Common copy number variations in fifty radiosensitive cell lines.

Hypersensitivity to radiation exposure is a major challenge to radiotherapy in the treatment of cancer patients. Copy number variations (CNVs) are believed to identify genomic regions of functional significance for radiosensitivity (RS) but have yet to be systematically investigated. We used Affymetrix 6.0 SNP arrays to survey common CNVs in a cohort of 50 radiosensitive lymphoblastoid cell lines (RS-LCLs) derived from patients with undiagnosed diseases. A total of 317 CNVs that were present in at least 10% of the studied cell lines were identified. Three hundred and eight CNVs overlapped with polymorphic CNVs, 13 of which were significantly enriched in the RS-LCLs compared to the reference. The remaining 9 CNVs were novel. The majority of these enriched and novel CNVs were chromosomal gains. The dominance of the chromosomal gains over losses is inconsistent with the traditional concept of molecular basis of RS and suggests more complex genetic mechanisms for RS.

[Fractal characteristics of visible spectra across a hilly area].

The spectral characteristic of remotely sensed image is mainly the results of integrative effects on spectrum from heterogeneous ground reflectors. Investigating its spatial distribution characteristics may be helpful for image interpreting and modeling based on remote sensing technique. In the present study, spatial heterogeneity of remotely sensed multispectral TM image across a hilly area in late October was studied by the combination of statistical method and multifractal analysis. The results showed that distribution of digital number (DN) values of visible spectra (0.45-0.69 microm) had statistical scale-invariance. The generalized fractal dimension function D(q) suggested that distribution of TM 2 (0.52-0.60 microm) DN values was monofractal type, whereas DN values of TM 1 (0.45-0.52 microm) and TM 3 (0.63-0.69 microm) had multifractal distribution characteristics. The parameters (alpha(max)-alpha(min)) and [f(a(max))-f(alpha(min))] of multifractal spectra further indicated that TM 3 DN values had the high est spatial heterogeneity and most abundant information, followed by TM 1, while the extremely narrow spectrum of TM 2 DN values showed its relatively low spatial heterogeneity and information capacity.

Human functional genetic studies are biased against the medically most relevant primate-specific genes.

BACKGROUND: Many functional, structural and evolutionary features of human genes have been observed to correlate with expression breadth and/or gene age. Here, we systematically explore these correlations. RESULTS: Gene age and expression breadth are strongly correlated, but contribute independently to the variation of functional, structural and evolutionary features, even when we take account of variation in mRNA expression level. Human genes without orthologs in distant species ('young' genes) tend to be tissue-specific in their expression. As computational inference of gene function often relies on the existence of homologs in other species, and experimental characterization is facilitated by broad and high expression, young, tissue-specific human genes are often the least characterized. At the same time, young genes are most likely to be medically relevant. CONCLUSIONS: Our results indicate that functional characterization of human genes is biased against young, tissue-specific genes that are mostly medically relevant. The biases should not be taken lightly because they may pose serious obstacles to our understanding of the molecular basis of human diseases. Future studies should thus be designed to specifically explore the properties of primate-specific genes.

cDNA cloning and expression pattern of two enolase genes from the Chinese oak silkworm, Antheraea pernyi.

In this study, two enolase genes were isolated and characterized from the Chinese oak silkworm, Antheraea perny, which were designated as enolase I and II, respectively. The enolase I cDNA sequence was 1712 bp with an open reading frame (ORF) of 1302 bp encoding 433 amino acids. The enolase II cDNA sequence was 1549 bp with an ORF of 1296 bp encoding 431 amino acids. The amino acid sequences of the two genes share several conserved features/sites of enolase. Antheraea pernyi enolase I shows 93%-97% sequence identity to enolases of lepidopterans available to date, 75%-82% identity to enolases of other invertebrates, 60%-72% identity to enolases of other organisms including vertebrates, plants, and fungi. Antheraea pernyi enolase II shows 84% identity to Bombyx mori enolase II, but 60% identity to A. pernyi enolase I. In the phylogenetic tree, enolase II sequences from A. pernyi and B. mori were clearly separated from the majority of enolase sequences of higher organisms including A. pernyi and B. mori enolase I sequences. By sequence comparisons and phylogenetic analysis, we suggest that enolase II from A. pernyi and B. mori may be a new member of the enolase superfamily. Antheraea pernyi enolase I mRNA was found in all tested tissues whereas enolase II mRNA was expressed specifically in the spermaries and ovaries, suggesting that the product of enolase II gene may be related to reproduction. The transcript abundance of A. pernyi enolase I gene was significantly down-regulated after cold shock and significantly up-regulated after heat shock, suggesting that A. pernyi enolase I gene may be inducible by temperature stress.

