Sub-megabase resolution tiling (SMRT) array-based comparative genomic hybridization profiling reveals novel gains and losses of chromosomal regions in Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma cell lines

Fadlelmola, Faisal M; Zhou, Minglong; de Leeuw, Ronald J; Dosanjh, Nirpjit S; Harmer, Karynn; Huntsman, David; Lam, Wan L; Banerjee, Diponkar

doi:10.1186/1476-4598-7-2

Molecular Cancer

Table 2 Gains and Losses of the regions and the genes reported to be differentiallyexpressed.

From: Sub-megabase resolution tiling (SMRT) array-based comparative genomic hybridization profiling reveals novel gains and losses of chromosomal regions in Hodgkin Lymphoma and Anaplastic Large Cell Lymphoma cell lines

Cytoband	Size (Mb)	Minimal region boundary clones	Number of refseq genes in region	Reported Copy number alterations	Genes known/found to be differentially expressed
1q25.2-q31.3	17.73	174994286–192721998	68	Gogusev et al. (2002)	ANGPTL1, LHX4, PNF2, RGS1, NEK7, PCTRK3, CTSE, MYOG, RGS2
1q42.2-q43	9.16	228621517–237777167	30	Gogusev et al. (2002)	LGALS8, NID, MTR, OPN3, GNG4, TBCE
2p16.2-p13.3	17.77	53587332–70354068	63	Joos et al. (2002)	REL, PNPT1, RPS27A, XPO1, SLC1A4, MSH6, MGC15407
2q23.1-q24.2	13.83	149314143–163139362	40	current study	TNFAIP6, GCA, LY75, SLC25A12, DCL-1, ITGB6, RBMS1
2q24.2-q31.3	18.76	163139362–181903843	81	Franke et al. (2001)	MTX2, DPP4, ATP5G3, TLK1, STAT1, BBS5, SCRN3, NFE2L2
5p15.32-p14.3	10	5257164–15261389	20	current study	DNAH5, DDX4, MGC5309, ARFRP2, CTNND2, MYO10
5q14.1-q15	18.99	79623141–98609560	48	Joos et al. (2003)	C5ORF12, CACH-1, RPS23, ANKRD32, TBCA, KIAA0372, RHOBTB3
7q11.1-q36.3	97.02	61369644–158387760	575	current study	PRSS1, TRY6, PRSS2, CDK6, CLDN4, HSPB1, HGF, mTERF, ING3, TPST1
8q23.3-24.12	5.08	116154379–121233686	19	Joos et al. (2003)	MYC, RAD21, DEPDC6, THRAP6, DCC1
9p24.3-p24.1	5.9	23994–5928516	28	Joos et al. (2003)	JAK2, RANBP6, UHRF2, C9orf46, C9orf123, MLANA, RCL1, AK3L1
9p21.3-p12	14.87	25192411–40063723	119	current study	PRSS3, DNAJA1, RPS6, CCDC2
11q22.1-q23.3	19.91	98410656–118317962	106	Falzetti et al. (1999)	ATM, DDX6, CRYAB, PDGFD
12q13.13-q14.1	8.64	53812697–62450135	114	current study	DDIT3, DTX3, KRT6IRS, HOXC4, HOXC5, LEMD3, TBK1, USP15
13q12.13-q12.3	5.49	25577047–31063440	25	current study	GTF3A, MTIF3, PAN3, APRIN, BRCA2
13q13.1-q21.32	35.16	31151386–66311960	108	Joos et al. (2002)	Ufm1, C13orf1, RCBTB1, KBTBD6, NARG1L, DDX26, NUDT15
13q31.1-q34	27.91	86156309–114062150	74	Joos et al. (2002)	STK24, DCT, GPC5, DZI, EFNB2, TM9SF2, RASA3, LOC196541
16q22.1-q24.1	19.68	65582104–85259588	170	Joos et al. (2002)	CIRH1A, CKLFSF3, DNCL12, BMO39
20p12.3-q13.11	33.93	8872139–42799402	185	current study	PCNA, SNAP25, FKBP1A, SNPH, TH1L, SPAG4L, TDE1, SLC2A10, C20orf52, EYA2
20q13.2-q13.32	6.95	50997916–57946927	31	current study	TFAP2C, CDH4, ZFP64, GNAS, ATP5E
18q21.32-q23	19.03	58644127–77673453	52	current study	*VPS4B, RTTN, PIGN* , ZCCHC2, BCL2, *FLJ25715, TXNL4A, ZNF516* , PARD6G

Aligned with data from the University of California, Santa Cruz Human Browser April 2003 Freeze. Novel regions are in underlined bold. Genes in italic and underlined are those that previously been reported {Joos et al. 2003 [19]; Gogusev et al. [20]; Joos et al. 2002 [29]; Franke et al. [54]; Falzetti et al. [55]}, whereas those in bold and italic are those found to be over-expressed and down regulated, respectively, in the current study.

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ISSN: 1476-4598

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