BioMed Central Blog

One for all and all for one: random monoallelic expression in Genome Biology

The term epigenetics was coined by Conrad Waddington in 1939, and recent advances in next generation sequencing technologies are now allowing genome-wide analyses of epigenetic regulation. A groundbreaking discovery in the field has been that a maternal or paternal allele of an autosomal gene can be randomly silenced, in a process termed random monoallelic expression (RMAE). In this way, RMAE is similar to X-inactivation, except that it is established at the level of a single gene as opposed to a whole chromosome. In 2007, it was shown that the expression of up to 10% of human genes, spanning a wide range of functions, may be influenced by RMAE. This raises the important question of the extent to which RMAE has been conserved across mammals. In a fascinating article by Andrew Chess and colleagues, published in this month’s issue of Genome Biology, this question has finally been answered.

Chess and colleagues first of all test whether genes are regulated by RMAE in other mammals by analysing genome-wide patterns of RMAE in mouse lines. Strikingly, they show that more than 15% of mouse genes surveyed are regulated by RMAE, and that there is a high level of conservation of RMAE between mouse and humans. These genes encode products with a wide variety of functions, just as has been shown for humans, suggesting that RMAE is not restricted to specific gene classes. They also find that genes affected by RMAE are distributed throughout the genome, and that active alleles are not influenced by the epigenetic state of adjacent loci. Once RMAE is established, allele specific expression is stably inherited through mitosis.

Crucially, they show that within a clone of cells, monoallelically expressed genes can be either maternally or paternally expressed, and are not influenced by the epigenetic state of neighboring cells. This means that the tissues of mammalian cells may resemble a patchwork quilt, with juxtaposed cells exhibiting different allelic expression patterns.

In one of their most interesting findings, they show that no gene classes are significantly enriched for RMAE in mouse, which is in contrast to previous work showing that in humans, transmembrane receptors are significantly enriched among genes displaying RMAE. This raises important questions about the differential functions of RMAE between mammalian species.

The results from Andrew Chess and colleagues strongly suggest that the regulatory mechanisms controlling RMAE were present in the last common ancestor of primates and rodents, which was thought to be roaming the earth 65-85 million years ago. It is clear that RMAE can cause differential expression between genetically identical cells, but it remains to be determined how RMAE is regulated, and what the adaptive advantage of RMAE is.

To read more about the results of Andrew Chess and colleagues, click here.

Posted by Gemma Bilsborough at 16:29    Comments (0)

From the Rhine to the Rift Valley: Human population genetics in Genome Biology

Has hypoxia adaptation in the Ethiopian highlands mirrored that seen in Tibet and the Andes? Is there a genetic definition for an Ashkenazi Jew? These are two questions on human diversity that can now be answered, thanks to new research articles published in this month's Genome Biology.

In the first article, the University of Pennsylvania's Tishkoff lab, in collaboration with Addis Ababa University, sought to identify genetic adaptations to high altitude present in the Amhara people of the Ethiopian Highlands. Two other high altitude populations – in Tibet and the Andes – have previously been studied in this way; obtaining Ethiopian samples, however, proved to be a challenging feat.

A set of strong candidate genes for high altitude selection were identified in the Amhara, whose samples were used both for genotyping and for physiological measurements. As with Tibetan and Andean populations, adaptations targeted the HIF-1 pathway, demonstrating the selective pressure brought about by the risk of hypoxia in high altitude environments. While the three populations share an adaptive pathway in common, the individual genetic changes underlying the hypoxia-resistant phenotype were different in the Ethiopian cohort to that seen in Tibetans or Andeans. This example of convergent evolution suggests that the HIF-1 pathway is an inevitable adaptation for any population under selection pressure for hypoxia.

The definition of what constitutes a Jew is an age-old question without a simple answer. The Ashkenazim are a subpopulation of the Jewish people descended from a small founder population based in Western Europe approximately 1,000 years ago; using the largest Ashkenazi genotyping cohort to date, Todd Lencz (The Feinstein Institute for Medical Research) and colleagues were able to determine a distinct genetic signature that can identify Ashkenazi Jews.

