Mapping chromosome band 11q23 in human acute leukemia with biotinylated probes: identification of 11q23 translocation breakpoints with a yeast artificial chromosome.

Abstract Partner sites of 14q32 translocations found in B-cell malignancies were detected by fluorescence in situ hybridization (FISH) using yeast artificial chromosome (YAC) clones, Y20 and Y6, containing the human Ig heavy chain (IgH) gene locus. Y20 spans a 160-kb upstream and 40-kb downstream region of the JH segments on chromosome band 14q32.33. Y6 is 300-kb upstream of Y20, and spans a further 320-kb telomeric region. The human DNA sequences amplified by Alu polymerase chain reaction of the YAC clones were used as probes for FISH to study six patients with non-Hodgkin's lymphoma (NHL), one patient with acute lymphoblastic leukemia, and one cell line FR4 established from a plasmacytoma. Three telomeric YAC clones each specific for 3q, 8q, and 18q were also used to further characterize 14q32 translocations. The IgH YACs were successfully applied to detect cytogenetically invisible subtelomeric translocation of the IgH gene locus to each partner site in t(14;18), t(8;14), and t(14;19), and to identify t(3;14) (q27;q32.33) in three patients with 14q32 translocation of unknown origin. Furthermore, complex translocations involving more than three chromosomes were detected in an NHL patient with t(8;14), and t(3;12), and in the FR4 with der(14)t(8;14), der(8)dic(1;8), and del(1)(q21). The technique would be a useful tool in elucidating the mechanisms of a 14q32 translocation in B-cell malignancies.

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Fluorescence in situ hybridization mapping of translocations and deletions involving the short arm of human chromosome 12 in malignant hematologic diseases

Blood ◽

10.1182/blood.v84.10.3473.bloodjournal84103473 ◽

1994 ◽

Vol 84 (10) ◽

pp. 3473-3482 ◽

Cited By ~ 3

Author(s):

H Kobayashi ◽

KT Montgomery ◽

SK Bohlander ◽

CN Adra ◽

BL Lim ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Cell Line ◽

Yeast Artificial Chromosome ◽

Artificial Chromosome ◽

Chromosome 12 ◽

Fish Analysis ◽

Translocation Breakpoints ◽

Hybridization Mapping

Translocations and deletions of the short arm of chromosome 12 [t(12p) and del(12p)] are common recurring abnormalities in a broad spectrum of hematologic malignant diseases. We studied 20 patients and one cell line whose cells contained 12p13 translocations and/or 12p deletions using fluorescence in situ hybridization (FISH) with phage, plasmid, and cosmid probes that we previously mapped and ordered on 12p12–13. FISH analysis showed that the 12p13 translocation breakpoints were clustered between two cosmids, D12S133 and D12S142, in 11 of 12 patients and in one cell line. FISH analysis of 11 patients with deletions demonstrated that the deletions were interstitial rather than terminal and that the distal part of 12p12, including the GDI-D4 gene and D12S54 marker, was deleted in all 11 patients. Moreover, FISH analysis showed that cells from 3 of these patients contained both a del(12p) and a 12p13 translocation and that the affected regions of these rearrangements appeared to overlap. We identified three yeast artificial chromosome (YAC) clones that span all the 12p13 translocation breakpoints mapped between D12S133 and D12S142. They have inserts of human DNA between 1.39 and 1.67 Mb. Because the region between D12S133 and D12S142 also represents the telomeric border of the smallest commonly deleted region of 12p, we also studied patients with a del(12p) using these YACs. The smallest YAC, 964c10, was deleted in 8 of 9 patients studied. In the other patient, the YAC labeled the del(12p) chromosome more weakly than the normal chromosome 12, suggesting that a part of the YAC was deleted. Thus, most 12p13 translocation breakpoints were clustered within the sequences contained in the 1.39 Mb YAC and this YAC appears to include the telomeric border of the smallest commonly deleted region. Whether the same gene is involved in both the translocations and deletions is presently unknown.