Clinical Genetic Testing for Fragile X Syndrome by Polymerase Chain Reaction Amplification and Southern Blot Analyses.

Fragile X syndrome (FXS) is characterized by mental retardation and in the vast majority of cases it is caused by expansion of CGG trinucleotide repeats in the 5' untranslated region (or UTR) in the FMR1 gene on the X chromosome. The size and methylation status of CGG repeats are correlated with the clinical phenotype of FMR1-related disorders. The methods used for clinical genetic testing of FXS include polymerase chain reaction (PCR) amplification and Southern blot analyses, which effectively detect alleles with repeats in the normal, intermediate, premutation, and full mutation size ranges, as well as the methylation status of FMR1 promoter region.

A comparison of isolated circulating tumor cells and tissue biopsies using whole-genome sequencing in prostate cancer.

Previous studies have demonstrated focal but limited molecular similarities between circulating tumor cells (CTCs) and biopsies using isolated genetic assays. We hypothesized that molecular similarity between CTCs and tissue exists at the single cell level when characterized by whole genome sequencing (WGS). By combining the NanoVelcro CTC Chip with laser capture microdissection (LCM), we developed a platform for single-CTC WGS. We performed this procedure on CTCs and tissue samples from a patient with advanced prostate cancer who had serial biopsies over the course of his clinical history. We achieved 30X depth and ≥ 95% coverage. Twenty-nine percent of the somatic single nucleotide variations (SSNVs) identified were founder mutations that were also identified in CTCs. In addition, 86% of the clonal mutations identified in CTCs could be traced back to either the primary or metastatic tumors. In this patient, we identified structural variations (SVs) including an intrachromosomal rearrangement in chr3 and an interchromosomal rearrangement between chr13 and chr15. These rearrangements were shared between tumor tissues and CTCs. At the same time, highly heterogeneous short structural variants were discovered in PTEN, RB1, and BRCA2 in all tumor and CTC samples. Using high-quality WGS on single-CTCs, we identified the shared genomic alterations between CTCs and tumor tissues. This approach yielded insight into the heterogeneity of the mutational landscape of SSNVs and SVs. It may be possible to use this approach to study heterogeneity and characterize the biological evolution of a cancer during the course of its natural history.

A transcriptome analysis of mitten crab testes (Eriocheir sinensis).

The identification of expressed genes involved in sexual precocity of the mitten crab (Eriocheir sinensis) is critical for a better understanding of its reproductive development. To this end, we constructed a cDNA library from the rapid developmental stage of testis of E. sinensis and sequenced 3,388 randomly picked clones. After processing, 2,990 high-quality expressed sequence tags (ESTs) were clustered into 2,415 unigenes including 307 contigs and 2,108 singlets, which were then compared to the NCBI non-redundant (nr) protein and nucleotide (nt) database for annotation with Blastx and Blastn, respectively. After further analysis, 922 unigenes were obtained with concrete annotations and 30 unigenes were found to have functions possibly related to the process of reproduction in male crabs - six transcripts relevant to spermatogenesis (especially Cyclin K and RecA homolog DMC1), two transcripts involved in nuclear protein transformation, two heat-shock protein genes, eleven transcription factor genes (a series of zinc-finger proteins), and nine cytoskeleton protein-related genes. Our results, besides providing valuable information related to crustacean reproduction, can also serve as a base for future studies of reproductive and developmental biology.