Consistent with previous reports, the article concludes that the founding Ashkenazi population likely included both Levantine Jewish and European Caucasian individuals. However, the results presented by Lencz and colleagues powerfully show that, since the founding event, the level of admixture with "host" European populations (and with other Jewish populations) has been extremely low.

The genetic signature also harbors an enrichment of genes associated with disease pathways known to be overrepresented in the Ashkenazi population, and so will therefore help to unravel the genetic basis by which these conditions (including cystic fibrosis and Usher syndrome) have become prevalent among Ashkenazim.

Posted by Naomi Attar at 13:35    Comments (0)

Genome Biology’s two-mile high epigenomic epiphanies

"A Lamarckian contribution to natural selection doesn't make much sense to me," says father-of-(modern) epigenetics Andy Feinberg as he opens his talk at the Keystone Symposium on Epigenomics.

Admittedly, expressing skepticism toward Lamarck’s theory on the heritability of acquired traits is hardly controversial in the 21st century, but a number of better accepted theories were also challenged during the meeting, which was held concurrently with the Keystone Symposium on Chromatin Dynamics January 17-22 in Keystone, CO.

Tim Bestor (Columbia) came fully armed and ready for a fight as he took on the prevailing truth in the literature that promoter CpG hypermethylation is a pathogenic feature of many tumors. But, strikingly, the audience response was one of agreement with Bestor's line of argument. An overreliance on tissue culture cell lines was blamed for the unrepresentative reporting of tumor cell methylation patterns.

The importance of avoiding generalizations from results observed in a given cellular context was a strong message from the meeting, and multiple presentations reported remarkably high cell-type specificity for a range of epigenomic features.

Another theory to find itself in the crosshairs was that of an independent functional significance for histone modifications; instead, it was argued that the distribution of these marks is merely reflective of polymerase activity and of chromatin openness.

The conference organizers believe that the turnout (~650 participants) is a world record for an epigenomics meeting, a clear sign that the field is in its ascendancy. Methodological innovations – such as the Dekker lab's HiC approach to mapping the genome in 3D, Paul Soloway's high-throughput fluorescent chromatin sorting, and high resolution DNA-protein interaction mapping methods developed by the Henikoff and Pugh* labs – show that there is plenty of potential for epigenomics to continue its upward momentum. Perfect timing, then, for this year's Genome Biology special issue focusing on epigenomics, for which we are now accepting submissions. BioMed Central is also the publisher of Epigenetics & Chromatin, an open access journal dedicated to this topic, which boasts Steve Henikoff and Frank Grosveld as hands-on Editors-in-Chief.

A final thought: maybe it was just the thin mountain air befuddling the mind, but some of the work presented on heritable epialleles and mobile sRNAs in plants did seem, after all, to offer renewed hope for a quasi-Lamarckian inheritance (propagation of an acquired trait for a few generations, if not in permanency).

*see our Research Highlight by Eric Mendenhall and Brad Bernstein on the Pugh lab's ChIP-exo method

See also:  Genome Biology's Twitter stream for a more detailed account of the Symposia

Posted by Naomi Attar at 16:59    Comments (0)

Genome Biology special issue on epigenomics

To showcase the exciting developments currently being made in the study of epigenomes, Genome Biology will publish a special issue on epigenomics in the late summer of 2012.

A call for papers has now been issued inviting Research, Method and Software submissions on topics including:

• methylomes (and hydroxymethylomes)

• histone modifications
• nucleosome positioning
• higher order chromatin structure
• genome-interacting non-coding RNAs

If you would like to enquire about the suitability of a manuscript for consideration, please email editorial@genomebiology.com. Potential submissions can also be discussed in person at the "Epigenomics and Chromatin Dynamics" and "Nuclear Events in Plant Gene Expression and Signaling" Keystone Symposia; if you are attending one of these conferences and would like to meet us, then please do get in touch. 

Posted by Naomi Attar at 18:38    Comments (0)

Genome Biology publishes MiSeq data

The pioneering genomicist Sydney Brenner has a sound bite that the most important -omics discipline of all is econ-omics.

