The precise breakpoints of a Filipino-type alpha-thalassemia-1 deletion found in two Japanese

A NovelGγAγ(δβ)0-Thalassemia with a 27 kb Deletion

A new (G)gamma(A)gamma(deltabeta)O-thalassemia (thal) was found in six unrelated Japanese individuals, and characterized by a method employing only polymerase chain reaction (PCR) and direct sequencing. This (G)gamma(A)gamma(deltabeta)O-thal mutation has removed a fragment of about 27 kb of DNA, that starts approximately 2.8 kb downstream of the Agamma-globin gene and ends in the L1 repeat sequence, 7.0 kb downstream of the beta-globin gene. The 5' breakpoint is similar to that of the previously reported Japanese (G)gamma(A)gamma(deltabeta)O-thal (called here Jpn type 1 for convenience). However, the 3' endpoint is quite different. This new Japanese deltabeta-thal, designated as Japanese type 2 (Jpn type 2), shows a deletion rather similar to Turkish type 3 deltabeta-thal but with 5' and 3' breakpoints located inside the deletion of Turkish type 3. A mutation-specific gap PCR was designed to diagnose patients with the Jpn type 2 (G)gamma(A)gamma(deltabeta)O-thal. The identified carriers exhibited a thalassemia minor.

A novel epsilon gamma delta beta thalassemia of 1.4 Mb deletion found in a Japanese patient

A novel large deletion, causing epsilon gamma delta beta thalassemia (here called, epsilon gamma delta beta thalassemia Jpn-I) was discovered in a 6-year-old Japanese boy. He was born uneventfully, but revealed thalassemia minor after birth. The mutation was inherited from his mother. The deletion, caused by an illegitimate recombination extended from 750 kb upstream to 660 kb downstream of e-globin gene, and removed about 1.4 Mb of DNA, the largest in epsilon gamma delta beta thalassemias. A 19-nucleotide orphan sequence and direct repeats were present at the junction. The deletion lost several functional genes, but no relevant symptoms manifested. The breakpoints were determined by relatively simple methods.

Human genomic deletions mediated by recombination between Alu elements

Recombination between Alu elements results in genomic deletions associated with many human genetic disorders. Here, we compare the reference human and chimpanzee genomes to determine the magnitude of this recombination process in the human lineage since the human-chimpanzee divergence approximately 6 million years ago. Combining computational data mining and wet-bench experimental verification, we identified 492 human-specific deletions (for a total of approximately 400 kb) attributable to this process, a significant component of the insertion/deletion spectrum of the human genome. The majority of the deletions (295 of 492) coincide with known or predicted genes (including 3 that deleted functional exons, as compared with orthologous chimpanzee genes), which implicates this process in creating a substantial portion of the genomic differences between humans and chimpanzees. Overall, we found that Alu recombination-mediated genomic deletion has had a much higher impact than was inferred from previously identified isolated events and that it continues to contribute to the dynamic nature of the human genome.

The role of Alu repeat clusters as mediators of recurrent chromosomal aberrations in tumors

There is increasing evidence for the involvement of repetitive DNA sequences as facilitators of some of the recurrent chromosomal rearrangements observed in human tumors. The high densities of repetitive DNA, such as Alu elements, at some chromosomal translocation breakpoint regions has led to the suggestion that these sequences could provide hot spots for homologous recombination, and could mediate the translocation process and elevate the likelihood of other types of chromosomal rearrangements taking place. The Alu core sequence itself has been suggested to promote DNA strand exchange and genomic rearrangement, and it has striking sequence similarity to chi (which has been shown to stimulate recBCD-mediated recombination in Escherichia coli). Alu repeats have been shown to be involved in the generation of many constitutional gene mutations in meiotic cells, attributed to unequal homologous recombination and consequent deletions and/or duplication events. It has recently been demonstrated that similar deletion events can take place in neoplasia because several types of leukemia-associated chromosomal rearrangements frequently have submicroscopic deletions immediately adjacent to the translocation breakpoint regions. Significantly, these types of deletions appear to be more likely to take place when the regions subject to rearrangement contain a high density of Alu repeats. With the completion of the Human Genome Project, it will soon be possible to create more comprehensive maps of the distribution and densities of repetitive sequences, such as Alu, throughout the genome. Such maps will offer unique insights into the relative distribution of cancer translocation breakpoints and the localization of clusters of repetitive DNA.

PCR-based diagnosis of the Filipino (--(FIL)) and Thai (--(THAI)) alpha-thalassemia-1 deletions

In southeast Asia, the carrier frequency of two-gene alpha-thalassemia deletions is quite high, ranging from 4% to 14% depending on the population. The most common alpha-thalassemia-1 deletion is the so-called southeast Asian deletion (--(SEA)). In addition, a significant proportion of cases involve two other deletions, the Filipino (--(FIL)) and Thai (--(THAI)) deletions. In this report, we identify the deletion breakpoints for the (--(FIL)) and (--(THAI)) deletions, and describe PCR-based protocols for rapid and reliable DNA diagnosis of these deletions.