A comparative transcriptomic analysis of uveal melanoma and normal uveal melanocyte.

BACKGROUND: Uveal melanoma is the most common primary intraocular tumor in adults in western countries. It is associated with very severe visual morbidity and may lead to distant metastases even after successful treatment of the primary tumor. In order to gain better insight into molecular mechanisms related to tumorigenesis and metastasis of uveal melanoma, we used next-generation sequencing technology (SOLiD, Life Technologies) to acquire global transcriptome alteration between posterior uveal melanoma cells and normal uveal melanocyte. RESULTS: From mRNAs of the cultured uveal melanoma cells and normal uveal melanocytes, we annotated more than 3.7 × 10(7) and 2.7 × 10(7) sequencing tags based on human Ensembl databases, respectively. For detailed analysis, we chose 5155 well-annotated genes mainly involved in the MAPK signaling pathway, cell cycle, cell adhesion junction, apoptosis, and P53 signaling pathways as well as melanogenesis. In an effort to confirm the authenticity of our sequencing results, we validated twenty-one identically differentially expressed genes by using quantitative real time PCR from cultured cell lines of other posterior uveal melanoma cells and normal uveal melanocytes. CONCLUSION: We have identified a large number of potentially interesting genes for biological investigation of uveal melanoma. The expression profiling also provides useful resources for other functional genomic and transcriptome studies. These 21 potential genes could discriminate between uveal melanoma cells and normal uveal melanocyte, which may be indicative of tumorigenesis process. Our results further suggest that high-throughput sequencing technology provides a powerful tool to study mechanisms of tumogenesis in the molecular level.

Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.

BACKGROUND: Over the past two decades, there have been several approximate methods that adopt different mutation models and used for estimating nonsynonymous and synonymous substitution rates (Ka and Ks) based on protein-coding sequences across species or even different evolutionary lineages. Among them, MYN method (a Modified version of Yang-Nielsen method) considers three major dynamic features of evolving DNA sequences-bias in transition/transversion rate, nucleotide frequency, and unequal transitional substitution but leaves out another important feature: unequal substitution rates among different sites or nucleotide positions. RESULTS: We incorporated a new feature for analyzing evolving DNA sequences-unequal substitution rates among different sites-into MYN method, and proposed a modified version, namely gamma (gamma)-MYN, based on an assumption that the evolutionary rate at each site follows a mode of gamma-distribution. We applied gamma-MYN to analyze the key estimator of selective pressure omega (Ka/Ks) and other relevant parameters in comparison to two other related methods, YN and MYN, and found that neglecting the variation of substitution rates among different sites may lead to biased estimations of omega. Our new method appears to have minimal deviations when relevant parameters vary within normal ranges defined by empirical data. CONCLUSION: Our results indicate that unequal substitution rates among different sites have variable influences on omega under different evolutionary rates while both transition/transversion rate ratio and unequal nucleotide frequencies affect Ka and Ks thus selective pressure omega.

A transcriptome analysis of mitten crab testes (Eriocheir sinensis)

The identification of expressed genes involved in sexual precocity of the mitten crab (Eriocheir sinensis) is critical for a better understanding of its reproductive development. To this end, we constructed a cDNA library from the rapid developmental stage of testis of E. sinensis and sequenced 3,388 randomly picked clones. After processing, 2,990 high-quality expressed sequence tags (ESTs) were clustered into 2,415 unigenes including 307 contigs and 2,108 singlets, which were then compared to the NCBI non-redundant (nr) protein and nucleotide (nt) database for annotation with Blastx and Blastn, respectively. After further analysis, 922 unigenes were obtained with concrete annotations and 30 unigenes were found to have functions possibly related to the process of reproduction in male crabs - six transcripts relevant to spermatogenesis (especially Cyclin K and RecA homolog DMC1), two transcripts involved in nuclear protein transformation, two heat-shock protein genes, eleven transcription factor genes (a series of zinc-finger proteins), and nine cytoskeleton protein-related genes. Our results, besides providing valuable information related to crustacean reproduction, can also serve as a base for future studies of reproductive and developmental biology.