Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

MSB: a mean-shift-based approach for the analysis of structural variation in the genome

Genome structural variation includes segmental duplications, deletions, and other rearrangements, and array-based comparative genomic hybridization (array-CGH) is a popular technology for determining this. Drawing relevant conclusions from array-CGH requires computational methods for partitioning the chromosome into segments of elevated, reduced, or unchanged copy number. Several approaches have been described, most of which attempt to explicitly model the underlying distribution of data based on particular assumptions. Often, they optimize likelihood functions for estimating model parameters, by expectation maximization or related approaches; however, this requires good parameter initialization through prespecifying the number of segments. Moreover, convergence is difficult to achieve, since many parameters are required to characterize an experiment. To overcome these limitations, we propose a nonparametric method without a global criterion to be optimized. Our method involves mean-shift-based (MSB) procedures; it considers the observed array-CGH signal as sampling from a probability-density function, uses a kernel-based approach to estimate local gradients for this function, and iteratively follows them to determine local modes of the signal. Overall, our method achieves robust discontinuity-preserving smoothing, thus accurately segmenting chromosomes into regions of duplication and deletion. It does not require the number of segments as input, nor does its convergence depend on this. We successfully applied our method to both simulated data and array-CGH experiments on glioblastoma and adenocarcinoma. We show that it performs at least as well as, and often better than, 10 previously published algorithms. Finally, we show that our approach can be extended to segmenting the signal resulting from the depth-of-coverage of mapped reads from next-generation sequencing.

Array-CGH für die Analyse von Tumorgenomen

Durch Array-CGH („comparative genomic hybridization“) können genomweit Kopienzahlveränderungen mit hoher Auflösung erfasst werden. In der letzten Dekade zeigte sich, dass diese in Tumorgenomen häufig und in größerer Anzahl vorliegen können. Über Abweichungen im Array-CGH-Profil einer Tumor-DNA können Tumorsuppressor- oder Protoonkogene kartiert werden, sodass krebsrelevante Gene identifiziert werden konnten. Weiterhin werden Aberrationsmuster erfasst, was zur molekularen Subklassifikation von Tumortypen mit diagnostischer Bedeutung führte. Auch zur Identifizierung neuer prognostischer Marker konnten Array-CGH-Analysen beitragen. In Zukunft werden eine Datenbewertung durch Einbeziehung von Analysen auf anderen molekularen Ebenen und eine gezielte Anwendung mit chromosomen- oder tumorspezifischen Mikroarrays wichtig sein.

Accurate whole human genome sequencing using reversible terminator chemistry

DNA sequence information underpins genetic research, enabling discoveries of important biological or medical benefit. Sequencing projects have traditionally used long (400-800 base pair) reads, but the existence of reference sequences for the human and many other genomes makes it possible to develop new, fast approaches to re-sequencing, whereby shorter reads are compared to a reference to identify intraspecies genetic variation. Here we report an approach that generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence. We demonstrate application of this approach to human genome sequencing on flow-sorted X chromosomes and then scale the approach to determine the genome sequence of a male Yoruba from Ibadan, Nigeria. We build an accurate consensus sequence from >30x average depth of paired 35-base reads. We characterize four million single-nucleotide polymorphisms and four hundred thousand structural variants, many of which were previously unknown. Our approach is effective for accurate, rapid and economical whole-genome re-sequencing and many other biomedical applications.

Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas

Brain tumors are the most common solid tumors of childhood, and pilocytic astrocytomas (PA) are the most common central nervous system tumor in 5 to 19 year olds. Little is known about the genetic alterations underlying their development. Here, we describe a tandem duplication of approximately 2 Mb at 7q34 occurring in 66% of PAs. This rearrangement, which was not observed in a series of 244 higher-grade astrocytomas, results in an in-frame fusion gene incorporating the kinase domain of the BRAF oncogene. We further show that the resulting fusion protein has constitutive BRAF kinase activity and is able to transform NIH3T3 cells. This is the first report of BRAF activation through rearrangement as a frequent feature in a sporadic tumor. The frequency and specificity of this change underline its potential both as a therapeutic target and as a diagnostic tool.

