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James R. Downing, MD

Member, St. Jude Faculty
Deputy Director, St. Jude Children's Research Hospital
Scientific Director and Executive Vice President, St. Jude Children's Research Hospital
Associate Director of Basic Research, Cancer Center
Co-Leader, Hematological Malignancies Program
Gignac Chair of Pathology
Director, Molecular Pathology Laboratory

See Faculty Bio

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.

Data

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.


Supplemental Data

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

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 USA 2009 Aug 4;106(31):12944-9.*

*See also: AML-SNP1

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

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

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.

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

Classification of Pediatric Acute Lymphoblastic Leukemia by Gene Expression Profile.
Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing.
Blood 2003 Oct 15;102(8):2951-9.

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 Jun;34(2):231.

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 Mar;1(2):109-10.