of Medicine-Tulsa and Laureate Psychiatric Clinic and Hospital, Tulsa, Oklahoma
| | - Edward S. Friedman
- Department of Psychiatry and Human Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Laszlo Gyulai
- Department of Psychiatry, University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | | | - Terence B. Ketter
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, California
| | - Lauren B. Marangell
- Eli Lilly and Company, Indianapolis, Indiana (work conducted at Baylor College of Medicine and not necessarily reflecting the views of Eli Lilly)
| | | | | | - Jayendra K. Patel
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Gary S. Sachs
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael E. Thase
- Department of Psychiatry, University of Pennsylvania Health System, Philadelphia, Pennsylvania
| | - Francine B. Molay
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts
| | - Michael A. Escamilla
- Department of Psychiatry, University of Texas Health Science Center, San Antonio, Texas,Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
| | - Vishwajit L. Nimgaonkar
- Department of Psychiatry and Human Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Pamela Sklar
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Boston, Massachusetts,Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts,Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts
| | - Nan M. Laird
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Jordan W. Smoller
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Boston, Massachusetts,Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts,Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts,Correspondence to: Jordan W. Smoller, M.D., Sc.D., Simches Research Building, 185, Cambridge St., 2nd Floor, Boston, MA 02114,
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