The holy grail of biomedical research is to translate scientific achievement into practical applications in the clinic. And for genomics to conquer the local hospital ward, it must not only be genom-ical – but also econ-omical.

2011 has seen economical genomics arrive one step closer with the unveiling of two sequencing machines of note that are designed to be affordable to small operations: Illumina's MiSeq and Life Technologies' Ion Torrent Personal Genome Machine.

A new article published in Genome Biology by Olivier Harismendy, Kelly Frazer and colleagues is one of the first publications to showcase MiSeq data. The focus of the article is an ultra-deep targeted sequencing method ('UDT-seq') for the detection of low prevalence mutations in heterogeneous tumor samples. In the article, the authors use calibrated human DNA samples to demonstrate the superior performance of MiSeq over Illumina's Genome Analyzer II platform, in terms of both sensitivity and speed.

The impressive quality of the data generated by MiSeq is an encouraging sign that routine sequencing in the clinic may soon become a reality, and that a new era of radically different diagnosis and pharmacology stratagies may be just around the corner.

As with all sequencing data described in Genome Biology articles, the MiSeq data are available in a public repository (NBCI SRA: SRP009487). The MiSeq vs GAII comparison is also nicely complemented by last month’s article from Heinz Himmelbauer and colleagues, which compared the errors and biases in GAII and Illumina HiSeq datasets.

Posted by Naomi Attar at 11:45    Comments (0)

GigaScience – a repository for large datasets

The recent explosion of genomics technology has revolutionized biology, but it is only really of use if people are able to analyze and use the resulting sequences. Storage of such vast quantities of data is problematic, as the ongoing uncertainty over the future of NCBI’s arm of the Sequence Read Archive shows (SRA). The BGI, in conjunction with BioMed Central, recently launched GigaScience, a journal aimed specifically at projects generating a lot of data, which can accommodate such large datasets alongside the articles describing them. GigaScience also anticipates becoming a repository for stand-alone datasets such as those resulting from genome sequencing projects. One such dataset has just been released, and it contains the assembled and annotated sequences of genomes from three strains of sorghum, a plant of huge economic importance in the developing world as a source of food, fodder, fuel and fiber. The article describing these data has been published in Genome Biology; the raw reads are available from the SRA, and the assembled reads from GigaScience. This is the first time that a genome dataset has been cited as a DoI in an article's reference list, so is the first step in the process leading to researchers getting citation credits for the data they generate.

Posted by Andrew Cosgrove at 12:12    Comments (4)

Genome Biology - highlights of the October issue

The October issue of Genome Biology is now available and, excitingly, it contains reports of three novel genome sequences.

Much attention has already surrounded our article from van Bakel et al. reporting the genome of Cannabis sativa. As well as sequencing and assembling the genome, the group also sequenced the transcriptomes of the Purple Kush marijuana strain and the Finola hemp strain to shed light on why marijuana is psychoactive and hemp is not. So as not to spoil the surprise, I won’t reveal the answer here – read the article, or our editorial by Naomi Attar, to find out.

The liver fluke Clonorchis sinensis is endemic in South East Asia and is the third most prevalent worm parasite of humans. The flukes are contracted through eating raw fish, and persistent infection has been linked with bile duct cancer. Xinbing Yu and colleagues have sequenced and assembled the genome of this parasite, which should lead to better therapies to combat worm infection and may provide insights into why colonization by the fluke is carcinogenic.

Anybody who has kept fish is probably familiar with the infectious disease white spot. The disease is caused by a ciliate protozoan called Ichthyophthirius multifiliis, or Ich for short, and is a major problem for the worldwide aquaculture industry. Coyne et al. have sequenced and assembled the Ich genome. The obligate parasitic nature of the Ich genome made this challenging, due to the difficulty in obtaining sufficient quantities for sequencing and the problem of contamination with fish DNA. Further complications were presented by the presence of bacterial endosymbionts, which provided another source of contaminating DNA. But Coyne and his co-workers overcame these problems to sequence the genome. Because Ich is closely related to the model ciliate Tetrahymena thermophila, comparison of the two genomes has shed light on the changes arising on adoption of the parasitic lifestyle, and it is hoped these could lead to therapeutic approaches against white spot.

