Sequence and Analysis of the Human ABL Gene, the BCR Gene, and Regions Involved in the Philadelphia Chromosomal Translocation

Chissoe, Stephanie L.; Bodenteich, Angelika; Wang, Yunfang; Wang, Ying‐Ping; Burian, Dennis; Clifton, Sandra W.; Crabtree, Judy S.; Freeman, Alexandra F.; Iyer, Kala; Li, Jian; Ma, Yichen; McLaury, Hei-Jen; Pan, Huaqin; Sarhan, Omayma H.; Toth, Steve; Wang, Zhili; Zhang, Guozhong; Heisterkamp, Nora; Groffen, John; Roe, Bruce A.

doi:10.1006/geno.1995.1008

Cited by 193 publications

(149 citation statements)

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“…60,61 DNA sequence analysis of the major breakpoint cluster region of Philadelphia chromosome in chronic myelogenous leukemia has revealed chi-like octamers. 62,63 Chi-like octamers were also identified in the bcl-2 major (mbr) and minor (mcr) breakpoint regions as well as their IgH reciprocal counterparts, which constitute the chromosomal translocation t(14;18)(q32;q31), the pathogenetic hallmark of follicular lymphoma. 64 Other sequences that favor chromosomal recombinations are repetitive ones, 11 like the SINEs 65-69 and the long interspersed nucleic elements (LINEs).…”

Section: Resultsmentioning

confidence: 99%

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

Papadopoulos

Benter

Anastassiou

et al. 2002

Intl Journal of Cancer

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Some types of cancer have been associated with abnormal DNA fingerprinting. We used random amplified polymorphic DNA (RAPD) to generate fingerprints that detect genomic alterations in human breast cancer. Primers were designed by choosing sequences involved in the development of DNA mutations. Seventeen primers in 44 different combinations were used to screen a total of 6 breast cancer DNA/normal DNA pairs and 6 uveal melanoma DNA/normal DNA pairs. Forty-five percent of these combinations reliably detected quantitative differences in the breast cancer pairs, while only 18% of these combinations detected differences in the uveal melanoma pairs. Fourteen (32%) and 12 (27%) primers generated a smear or did not produce any band patterns in the first and second cases, respectively. Taking into account the ability of RAPD to screen the whole genome, our results suggest that the genomic damage in breast cancer is significantly higher than in uveal melanoma. Our study confirms other reports that the molecular karyotypes produced with random priming, called amplotypes, are very useful for assessing genomic damage in cancer. Genomic instability is a hallmark of neoplastic transformation and a herald of genomic damage. The existence of an additional type of genomic instability has been described, the microsatellite mutator phenotype pathway. Progress in molecular cancer genetics has facilitated the detection of these mutations. In the last decade, representation differential analysis and comparative genomic hybridization (CGH) were added to methods like flow cytometry, restriction fragment length polymorphisms of polymorphic minisatellite loci and allelotyping, a PCR amplification of informative microsatellite loci.Another promising approach has been introduced, arbitrarily primed PCR 1 combined with random amplified polymorphic DNA (RAPD). 2 Both PCR-based techniques, called amplotyping, use fingerprinting to quantitatively and qualitatively evaluate band alterations. 3 This random priming method allows comparison of normal and tumor tissues at a minimum of 20 -40 genome sites in a single PCR, though evidence suggests that the number of compared loci runs into the hundreds if we take into account that a gel band consists of many comigrating fragments. 4,5 It also includes internal controls and detects moderate gains of chromosomal sequences (trisomy/tetrasomy) that would otherwise escape detection.Previously, we addressed the problems of reproducibility and contamination in random priming. In the present work, we used RAPD fingerprinting to assess the genomic damage present in breast cancer and in uveal melanoma cells. For this task, we designed primers based on sequences that are supposed to play an important role in the mechanisms leading to DNA alterations. Human gene mutations appear to be caused by multiple mechanisms whose relative importance is probably governed by local primary and secondary DNA structure. 7 We have searched for consensus sequences located in the immediate vicinity of gene mutations and for "hot s...

