GM01416

GM01416 LCL from B-Lymphocyte

Description:

XXXX SYNDROME
ANEUPLOID CHROMOSOME NUMBER - NON-TRISOMIC
COPY NUMBER VARIATION (CNV) REFERENCE PANEL

Affected:

No Data

Sex:

Female

Age:

27 YR (At Sampling)

Overview

Repository

NIGMS Human Genetic Cell Repository

Subcollection

Chromosome Abnormalities
dbGaP

Biopsy Source

Peripheral vein

Cell Type

B-Lymphocyte

Tissue Type

Blood

Transformant

Epstein-Barr Virus

Sample Source

LCL from B-Lymphocyte

Race

White

Family Member

Relation to Proband

proband

Confirmation

Clinical summary/Case history

ISCN

48,XXXX

Species

Homo sapiens

Common Name

Human

Remarks

Developmental delay; moderate retardation; delayed language development; abnormal dermatoglyphics; bilateral epicanthal folds; small mandible; bilateral dermato-lipomas; lens opacities; high arched palate; mildly hypotonic; normal menses; see GM01415E Fibroblast.

Characterizations

IDENTIFICATION OF SPECIES OF ORIGIN

Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis and by Chromosome Analysis

CNVPANEL

For more information click here:CNVPANEL01

Phenotypic Data

Remarks

Publications

Nyaga DM, Tsai P, Gebbie C, Phua HH, Yap P, Le Quesne Stabej P, Farrow S, Rong J, Toldi G, Thorstensen E, Stark Z, Lunke S, Gamet K, Van Dyk J, Greenslade M, O'Sullivan JM, Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand NPJ genomic medicine9:57 2024

PubMed ID: 39516456

Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A, Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation Human molecular genetics9:57 2021

PubMed ID: 35394024

Tang Z, Berlin DS, Toji L, Toruner GA, Beiswanger C, Kulkarni S, Martin CL, Emanuel BS, Christman M, Gerry NP, A dynamic database of microarray-characterized cell lines with various cytogenetic and genomic backgrounds G3 (Bethesda, Md)3:1143-9 2013

PubMed ID: 23665875

Yim SH, Chung YJ, Jin EH, Shim SC, Kim JY, Kim YS, Hu HJ, Shin SH, Pae HO, Zouali M, Chung HT, The potential role of VPREB1 gene copy number variation in susceptibility to rheumatoid arthritis Molecular immunology48:1338-43 2010

PubMed ID: 21144590

Weaver S, Dube S, Mir A, Qin J, Sun G, Ramakrishnan R, Jones RC, Livak KJ, Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution Methods (San Diego, Calif)50:271-6 2009

PubMed ID: 20079846

Isaksson M, Stenberg J, Dahl F, Thuresson AC, Bondeson ML, Nilsson M, MLGA--a rapid and cost-efficient assay for gene copy-number analysis Nucleic acids research35:e115 2007

PubMed ID: 17823203

Ji H, Kumm J, Zhang M, Farnam K, Salari K, Faham M, Ford JM, Davis RW, Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma Cancer research66:7910-9 2006

PubMed ID: 16912164

Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL, High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping Genome research16:1136-48 2006

PubMed ID: 16899659

Lieu PT, Jozsi P, Gilles P, Peterson T, Development of a DNA-labeling system for array-based comparative genomic hybridization Journal of biomolecular techniques : JBT16:104-11 2005

PubMed ID: 16030317

Wang Y, Moorhead M, Karlin-Neumann G, Falkowski M, Chen C, Siddiqui F, Davis RW, Willis TD, Faham M, Allele quantification using molecular inversion probes (MIP) Nucleic acids research33:e183 2005

PubMed ID: 16314297

Bignell GR, Huang J, Greshock J, Watt S, Butler A, West S, Grigorova M, Jones KW, Wei W, Stratton MR, Futreal PA, Weber B, Shapero MH, Wooster R, High-resolution analysis of DNA copy number using oligonucleotide microarrays. Genome Res14(2):287-95 2004

PubMed ID: 14762065

Omran H, Haffner K, Burth S, Fernandez C, Fargier B, Villaquiran A, Nothwang HG, Schnittger S, Lehrach H, Woo D, Brandis M, Sudbrak R, Hildebrandt F, Human adolescent nephronophthisis: gene locus synteny with polycystic kidney disease in pcy mice. J Am Soc Nephrol12(1):107-13 2001

