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LDI-PCR in Cancer Translocation Mapping

 

Björn Schneider, Hans G Drexler, Roderick AF MacLeod

Corresponding author:
Björn Schneider, PhD,
DSMZ - German Collection of Microorganisms and Cell Cultures,
Department of Human and Animal Cell Cultures,
Inhoffenstr. 7b,
38124 Braunschweig, Germany
Tel: +495312616151
Fax: +495312616150
Email: bsc06@dsmz.de

 

April 2010

 

 

Abstract
Identification of genes in oncogenic chromosome translocations by Fluorescence In Situ Hybridization (FISH) screening using genomic tilepath clones, is often laborious, notably if the region of interest is gene-dense. Other molecular methods for partner identification also suffer limitations; for instance, genomic PCR screening requires prior knowledge of both sets of breakpoints, while Rapid Amplification of cDNA Ends (RACE) is limited to translocations causing mRNA fusion and delivers no breakpoint data. With Long Distance Inverse (LDI)-PCR, however, it is possible to identify unknown translocation partners and to map breakpoints at the base-pair level. Applying LDI-PCR merely requires approximate sequence information on one partner, rendering it ideal for use in combination with FISH to extend and refine cytogenetic breakpoint data.

Introduction
Recurrent chromosomal rearrangements characterize many different types of cancer.
Specific cytogenetic translocations are key events, widely considered to be diagnostically and prognostically significant in leukemia and lymphoma, and increasingly so in solid tumors (Mitelman et al., 2007). Hitherto, most cancer genes have been identified following analysis of recurrent chromosome translocations (Futreal et al., 2004). The pathological significance and usefulness of such rearrangements depend on two key features: a) whether rearrangements display distinct patterns of recurrence within specific tumors, e.g. t(8;14)(q24;q32) which is restricted to B-cell neoplasia; and b) how clustered are the chromosomal breakpoints therein. The significance accorded to breakpoint data depends on their ascertainment precision, from megabase- and kilobase-, down to single base-pair levels, when ascertained by classical cytogenetics, fluorescence in situ hybridization (FISH), and sequence-based methods, respectively.
Chromosome translocations fall into three broad categories. The first causes the physical fusion of the two mRNAs expressed by the participating genes, thus creating novel fusion proteins translated from exons emanating from both genes, e.g. BCR (at [chromosome]-22-[band]-q11) with ABL1 (at 9q34) fused by t(9;22)(q34;q11) in chronic myeloid leukemia (CML) and in some cases of acute lymphoblastic leukemias (ALL) (Turhan, 2008a,b). The second category also fuses mRNA from genes at separate loci but, in this case, serving to deregulate a developmentally silenced partner by exchanging promoters with more active partners, e.g. BCL6 (at 3q27) which is activated by translocations with any one of many partners, chiefly in diffuse large B-cell lymphoma (DLBCL) (Knezevich, 2007).
The third class of chromosome translocation again results in the activation of the normally silent partner, this time by juxtaposition with another constitutively active partner without mRNA fusion, e.g. the neighboring homeobox genes, TLX3 (at 5q35.1) and NKX2-5 (at 5q35.2). According to the proximity of the breakpoint involved, either (but not both) genes may be activated in T-cell ALL by the recurrent t(5;14)(q35;q32.2) by which these are juxtaposed with regulatory regions from BCL11B (at 14q32.2) to stimulate transcription (Bernard et al., 2001; MacLeod et al., 2003; Nagel et al., 2007).