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Section: Resultsmentioning

confidence: 99%

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

Papadopoulos

Benter

Anastassiou

et al. 2002

Intl Journal of Cancer

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“…The detailed procedures for cosmid DNA isolation, random shotgun cloning, fluorescent-based DNA sequencing and subsequent analysis have been described (Bodenteich et al, 1993;Pan et al, 1994;Chissoe et al, 1995). Briefly, the cosmid 36 DNA was isolated free from host genomic DNA via a cleared lysate-diatomaceous earth-based protocol (Pan et al, 1994).…”

Section: Dna Sequencingmentioning

confidence: 99%

Analyses of the cag pathogenicity island of Helicobacter pylori

Akopyants¹,

Clifton²,

Kersulyte³

et al. 1998

Molecular Microbiology

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677

331

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SummaryMost strains of Helicobacter pylori from patients with peptic ulcer disease or intestinal-type gastric cancer carry cagA, a gene that encodes an immunodominant protein of unknown function, whereas many of the strains from asymptomatically infected persons lack this gene. Recent studies showed that the cagA gene lies near the right end of a Ϸ37 kb DNA segment (a pathogenicity island, or PAI) that is unique to cagA þ strains and that the cag PAI was split in half by a transposable element insertion in the reference strain NCTC11638. In complementary experiments reported here, we also found the same cag PAI, and sequenced a 39 kb cosmid clone containing the left 'cagII' half of this PAI. Encoded in cagII were four proteins each with homology to four components of multiprotein complexes of Bordetella pertussis ('Ptl'), Agrobacterium tumefaciens ('Vir'), and conjugative plasmids ('Tra') that help deliver pertussis toxin and T (tumour inducing) and plasmid DNA, respectively, to target eukaryotic or prokaryotic cells, and also homologues of eukaryotic proteins that are involved in cytoskeletal structure. To the left of cagII in this cosmid were genes for homologues of HslU (heat-shock protein) and Era (essential GTPase); to the right of cagII were homologues of genes for a type I restriction endonuclease and ion transport functions. Deletion of the cag PAI had no effect on synthesis of the vacuolating cytotoxin, but this deletion and several cag insertion mutations blocked induction of synthesis of proinflammatory cytokine IL-8 in gastric epithelial cells. Comparisons among H. pylori strains indicated that cag PAI gene content and arrangement are rather well conserved. We also identified two genome rearrangements with end-points in the cag PAI. One, in reference strain NCTC11638, involved IS605, a recently described transposable element (as also found by others). Another rearrangement, in 3 of 10 strains tested (including type strain NCTC11637), separated the normally adjacent cagA and picA genes and did not involve IS605. Our results are discussed in terms of how cagencoded proteins might help trigger the damaging inflammatory responses in the gastric epithelium and possible contributions of DNA rearrangements to genome evolution.

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“…However, the source of the inserted sequence in our patient has not been found in a gene databank search, possibly because not all of the human ABL gene has been sequenced 17 or may have arisen due to a mutation in the patient. The inserted sequence has, however, remained unchanged and unique, from diagnosis until remission several years later.…”

Section: Discussionmentioning

confidence: 99%

A novel BCR-ABL rearrangement in a Philadelphia chromosome-positive chronic myelogenous leukaemia variant with thrombocythaemia

Rubinstein

1998

Leukemia

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Reverse transcription polymerase chain reaction was used to detect an unusual BCR/ABL transcript in a patient who presented with thrombocythaemia and was Philadelphia chromosome positive but weakly reactive to conventional BCR/ABL fusion probes. Sequencing revealed the presence of a 12 bp insert between BCR exon2 (b2) and ABL exon2 (a2). In such cases the use of conventional BCR/ABL probes may lead to false negative results. This is the first report of this transcript. Clinically the patient has responded well to therapy.

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Sequence and Analysis of the Human ABL Gene, the BCR Gene, and Regions Involved in the Philadelphia Chromosomal Translocation

Cited by 193 publications

References 0 publications

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

Assessment of genomic instability in breast cancer and uveal melanoma by random amplified polymorphic DNA analysis

Analyses of the cag pathogenicity island of Helicobacter pylori

A novel BCR-ABL rearrangement in a Philadelphia chromosome-positive chronic myelogenous leukaemia variant with thrombocythaemia

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