Similar difficulties of obtaining uncontaminated nucleic acid from an obligate intracellular parasite were faced by Thomas Rudel and colleagues in their attempts to sequence the transcriptome of Chlamydia pneumoniae, and necessitated a complex methodology that included a sucrose gradient purification step and differential RNA-seq. The resulting transcriptome adds useful information on gene structure and expression to the existing genome sequence of this pathogen.

Other research articles this month include a study by Edwin Cuppen and colleagues looking at catastrophic chromosomal rearrangements in colorectal cancer and a transcriptomic study of Rhizobium leguminosarum by Philip Poole and colleagues, and we have also published several methods, including those for detecting condition-specific gene expression and for performing high-throughput shRNA screens. As well as genomes, October has also been a bumper month for reviews: among others, Julian Parkhill and Brendan Wren discuss what genome sequencing can tell us about bacterial epidemics, and Justin Borevitz and colleagues tell us about the success of GWAS in plants.

Posted by Andrew Cosgrove at 15:29    Comments (0)

Putting the high into high-throughput sequencing: the cannabis genome

The cannabis plant has been exploited by humanity primarily for textiles and for intoxication, with hemp strains used for fabrics and marijuana strains for altering the mind. The changes to the genome that led to drug-producing plants is a mystery of cannabis evolution, but one that has now been solved, thanks to an article published in Genome Biology.

In the article, a team of Canadian researchers describe the first cannabis genome sequence, which they assembled using reads from a number of high-throughput sequencing strategies. Using DNA from the potent Purple Kush marijuana strain, obtained from a patient prescribed cannabis for medicinal purposes, the researchers scanned the assembled genome for mutations that differed from hemp strains. They reasoned that such mutations might be why Purple Kush produces THCA, which is the active ingredient of cannabis, while hemp strains do not.

Frustrated in their search for mutations, which didn’t turn up a smoking gun, the researchers instead analyzed the transcriptome sequence – and struck the jackpot.

The transcriptome showed that, while both hemp and marijuana have the THCA synthase genes in their genomes, the gene is strongly expressed in marijuana but not transcribed in hemp. THCA synthase is a gene that codes for an essential enzyme in THCA production; thanks to the Genome Biology article, we now know that making more of this enzyme is how hemp got high.

See also: our editorial

Posted by Naomi Attar at 11:06    Comments (0)

Sequencing from Starbucks and the not-so-patently obvious: Genome Biology attends ICHG 2011

Who owns your DNA sequence? "You do" might seem like the obvious answer, but it wasn’t one that everyone attending the 12th International Congress of Human Genetics in Montreal could agree on.

In a debate on gene patenting, the conference heard how an astonishing 20% of human genes currently have intellectual property claims on them and how Myriad Genetics has had some success defending its patents on breast cancer genes BRCA1 and BRCA2 in the US courts (and, to a more limited extent, in the European Patent Office).

Even the 80% of your gene sequences that have escaped patenting do not belong to you, according to Radoje Drmanac of Complete Genomics, who espoused the view that genomes do not belong to sequenced individuals but to computers. Speaking in a debate on how clinicians can best adapt to the coalescence between high-throughput sequencing and personalized medicine, Drmanac was one of many to claim that patients should not be given access to their DNA sequence.

This coalescence was a notable feature of the conference, with many reports of novel mutations identified by high-throughput sequencing technologies. In particular, exome sequencing has made massively parallel sequencing accessible to a wide range of clinicians and researchers, due to the reduced cost relative to whole genome sequencing. To put a measure on this phenomenon, no less than 387 submitted abstracts were tagged with "exome/s" as a keyword. In light of this, it was no wonder that free copies of Genome Biology’s special issue on exome sequencing were a big hit.

The expansion of high-throughput sequencing in the clinic looks set to continue at a rapid pace, thanks to new affordable "desktop" sequencers exhibited by Illumina (MiSeq) and Life Technologies (IonTorrent) – a development analogous to the appearance of IBM's personal computer.

A demonstration of MiSeq showed that it has been designed with a non-scientist user in mind – and maybe a lazy user, too, given that a smartphone app can provide real time updates while you sit out your sequencing run in the comfort of a coffee shop.