Some "promiscuous" genes engage with multiple partners: notably MLL with 64 known partners (Meyer et al., 2009b), BCL6 with 28 (Knezevich, 2007), RUNX1 with 39 (Huret and Senon, 2003), NUP98 with 29 (Kearney, 2002), and the IgH-locus with 40 (Lefranc, 2003). Although, promiscuity may reflect the dependence of tumors on the inappropriate oncogene expression without overly caring how deregulation is accomplished, the role of the partner genes has come under renewed scrutiny. Choice of partner gene may not only reveal in which types of precancerous cells primary oncogenic rearrangements occur, but also by looking for conserved DNA or protein motifs, yield clues to the mechanisms underlying their formation or their functional contribution to neoplasia. In addition, the roles of biologically important genes, e.g. BCL11B, a key regulator of both differentiation and survival during thymocyte development, are often first rendered visible by their participation in cancer rearrangements (MacLeod et al., 2003).
Both the identities of each partner gene and their precise breakpoints at the DNA base-pair level, may be useful not only to characterize potential fusion genes/products but also to ascertain whether additional non protein-coding genomic entities, such as chromosomal fragile sites (Schneider et al., 2008), microRNA loci, putative genes, unspliced "expressed sequence tags", or regulatory non-coding regions may be involved.
Clues to the biological mechanisms generating chromosome rearrangements are given by breakpoint sequences, including T- and B-cell receptor gene (VDJ) rearrangement, Alu-mediated recombination, non-homologous end joining, etc. VDJ genes are flanked by recombination signal sequences composed of heptamers followed, in turn, by a spacer containing either 12 or 23 unconserved nucleotides and a conserved nonamer. Spacers of 12 nucleotides undergo physiological recombination with those containing 23 in order to obey the so-called "12/23 rule". The presence of these or related sequences has been reported in connection with cancer translocations to reveal how physiologic processes may be abused to cause genomic rearrangements (Gu et al., 1992).
Genomic fusion sequences may also be used to aid cell line authentication - an omnipresent problem confronting cell culturists, given that an unexpectedly (and unacceptably) high percentage of new cell lines has been misidentified, or cross-contaminated by older cell lines (MacLeod et al., 1999). While mRNA fusion sequences are constrained by splicing, their genomic equivalents allow sufficient variation to provide "fingerprints" unique to individual cell lines to serve as potential identifiers. For analyzing patient tumors, knowledge of the exact fusion sequence allows design of patient-specific quantitative (q)PCR used for monitoring minimal residual disease with high sensitivity (Burmeister et al., 2006), to follow up therapeutic responses thus enabling early detection of relapse.
Cancer gene promiscuity enables oncogenic chromosome rearrangements, "smoking guns" of cancer genes, to be distinguished from random changes. FISH is initially used to confirm rearrangement of a contextually appropriate oncogene residing at the locus in question. Hence, a breakpoint at 9q34 might throw suspicion onto NOTCH1 in a T-cell-, ABL1 in myeloid- neoplasia, and NUP214 in either entity. While such an approach is less helpful among solid tumors where oncogene rearrangements are less informative, at this locus TSC1 might be deemed a candidate in tuberous sclerosis cells. Even when the index breakpoint is precisely known, determination of its partner by FISH requires time-consuming and laborious procedures for those not afforded immediate blanket tilepath-clone coverage with which to quarter the region of interest.
PCR screening with hit-lists of known and potential partner genes is quite as laborious as FISH, and is liable to miss unknown translocation partners, or those with breakpoints lying outside their respective cluster regions. When there are grounds to suspect transcriptional fusion (as among partners of genes prone to this type of gene rearrangement, e.g. ABL1, ETV6, NUP98, etc.) a mRNA-based method, rapid amplification of cDNA ends (RACE), may be used to detect novel fusion partners (Frohman et al., 1988). A drawback of RACE is its inability to supply genomic breakpoint data, and the risk of overlooking some splice variants. Hence, the technique of choice for identifying unknown partner genes and their breakpoints should not require prior knowledge of the partner gene, yet provide breakpoint data at the DNA base pair level.
Long Distance Inverse (LDI)-PCR satisfies these needs. LDI-PCR was developed from the earlier inverse-PCR (Ochman et al., 1988) to allow the amplification of large DNA fragments comprised of known and unknown sequences (Willis et al., 1997) using re-ligated circular restriction fragments as templates. Primers are set in opposition within the known sequence. The unknown sequence is flanked on both sides by known sequences following re-ligation in the resultant amplicon (Fig. 1). When a restriction fragment length polymorphism (RFLP) distinguishing the wild type and derivative alleles is generated by the genomic alteration, the two resulting amplicons should be separable by gel electrophoresis, enabling their respective sequences to be compared (Fig. 2). Sequencing with one of the PCR-primers directed towards the restriction site allows immediate identification of the partner gene. Sequencing in the other direction allows precise mapping of the breakpoint. While easier to perform for genes with well defined, short breakpoint cluster regions, LDI-PCR may be applied to any gene or region involved in a translocation and has, therefore, been applied to a wide variety of translocations involving both frequently rearranged promiscuous oncogenes, but also as single events. Table 1 gives an overview of genes analyzed by LDI-PCR according to literature databases and the respective references.

