Supplemental Data    

Investigators at St. Jude Children's Research Hospital have performed several large scale projects interrogating genomic alterations in acute leukemia and related disorders using a variety of complementary approaches. These include examination of DNA copy number alterations and loss of heterozygosity using single nucleotide polymorphism arrays and oligonucleotide array-CGH; gene expression profiling; methylation analysis, and gene resequencing. A list of recent publications describing these data are provided below. Much of the Affymetrix Gene Expression and SNP microarray data was initially deposited in the NCBI Gene Expression Omnibus (GEO). Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the link below.

The data is provided as Affymetrix .CEL and .CHP (and/or SNP call TXT) files. SNP genotyping and the generation of .CHP and .TXT files has been performed by standard means (Affymetrix GTYPE v4, and birdseed v2 implemented in Affymetrix Genotyping Console) Chip identifiers linking the chips to samples described in each publication are also provided.

• Primary Genomic Data (Download Request)
  The repository includes primary SNP array data for the publications listed below.

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• Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia.
  Figueroa ME, Chen SC, Andersson AK, Phillips LA, Li Y, Sotzen J, Kundu M, Downing JR, Melnick A, Mullighan CG. 
  J Clin Invest. 2013 June.
• Rearrangement of CRLF2 in B-progenitor- and Down syndrome-associated acute lymphoblastic leukemia.
  Mullighan CG, Collins-Underwood JR, Phillips LA, Loudin MG, Liu W, Zhang J, Ma J, Coustan-Smith E, Harvey RC, Willman CL, Mikhail FM, Meyer J, Carroll AJ, Williams RT, Cheng J, Heerema NA, Basso G, Pession A, Pui CH, Raimondi SC, Hunger SP, Downing JR, Carroll WL, Rabin KR.
  Nature Genetics 2009 Nov;41(11):1243-6.*

*See also: ALL-SNP5

• Reference Alignment of SNP Microarray Signals for Copy Number Analysis of Tumors.
  Pounds S, Cheng C, Mullighan C, Raimondi SC, Shurtleff S, Downing JR.
  Bioinformatics 2009 Feb 1;25(3):315-21. Epub 2008 Dec 3.
  
• Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia.
  Mullighan CG, Su X, Zhang J, Radtke I, Phillips LA, Miller CB, Ma J, Liu W, Cheng C, Schulman BA, Harvey RC, Chen I-M, Clifford RJ, Carroll WL, Reaman G, Bowman WP, Devidas M, Gerhard DS, Yang W, Relling MV, Shurtleff SA, Campana D, Borowitz M, Pui C-H, Smith M, Hunger SP, Willman C, Downing JR, and the Children's Oncology Group.
  N Engl J Med 2009;360:470-80.*
  

*See also: ALL-SNP4

• Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.
  Mullighan CG, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, Downing JR.
  Science 2008;322:1377-80

See also: ALL-SNP3

• BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros.
  Mullighan CG, Miller CB, Radtke I, Phillips LA, Dalton J, Ma J, White D, Hughes TP, Le Beau MM, Pui C.-H., Relling MV, Shurtleff, SA, Downing JR.
  Nature 2008;453:110-114.*

*See also: ALL-SNP2

• Genes regulating B cell development are mutated in acute lymphoid leukaemia.
  Charles G. Mullighan, Salil Goorha, Ina Radtke, Christopher B. Miller, Elaine Coustan-Smith, James D. Dalton, Kevin Girtman, Susan Mathew, Jing Ma, Stanley B. Pounds, Xiaoping Su, Ching-Hon Pui, Mary V. Relling, William E. Evans, Sheila A. Shurtleff, James R. Downing
  Nature. 2007 Apr 12;446(7137):758-64.
• Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia.
  Mullighan CG, Goorha S, Radtke I, Miller CB, Coustan-Smith E, Dalton JD, Girtman K, Mathew S, Ma J, Pounds SB, Su X, Pui C-H, Relling MV, Evans WE, Shurtleff SA, Downing JR.
  Nature 2007;446:758-64, 2007.*
  

*See also: ALL-SNP1

Charles Mullighan, MBBS(Hons), MSc, MD
Member, St. Jude Faculty
St. Jude Children's Research Hospital
Department of Pathology
262 Danny Thomas Place
Pathology, Mail Stop 342, Room D4047E
Memphis, TN, 38105
T: 901-595-3387
F: 901-595-5947
charles.mullighan@stjude.org
www.stjude.org/mullighan