It is easy to imagine that every hospital and clinic in the developed world will have access to desktop sequencers in the not-too-distant feature; for the developing world, a protoype of a handheld DNA sequencer was presented that uses nanowires for gene sequencing at a projected cost of $400 per device.

Controversies were not limited to genome ownership. Jim Watson caused a stir by branding swathes of humanity as "genetic losers". Michael Hayden, of the University of British Columbia, countered that "we are all brothers and sisters in genetic mutation" and that his greatest source of inspiration has been those who have borne their burdens of genetic disease with quiet dignity.

Controversial to this observer was Lynn B. Jorde’s baffling decision to turn down an invited appearance on The Jerry Springer Show. Jorde’s address as President of the American Society of Human Genetics (whose 61st annual meeting ran concurrently with the conference) discussed, in TV-friendly dulcet tones, his genetics education workshops run for the judiciary. Judge Robert Sweet, who heard the Myriad Genetics patent case in his court, may not have needed Jorde’s help because, as fate would have it, his clerk at the time had a PhD in molecular biology (another former clerk was disgraced New York governor Eliot Spitzer).

The 13th Congress will take place in Yokohama, Japan – but not until 2016; the 62nd meeting of the American Society, ASHG 2012, will be held next year in San Francisco. In the mean time, why not listen to Genome Biology’s podcast on the sequencing of disease variants, which features discussions with Jim Lupski, Joris Veltman, Jay Shendure and Elaine Mardis on many of the themes central to this year’s conference.

Posted by Naomi Attar at 11:50    Comments (0)

Introducing the Genome Biology podcast – sequencing and disease mutations

To accompany the recent Genome Biology special issue on exome sequencing, we have made a podcast focusing on the challenges of identifying disease genes using exome sequencing and whole genome sequencing (you can read more about our special issue on exome sequencing in our previous blog post.)

In the podcast we speak with Jim Lupski about his journey to identify the genetic cause of his Charcot Marie Tooth Syndrome. Identifying the cause of this genetically heterogenous disease proved difficult; partially because there are many genes that can be mutated causing this disease, partially because of the specific type of mutation that often causes it – a gene copy number variation.

Jay Shendure discusses how he developed exome sequencing, and how his team gambled upon its use in identifying disease mutations. This technique has proven very successful thus far in identifying causes of Mendelian disease and Joris Veltman spoke with us about his work on mutations in Mental Retardation.

We also chatted with Elaine Mardis about the suitability of exome sequencing for identifying mutations in cancer.

Furthermore, we add to the general debate surrounding the application of sequencing techniques in the clinic and whether there is an expiry date on exome sequencing.

The podcast is available to stream below (or download here, 35.8MB) and is also available on iTunes.

Hannah Stower
Genome Biology Special Issues Editor

Posted by Naomi Attar at 13:41    Comments (0)

Help from a model organism in Genome Biology’s special issue on exome sequencing

In a special issue of Genome Biology focusing on exome sequencing published online today , an article by Karen Avraham and colleagues identifies the genes responsible for hereditary deafness in Jewish Israeli and Palestinian Arab populations.

Most early onset hearing loss is genetic. However, the genes that are involved in this hereditary hearing loss are many and are specific to different populations, making the identification of human hearing loss genes a complex problem. The development of a screen for these genetic mutations would not only aid in the accurate diagnosis of hereditary hearing loss, but also will allow further mutations to be identified in different populations.

Karen Avraham and colleagues identify genes associated with deafness in Jewish Israeli and Palestinian Arab populations using a novel screening approach. To probe for hearing loss genes the authors used known human hereditary hearing loss genes as bait and then sequenced the genes that they captured to identify mutations in the populations.  As additional bait, the authors also used the human houmolog of mouse genes that had previously been shown to be involved in hearing loss. They applied this approach in 11 individuals of Jewish Israeli and Palestinian Arab origin. They identified multiple mutations responsible for hearing loss and so by broadening their approach to include clues from one of our best researched model organisms, the authors now have a tool for diagnosis and researching hereditary deafness.