Gene No. of Partners References describing LDI-PCR analysis
ALK 14 (Allouche, 2010) Ma et al., 2000
ANTXR1 1 (Oberthuer et al., 2005) Oberthuer et al., 2005
API2 1 (Mathijs and Marynen, 2001) Dierlamm et al., 1999
BCL6 28 (Knezevich, 2007)

Akasaka H et al., 2000
Akasaka T et al., 2000
Kurata et al., 2002
Akasaka et al., 2003
Chen et al., 2003
Montesinos-Rongen et al., 2003
Chen et al., 2006
Schneider et al., 2008

BRD4 1 (Collin, 2007) Haruki et al., 2005
CALL 1 (Frints et al., 2003) Frints et al., 2003
E2A 5 (Huret, 1997) Wiemels et al., 2002a
ETV6 28 (Knezevich, 2005) Wiemels et al., 1999a
Wiemels et al., 1999b
Wiemels and Greaves, 1999
Wiemels et al., 2008
IGH 40 (Lefranc, 2003) Willis et al., 1997
Willis et al., 1998
Nardini et al., 2000
Satterwhite et al., 2001
Sonoki et al., 2001
Bichi et al., 2002
Sanchez-Izquierdo et al., 2003
Sonoki et al., 2004
Akasaka et al., 2007
Lenz et al., 2007
Souabni et al., 2007
d'Amore et al., 2008
Ishizaki et al., 2008
Russell et al., 2008
Vieira et al., 2008
Vinatzer et al., 2008
Nagel et al., 2009
Russell et al., 2009
Yin et al., 2009
Hu et al., 2010
let-7a-2, miR-100 1 (Bousquet, 2008) Bousquet et al., 2008
MLH1 1 (Meyer et al., 2009b) Meyer et al., 2009a
MLL 64 (Meyer et al., 2009b) Blanco et al., 2001
Meyer et al., 2005
Teuffel et al., 2005
Attarbaschi et al., 2006
Burmeister et al., 2006
Matsuda et al., 2006
Meyer et al., 2006a
Meyer et al., 2006b
Strehl et al., 2006
Burmeister et al., 2008
Balgobind et al., 2009
Bueno et al., 2009
Burmeister et al., 2009
Matsuda et al., 2009
Meyer and Marschalek, 2009
Cóser et al., 2010
De Braekeleer et al., 2010
Lee et al., 2010
NOTCH1 2 (Suzuki et al., 2009) Suzuki et al., 2009
PAX5 6 (Strehl, 2005) An et al., 2008
An et al., 2009
PDGFRA 6 (Dessen, 2009) Cools et al., 2003
PDGFRB 20 (Vizmanos, 2005) Walz et al., 2007
Walz et al., 2009
RUNX1 / AML1 39 (Huret and Senon, 2003) Xiao et al., 2001
Wiemels et al., 2002b

Table 1: Genes involved in translocations analyzed by LDI-PCR, numbers of yet known translocation partner genes and references wherein the analysis of the particular gene is described.

Limitations are set by the performance of the DNA polymerase since lengthier fragments may resist amplification, and by the placement of the RFLP, as fragments similar in size cannot be readily distinguished by gel electrophoresis. If primary patient tumor material is analyzed, it should be noted that the samples used for analysis not only contain tumor material, but also normal bystander cells devoid of tumor rearrangement. Detection attempted at lower tumor infiltration rates risk false negative results.
In contrast to other PCR methods suitable for detection of unknown fusion sequences, such as panhandle PCR (Megonigal et al., 2000) or analogous techniques requiring adaptor ligations (reviewed in Tonooka and Fujishima, 2009), LDI-PCR is independent of any additional adaptors or anchors which have to be ligated to the restricted fragments, reducing the number of steps required, while remaining sufficiently flexible to allow a wide choice of restriction enzymes.
In the future, translocation analysis by next generation sequencing should overcome these limitations and suitable algorithms have been developed to recognize novel derivative breakpoint-flanking sequences and thereby identify novel cancer translocations and other synonymous rearrangements, including a subset of fusogenic microdeletions (Campbell et al., 2008).

Figure 1: Amplifying Genomic Fusions of Unknown Sequence.
The schema summarizes how the genomic DNA is first restricted, then re-ligated to the circular template, and how the resulting amplicon should appear. Note unknown region (red) flanked by known sequences (black). R: restriction site, BP: breakpoint; arrows: forward (FW) and reverse (REV) primers.

 

Figure 2: How to Interpret LDI-PCR Gels.
Left figure shows the wild type configuration where twin circular templates identical in size would yield a single band by agarose gel electrophoresis. Translocation bearing cells (right figure) yield both wild type and derivative templates, differing in size and detectible as two bands on the gel. The derivative band is indicated by an arrow. Known regions are outlined in black, unknown in red. R: Restriction site, REV: reverse primer, FW: forward primer.