PubMed ID: 11134256

Esposito T, Gianfrancesco F, Ciccodicola A, Montanini L, Mumm S, D'Urso M, Forabosco A, A novel pseudoautosomal human gene encodes a putative protein similar to Ac-like transposases. Hum Mol Genet8(1):61-7 1999

PubMed ID: 9887332

Gianfrancesco F, Esposito T, Montanini L, Ciccodicola A, Mumm S, Mazzarella R, Rao E, Giglio S, Rappold G, Forabosco A, A novel pseudoautosomal gene encoding a putative GTP-binding protein resides in the vicinity of the Xp/Yp telomere. Hum Mol Genet7:407-14 1998

PubMed ID: 9466997

Potier M, Dutriaux A, Orti R, Groet J, Gibelin N, Karadima G, Lutfalla G, Lynn A, Van Broeckhoven C, Chakravarti A, Petersen M, Nizetic D, Delabar J, Rossier J, Two sequence-ready contigs spanning the two copies of a 200-kb duplication on human 21q: partial sequence and polymorphisms. Genomics51:417-26 1998

PubMed ID: 9721212

Yoshikawa H, Fujiyama A, Nakai K, Inazawa J, Matsubara K, Detection and isolation of a novel human gene located on Xp11.2-p11.4 that escapes X-inactivation using a two-dimensional DNA mapping method. Genomics49:237-46 1998

PubMed ID: 9598311

Stranick KS, Zambas DN, Uss AS, Egan RW, Billah MM, Umland SP, Identification of transcription factor binding sites important in the regulation of the human interleukin-5 gene. J Biol Chem272:16453-65 1997

PubMed ID: 9195954

D'Esposito M, Ciccodicola A, Gianfrancesco F, Esposito T, Flagiello L, Mazzarella R, Schlessinger D, D'Urso M, A synaptobrevin-like gene in the Xq28 pseudoautosomal region undergoes X inactivation. Nat Genet13:227-9 1996

PubMed ID: 8640232

Hewitt JE, Lyle R, Clark LN, Valleley EM, Wright TJ, Wijmenga C, van Deutekom JC, Francis F, Sharpe PT, Hofker M, et al, Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular dystrophy. Hum Mol Genet3:1287-95 1994

PubMed ID: 7987304

Janne PA, Dutra AS, Dracopoli NC, Charnas LR, Puck JM, Nussbaum RL, Localization of the 75-kDa inositol polyphosphate-5-phosphatase (INPP5B) to human chromosome band 1p34. Cytogenet Cell Genet66:164-6 1994

PubMed ID: 8125013

Kvaloy K, Galvagni F, Brown WR, The sequence organization of the long arm pseudoautosomal region of the human sex chromosomes. Hum Mol Genet3:771-8 1994

PubMed ID: 8081364

Wang Q, Ishikawa-Brush Y, Monaco AP, Nelson DL, Caskey CT, Pauly SP, Lenoir GM, Sylla BS, Physical mapping of Xq24-25 around loci closely linked to the X-linked lymphoproliferative syndrome locus: an overlapping YAC map and linkage between DXS12, DXS42, and DXS37. Eur J Hum Genet1:64-71 1993

PubMed ID: 8069652

Ward JR, Cottrell S, Thomas HJ, Jones TA, Howe CM, Hampton GM, Deaven L, Sheer D, Bodmer WF, Solomon E, et al, A long-range restriction map of human chromosome 5q21-q23. Genomics17:15-24 1993

PubMed ID: 8104865

Carlock L, Wisniewski D, Lorincz M, Pandrangi A, Vo T, An estimate of the number of genes in the Huntington disease gene region and the identification of 13 transcripts in the 4p16.3 segment. Genomics13:1108-18 1992

PubMed ID: 1387107

Ragoussis J, Senger G, Trowsdale J, Campbell IG, Genomic organization of the human folate receptor genes on chromosome 11q13. Genomics14:423-30 1992

PubMed ID: 1330883

Bell MV, Hirst MC, Nakahori Y, MacKinnon RN, Roche A, Flint TJ, Jacobs PA, Tommerup N, Tranebjaerg L, Froster-Iskenius U, et al, Physical mapping across the fragile X: hypermethylation and clinical expression of the fragile X syndrome. Cell64:861-6 1991

