St. Jude Research/Authors/James R. Downing, MD

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.

Link to Primary Genomic Data
*The repository includes primary SNP array data for the publications listed below.

Genomic analysis reveals few genetic alterations in pediatric acute myeloid leukemia
Radtke I, Mullighan CG, Ishii M, Su X, Cheng J, Ma J, Ganti R, Cai Z, Goorha S, Pounds SB, Cao X, Obert C, Armstrong J, Zhang J, Song G, Ribeiro RC, Rubnitz JE, Raimondi SC, Shurtleff SA, Downing JR.
Proc Natl Acad Sci U S A 2009 Aug 4;106(31):12944-9.
See also: AML-SNP1

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

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 360:470-80, 2009.
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 453:110-114, 2008.
See also: ALL-SNP2

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 446:758-64, 2007*.
See also: ALL-SNP1

Pediatric Lymphoblastic Leukemia by Gene Expression Profiling
Eng-Juh Yeoh, Mary E. Ross, Shelia A. Shurtleff, W. Kent Williams, Divyen Patel, Rami Mahfouz, Fred G. Behm, Susana C. Raimondi, Mary V. Relling, Anami Patel, Cheng Cheng, Dario Campana, Dawn Wilkins, Xiaodong Zhou, Jinyan Li, Huiqing Liu, Ching-Hon Pui, William E. Evans, Clayton Naeve, Limsoon Wong, James R. Downing
Cancer Cell 2002 Volume 1:133-143

Treatment-specific Changes in Gene Expression Discriminate in vivo Drug
response in Human Leukemia Cells
Meyling H. Cheok, Wenjian Yang, Ching Hon Pui, James R. Downing, CHeng Cheng, Clayton W. Naeve, Mary V. Relling, William E. Evans
Nature Genetics 2003

Classification of Pediatric Acute Lymphoblastic Leukemia by Gene Expression Profile
Mary E. Ross, Xiadong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, James R. Downing
Blood 2003

Gene Expression Profiling of Pediatric Acute Myelogenous Leukemia
Mary E. Ross, Rami Mahfouz, Mihaela Onciu, Hsi-Che Liu, Xiadong Zhou, Guangchun Song, Shelia A. Shurtleff, Stanley Pounds, Cheng Cheng, Jing Ma, Raul C. Riberiro, Jeffrey E. Rubnitz, Kevin Girtman, W. Kent Williams, Susana C. Raimondi, Der-Chemg Liang, Lee-Yung Shih, CHing-Hon Pui & James R. Downing
Blood 2004

Expression of the outcome predictor in acute leukemia 1 (OPAL1) gene is not an independent prognostic factor in patients treated according to COALL or St Jude protocols.
Holleman A, den Boer ML, Cheok MH, Kazemier KM, Pei D, Downing JR, Janka-Schaub GE, Gobel U, Graubner UB, Pui CH, Evans WE, Pieters R.
Blood 2006 Sep 15;108(6): 1984-90.