Methology
In principle, LDI-PCR utilizes digested and re-ligated circular templates, which are of different sizes, due to RFLP caused by genomic rearrangements. This size difference renders the amplicons separable by gel electrophoresis (Fig. 2).
For a successful analysis, the LDI-PCR has to be designed carefully. The sequence covering the genomic region of interest should be selected from a genome browser (ENSEMBL, UCSC, NCBI) and then pasted into the query box of a restriction map generator (BioEdit, multiple online tools: SMS, RestrictionMapper). Restriction enzymes should be chosen to yield fragments in a size range of 2-5 kb. If using a double-digest strategy with enzymes producing sticky ends, these ends must be compatible. Ensure that both enzymes perform well in the same buffer and at the same temperature. Primer pairs have to be designed in such a way that one primer is directed towards the restriction site, the other one in the opposite direction (see Figures). The sequence lying between the primer tails is not subject to amplification, so the gap should not be excessive, ideally 30-50 bp. A breakpoint lying therein cannot be detected unless another primer pair, e.g. at the other end of the restriction fragment is used. For longer fragments (greater than 5 kb, say) use of a primer set consisting of one forward and multiple reverse primers (or vice versa) can be helpful. The oligonucleotides should be ~30 bp with a Tm ~65°C and a GC-content of 40-60%.
For LDI-PCR template preparation high quality genomic DNA should be used, meaning high purity (260/280 1.8-2.0 and 260/230 > 2) and high integrity without degradation. One microgram of DNA is then digested with 30-50 U of each restriction enzyme in the presence of the appropriate digestion buffer in a total volume of 100 μl for 3-4 h at the temperature suitable for the chosen enzymes (mostly 37°C), followed by heat inactivation (where applicable) and purification, preferably with a column based purification kit. Phenol / chloroform purification followed by precipitation may also be performed, but residual phenol can disturb downstream processes. To form the circular templates, the restriction fragments are then religated with 5 U T4 ligase overnight at 4-8°C in a total volume of 80 μL, terminated by heat inactivation. These conditions favor the desired self-ligation.
The PCR is performed best using a PCR kit suitable for amplification of long templates and using 5 μL (62.5 ng) of the digested and re-ligated DNA.
The PCR products are analyzed by gel electrophoresis. Discrepant bands not corresponding to the calculated amplicon size may represent amplicons of translocated fragments. These are excised from the gel, purified and subjected to sequence analysis and, unless artefacts, may reveal the translocation partner and the exact breakpoint of the rearrangement subject to analysis.

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Atlas Genet Cytogenet Oncol Haematol. August 2005. URL: http://AtlasGeneticsOncology.org/Genes/PAX5ID62.html
 
Clonal expansion of a new MLL rearrangement in the absence of leukemia.
Teuffel O, Betts DR, Thali M, Eberle D, Meyer C, Schneider B, Marschalek R, Trakhtenbrot L, Amariglio N, Niggli FK, Schafer BW.
Blood. 2005 May 15;105(10):4151-2.
PMID 15867425
 
PDGFRB (platelet-derived growth factor receptor, beta polypeptide).
Vizmanos JL.
Atlas Genet Cytogenet Oncol Haematol. July 2005. URL: http://AtlasGeneticsOncology.org/Genes/PDGFRBID21ch5q32.html
 
Mixed lineage leukemia-rearranged childhood pro-B and CD10-negative pre-B acute lymphoblastic leukemia constitute a distinct clinical entity.
Attarbaschi A, Mann G, Konig M, Steiner M, Strehl S, Schreiberhuber A, Schneider B, Meyer C, Marschalek R, Borkhardt A, Pickl WF, Lion T, Gadner H, Haas OA, Dworzak MN.
Clin Cancer Res. 2006 May 15;12(10):2988-94.
PMID 16707593
 
Monitoring minimal residual disease by quantification of genomic chromosomal breakpoint sequences in acute leukemias with MLL aberrations.
Burmeister T, Marschalek R, Schneider B, Meyer C, Gokbuget N, Schwartz S, Hoelzer D, Thiel E.
Leukemia. 2006 Mar;20(3):451-7.
PMID 16424875
 
High BCL6 expression predicts better prognosis, independent of BCL6 translocation status, translocation partner, or BCL6-deregulating mutations, in gastric lymphoma.
Chen YW, Hu XT, Liang AC, Au WY, So CC, Wong ML, Shen L, Tao Q, Chu KM, Kwong YL, Liang RH, Srivastava G.
Blood. 2006 Oct 1;108(7):2373-83. Epub 2006 Jun 13.
PMID 16772602
 
A case of acute myelogenous leukemia with MLL-AF10 fusion caused by insertion of 5' MLL into 10p12, with concurrent 3' MLL deletion.
Matsuda K, Hidaka E, Ishida F, Yamauchi K, Makishima H, Ito T, Suzuki T, Imagawa E, Sano K, Katsuyama T, Ota H.
Cancer Genet Cytogenet. 2006 Nov;171(1):24-30.
PMID 17074587
 
