Sequence patterns and hybridization analysis of clones generated by<i>Alu</i>-PCR

Müllenbach, Roman; Tisborn, Sabine; Blin, Nikolaus

doi:10.3109/10425179409020848

DNA Sequence

1994

DOI: 10.3109/10425179409020848

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Sequence patterns and hybridization analysis of clones generated byAlu-PCR

Roman Müllenbach¹,

Sabine Tisborn²,

Nikolaus Blin³

Abstract: A series of clones from an Alu-PCR library were analysed in more detail. Characterization by Southern blot hybridization and sequencing displayed several features common to all probes generated by this approach: Short length of the PCR-products as well as the presence of homologous regions on both ends resulted in a limited feasibility for filter hybridization and a low probability of restriction length polymorphisms. In addition, a series of different short repeats at the 3'-ends of Alu-repeats and present in… Show more

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Cited by 2 publications

References 17 publications

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Characterization and population diversity of interspersed repeat sequence variants (IRS-morphs)

Kass¹,

Batzer²,

Deininger³

1996

Genome

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Inter-Alu PCR is increasingly useful in human genome mapping studies. One use is the generation of alumorphs, polymorphisms resulting from the presence or absence of inter-Alu PCR products. In this study, we have increased the proportion of the genome that can be analyzed by this technique with the use of long interspersed elements (LINEs). The set of polymorphisms detected by both Alu and LINE primers are referred to as interspersed repetitive sequence variants or IRS-morphs. Since a presence-absence variant may have been the result of a recent Alu or LINE insertion, we analyzed 7 isolated IRS-morphs that were generated, in part, with a primer derived from either a consensus LINE or a young Alu subfamily specific sequence, and observed by Southern blot analysis that these variants resulted from other types of genomic alterations. The use of these primers, however, reduces background from the numerous LINEs and Alu elements in the genome, providing sharp DNA fingerprint profiles. We have demonstrated the potential usefulness of these IRS-morph profiles in human population studies. We compared 12 IRS-morphs from a single amplification reaction from five distinct population groups (Caucasian (northern European descent), Hispanic (Mexican-American), Hindu-Indian, Papua New Guinean, and Greenland Eskimo) and observed that most have variable allelic frequencies among populations. The utilization of additional IRS-morph profiles will perpetuate this technique as a tool for DNA fingerprinting and for the analysis of human populations. Key words : Alu elements, DNA fingerprint, human populations, LINEs, SINEs.

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Characterization and population diversity of interspersed repeat sequence variants (IRS-morphs)

Kass¹,

Batzer²,

Deininger³

1996

Genome

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Extranodal Marginal Zone B-Cell Lymphoma Genotyping byAlu— Polymerase Chain Reaction

Bertoni

Müllenbach

Broggini

et al. 2000

Leukemia & Lymphoma

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DNA amplification by polymerase chain reaction (PCR) with primers designed on the widely distributed Alu sequences allows the production of specific inter-Alu DNA-fingerprints. Amplification of tumour and matched normal DNA can show differences due to genetic alterations within the tumour genome. We applied this approach to study low-grade extranodal marginal zone B-cell lymphoma (of MALT type). After digestion with restriction enzymes, DNA samples were separately amplified by PCR with three different Alu-primers. A comparison between the fingerprint pattern from lymphoma and normal samples was made. Inter-Alu bands differing between the two samples were excised from the gel, cloned and sequenced. Nine cases of low-grade MALT-lymphomas have been analysed, giving seventeen different bands between tumour and normal. DNA sequence analysis showed identities for three of them with sequences available at the GenBank. The methodology of Alu-PCR to detect DNA-based abnormalities, in addition or combination with RNA-based methods, is a powerful tool to identify candidate regions frequently altered in tumours. With the increased available genomic sequences through the Human Genome Project, there will be an increasing probability of picking up perfect homologies with these sequences using cloned differential Alu-PCR bands in BLAST searches through genome databases.

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Sequence patterns and hybridization analysis of clones generated byAlu-PCR

Cited by 2 publications

References 17 publications

Characterization and population diversity of interspersed repeat sequence variants (IRS-morphs)

Characterization and population diversity of interspersed repeat sequence variants (IRS-morphs)

Extranodal Marginal Zone B-Cell Lymphoma Genotyping byAlu— Polymerase Chain Reaction

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