An STS-Based Radiation Hybrid Map of the Human Genome

Stewart, Elizabeth A.; McKusick, Kathleen B.; Aggarwal, Amita; Bajorek, E.; Brady, Shannon D.; Chu, Angela M.; Fang, N.; Hadley, David; Harris, Mark; Hussain, Syed Yasir; Lee, Richard S.; Maratukulam, A.; O`Connor, K.; Perkins, S.; Piercy, Mark; Qin, Fawn; Reif, Tim; Sanders, C.; She, Xiaohong; Sun, Wei; Tabar, P.; Voyticky, S.; Cowles, Sid; Fan, Jie; Mader, Chris; Quackenbush, John; Myers, R; Cox, David

doi:10.1101/gr.7.5.422

Cited by 309 publications

(231 citation statements)

References 27 publications

(31 reference statements)

Supporting

Mentioning

213

Contrasting

Unclassified

Order By: Relevance

“…The sequence of the partner DNA in the treatment-related ALL did not share homology with known sequences of AF-4. Nonetheless, the closest framework marker to the AF-4 gene (24) and to the partner DNA in the treatment-related ALL was the same. These results suggest that panhandle PCR amplified either a previously uncharacterized intronic region of the AF-4 gene or, alternatively, another genomic region in close proximity to AF-4.…”

Section: Discussionmentioning

confidence: 91%

See 1 more Smart Citation

Panhandle PCR strategy to amplify MLL genomic breakpoints in treatment-related leukemias

Megonigal

Rappaport

Jones

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Panhandle PCR amplifies genomic DNA with known 5 and unknown 3 sequences from a template with an intrastrand loop schematically shaped like a pan with a handle. We used panhandle PCR to clone MLL genomic breakpoints in two pediatric treatment-related leukemias. The karyotype in a case of treatment-related acute lymphoblastic leukemia showed the t(4;11)(q21;q23). Panhandle PCR amplified the translocation breakpoint at position 2158 in intron 6 in the 5 MLL breakpoint cluster region (bcr). The karyotype in a case of treatment-related acute myeloid leukemia was normal, but Southern blot analysis showed a single MLL gene rearrangement. Panhandle PCR amplified the breakpoint at position 1493 in MLL intron 6. Screening of somatic cell hybrid and radiation hybrid DNAs by PCR and reverse transcriptase-PCR analysis of the leukemic cells indicated that panhandle PCR identified a fusion of MLL intron 6 with a previously uncharacterized sequence in MLL intron 1, consistent with a partial duplication. In both cases, the breakpoints in the MLL bcr were in Alu repeats, and there were Alu repeats in proximity to the breakpoints in the partner DNAs, suggesting that Alu sequences were relevant to these rearrangements. This study shows that panhandle PCR is an effective method for cloning MLL genomic breakpoints in treatment-related leukemias. Analysis of additional pediatric cases will determine whether breakpoint distribution deviates from the predilection for 3 distribution in the bcr that has been found in adult cases.DNA topoisomerase II catalyzes transient cleavage and rejoining of both strands of the DNA double helix (1). Epipodophyllotoxins form a complex with the DNA and DNA topoisomerase II, decrease DNA rejoining, and cause chromosomal breakage (2). Epipodophyllotoxins and other DNA topoisomerase II inhibitors are associated with leukemias with translocations of a breakpoint cluster region (bcr) of the MLL gene at chromosome band 11q23 (3-10). One suggested model for the translocations involving MLL entails DNA topoisomerase II-mediated chromosomal breakage followed by fusion of DNA free ends from different chromosomes through DNA repair (11). A better understanding of the translocation mechanism may come through genomic breakpoint cloning in many other cases.However, MLL genomic breakpoint cloning by PCR is difficult because MLL has myriad partner genes, and karyotype analysis does not detect the rearrangement or give information about potential translocation partners in onethird of cases (8). Other rearrangements result from partial duplication of several exons of the MLL gene (12-19). Panhandle PCR amplifies genomic DNA with known 5Ј and unknown 3Ј sequences and does not require specific primers for the many partner genes of MLL (20,21). In the present study, we used panhandle PCR to surmount the problem of MLL genomic breakpoint cloning in two pediatric DNA topoisomerase II inhibitor-related leukemias. To validate the method, we first used panhandle PCR in a treatment-related leukemia in which the cytogeneti...

show abstract

Section: Discussionmentioning

confidence: 91%

“…However, screening of radiation hybrid panel DNAs previously indicated that the nearest linked marker to the AF-4 gene was also D4S1542 (24), suggesting that the partner DNA in the treatment-related ALL was derived from either AF-4 or from a genomic sequence in close proximity to AF-4.…”