The MLL recombinome of acute leukemias.
Meyer C, Schneider B, Jakob S, Strehl S, Attarbaschi A, Schnittger S, Schoch C, Jansen MW, van Dongen JJ, den Boer ML, Pieters R, Ennas MG, Angelucci E, Koehl U, Greil J, Griesinger F, Zur Stadt U, Eckert C, Szczepan'ski T, Niggli FK, Schafer BW, Kempski H, Brady HJ, Zuna J, Trka J, Nigro LL, Biondi A, Delabesse E, Macintyre E, Stanulla M, Schrappe M, Haas OA, Burmeister T, Dingermann T, Klingebiel T, Marschalek R.
Leukemia. 2006a May;20(5):777-84.
PMID 16511515
 
Genomic DNA of leukemic patients: target for clinical diagnosis of MLL rearrangements.
Meyer C, Kowarz E, Schneider B, Oehm C, Klingebiel T, Dingermann T, Marschalek R.
Biotechnol J. 2006b Jun;1(6):656-63.
PMID 16892314
 
Molecular dissection of t(11;17) in acute myeloid leukemia reveals a variety of gene fusions with heterogeneous fusion transcripts and multiple splice variants.
Strehl S, Konig M, Meyer C, Schneider B, Harbott J, Jager U, von Bergh AR, Loncarevic IF, Jarosova M, Schmidt HH, Moore SD, Marschalek R, Haas OA.
Genes Chromosomes Cancer. 2006 Nov;45(11):1041-9.
PMID 16897742
 
BRD4 (bromodomain containing 4).
Collin A.
Atlas Genet Cytogenet Oncol Haematol. February 2007. URL: http://AtlasGeneticsOncology.org/Genes/BRD4ID837ch19p13.html
 
Five members of the CEBP transcription factor family are targeted by recurrent IGH translocations in B-cell precursor acute lymphoblastic leukemia (BCP-ALL).
Akasaka T, Balasas T, Russell LJ, Sugimoto KJ, Majid A, Walewska R, Karran EL, Brown DG, Cain K, Harder L, Gesk S, Martin-Subero JI, Atherton MG, Bruggemann M, Calasanz MJ, Davies T, Haas OA, Hagemeijer A, Kempski H, Lessard M, Lillington DM, Moore S, Nguyen-Khac F, Radford-Weiss I, Schoch C, Struski S, Talley P, Welham MJ, Worley H, Strefford JC, Harrison CJ, Siebert R, Dyer MJ.
Blood. 2007 Apr 15;109(8):3451-61. Epub 2006 Dec 14.
PMID 17170124
 
BCL6 (B-Cell Lymphoma 6).
Knezevich S.
Atlas Genet Cytogenet Oncol Hematol. 2007. URL: http://AtlasGeneticsOncology.org/Genes/BCL6ID20.html
 
Aberrant immunoglobulin class switch recombination and switch translocations in activated B cell-like diffuse large B cell lymphoma.
Lenz G, Nagel I, Siebert R, Roschke AV, Sanger W, Wright GW, Dave SS, Tan B, Zhao H, Rosenwald A, Muller-Hermelink HK, Gascoyne RD, Campo E, Jaffe ES, Smeland EB, Fisher RI, Kuehl WM, Chan WC, Staudt LM.
J Exp Med. 2007 Mar 19;204(3):633-43. Epub 2007 Mar 12.
PMID 17353367
 
The impact of translocations and gene fusions on cancer causation.
Mitelman F, Johansson B, Mertens F.
Nat Rev Cancer. 2007 Apr;7(4):233-45. Epub 2007 Mar 15.
PMID 17361217
 
Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1.
Nagel S, Scherr M, Kel A, Hornischer K, Crawford GE, Kaufmann M, Meyer C, Drexler HG, MacLeod RA.
Cancer Res. 2007 Feb 15;67(4):1461-71.
PMID 17308084
 
Oncogenic role of Pax5 in the T-lymphoid lineage upon ectopic expression from the immunoglobulin heavy-chain locus.
Souabni A, Jochum W, Busslinger M.
Blood. 2007 Jan 1;109(1):281-9. Epub 2006 Sep 12.
PMID 16968900
 
Characterization of three new imatinib-responsive fusion genes in chronic myeloproliferative disorders generated by disruption of the platelet-derived growth factor receptor beta gene.
Walz C, Metzgeroth G, Haferlach C, Schmitt-Graeff A, Fabarius A, Hagen V, Prummer O, Rauh S, Hehlmann R, Hochhaus A, Cross NC, Reiter A.
Haematologica. 2007 Feb;92(2):163-9.
PMID 17296564
 
Variable breakpoints target PAX5 in patients with dicentric chromosomes: a model for the basis of unbalanced translocations in cancer.
An Q, Wright SL, Konn ZJ, Matheson E, Minto L, Moorman AV, Parker H, Griffiths M, Ross FM, Davies T, Hall AG, Harrison CJ, Irving JA, Strefford JC.
Proc Natl Acad Sci U S A. 2008 Nov 4;105(44):17050-4. Epub 2008 Oct 28.
PMID 18957548
 
