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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jul 12, 2011 |
Title |
Genomic profiling in Down syndrome pediatric acute lymphoblastic leukemia |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by array Methylation profiling by array SNP genotyping by SNP array Genome variation profiling by SNP array
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Summary |
Patients with Down syndrome (DS) and acute lymphoblastic leukemia (ALL) have distinct clinical and biological features. Whereas most DS-ALL cases lack the sentinel cytogenetic lesions that guide risk assignment in childhood ALL, JAK2 mutations and CRLF2 overexpression are highly enriched. To further characterize the unique biology of DS-ALL, we performed genome-wide profiling of 58 DS-ALL and 35 non-Down syndrome (NDS) ALL cases by DNA copy number, loss of heterozygosity, gene expression, and methylation analyses. We report novel deletions within the 6p22 histone gene cluster as significantly more frequent in DS-ALL, occurring in 12 DS (24%) and only a single NDS case (3%) (Fisher’s exact p = 0.013). Homozygous deletions yielded significantly lower histone expression levels, and were associated with higher methylation levels, distinct spatial localization of methylated promoters, and enrichment of highly methylated genes for specific pathways and transcription factor binding motifs. Gene expression profiling identified CRLF2 overexpression in nearly half DS-ALL cases, and supervised analysis identified an associated 39-gene signature. However, no expression signature was identified for DS-ALL overall, nor for histone status, suggesting that DS-ALL constitutes several, heterogeneous molecular entities. Characterization of pathways associated with histone deletions and high CRLF2 expression may identify opportunities for novel targeted interventions.
This SuperSeries is composed of the SubSeries listed below.
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Overall design |
Refer to individual Series.
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Contributor(s) |
Rabin KR, Loudin MG, Wang J, Leung HE, Gurusiddappa S, Meyer J, Condos G, Morrison D, Tsimelzon A, Devidas M, Heerema NA, Carroll AJ, Plon SE, Hunger SP, Basso G, Pession A, Bhojwani D, Carroll WL |
Citation(s) |
21647151 |
Submission date |
Mar 27, 2010 |
Last update date |
Mar 25, 2019 |
Contact name |
Hon-chiu Eastwood Leung |
E-mail(s) |
exleung@txccc.org
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Phone |
832-824-4373
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Fax |
832-825-4038
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URL |
http://www.txccc.org/content.cfm?content_id=1405
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Organization name |
Baylor College of Medicine
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Department |
Pediatrics
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Lab |
Genomics and Proteomics Core Laboratory