PubMed ID: 1997211

Dietrich A, Kioschis P, Monaco AP, Gross B, Korn B, Williams SV, Sheer D, Heitz D, Oberle I, Toniolo D, et al, Molecular cloning and analysis of the fragile X region in man. Nucleic Acids Res19:2567-72 1991

PubMed ID: 2041732

Bates GP, MacDonald ME, Baxendale S, Sedlacek Z, Youngman S, Romano D, Whaley WL, Allitto BA, Poustka A, Gusella JF, et al, A yeast artificial chromosome telomere clone spanning a possible location of the Huntington disease gene. Am J Hum Genet46:762-75 1990

PubMed ID: 2138410

Brown WR, MacKinnon PJ, Villasante A, Spurr N, Buckle VJ, Dobson MJ, Structure and polymorphism of human telomere-associated DNA. Cell63:119-32 1990

PubMed ID: 2208276

Fisher EM, Beer-Romero P, Brown LG, Ridley A, McNeil JA, Lawrence JB, Willard HF, Bieber FR, Page DC, Homologous ribosomal protein genes on the human X and Y chromosomes: escape from X inactivation and possible implications for Turner syndrome. Cell63:1205-18 1990

PubMed ID: 2124517

Malaspina P, Persichetti F, Novelletto A, Iodice C, Terrenato L, Wolfe J, Ferraro M, Prantera G, The human Y chromosome shows a low level of DNA polymorphism. Ann Hum Genet54 ( Pt 4):297-305 1990

PubMed ID: 1980996

Palmer MS, Berta P, Sinclair AH, Pym B, Goodfellow PN, Comparison of human ZFY and ZFX transcripts. Proc Natl Acad Sci U S A87:1681-5 1990

PubMed ID: 2308929

Brown RM, Dahl HH, Brown GK, X-chromosome localization of the functional gene for the E1 alpha subunit of the human pyruvate dehydrogenase complex. Genomics4:174-81 1989

PubMed ID: 2737678

Merry DE, Lesko JG, Sosnoski DM, Lewis RA, Lubinsky M, Trask B, van den Engh G, Collins FS, Nussbaum RL, Choroideremia and deafness with stapes fixation: a contiguous gene deletion syndrome in Xq21. Am J Hum Genet45:530-40 1989

PubMed ID: 2491012

Cariello NF, Scott JK, Kat AG, Thilly WG, Keohavong P, Resolution of a missense mutant in human genomic DNA by denaturing gradient gel electrophoresis and direct sequencing using in vitro DNA amplification: HPRT Munich. Am J Hum Genet42:726-34 1988

PubMed ID: 3358423

Lubahn DB, Joseph DR, Sullivan PM, Willard HF, French FS, Wilson EM, Cloning of human androgen receptor complementary DNA and localization to the X chromosome. Science240:327-30 1988

PubMed ID: 3353727

Reilly DS, Lewis RA, Ledbetter DH, Nussbaum RL, Tightly linked flanking markers for the Lowe oculocerebrorenal syndrome, with application to carrier assessment. Am J Hum Genet42:748-55 1988

PubMed ID: 2895982

Wiles MV, Alexander CM, Goodfellow PN, Isolation of an abundantly expressed sequence from the human X chromosome by differential screening. Somat Cell Mol Genet14:31-9 1988

PubMed ID: 2829364

Ballabio A, Parenti G, Carrozzo R, Sebastio G, Andria G, Buckle V, Fraser N, Craig I, Rocchi M, Romeo G, et al, Isolation and characterization of a steroid sulfatase cDNA clone: genomic deletions in patients with X-chromosome-linked ichthyosis. Proc Natl Acad Sci U S A84:4519-23 1987

PubMed ID: 3474618

Buckle VJ, Boyd Y, Fraser N, Goodfellow PN, Goodfellow PJ, Wolfe J, Craig IW, Localisation of Y chromosome sequences in normal and 'XX' males. J Med Genet24:197-203 1987

PubMed ID: 3035183

Nussbaum RL, Lesko JG, Lewis RA, Ledbetter SA, Ledbetter DH, Isolation of anonymous DNA sequences from within a submicroscopic X chromosomal deletion in a patient with choroideremia, deafness, and mental retardation. Proc Natl Acad Sci U S A84:6521-5 1987