Myeloid cell differentiation arrest by miR-125b-1 in myelodysplastic syndrome and acute myeloid leukemia with the t(2;11)(p21;q23) translocation.
Bousquet M, Quelen C, Rosati R, Mansat-De Mas V, La Starza R, Bastard C, Lippert E, Talmant P, Lafage-Pochitaloff M, Leroux D, Gervais C, Viguie F, Lai JL, Terre C, Beverlo B, Sambani C, Hagemeijer A, Marynen P, Delsol G, Dastugue N, Mecucci C, Brousset P.
J Exp Med. 2008 Oct 27;205(11):2499-506. Epub 2008 Oct 20.
PMID 18936236
 
A MLL-KIAA0284 fusion gene in a patient with secondary acute myeloid leukemia and t(11;14)(q23;q32).
Burmeister T, Meyer C, Thiel G, Reinhardt R, Thiel E, Marschalek R.
Blood Cells Mol Dis. 2008 Sep-Oct;41(2):210-4. Epub 2008 Jul 18.
PMID 18640063
 
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing.
Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PA, Bignell GR, Stratton MR, Futreal PA.
Nat Genet. 2008 Jun;40(6):722-9. Epub 2008 Apr 27.
PMID 18438408
 
Clonal evolution in t(14;18)-positive follicular lymphoma, evidence for multiple common pathways, and frequent parallel clonal evolution.
d'Amore F, Chan E, Iqbal J, Geng H, Young K, Xiao L, Hess MM, Sanger WG, Smith L, Wiuf C, Hagberg O, Fu K, Chan WC, Dave BJ.
Clin Cancer Res. 2008 Nov 15;14(22):7180-7.
PMID 19010834
 
Usefulness of long-distance inverse polymerase chain reaction for molecular detection of 14q32 translocation in a clinical setting.
Ishizaki A, Sugahara K, Tsuruda K, Hasegawa H, Yanagihara K, Tsukasaki K, Yamada Y, Kamihira S.
Scand J Clin Lab Invest. 2008;68(7):519-25.
PMID 19378422
 
t(6;14)(p22;q32): a new recurrent IGH@ translocation involving ID4 in B-cell precursor acute lymphoblastic leukemia (BCP-ALL).
Russell LJ, Akasaka T, Majid A, Sugimoto KJ, Loraine Karran E, Nagel I, Harder L, Claviez A, Gesk S, Moorman AV, Ross F, Mazzullo H, Strefford JC, Siebert R, Dyer MJ, Harrison CJ.
Blood. 2008 Jan 1;111(1):387-91. Epub 2007 Oct 16.
PMID 17940204
 
T(3;7)(q27;q32) fuses BCL6 to a non-coding region at FRA7H near miR-29.
Schneider B, Nagel S, Kaufmann M, Winkelmann S, Bode J, Drexler HG, MacLeod RA.
Leukemia. 2008 Jun;22(6):1262-6. Epub 2007 Nov 8.
PMID 17989715
 
BCR (Breakpoint cluster region).
Turhan AG.
Atlas Genet Cytogenet Oncol Haematol. 2008a. URL: http://AtlasGeneticsOncology.org/Genes/BCR.html
 
ABL1 (v-abl Abelson murine leukemia viral oncogene homolog 1).
Turhan AG.
Atlas Genet Cytogenet Oncol Haematol. 2008b. URL: http://AtlasGeneticsOncology.org/Genes/ABL.html
 
Combined molecular diagnosis of B-cell lymphomas with t(11;14)(q13;q32) or t(14;18)(q32;q21) using multiplex- and long distance inverse-polymerase chain reaction.
Vieira L, Martinho A, Antunes O, Silva E, Ambrosio AP, Geraldes MC, Nascimento R, Silva C, Pereira JM, Junior EC, Jordan P.
Diagn Mol Pathol. 2008 Jun;17(2):73-81.
PMID 18382373
 
Mucosa-associated lymphoid tissue lymphoma: novel translocations including rearrangements of ODZ2, JMJD2C, and CNN3.
Vinatzer U, Gollinger M, Mullauer L, Raderer M, Chott A, Streubel B.
Clin Cancer Res. 2008 Oct 15;14(20):6426-31.
PMID 18927281
 
Chromosome 12p deletions in TEL-AML1 childhood acute lymphoblastic leukemia are associated with retrotransposon elements and occur postnatally.
Wiemels JL, Hofmann J, Kang M, Selzer R, Green R, Zhou M, Zhong S, Zhang L, Smith MT, Marsit C, Loh M, Buffler P, Yeh RF.
Cancer Res. 2008 Dec 1;68(23):9935-44.
PMID 19047175
 
