Differences between individual human genomes, or between human and cancer genomes, range in scale from single nucleotide variants (SNVs) through intermediate and large-scale duplications, deletions, and rearrangements of genomic segments. The latter class, called structural variants (SVs), have received considerable attention in the past several years as they are a previously under appreciated ...

Species evolution is indirectly registered in their genomic structure. The emergence and advances in sequencing technology provided a way to access genome information, namely to identify and study evolutionary macro-events, as well as chromosome alterations for clinical purposes. This paper describes a completely alignment-free computational method, based on a blind unsupervised approach, to de...

Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome sequencing provides an unprecedented level of detailed sequence data to infer genom...

Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the zebra finch, provides, for the first time, an ideal opportunity to analyze the ...

Motivation: There are many different forms of genomic structural variation that can be broadly classified into two groups as copy number variation (CNV) and balanced rearrangements. Although many algorithms are now available in the literature that aim to characterize CNVs, discovery of balanced rearrangements (inversions and translocations) remains an open problem. This is mainly because the br...

We have developed a restriction map of the chromosome 21 breakpoint region involved in t(8;21)(q22;q22.3) acute myelogenous leukemia (AML) and have isolated a genomic junction clone containing chromosome 8 and 21 material. Using probes from these regions, rearrangements have been identified in each of nine cases of t(8;21) AML examined. In addition, we have isolated cDNA clones from a t(8;21) A...

In this issue of Blood, Lin and colleagues address in detail the nature and severity of telomere disruption in chronic lymphocytic leukemia (CLL).1 Using sophisticated methods for telomere length determination, the authors show that critical telomere shortening occurs in a proportion of CLL samples and correlates with the presence of large-scale genomic rearrangements occurring in telomeric reg...

The recent plethora of sequenced genomes has just ushered in a new era of genetics-based research. Although an impressive number of species have been, or are planned to be sequenced, the full value of such efforts will be fully accrued when patterns of variation can be discerned and annotated for many strains or isolates within a given species. As such, bacteria are an ideal place to start inve...

Background De novo copy number variation (CNV) can occur constitutionally in gametogenesis or in early development leading to sporadic genomic disorders. Such de novo CNVs appear to also be important in somatic mutagenesis relevant to cancer and population events important to species evolution. Since large pathological CNVs are rarely observed at more than one locus in a single patient, and are...

SUMMARY We present SVDetect, a program designed to identify genomic structural variations from paired-end and mate-pair next-generation sequencing data produced by the Illumina GA and ABI SOLiD platforms. Applying both sliding-window and clustering strategies, we use anomalously mapped read pairs provided by current short read aligners to localize genomic rearrangements and classify them accord...