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Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data.

Xu C, Zhang J, Wang YP, Deng HW, Li J - Genome Biol Evol (2014)

Bottom Line: We identified 16 translocation hot regions, among which two regions did not contain repetitive fragments.Results of our study overlapped with a majority of previous results, containing approximately 79% of approximately 2,340 translocations characterized in three available translocation databases.Our results will be helpful for an accurate characterization of translocations in human genomes, and contribute as a resource for future studies of the roles of translocations in human disease etiology and mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University.

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Size distribution of the identified translocated DNA fragments. X axis indicates the size groups of the identified translocated DNA fragments. Y axis represents the corresponding frequencies.
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evu234-F1: Size distribution of the identified translocated DNA fragments. X axis indicates the size groups of the identified translocated DNA fragments. Y axis represents the corresponding frequencies.

Mentions: The size distribution of all translocated fragment pairs was shown in figure 1, ranging from 65 to 1,886 bp with an average of approximately 102 bp and a median of 101 bp. In total, 4,895 pairs were greater than 1 kb, which we defined as >1 kb translocations. The numbers of translocated fragment pairs on individual study subjects were shown in figure 2, with 95.0% of these numbers ranging from 177 to 49,235 and an average of 10,364 pairs per subject. The detected translocated fragments covered about 57.3% of the whole genome (including both autosomal and X chromosomes). For regions covered by the translocated fragments, approximately 44.9% were genic regions and approximately 34.5% were coding sequence regions (based on NCBI annotations, December 2012 version), consistent with results from previous studies (Chiarle et al. 2011). Approximately 52.9% of the translocated fragments overlapped with G-positive regions. For each subject, approximately 0.069% of his/her genome were covered by translocated fragments.Fig. 1.—


Characterization of human chromosomal material exchange with regard to the chromosome translocations using next-generation sequencing data.

Xu C, Zhang J, Wang YP, Deng HW, Li J - Genome Biol Evol (2014)

Size distribution of the identified translocated DNA fragments. X axis indicates the size groups of the identified translocated DNA fragments. Y axis represents the corresponding frequencies.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4255766&req=5

evu234-F1: Size distribution of the identified translocated DNA fragments. X axis indicates the size groups of the identified translocated DNA fragments. Y axis represents the corresponding frequencies.
Mentions: The size distribution of all translocated fragment pairs was shown in figure 1, ranging from 65 to 1,886 bp with an average of approximately 102 bp and a median of 101 bp. In total, 4,895 pairs were greater than 1 kb, which we defined as >1 kb translocations. The numbers of translocated fragment pairs on individual study subjects were shown in figure 2, with 95.0% of these numbers ranging from 177 to 49,235 and an average of 10,364 pairs per subject. The detected translocated fragments covered about 57.3% of the whole genome (including both autosomal and X chromosomes). For regions covered by the translocated fragments, approximately 44.9% were genic regions and approximately 34.5% were coding sequence regions (based on NCBI annotations, December 2012 version), consistent with results from previous studies (Chiarle et al. 2011). Approximately 52.9% of the translocated fragments overlapped with G-positive regions. For each subject, approximately 0.069% of his/her genome were covered by translocated fragments.Fig. 1.—

Bottom Line: We identified 16 translocation hot regions, among which two regions did not contain repetitive fragments.Results of our study overlapped with a majority of previous results, containing approximately 79% of approximately 2,340 translocations characterized in three available translocation databases.Our results will be helpful for an accurate characterization of translocations in human genomes, and contribute as a resource for future studies of the roles of translocations in human disease etiology and mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Center for Bioinformatics and Genomics, Department of Biostatistics and Bioinformatics, School of Public Health and Tropical Medicine, Tulane University.

Show MeSH
Related in: MedlinePlus