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Street address |
1102 Bates Street Room C1030.09
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City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030 |
Country |
USA |
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Platforms (3) |
GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
GPL6986 |
Illumina HumanCNV370-Duov1 DNA Analysis BeadChip (HumanCNV370v1) |
GPL8490 |
Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2) |
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Samples (233)
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GSM521939 |
ALL_DS_506 |
GSM521940 |
ALL_DS_542 |
GSM521941 |
ALL_NDS_655 |
GSM521942 |
ALL_DS_92 |
GSM521943 |
ALL_DS_D13 |
GSM521944 |
ALL_DS_D17 |
GSM521945 |
DS_D18 |
GSM521946 |
ALL_DS_D23 |
GSM521947 |
ALL_DS_D26 |
GSM521948 |
DS_D27 |
GSM521949 |
ALL_DS_D45 |
GSM521950 |
ALL_NDS_N1 |
GSM521951 |
ALL_NDS_N10 |
GSM521952 |
NDS_N2 |
GSM521953 |
ALL_NDS_N23 |
GSM521954 |
ALL_NDS_N27 |
GSM521955 |
ALL_NDS_N57 |
GSM521956 |
NDS_N58 |
GSM521957 |
ALL_NDS_N59 |
GSM521958 |
NDS_N9 |
GSM523115 |
ALL_DS, K1 011409 |
GSM523116 |
ALL_DS, K12 012109 |
GSM523117 |
ALL_NDS, K13 011609 |
GSM523118 |
ALL_DS, K15 011509 |
GSM523119 |
ALL_DS, K16 011409 |
GSM523120 |
ALL_DS, K17 011409 |
GSM523121 |
ALL_DS, K18 011409 |
GSM523122 |
ALL_DS, K19 011409 |
GSM523123 |
ALL_DS, K2 011609 |
GSM523124 |
ALL_DS, K21 011509 |
GSM523125 |
ALL_DS, K23 011409 |
GSM523126 |
ALL_DS, K24 011609 |
GSM523127 |
ALL_DS, K25 011509 |
GSM523128 |
ALL_DS, K26 011609 |
GSM523129 |
ALL_DS, K28 011409 |
GSM523130 |
ALL_DS, K29 011509 |
GSM523131 |
ALL_DS, K3 012109 |
GSM523132 |
ALL_DS, K30 012109 |
GSM523133 |
ALL_DS, K31 012109 |
GSM523134 |
ALL_NDS, K32 011609 |
GSM523135 |
ALL_NDS, K33 011609 |
GSM523136 |
ALL_NDS, K34 011409 |
GSM523137 |
ALL_NDS, K35 011409 |
GSM523138 |
ALL_NDS, K36 011609 |
GSM523139 |
ALL_NDS, K37 011609 |
GSM523140 |
ALL_NDS, K38 011409 |
GSM523141 |
ALL_NDS, K39 011509 |
GSM523142 |
ALL_DS, K4 011509 |
GSM523143 |
ALL_NDS, K40 012109 |
GSM523144 |
ALL_NDS, K41 011509 |
GSM523145 |
ALL_NDS, K42 011509 |
GSM523146 |
ALL_NDS, K43 012109 |
GSM523147 |
ALL_NDS, K48 011409 |
GSM523148 |
ALL_NDS, K49 011509 |
GSM523149 |
ALL_DS, K5 012109 |
GSM523150 |
ALL_NDS, K50 011409 |
GSM523151 |
ALL_NDS, K51 011509 |
GSM523152 |
ALL_NDS, K52 011609 |
GSM523153 |
ALL_NDS, K54 011509 |
GSM523154 |
ALL_NDS, K55 012109 |
GSM523155 |
ALL_DS, K56 011409 |
GSM523156 |
ALL_DS, K57 011509 |
GSM523157 |
ALL_NDS, K58 011509 |
GSM523158 |
ALL_NDS, K59 011509 |
GSM523159 |
ALL_DS, K6 011509 |
GSM523160 |
ALL_NDS, K60 011409 |
GSM523161 |
ALL_NDS, K61 011509 |
GSM523162 |
ALL_NDS, K62 011409 |
GSM523163 |
ALL_NDS, K63 011409 |
GSM527317 |
DS ALL (4064204001_A) |
GSM527318 |
DS ALL (4064204001_B) |
GSM527319 |
nl (4064204003_A) |
GSM527320 |
nl (4064204003_B) |
GSM527321 |
DS ALL (4064204012_A) |
GSM527322 |
DS ALL (4064204012_B) |
GSM527323 |
DS (4064204013_A) |
GSM527324 |
DS (4064204013_B) |
GSM527325 |
NDS ALL (4064204014_A) |
GSM527326 |
DS ALL (4064204014_B) |