PubMed ID: 3476958

Cate RL, Mattaliano RJ, Hession C, Tizard R, Farber NM, Cheung A, Ninfa EG, Frey AZ, Gash DJ, Chow EP, et al, Isolation of the bovine and human genes for Mullerian inhibiting substance and expression of the human gene in animal cells. Cell45:685-98 1986

PubMed ID: 3754790

Darling SM, Banting GS, Pym B, Wolfe J, Goodfellow PN, Cloning an expressed gene shared by the human sex chromosomes. Proc Natl Acad Sci U S A83:135-9 1986

PubMed ID: 2934738

Nussbaum RL, Boggs BA, Beaudet AL, Doyle S, Potter JL, O'Brien WE, New mutation and prenatal diagnosis in ornithine transcarbamylase deficiency. Am J Hum Genet38:149-58 1986

PubMed ID: 3004207

Oberle I, Camerino G, Kloepfer C, Moisan JP, Grzeschik KH, Hellkuhl B, Hors-Cayla MC, Van Cong N, Weil D, Mandel JL, Characterization of a set of X-linked sequences and of a panel of somatic cell hybrids useful for the regional mapping of the human X chromosome. Hum Genet72:43-9 1986

PubMed ID: 3002952

Riddell DC, Wang HS, Beckett J, Chan A, Holden JJ, Mulligan LM, Phillips MA, Simpson NE, Wrogemann K, Hamerton JL, et al, Regional localization of 18 human X-linked DNA sequences. Cytogenet Cell Genet42:123-8 1986

PubMed ID: 3460742

Riley DE, Goldman MA, Gartler SM, Chromatin structure of active and inactive human X-linked phosphoglycerate kinase gene. Somat Cell Mol Genet12:73-80 1986

PubMed ID: 3456175

Riley DE, Reeves R, Gartler SM, Xrep, a plasmid-stimulating X chromosomal sequence bearing similarities to the BK virus replication origin and viral enhancers. Nucleic Acids Res14:9407-23 1986

PubMed ID: 3025813

Buckle V, Mondello C, Darling S, Craig IW, Goodfellow PN, Homologous expressed genes in the human sex chromosome pairing region. Nature317:739-41 1985

PubMed ID: 4058580

Koenig M, Moisan JP, Heilig R, Mandel JL, Homologies between X and Y chromosomes detected by DNA probes: localisation and evolution. Nucleic Acids Res13:5485-501 1985

PubMed ID: 2994000

Michelson AM, Blake CC, Evans ST, Orkin SH, Structure of the human phosphoglycerate kinase gene and the intron- mediated evolution and dispersal of the nucleotide-binding domain. Proc Natl Acad Sci U S A82:6965-9 1985

PubMed ID: 2995995

Rees DJ, Rizza CR, Brownlee GG, Haemophilia B caused by a point mutation in a donor splice junction of the human factor IX gene. Nature316:643-5 1985

PubMed ID: 4033760

Hutz MH, Michelson AM, Antonarakis SE, Orkin SH, Kazazian HH Jr, Restriction site polymorphism in the phosphoglycerate kinase gene on the X chromosome. Hum Genet66:217-9 1984

PubMed ID: 6325324

Patel PI, Nussbaum RL, gramson PE, Ledbetter DH, Caskey CT, Chinault AC, Organization of the HPRT gene and related sequences in the human genome. Somat Cell Mol Genet10:483-93 1984

PubMed ID: 6089358

Nussbaum RL, Crowder WE, Nyhan WL, Caskey CT, A three-allele restriction-fragment-length polymorphism at the hypoxanthine phosphoribosyltransferase locus in man. Proc Natl Acad Sci U S A80:4035-9 1983

PubMed ID: 6306659

Krumlauf R, Jeanpierre M, Young BD, Construction and characterization of genomic libraries from specific human chromosomes. Proc Natl Acad Sci U S A79:2971-5 1982

PubMed ID: 6953442

Davies KE, Young BD, Elles RG, Hill ME, Williamson R, Cloning of a representative genomic library of the human X chromosome after sorting by flow cytometry. Nature293:374-6 1981

PubMed ID: 6456416