Pubmed highlight: review on ngs data format, visualization and analysis tools

"Unraveling genomic variation from next generation sequencing data."
http://feedly.com/k/18GOEVs

Pubmed Highlight: silencing the extra copy of chromosome 21 in Down’s syndrome cells using the XIST gene

Having been been part in 1991 of the team who originally cloned the mouse Xist gene, I've been really excited by the news. Scientists at the University of Massachusetts discovered that XIST, the gene involved in X-chromosome inactivation, can be used to turn off the extra chromosome 21 in Down syndrome.

The study has been published on the latest issue of Nature.

Nature. 2013 Jul 17. doi: 10.1038/nature12394.

Translating dosage compensation to trisomy 21.

Jiang J, Jing Y, Cost GJ, Chiang JC, Kolpa HJ, Cotton AM, Carone DM, Carone BR, Shivak DA, Guschin DY, Pearl JR, Rebar EJ, Byron M, Gregory PD, Brown CJ, Urnov FD, Hall LL, Lawrence JB.

Source

Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA.

Abstract

Down's syndrome is a common disorder with enormous medical and social costs, caused by trisomy for chromosome 21. We tested the concept that gene imbalance across an extra chromosome can be de facto corrected by manipulating a single gene, XIST (the X-inactivation gene). Using genome editing with zinc finger nucleases, we inserted a large, inducible XIST transgene into the DYRK1A locus on chromosome 21, in Down's syndrome pluripotent stem cells. The XIST non-coding RNA coats chromosome 21 and triggers stable heterochromatin modifications, chromosome-wide transcriptional silencing and DNA methylation to form a 'chromosome 21 Barr body'. This provides a model to study human chromosome inactivation and creates a system to investigate genomic expression changes and cellular pathologies of trisomy 21, free from genetic and epigenetic noise. Notably, deficits in proliferation and neural rosette formation are rapidly reversed upon silencing one chromosome 21. Successfultrisomy silencing in vitro also surmounts the major first step towards potential development of 'chromosome therapy'.

PMID:

 

23863942

PubMed Highlight: A new type of viruses, the Pandoraviruses.

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

1. Nadège Philippe1,2,*, 
2. Matthieu Legendre1,*, 
3. Gabriel Doutre1, 
4. Yohann Couté3, 
5. Olivier Poirot1, 
6. Magali Lescot1,
7. Defne Arslan1, 
8. Virginie Seltzer1, 
9. Lionel Bertaux1, 
10. Christophe Bruley3, 
11. Jérome Garin3, 
12. Jean-Michel Claverie1,†,
13. Chantal Abergel1,†

Abstract:

Ten years ago, the discovery of Mimivirus, a virus infecting Acanthamoeba, initiated a reappraisal of the upper limits of the viral world, both in terms of particle size (>0.7 micrometers) and genome complexity (>1000 genes), dimensions typical of parasitic bacteria. The diversity of these giant viruses (the Megaviridae) was assessed by sampling a variety of aquatic environments and their associated sediments worldwide. We report the isolation of two giant viruses, one off the coast of central Chile, the other from a freshwater pond near Melbourne (Australia), without morphological or genomic resemblance to any previously defined virus families. Their micrometer-sized ovoid particles contain DNA genomes of at least 2.5 and 1.9 megabases, respectively. These viruses are the first members of the proposed “Pandoravirus” genus, a term reflecting their lack of similarity with previously described microorganisms and the surprises expected from their future study.

PubMed Highlight: RNA-Seq analysis made simple

Use of RNA-Seq data to asses differential expression and analyze variation in splicing and isoforms is becoming a recurrent task for many lab interested in gene expression. As usual with NGS, generate the is quite fast and simple but strong bioinformatic know-how is required to actually answer the biological question.
With this paper published in BMC Bioinformatics, Boria et al. provide a simple and automated analysis pipeline for RNA-Seq data, with the ability to detect deferentially expressed genes, differential splicing events and new gene transcripts. The suite is freely available upon registration at this web address.

BMC Bioinformatics. 2013 Apr 22;14 Suppl 7:S10.

NGS-Trex: Next Generation Sequencing Transcriptome profile explorer. 

Boria I, Boatti L, Pesole G, Mignone F. 