Section: Resultsmentioning

confidence: 99%

Panhandle PCR strategy to amplify MLL genomic breakpoints in treatment-related leukemias

Megonigal

Rappaport

Jones

et al. 1997

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…The Coriell Monochromosomal Panel 2 (Coriell Cell Repositories, Camden, NJ) was PCR screened with primers IPF85 and IPB83 to establish a gross chromosomal localization. A finer localization was achieved by a PCR screen with the same primers against the Stanford Human Genome Center G3 radiation hybrid panel (Stewart et al, 1997). PCR primers were also designed within putative coding regions of the genomic sequence as determined by homology to Xenopus melanopsin (primer I PF70, 5Ј-GACACCC TACATGAGC -TCGG-3Ј; primer IPB64, 5Ј-CTGTACTTGGGGTGGGTGAT-3Ј).…”

Section: Methodsmentioning

confidence: 99%

A Novel Human Opsin in the Inner Retina

et al. 2000

View full text Add to dashboard Cite

Here we report the identification of a novel human opsin, melanopsin, that is expressed in cells of the mammalian inner retina. The human melanopsin gene consists of 10 exons and is mapped to chromosome 10q22. This chromosomal localization and gene structure differs significantly from that of other human opsins that typically have four to seven exons. A survey of 26 anatomical sites indicates that, in humans, melanopsin is expressed only in the eye. In situ hybridization histochemistry shows that melanopsin expression is restricted to cells within the ganglion and amacrine cell layers of the primate and murine retinas. Notably, expression is not observed in retinal photoreceptor cells, the opsin-containing cells of the outer retina that initiate vision. The unique inner retinal localization of melanopsin suggests that it is not involved in image formation but rather may mediate nonvisual photoreceptive tasks, such as the regulation of circadian rhythms and the acute suppression of pineal melatonin. The anatomical distribution of melanopsinpositive retinal cells is similar to the pattern of cells known to project from the retina to the suprachiasmatic nuclei of the hypothalamus, a primary circadian pacemaker.

show abstract

“…Each cell line was analyzed by PCR amplification and the products were resolved on 6% polyacrylamide gels and silverstained. The second approach made use of the Stanford G3 humanhamster radiation hybrid somatic cell panel (Cox et al 1990;Stewart et al 1997), which was purchased from Research Genetics (Huntsville, AL, USA). The amplification products were resolved using a denaturing 6% polyacrylamide gel on the ALFExpress sequencer (Pharmacia).…”

Section: Chromosomal Mapping Of the Six Y Microsatellite Locimentioning

confidence: 99%

Divergent Human Y-Chromosome Microsatellite Evolution Rates

et al. 1999

View full text Add to dashboard Cite

Abstract:In this work, we analyze several characteristics influencing the low variability of the microsatellite DYS19 in the major founder Amerindian Y chromosome lineage containing the point mutation DYS199-T. Variation of DYS19 was compared with that of five other Y-linked tetranucleotide repeat loci (DYS389A, DYS389B, DYS390, DYS391, and DYS393) in the DYS199-T lineage. All the other microsatellites showed significantly higher levels of variability than DYS19 as measured by gene diversity and repeat number variance. Moreover, we had previously shown that DYS19 had high diversity in Brazilians and in several other populations worldwide. Thus, the slow DYS19 evolution in the DYS199-T lineage seems to be both locus and allele specific. To understand the slow DYS19 evolutionary rate, the microsatellite loci were compared according to their mapping on the Y chromosome and also on the basis of structural aspects such as the base composition of the repeat motif and flanking regions and the degree of perfection and size (repeat number) of the variable blocks. The only observed difference that might be related to the low DYS19 variability is its small average number of repeats, a value expected to be closer to the founder DYS19 allele in the DYS199-T lineage. These data were also compared to other derived Y lineages. The Tat-C lineage displayed a lower DYS19 variability correlated to a small average repeat number, while in the DYS234-G lineage, a high DYS19 variability was found associated to a larger average repeat number. This approach reveals that evolution of Y microsatellites in lineages defined by slowly evolving markers, such as point mutations, can be greatly influenced by the size (number of repeats of the variable block) of the founder allele in each microsatellite locus. Thus lineage-dating methods using microsatellite variation should be practiced with great care.

show abstract

An STS-Based Radiation Hybrid Map of the Human Genome

Cited by 309 publications

References 27 publications

Panhandle PCR strategy to amplify MLL genomic breakpoints in treatment-related leukemias

Panhandle PCR strategy to amplify MLL genomic breakpoints in treatment-related leukemias

A Novel Human Opsin in the Inner Retina

Divergent Human Y-Chromosome Microsatellite Evolution Rates

Contact Info

Product

Resources

About