Mapping short DNA sequencing reads and calling variants using mapping quality scores

New sequencing technologies promise a new era in the use of DNA sequence. However, some of these technologies produce very short reads, typically of a few tens of base pairs, and to use these reads effectively requires new algorithms and software. In particular, there is a major issue in efficiently aligning short reads to a reference genome and handling ambiguity or lack of accuracy in this alignment. Here we introduce the concept of mapping quality, a measure of the confidence that a read actually comes from the position it is aligned to by the mapping algorithm. We describe the software MAQ that can build assemblies by mapping shotgun short reads to a reference genome, using quality scores to derive genotype calls of the consensus sequence of a diploid genome, e.g., from a human sample. MAQ makes full use of mate-pair information and estimates the error probability of each read alignment. Error probabilities are also derived for the final genotype calls, using a Bayesian statistical model that incorporates the mapping qualities, error probabilities from the raw sequence quality scores, sampling of the two haplotypes, and an empirical model for correlated errors at a site. Both read mapping and genotype calling are evaluated on simulated data and real data. MAQ is accurate, efficient, versatile, and user-friendly. It is freely available at http://maq.sourceforge.net.

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Background

Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes.

Results

We have analyzed aspects of the information content of Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Saccharomyces cerevisiae, and Escherichia coli (K-12) genomes. Virtually all possible (> 98%) 12 bp oligomers appear in vertebrate genomes while < 2% of 19 bp oligomers are present. Other species showed different ranges of > 98% to < 2% of possible oligomers in D. melanogaster (12–17 bp), C. elegans (11–17 bp), A. thaliana (11–17 bp), S. cerevisiae (10–16 bp) and E. coli (9–15 bp). Frequencies of unique oligomers in the genomes follow similar patterns. We identified a set of 2.6 M 15-mers that are more than 1 nucleotide different from all 15-mers in the human genome and so could be used as probes to detect microbes in human samples. In a human sample, these probes would detect 100% of the 433 currently fully sequenced prokaryotes and 75% of the 3065 fully sequenced viruses. The human genome is significantly more compact in sequence space than a random genome. We identified the most frequent 5- to 20-mers in the human genome, which may prove useful as PCR primers. We also identified a bacterium, Anaeromyxobacter dehalogenans, which has an exceptionally low diversity of oligomers given the size of its genome and its GC content. The entropy of coding regions in the human genome is significantly higher than non-coding regions and chromosomes. However chromosomes 1, 2, 9, 12 and 14 have a relatively high proportion of coding DNA without high entropy, and chromosome 20 is the opposite with a low frequency of coding regions but relatively high entropy.

Conclusion

Measures of the frequency of oligomers are useful for designing PCR assays and for identifying chromosomes and organisms with hidden structure that had not been previously recognized. This information may be used to detect novel microbes in human tissues.

Variable breakpoints target PAX5 in patients with dicentric chromosomes: a model for the basis of unbalanced translocations in cancer

The search for target genes involved in unbalanced acquired chromosomal abnormalities has been largely unsuccessful, because the breakpoints of these rearrangements are too variable. Here, we use the example of dicentric chromosomes in B cell precursor acute lymphoblastic leukemia to show that, despite this heterogeneity, single genes are targeted through a variety of mechanisms. FISH showed that, although they were heterogeneous, breakpoints on 9p resulted in the partial or complete deletion of PAX5. Molecular copy number counting further delineated the breakpoints and facilitated cloning with long-distance inverse PCR. This approach identified 5 fusion gene partners with PAX5: LOC392027 (7p12.1), SLCO1B3 (12p12), ASXL1 (20q11.1), KIF3B (20q11.21), and C20orf112 (20q11.1). In each predicted fusion protein, the DNA-binding paired domain of PAX5 was present. Using quantitative PCR, we demonstrated that both the deletion and gene fusion events resulted in the same underexpression of PAX5, which extended to the differential expression of the PAX5 target genes, EBF1, ALDH1A1, ATP9A, and FLT3. Further molecular analysis showed deletion and mutation of the homologous PAX5 allele, providing further support for the key role of PAX5. Here, we show that specific gene loci may be the target of heterogeneous translocation breakpoints in human cancer, acting through a variety of mechanisms. This approach indicates an application for the identification of cancer genes in solid tumours, where unbalanced chromosomal rearrangements are particularly prevalent and few genes have been identified. It can be extrapolated that this strategy will reveal that the same mechanisms operate in cancer pathogenesis in general.