GSM527332 |
DS ALL (4064204015_A) |
GSM527333 |
DS ALL (4064204015_B) |
GSM527334 |
DS ALL (4064204022_A) |
GSM527335 |
DS ALL (4064204022_B) |
GSM527336 |
nl (4064204023_A) |
GSM527337 |
nl (4064204023_B) |
GSM527338 |
DS ALL (4064204035_A) |
GSM527339 |
DS ALL (4064204035_B) |
GSM527340 |
DS ALL (4064204036_A) |
GSM527341 |
nl (4064204036_B) |
GSM527342 |
NDS ALL (4064204052_A) |
GSM527343 |
NDS ALL (4064204052_B) |
GSM527344 |
DS ALL (4064204053_A) |
GSM527345 |
DS ALL (4064204053_B) |
GSM527346 |
nl (4064204058_A) |
GSM527347 |
DS ALL (4064204058_B) |
GSM527348 |
DS (4064204059_A) |
GSM527349 |
DS (4064204059_B) |
GSM527350 |
nl (4064204070_A) |
GSM527351 |
DS ALL (4064204070_B) |
GSM527352 |
NDS ALL (4064204085_A) |
GSM527353 |
NDS (4064204085_B) |
GSM527354 |
nl (4064204087_A) |
GSM527355 |
nl (4064204087_B) |
GSM527356 |
NDS ALL (4064204091_A) |
GSM527357 |
NDS (4064204091_B) |
GSM527358 |
DS ALL (4064204092_A) |
GSM527359 |
DS ALL (4064204092_B) |
GSM527360 |
DS ALL (4064204102_A) |
GSM527361 |
DS ALL (4064204102_B) |
GSM527362 |
DS ALL (4094577059_A) |
GSM527363 |
DS ALL (4094577059_B) |
GSM527364 |
DS ALL (4094577062_A) |
GSM527365 |
DS ALL (4094577062_B) |
GSM527366 |
DS ALL (4094577113_A) |
GSM527367 |
DS ALL (4094577113_B) |
GSM527368 |
DS ALL (4094577134_A) |
GSM527369 |
DS ALL (4094577134_B) |
GSM527370 |
DS ALL (4256134180_A) |
GSM527371 |
DS (4256134180_B) |
GSM527372 |
DS ALL (4256134250_A) |
GSM527373 |
DS ALL (4256134250_B) |
GSM527374 |
DS ALL (4256134252_A) |
GSM527375 |
DS (4256134252_B) |
GSM527376 |
DS (4256134253_A) |
GSM527377 |
DS ALL (4256134253_B) |
GSM527378 |
NDS ALL (4256134305_A) |
GSM527379 |
NDS ALL (4256134305_B) |
GSM527380 |
DS ALL (4256134364_A) |
GSM527381 |
DS (4256134364_B) |
GSM527385 |
DS ALL (4256134365_A) |
GSM527386 |
DS (4256134365_B) |
GSM527387 |
DS ALL (4256134405_A) |
GSM527388 |
DS (4256134405_B) |
GSM527389 |
NDS ALL (4256134444_A) |
GSM527390 |
NDS (4256134444_B) |
GSM527391 |
DS ALL (4256134446_A) |
GSM527392 |
DS ALL (4256134446_B) |
GSM527393 |
NDS ALL (4256134462_A) |
GSM527394 |
NDS (4256134462_B) |
GSM527395 |
NDS (4256134464_A) |
GSM527396 |
NDS ALL (4256134464_B) |
GSM527397 |
NDS ALL (4256134467_A) |
GSM527398 |
NDS ALL (4256134467_B) |
GSM527399 |
NDS ALL (4256134474_A) |
GSM527400 |
NDS ALL (4256134474_B) |
GSM527401 |
NDS ALL (4256134489_A) |
GSM527402 |
NDS (4256134489_B) |
GSM527403 |
NDS ALL (4256134505_A) |
GSM527404 |
NDS (4256134505_B) |
GSM527405 |
DS ALL (4256134507_A) |
GSM527406 |
DS (4256134507_B) |
GSM527407 |
DS ALL (4256134520_A) |
GSM527408 |
DS (4256134520_B) |
GSM527409 |
DS ALL (4256134539_A) |
GSM527410 |
DS (4256134539_B) |
GSM527411 |
DS ALL (4256134540_A) |
GSM527412 |
DS (4256134540_B) |
GSM527413 |
DS ALL (4281807008_A) |
GSM527414 |
DS (4281807008_B) |
GSM527415 |
DS (4281807035_A) |
GSM527416 |
NDS ALL (4281807035_B) |
GSM527417 |
NDS ALL (4281807051_A) |
GSM527418 |
NDS ALL (4281807051_B) |
GSM527419 |
NDS ALL (4281807089_A) |
GSM527420 |
NDS ALL (4281807089_B) |
GSM527421 |
DS (4281807090_A) |