Heterogeneous breakpoints in patients with acute lymphoblastic leukemia and the dic(9;20)(p11-13;q11) show recurrent involvement of genes at 20q11.21.
An Q, Wright SL, Moorman AV, Parker H, Griffiths M, Ross FM, Davies T, Harrison CJ, Strefford JC.
Haematologica. 2009 Aug;94(8):1164-9. Epub 2009 Jul 7.
PMID 19586940
 
NRIP3: a novel translocation partner of MLL detected in a pediatric acute myeloid leukemia with complex chromosome 11 rearrangements.
Balgobind BV, Zwaan CM, Meyer C, Marschalek R, Pieters R, Beverloo HB, Van den Heuvel-Eibrink MM.
Haematologica. 2009 Jul;94(7):1033. Epub 2009 May 19.
PMID 19454493
 
Etoposide induces MLL rearrangements and other chromosomal abnormalities in human embryonic stem cells.
Bueno C, Catalina P, Melen GJ, Montes R, Sanchez L, Ligero G, Garcia-Perez JL, Menendez P.
Carcinogenesis. 2009 Sep;30(9):1628-37. Epub 2009 Jul 8.
PMID 19587093
 
The MLL recombinome of adult CD10-negative B-cell precursor acute lymphoblastic leukemia: results from the GMALL study group.
Burmeister T, Meyer C, Schwartz S, Hofmann J, Molkentin M, Kowarz E, Schneider B, Raff T, Reinhardt R, Gokbuget N, Hoelzer D, Thiel E, Marschalek R.
Blood. 2009 Apr 23;113(17):4011-5. Epub 2009 Jan 14.
PMID 19144982
 
PDGFRA (platelet-derived growth factor receptor, alpha polypeptide)
Dessen P.
Atlas Genet Cytogenet Oncol Haematol. 2009. URL: http://atlasgeneticsoncology.org/Genes/GC_PDGFRA.html
 
Cryptic insertion into 11q23 of MLLT10 not involved in t(1;15;11;10)(p36;q11;q23;q24) in infant acute biphenotypic leukemia.
Matsuda K, Tanaka M, Araki S, Yanagisawa R, Yamauchi K, Koike K.
Cancer Genet Cytogenet. 2009 Apr 15;190(2):113-20.
PMID 19380030
 
An interstitial deletion at 3p21.3 results in the genetic fusion of MLH1 and ITGA9 in a Lynch syndrome family.
Meyer C, Brieger A, Plotz G, Weber N, Passmann S, Dingermann T, Zeuzem S, Trojan J, Marschalek R.
Clin Cancer Res. 2009a Feb 1;15(3):762-9.
PMID 19188145
 
New insights to the MLL recombinome of acute leukemias.
Meyer C, Kowarz E, Hofmann J, Renneville A, Zuna J, Trka J, Ben Abdelali R, Macintyre E, De Braekeleer E, De Braekeleer M, Delabesse E, de Oliveira MP, Cave H, Clappier E, van Dongen JJ, Balgobind BV, van den Heuvel-Eibrink MM, Beverloo HB, Panzer-Grumayer R, Teigler-Schlegel A, Harbott J, Kjeldsen E, Schnittger S, Koehl U, Gruhn B, Heidenreich O, Chan LC, Yip SF, Krzywinski M, Eckert C, Moricke A, Schrappe M, Alonso CN, Schafer BW, Krauter J, Lee DA, Zur Stadt U, Te Kronnie G, Sutton R, Izraeli S, Trakhtenbrot L, Lo Nigro L, Tsaur G, Fechina L, Szczepanski T, Strehl S, Ilencikova D, Molkentin M, Burmeister T, Dingermann T, Klingebiel T, Marschalek R.
Leukemia. 2009 Aug;23(8):1490-9. Epub 2009 Mar 5.
PMID 19262598
 
LDI-PCR: identification of known and unknown gene fusions of the human MLL gene.
Meyer C, Marschalek R.
Methods Mol Biol. 2009;538:71-83.
PMID 19277576
 
Identification of the gene encoding cyclin E1 (CCNE1) as a novel IGH translocation partner in t(14;19)(q32;q12) in diffuse large B-cell lymphoma.
Nagel I, Akasaka T, Klapper W, Gesk S, Bottcher S, Ritgen M, Harder L, Kneba M, Dyer MJ, Siebert R.
Haematologica. 2009 Jul;94(7):1020-3. Epub 2009 May 19.
PMID 19454496
 