Keeping up with the next generation: massively parallel sequencing in clinical diagnostics

The speed, accuracy, efficiency, and cost-effectiveness of DNA sequencing have been improving continuously since the initial derivation of the technique in the mid-1970s. With the advent of massively parallel sequencing technologies, DNA sequencing costs have been dramatically reduced. No longer is it unthinkable to sequence hundreds or even thousands of genes in a single individual with a suspected genetic disease or complex disease predisposition. Along with the benefits offered by these technologies come a number of challenges that must be addressed before wide-scale sequencing becomes accepted medical practice. Molecular diagnosticians will need to become comfortable with, and gain confidence in, these new platforms, which are based on radically different technologies compared to the standard DNA sequencers in routine use today. Experience will determine whether these instruments are best applied to sequencing versus resequencing. Perhaps most importantly, along with increasing read lengths inevitably comes increased ascertainment of novel sequence variants of uncertain clinical significance, the postanalytical aspects of which could bog down the entire field. But despite these obstacles, and as a direct result of the promises these sequencing advances present, it will likely not be long before next-generation sequencing begins to make an impact in molecular medicine. In this review, technical issues are discussed, in addition to the practical considerations that will need to be addressed as advances push toward personal genome sequencing.

Functional genomics of cancer

Cancer genomics has focused on the discovery of genetic mutations and chromosomal structural rearrangements that either increase susceptibility to cancer or support the cancer phenotype. Though each individual mutation may induce specific cancer phenotypes, it is the interaction of the functional changes in transcription and proteins that give the characteristics of cancer. Whereas molecular biology focuses on the impact of individual genes on the cancer state, functional genomics assesses the comprehensive genetic alterations in a cancer cell and seeks to integrate the dynamic changes in these networks so that cancer phenotypes can be explained. Most commonly, the transcriptome is the target of analysis because of the maturity, completeness, and speed of the technologies, but progressively the proteome is being studied in the same comprehensive manner. The focus of this review, however, will be on the functional consequences of cancer genomic alterations with special reference to the transcriptome and in the perturbed gene expression found in cancer states. The developments in the past two years (which is our time horizon) have been heavily driven by the applications of the new ultra high-throughput sequencing approaches assisted by computational discovery strategies. The precision and comprehensiveness of the analyses are astonishing. The collective results, when taken together, suggest that despite the large range of mutational and epigenetic events, there is a convergence onto a finite number of pathways that drive cancer behavior. Moreover, the interconnectivity of regulatory control mechanisms suggest that the earlier concepts distinguishing driver from passenger abnormalities may undervalue the contribution of the numerous aberrations that have small but additive effects on cancer virulence.

Molecular biology: power sequencing

Advances in DNA-sequencing technology provide unprecedented insight into the entire collection of four genomes' transcribed sequences; they herald a new era in the study of gene regulation and genome function.

Translating insights from the cancer genome into clinical practice

Cancer cells have diverse biological capabilities that are conferred by numerous genetic aberrations and epigenetic modifications. Today's powerful technologies are enabling these changes to the genome to be catalogued in detail. Tomorrow is likely to bring a complete atlas of the reversible and irreversible alterations that occur in individual cancers. The challenge now is to work out which molecular abnormalities contribute to cancer and which are simply 'noise' at the genomic and epigenomic levels. Distinguishing between these will aid in understanding how the aberrations in a cancer cell collaborate to drive pathophysiology. Past successes in converting information from genomic discoveries into clinical tools provide valuable lessons to guide the translation of emerging insights from the genome into clinical end points that can affect the practice of cancer medicine.