Abstract

BACKGROUND: Next-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner. Nevertheless, NGS data analysis requires bioinformatics skills and computational resources well beyond the possibilities of many "wet biology" laboratories. Moreover, most of projects only require few sequencing cycles and standard tools or workflows to carry out suitable analyses for the identification and annotation of genes, transcripts and splice variants found in the biological samples under investigation. These projects can take benefits from the availability of easy to use systems to automatically analyse sequences and to mine data without the preventive need of strong bioinformatics background and hardware infrastructure. RESULTS: To address this issue we developed an automatic system targeted to the analysis of NGS data obtained from large-scale transcriptome studies. This system, we named NGS-Trex (NGS Transcriptome profile explorer) is available through a simple web interface http://www.ngs-trex.org and allows the user to upload raw sequences and easily obtain an accurate characterization of the transcriptome profile after the setting of few parameters required to tune the analysis procedure. The system is also able to assess differential expression at both gene and transcript level (i.e. splicing isoforms) by comparing the expression profile of different samples.By using simple query forms the user can obtain list of genes, transcripts, splice sites ranked and filtered according to several criteria. Data can be viewed as tables, text files or through a simple genome browser which helps the visual inspection of the data. CONCLUSIONS: NGS-Trex is a simple tool for RNA-Seq data analysis mainly targeted to "wet biology" researchers with limited bioinformatics skills. It offers simple data mining tools to explore transcriptome profiles of samples investigated taking advantage of NGS technologies.

PubMed Highlight: Evaluation of bioinformatic tools for prediction of functional impact of missense variants

This interesting paper evaluates the performance (sensitivity and specificity) of 9 different tools commonly used in bioinformatics to predict the functional effect of a missense mutation. The authors also developed a publicly available Web-tool (Variant Effect Prediction) to estimate a consensus score taking into account the results from four different tools (SIFT, PolyPhen2, SNPs&GO and Mutation Assessor).
Since the automated prediction of functional impact is part of most SNV prioritization pipelines, this paper could certainly be useful to develop a robust NGS secondary analysis.

Genomics. 2013 Jul 3. pii: S0888-7543(13)00126-2
Predicting the functional consequences of non-synonymous DNA sequence variants - evaluation of bioinformatics tools and development of a consensus strategy.

Frousios K, Iliopoulos CS, Schlitt T, Simpson MA. 

Abstract

The study of DNA sequence variation has been transformed by recent advances in DNA sequencing technologies. Determination of the functional consequences of sequence variant alleles offers potential insight as to how genotype may influence phenotype. Even within protein coding regions of the genome, establishing the consequences of variation on gene and protein function is challenging and often requires substantial laboratory investigation. However, a series of bioinformatics tools have been developed to predict whether non-synonymous variants are neutral or disease-causing. In this study we evaluate the performance of nine such methods (SIFT, PolyPhen2, SNPs&GO, PhD-SNP, PANTHER, Mutation Assessor, MutPred, Condel and CAROL) and developed CoVEC (Consensus Variant Effect Classification), a tool that integrates the prediction results from four of these methods. We demonstrate that the CoVEC approach outperforms most individual methods and highlights the benefit of combining results from multiple tools.

Made with Love (and Science): first child born following embryo screening with NGS

Above is picture of Connor Levy from NewsWorks

The news has been reported on July 8 at the annual meeting of European Society of Human Reproduction and Embryology (ESHRE) by Dr Dagan Wells of the NIHR Biomedical Research Centre at the University of Oxford, UK.
According to The Guardian, after standard treatment at a US clinic a Philadelphia couple had 13 in vitro fertilization embryos embryos to choose from. The doctors cultured the embryos for five days, took a few cells from each and sent them to Dr. Wells in Oxford for genetic screening. Tests performed using NGS on a Ion Torrent platform showed that while most of the embryos looked healthy, only three had the right number of chromosomes. Based on the screening results, the US doctors transferred one of the healthy embryos into the mother and left the rest in cold storage. The single embryo implanted, and on 18 May 2013 a healthy boy, named Connor, was born.
Apparently the Oxford team has used NGS for testing for aneuploidy, mutations in the cystic fibrosis gene and mtDNA.
Dr Wells, who led the international research team behind the study, said: "Many of the embryos produced during infertility treatments have no chance of becoming a baby because they carry lethal genetic abnormalities. Next generation sequencing improves our ability to detect these abnormalities and helps us identify the embryos with the best chances of producing a viable pregnancy. Potentially, this should lead to improved IVF success rates and a lower risk of miscarriage".
The abstract of the ESHRE communication can be downloaded here.

Incredible But True: Life Technologies introduces an amplicon-based exome sequencing kit

Life Technologies has launched an exome capture kit that makes use of its AmpliSeq technology.
According to the manufacturer, the AmpliSeq™ Exome Kit minimizes the high cost and complexity of exome sequencing enabling the enrichment and sequencing of ~294,000 amplicons (!!!).
The kit targets 97% of coding regions, as described by Consensus Coding Sequences

(CCDS) annotation, in 12 primer pools for highly specific enrichment of exons within the human genome totaling ~58 Mb (it is not clear to me if the amplicons include sequences like UTRs and miRNA).  The novel technology, designed for the Ion Proton platform, delivers >94% of targeted bases covered at 10x even with two exomes per Ion PI  chip. Total workflow from DNA to annotated variants of an exome can be achieved in two days, including six hours for exome library preparation and three hours of sequencing time. Compared to hybridization approaches for exome sequencing, one advantage of an amplicon-based approached is that the input amount is small (as little as 50 nanograms).
Additional information can be found in this Life Technologies' Application Note.