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Molecular cloning of translocation breakpoints in a case of constitutional translocation t(11;22)(q23;q11) and preparation of probes for preimplantation genetic diagnosis

Reproduction Fertility and Development ◽

10.1071/rd98110 ◽

1999 ◽

Vol 11 (1) ◽

pp. 17 ◽

Cited By ~ 6

Author(s):

Jingly Fung ◽

Santiago Munné ◽

Jaqueline Garcia ◽

Ung-Jin Kim ◽

Heinz-Ulli G. Weier

Keyword(s):

Preimplantation Genetic Diagnosis ◽

Yeast Artificial Chromosome ◽

Chromosomal Abnormalities ◽

Genetic Diagnosis ◽

Artificial Chromosome ◽

Preimplantation Embryos ◽

Cytogenetic Map ◽

Additional Time ◽

Interphase Cell ◽

Translocation Breakpoints

In vitro fertilization (IVF) centres with preimplantation genetic diagnosis (PGD) programmes are often confronted with the problem of identifying chromosomal abnormalities in interphase cells biopsied from preimplantation embryos of carriers of a reciprocal translocation. The present authors have developed a DNA testing based approach to analyse embryos from translocation carriers, and this report describes breakpoint-spanning probes to detect abnormalities in cases of the most common human translocation (i.e. the t(11;22)(q23;q11)). Screening a yeast artificial chromosome (YAC) library for probes covering the respective breakpoint regions in the patient lead to probes for the breakpoint on chromosome 11q23. The physically mapped YAC and bacterial artificial chromosome (BAC) clones from chromosome 22 were then integrated with the cytogenetic map, which allowed localization of the breakpoint on chromosome 22q11 to an interval of less than 84 kb between markers D22S184 and KI457 and to prepare probes suitable for interphase cell analysis. In summary, breakpoint localization could be accomplished in about 4 weeks with additional time needed to optimize probes for use in PGD.

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Fluorescence in situ hybridization mapping of translocations and deletions involving the short arm of human chromosome 12 in malignant hematologic diseases

Blood ◽

10.1182/blood.v84.10.3473.3473 ◽

1994 ◽

Vol 84 (10) ◽

pp. 3473-3482 ◽

Cited By ~ 52

Author(s):

H Kobayashi ◽

KT Montgomery ◽

SK Bohlander ◽

CN Adra ◽

BL Lim ◽

...

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Cell Line ◽

Yeast Artificial Chromosome ◽

Artificial Chromosome ◽

Chromosome 12 ◽

Fish Analysis ◽

Translocation Breakpoints ◽

Hybridization Mapping

Abstract Translocations and deletions of the short arm of chromosome 12 [t(12p) and del(12p)] are common recurring abnormalities in a broad spectrum of hematologic malignant diseases. We studied 20 patients and one cell line whose cells contained 12p13 translocations and/or 12p deletions using fluorescence in situ hybridization (FISH) with phage, plasmid, and cosmid probes that we previously mapped and ordered on 12p12–13. FISH analysis showed that the 12p13 translocation breakpoints were clustered between two cosmids, D12S133 and D12S142, in 11 of 12 patients and in one cell line. FISH analysis of 11 patients with deletions demonstrated that the deletions were interstitial rather than terminal and that the distal part of 12p12, including the GDI-D4 gene and D12S54 marker, was deleted in all 11 patients. Moreover, FISH analysis showed that cells from 3 of these patients contained both a del(12p) and a 12p13 translocation and that the affected regions of these rearrangements appeared to overlap. We identified three yeast artificial chromosome (YAC) clones that span all the 12p13 translocation breakpoints mapped between D12S133 and D12S142. They have inserts of human DNA between 1.39 and 1.67 Mb. Because the region between D12S133 and D12S142 also represents the telomeric border of the smallest commonly deleted region of 12p, we also studied patients with a del(12p) using these YACs. The smallest YAC, 964c10, was deleted in 8 of 9 patients studied. In the other patient, the YAC labeled the del(12p) chromosome more weakly than the normal chromosome 12, suggesting that a part of the YAC was deleted. Thus, most 12p13 translocation breakpoints were clustered within the sequences contained in the 1.39 Mb YAC and this YAC appears to include the telomeric border of the smallest commonly deleted region. Whether the same gene is involved in both the translocations and deletions is presently unknown.