The special issue of Genome Biology is guest edited by Jay Shendure, his editorial includes an overview of exome sequencing development and future directions. The issue also includes other reviews and opinions from leaders in the field and articles applying exome sequencing. To find out more about what the issue contains, please do read my editorial – we’re very excited about this issue. Printed editions will be available at Beyond the Genome and the International Congress of Human Genetics conferences.

Posted by Hannah Stower at 15:32    Comments (0)

Genome Biology - lots of exciting software this month

The August issue of Genome Biology is now available on our website, and it’s a bumper issue this month. As well as several high-quality research articles (such as the wallaby genome sequence, the transcriptome of regenerating heads in planarians and a comprehensive screen for substrates of the Chk1 checkpoint kinase), we have a number of exciting computational methods for analyzing high throughput genomics data.

Kim and Salzberg present TopHat-Fusion, a modified version of the popular TopHat package for analyzing RNA-seq datasets, that can identify transcripts from fusion genes. As fusion genes are often important in carcinogenesis (such as the canonical BCR-Abl fusion from the Philadelphia chromosome in some leukemias), this has important medical applications.

Uwe Ohler and colleagues present PARalyzer, a package for analyzing PAR-CLIP data. PAR-CLIP is a relatively new method for identifying where specific proteins bind to RNA molecules. PAR-CLIP stands for ‘Photoactivatable Ribonucleoside-enhanced Cross-Linking and Immuno-Precipitation’. Crosslinks are induced between proteins and RNA, and specific proteins pulled down using antibodies. The RNA fragments attached to the proteins can be determined using high throughput sequencing. Until now, packages for analyzing these data have been few, but the new method from Ohler’s group will help researchers interpret their results.

Shirley Liu and colleagues give us CISTROME, in which they have integrated 29 different packages to provide a complete suite for the analysis of ChIP-chip and ChIP-seq data at all stages, from preliminary peak calling, to downstream genome feature association, gene expression analyses and motif discovery. These have all been combined into an easy-to-use application based on the Galaxy open source framework.

After Jason Lieb’s ZINBA program that we published last month this goes to show that Genome Biology’s support for first-rate data analysis applications goes from strength to strength.

Posted by Andrew Cosgrove at 18:20    Comments (0)

Tying the kangaroo genome down

If the date is January 22nd and you happen to be a tammar wallaby, the chances are high that it will be your birthday – as well as the anniversary of your conception. In between these two events, you will have spent eleven months in suspended animation, followed by a short one month gestation (in which you only grew to the size of a kidney bean).

These quirks of tammar reproduction are just some of the many fascinating biological features whose underlying genetics may now be explained, thanks to the publication in Genome Biology of the tammar wallaby genome and transcriptome sequences.

The article, which is accompanied by a number of companion articles in BMC Genomics, BMC Molecular Biology, BMC Immunology, BMC Genetics, BMC Developmental Biology, BMC Evolutionary Biology and EvoDevo (not to mention a Research Highilight in Genome Biology), represents the first kangaroo, second Australian marsupial and third marsupial published genome sequence.

 
Australian marsupial phylogeny (millions of years)

The tammar wallaby is well chosen as the subject of a genome sequencing project, as it is a model marsupial organism studied for insights into immunity, development and reproduction that may have parallels in human health. Its location in the mammalian phylogeny also renders it an invaluable organism for comparative genomics, affording scientists the luxury of asking the important human interest questions exploring what separates the evolutionary trail leading to Homo sapiens from those leading to other mammals.

The first kangaroo genome is a landmark in Australian science, and so it is fitting that the international consortium responsible for its sequencing has Australian researchers at its head. One of the project leaders, Marilyn Renfree (The University of Melbourne), summarizes the Genome Biology article as providing scientists “with many possibilities for understanding how marsupials are so different to us.” She also underscores the potential of translating tammar strategies for survival to the treatment of human disease.

When reading BioMed Central’s tammar wallaby genome and transcriptome article series, gems to look out for include innovations in the immune system, and a sex chromosome system likely to be more akin to that of the ancestral mammal than is the eutherian XY pair. Another highlight is the finding that the tammar’s two thymuses do not have distinct transcriptomes. There may be many more yet to be discovered clues in the sequences and, as all datasets have been made publicly available, the kangaroo genome’s secrets are now ripe for the picking.