GSM527422 |
DS ALL (4281807090_B) |
GSM527423 |
DS ALL (4281807098_A) |
GSM527424 |
DS ALL (4281807098_B) |
GSM527427 |
NDS ALL (4281807099_A) |
GSM527428 |
NDS ALL (4281807099_B) |
GSM527429 |
NDS ALL (4281807101_A) |
GSM527430 |
NDS ALL (4281807101_B) |
GSM527431 |
DS ALL (4281807102_A) |
GSM527432 |
DS (4281807102_B) |
GSM527433 |
NDS ALL (4281807103_A) |
GSM527434 |
NDS ALL (4281807103_B) |
GSM527435 |
DS ALL (4281807117_A) |
GSM527436 |
DS (4281807117_B) |
GSM527437 |
DS ALL (4281807140_A) |
GSM527438 |
DS (4281807140_B) |
GSM527439 |
DS ALL (4281807141_A) |
GSM527440 |
DS (4281807141_B) |
GSM527441 |
DS ALL (4281807166_A) |
GSM527442 |
DS (4281807166_B) |
GSM527443 |
NDS (4281807167_A) |
GSM527444 |
NDS ALL (4281807167_B) |
GSM527445 |
DS ALL (4281807578_A) |
GSM527446 |
DS (4281807578_B) |
GSM527447 |
NDS ALL (4281807626_A) |
GSM527448 |
NDS (4281807626_B) |
GSM527449 |
NDS ALL (4281807792_A) |
GSM527450 |
NDS (4281807792_B) |
GSM527451 |
NDS (4281807793_A) |
GSM527452 |
NDS ALL (4281807793_B) |
GSM527453 |
NDS (4281807875_A) |
GSM527454 |
NDS ALL (4281807875_B) |
GSM676326 |
NDS ALL (4281807254_A) |
GSM676327 |
NDS ALL (4281807254_B) |
GSM676328 |
NDS ALL (4281807259_A) |
GSM676329 |
NDS ALL (4281807259_B) |
GSM676330 |
NDS ALL (4281807260_A) |
GSM676331 |
NDS ALL (4281807260_B) |
GSM676332 |
NDS ALL (4281807342_A) |
GSM676333 |
NDS ALL (4281807342_B) |
GSM676334 |
NDS ALL (4281807368_A) |
GSM676335 |
NDS ALL (4281807368_B) |
GSM676336 |
NDS ALL (4281807370_A) |
GSM676337 |
NDS ALL (4281807370_B) |
GSM676338 |
NDS ALL (4281807377_A) |
GSM676339 |
NDS ALL (4281807377_B) |
GSM676340 |
NDS ALL (4281807378_A) |
GSM676341 |
NDS ALL (4281807378_B) |
GSM676342 |
NDS ALL (4281807379_A) |
GSM676343 |
NDS ALL (4281807379_B) |
GSM676344 |
NDS ALL (4281807415_A) |
GSM676345 |
NDS ALL (4281807422_A) |
GSM676346 |
NDS ALL (4281807422_B) |
GSM676347 |
NDS ALL (4281807465_B) |
GSM676348 |
NDS ALL (4281807488_A) |
GSM676349 |
NDS ALL (4281807488_B) |
GSM676350 |
NDS ALL (4281807491_A) |
GSM676351 |
NDS ALL (4281807491_B) |
GSM676352 |
NDS ALL (4286608035_A) |
GSM676353 |
NDS ALL (4286608035_B) |
GSM676354 |
NDS ALL (4286608048_A) |
GSM676355 |
NDS ALL (4286608048_B) |
GSM676356 |
NDS ALL (4286608260_A) |
GSM676357 |
NDS ALL (4286608260_B) |
GSM676358 |
NDS ALL (4286608262_A) |
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This SuperSeries is composed of the following SubSeries: |
GSE20872 |
Methylation data from Down syndrome and non-Down syndrome pediatric acute lymphoblastic leukemia cases and controls |
GSE20910 |
Expression data from Down syndrome and non-Down syndrome pediatric acute lymphoblastic leukemia cases |
GSE21091 |
SNP data from Down syndrome and non-Down syndrome pediatric acute lymphoblastic leukemia cases and controls |
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Relations |
BioProject |
PRJNA126695 |
Supplementary file |
Size |
Download |
File type/resource |
GSE21094_RAW.tar |
352.5 Mb |
(http)(custom) |
TAR (of CEL, TXT) |
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