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Protein tyrosine phosphatase receptor type C polypeptide (PTPRC) on human chromosome band 1q31→q32 localizes with marker D1S4131 on a 610-kb yeast artificial chromosome

Cytogenetic and Genome Research ◽

10.1159/000015431 ◽

1999 ◽

Vol 87 (3-4) ◽

pp. 223-224

Author(s):

L.K. Goff ◽

S. van Soest ◽

M. Timón ◽

E. Tchilian ◽

P.C.L. Beverley

Keyword(s):

Human Chromosome ◽

Protein Tyrosine Phosphatase ◽

Yeast Artificial Chromosome ◽

Tyrosine Phosphatase ◽

Artificial Chromosome ◽

Receptor Type ◽

Chromosome Band ◽

Protein Tyrosine ◽

Type C ◽

Human Chromosome Band

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Structure of the Chromosome VII Centromere Region in Neurospora crassa: Degenerate Transposons and Simple Repeats

Molecular and Cellular Biology ◽

10.1128/mcb.18.9.5465 ◽

1998 ◽

Vol 18 (9) ◽

pp. 5465-5477 ◽

Cited By ~ 69

Author(s):

Edward B. Cambareri ◽

Rafael Aisner ◽

John Carbon

Keyword(s):

Neurospora Crassa ◽

Yeast Artificial Chromosome ◽

Fragment Length Polymorphism ◽

Artificial Chromosome ◽

Polymorphism Analysis ◽

Dna Repeats ◽

Centromere Region ◽

Simple Repeats ◽

Restriction Fragment Length ◽

Repeat Induced Point Mutation

ABSTRACT DNA from the centromere region of linkage group (LG) VII ofNeurospora crassa was cloned previously from a yeast artificial chromosome library and was found to be atypical ofNeurospora DNA in both composition (AT rich) and complexity (repetitive). We have determined the DNA sequence of a small portion (∼16.1 kb) of this region and have identified a cluster of three new retrotransposon-like elements as well as degenerate fragments from the 3′ end of Tad, a previously identified LINE-like retrotransposon. This region contains a novel full-length but nonmobilecopia-like element, designated Tcen, that is only associated with centromere regions. Adjacent DNA contains portions of a gypsy-like element designated Tgl1. A third new element, Tgl2, shows similarity to theTy3 transposon of Saccharomyces cerevisiae. All three of these elements appear to be degenerate, containing predominantly transition mutations suggestive of the repeat-induced point mutation (RIP) process. Three new simple DNA repeats have also been identified in the LG VII centromere region. While Tcenelements map exclusively to centromere regions by restriction fragment length polymorphism analysis, the defective Tad elements appear to occur most frequently within centromeres but are also found at other loci including telomeres. The characteristics and arrangement of these elements are similar to those seen in theDrosophila centromere, but the relative abundance of each class of repeats, as well as the sequence degeneracy of the transposon-like elements, is unique to Neurospora. These results suggest that the Neurospora centromere is heterochromatic and regional in character, more similar to centromeres of Drosophila than to those of most single-cell yeasts.

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Entire maize chloroplast genome is stably maintained in a yeast artificial chromosome

Plant Molecular Biology ◽

10.1007/bf00040631 ◽

1991 ◽

Vol 17 (3) ◽

pp. 361-369 ◽

Cited By ~ 6

Author(s):

Manju Gupta ◽

Brad Hoo

Keyword(s):

Chloroplast Genome ◽

Yeast Artificial Chromosome ◽

Artificial Chromosome ◽

Maize Chloroplast

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Chromosomal localization of human genes for arylamine N-acetyltransferase

Biochemical Journal ◽

10.1042/bj2970441 ◽

1994 ◽

Vol 297 (3) ◽

pp. 441-445 ◽

Cited By ~ 64

Author(s):

D Hickman ◽

A Risch ◽

V Buckle ◽

N K Spurr ◽

S J Jeremiah ◽

...

Keyword(s):

Bladder Cancer ◽

In Situ Hybridization ◽

Yeast Artificial Chromosome ◽

Chromosomal Localization ◽

Artificial Chromosome ◽

Acetylator Phenotype ◽

Chromosome 8 ◽

Slow Acetylator ◽

Human Genes

Arylamine N-acetyltransferase is encoded at two loci, AAC-1 and AAC-2, on human chromosome 8. The products of the two loci are able to catalyse N-acetylation of arylamine carcinogens, such as benzidine and other xenobiotics. AAC-2 is polymorphic and individuals carrying the slow-acetylator phenotype are more susceptible to benzidine-induced bladder cancer. We have identified yeast artificial chromosome clones encoding AAC-1 and AAC-2 and have used the cloned DNAs as fluorescent probes for in situ hybridization. The hybridization patterns allow assignment of AAC-1 and AAC-2 to chromosome 8p21.3-23.1, a region in which deletions have been associated with bladder cancer [Knowles, Shaw and Proctor (1993) Oncogene 8, 1357-1364].

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