Kangaroo Island, South Australia: home to the individual tammar whose genome was sequenced

Posted by Naomi Attar at 16:57    Comments (0)

Genome Biology’s Viennese waltz at the ISMB

The organizers of the 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) could not have predicted that the funeral of an heir to the imperial Hapsburg throne would draw the eyes of the world to Vienna on the 16th July 2011, but so it was that the Viennese streets were overflowing with computational biologists just in time for the city to spend a day in the global spotlight.

The ISMB, which this year was held jointly with the 10th Annual European Conference on Computational Biology, is perhaps the major event of the computational biology calendar. Among the more than 1,700 delegates attending ISMB 2011 were keynote speakers Bonnie Berger, Alfonso Valencia, Luis Serrano, Janet Thornton and Michael Ashburner – not forgetting Olga Troyanskaya, whose post-keynote presentation Q&A from Princeton via Skype would have been a pipedream when the inaugural ISMB was held in 1993.

Hot topics at the conference included RNA-seq, talks on which attracted so many attendees that capacity was stretched beyond standing room only. Related to this, the “data deluge” brought about by high throughput technologies, such as RNA-seq, was a challenge being tackled from a computational standpoint by a number of delegates. To highlight the data problem, Janet Thornton estimated the time taken to transfer the entire 1,000 Genomes Project dataset to Australia as 6 months – a figure made more alarming when you consider that China’s BGI running its machines at full tilt can sequence 2,000 human genomes per day.

Another strong theme of the research presented was personalized medicine. Work being done on this area ranges from systems biology on gene networks in the context of disease to synthetic biology approaches in which “smart” viruses compute therapeutic instructions to give transduced cells dependent on a biological input. Personalized medicine is just one example of a traditionally non-computational research discipline that is being revolutionized by recent advances in bioinformatics. Michal Linial, one of three conference chairs, explained that computational biology is currently “changing all classical biology.”

Computational biologists are perhaps more aware than most of the need to share data as widely as possible, in a way that makes re-use of the data user friendly. Two initiatives to promote data sharing held workshops at the conference: BioSharing and ELIXIR. At the BioSharing workshop, which discussed the bioDBcore database cataloging project, Genome Biology appeared on the panel as a voice of open access publishing and representative of BioMed Central. In addition to Genome Biology, BioMed Central had several other journals represented at the ISMB, including a strong presence from BMC Bioinformatics and GigaScience.

Next year’s ISMB will be held at Long Beach, California, while ECCB 2012 will take place in Basel. Early birds can find out more at http://www.iscb.org/ismb2012 and http://www.bc2.ch/2012/. Genome Biology’s own conference – “Beyond the Genome 2011” – includes a Genome Informatics pre-meeting to be held 19th September in Washington, DC.

Posted by Naomi Attar at 18:09    Comments (0)

The first Chinese Rhesus macaque genome

The Rhesus macaque (Macaca mulatta) is an Asian monkey that shares 93% of its DNA sequence with humans and, due to this similarity, is an important species for scientific study. Until now, work on the Rhesus macaque has largely focused on the Indian subspecies, but an article published in Genome Biology reports, for the first time, the genome sequence of a Chinese Rhesus macaque.

In the article, researchers from the BGI (China’s premier genomics institute) and the Kunming Institute of Zoology identify millions of DNA sequence variations between the Indian and Chinese Rhesus macaque genomes, including 5.5 million one letter variations known as single nucleotide polymorphisms, or SNPs. A website to enable browsing of these SNPs accompanies the article and provides a valuable new resource cataloging the differences between the two subspecies.

Our understanding of genomic diversity in the Rhesus macaque is also enhanced by a recent article published in BMC Genomics, which compares the genome sequences of three Indian Rhesus macaques, identifying 3 million SNPs. Together, the Genome Biology and BMC Genomics datasets represent a significant advance in primate genomics and will inform future research in fields ranging from human evolution to HIV virology.

Posted by Naomi Attar at 13:57    Comments (0)