Deregulated expression of cytokine receptor gene, CRLF2, is involved in lymphoid transformation in B-cell precursor acute lymphoblastic leukemia.
Russell LJ, Capasso M, Vater I, Akasaka T, Bernard OA, Calasanz MJ, Chandrasekaran T, Chapiro E, Gesk S, Griffiths M, Guttery DS, Haferlach C, Harder L, Heidenreich O, Irving J, Kearney L, Nguyen-Khac F, Machado L, Minto L, Majid A, Moorman AV, Morrison H, Rand V, Strefford JC, Schwab C, Tonnies H, Dyer MJ, Siebert R, Harrison CJ.
Blood. 2009 Sep 24;114(13):2688-98. Epub 2009 Jul 29.
PMID 19641190
 
A second NOTCH1 chromosome rearrangement: t(9;14)(q34.3;q11.2) in T-cell neoplasia.
Suzuki S, Nagel S, Schneider B, Chen S, Kaufmann M, Uozumi K, Arima N, Drexler HG, MacLeod RA.
Leukemia. 2009 May;23(5):1003-6. Epub 2009 Jan 8.
PMID 19151773
 
Comparison and critical evaluation of PCR-mediated methods to walk along the sequence of genomic DNA.
Tonooka Y, Fujishima M.
Appl Microbiol Biotechnol. 2009 Nov;85(1):37-43. (REVIEW)
PMID 19714325
 
Identification of a MYO18A-PDGFRB fusion gene in an eosinophilia-associated atypical myeloproliferative neoplasm with a t(5;17)(q33-34;q11.2).
Walz C, Haferlach C, Hanel A, Metzgeroth G, Erben P, Gosenca D, Hochhaus A, Cross NC, Reiter A.
Genes Chromosomes Cancer. 2009 Feb;48(2):179-83.
PMID 19006078
 
Chronic lymphocytic leukemia With t(2;14)(p16;q32) involves the BCL11A and IgH genes and is associated with atypical morphologic features and unmutated IgVH genes.
Yin CC, Lin KI, Ketterling RP, Knudson RA, Medeiros LJ, Barron LL, Huh YO, Luthra R, Keating MJ, Abruzzo LV.
Am J Clin Pathol. 2009 May;131(5):663-70.
PMID 19369625
 
ALK (anaplastic lymphoma receptor tyrosine kinase).
Allouche M.
Atlas Genet Cytogenet Oncol Haematol. February 2010. URL: http://AtlasGeneticsOncology.org/Genes/ALK.html
 
Nebulette is the second member of the nebulin family fused to the MLL gene in infant leukemia.
Coser VM, Meyer C, Basegio R, Menezes J, Marschalek R, Pombo-de-Oliveira MS.
Cancer Genet Cytogenet. 2010 Apr 15;198(2):151-4.
PMID 20362230
 
Complex and cryptic chromosomal rearrangements involving the MLL gene in acute leukemia: a study of 7 patients and review of the literature.
De Braekeleer E, Meyer C, Douet-Guilbert N, Morel F, Le Bris MJ, Berthou C, Arnaud B, Marschalek R, Ferec C, De Braekeleer M.
Blood Cells Mol Dis. 2010 Apr 15;44(4):268-74. Epub 2010 Mar 4.
PMID 20206559
 
CD44 activation in mature B-cell malignancies by a novel recurrent IGH translocation.
Hu XT, Chen YW, Liang AC, Au WY, Wong KY, Wan TS, Wong ML, Shen L, Chan KK, Guo T, Chu KM, Tao Q, Chim CS, Loong F, Choi WW, Lu L, So CC, Chan LC, Kwong YL, Liang RH, Srivastava G.
Blood. 2010 Mar 25;115(12):2458-61. Epub 2010 Jan 21.
PMID 20093404
 
Three-way translocation involving MLL, MLLT1, and a novel third partner, NRXN1, in a patient with acute lymphoblastic leukemia and t(2;19;11) (p12;p13.3;q23).
Lee SG, Park TS, Won SC, Song J, Lee KA, Choi JR, Marschalek R, Meyer C.
Cancer Genet Cytogenet. 2010 Feb;197(1):32-8.
PMID 20113834
 
Written2010-04Björn Schneider, Hans G Drexler, Roderick AF MacLeod
German Collection of Microorganisms, Cell Cultures, Department of Human, Animal Cell Cultures, Inhoffenstr. 7b, 38124 Braunschweig, Germany

Citation

This paper should be referenced as such :
Schneider, B ; Drexler, HG ; MacLeod, RAF
LDI-PCR in Cancer Translocation Mapping
Atlas Genet Cytogenet Oncol Haematol. 2011;15(1):106-114.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Deep/LDI-PCRinCancerID20087.htm

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