Looking Back at SFAF in Santa Fe

Finishing in the FutureWe recently attended the Sequencing, Finishing, and Analysis in the Future (SFAF) meeting, hosted by the Los Alamos National Laboratory from May 29-31 in Santa Fe. DNAnexus was a sponsor of this year’s event, which included a star-studded roster of scientific speakers.

Among the great keynote presenters were Baylor’s Richard Gibbs; Mark Adams from the Venter Institute; and the NCBI’s Deanna Church.

As the conference name suggests, data analysis was a pillar of the event. There were several presentations on various hardware and software options, including data management and cloud computing. Other areas of interest included genome annotation pipelines and analytical tools for comparative genomics, structural variation, and more.

There were also a number of talks and posters centered on de novo bacterial and human genome sequence assembly methods, as well as metagenomic studies.

Andrey Kislyuk, one of our Senior Software Engineers, presented on deploying genomic applications in the cloud on DNAnexus. Anton Korobeynikov from the Algorithmic Biology Laboratory at the St. Petersburg Academic University, also presented on the improved SPAdes [1] , a new assembly tool (published in 2012) that has been ported as an app into the DNAnexus platform and is now available to all DNAnexus users.

SPAdes, which was recently recognized as a top performing assembler in the GAGE-B Evaluation, was designed specifically for single-cell genomics. Genome sequences from single cells have their own computational challenges, including lack of uniformity in read coverage and elevated numbers of chimeric reads and sequencing errors. Assemblers for next-gen sequencing are often confused by this data, which may have 100 times more coverage of erroneous segments than correct segments. SPAdes generates single-cell assemblies, providing information about genomes of bacteria that can’t be cultured that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is intended for both standard isolates and single-cell bacteria assemblies.

You can try SPAdes and a number of other apps today by signing up for a free DNAnexus beta account.

Interested in developing your own app? DNAnexus is currently accepting new members for our developer program. If interested, please contact us at developers@dnanexus.com to enroll.

Our new developer portal provides lots of information including FAQs, quick start guides, sample code, and other technical resources.

[1]  Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, Sergey I. Nikolenko, Son Pham, Andrey D. Prjibelski, Alexey V. Pyshkin, Alexander V. Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner. Journal of Computational Biology. May 2012, 19(5): 455-477. doi:10.1089/cmb.2012.0021.

Just Launched: The DNAnexus Developer Program

Join a dynamic app incubator community!

Software Development KitCalling all bioinformaticians, computational scientists and hackers! DNAnexus, a company leveraging cloud computing to facilitate the analysis of extremely large biological data sets, has kicked off an app developer program and is looking to add novel genomics tools for users of our new platform.

Genomic data is the next frontier in truly challenging, Big Data problems. Our platform is designed to help scientists collaborate and analyze DNA data within a secure, web-based environment. Users will be able to upload or build workflows and project pipelines, choosing from their own tools, DNAnexus-provided apps, and now apps contributed by external developers like you.

Why should you care?

Uploading your app to the DNAnexus platform offers lots of advantages:

  • The DNAnexus platform is the most flexible and configurable API-based infrastructure for enabling genomic data analysis and data sharing.
  • The DNAnexus platform accepts DNA data from any sequencing instrument, so you can write for multiple sequencers and gain users among a much broader audience than a vendor-specific environment.
  • Join early and incur no out-of-pocket expenses for developing and testing your app. Receive a $1,000 credit toward cloud storage and compute resources.
  • Get recognition! We’ll be profiling our best-contributed apps and the genius developers behind them as we roll out the platform.
  • Easily showcase your app and its functionality on behemoth data sets.
  • Working with DNAnexus is easy and we are more than happy to provide free technical support while you are developing your app.
  • DNAnexus is building in monetization opportunities, so as the platform comes out of beta your app can create a flow of income.

Join Today!genomics hackers

Interested in learning more? Email developers@dnanexus.com with questions. Send the following information to join the program:

1. Your name and institution
2. Briefly explain the problem you aim to solve
3. Describe the genomics tool you plan to build

Publication Watch: In Early 2013, Nice Flow of New Papers from DNAnexus Users

It’s been awhile since we checked in on publications using DNAnexus, so we headed over to PubMed to provide an update. With so many great new papers coming out — more than 10 just in the past few months — we wanted to take the opportunity to look at a few of them and see how they’re making use of DNAnexus.

 

In the Journal of Medical Genetics, scientists from Hebrew University Medical Center and colleagues at other organizations published a paper entitled “Agenesis of corpus callosum and optic nerve hypoplasia due to mutations in SLC25A1 encoding the mitochondrial citrate transporter” (published online February 2013). Lead author Simon Edvardson et al. report on the first known patient with agenesis of corpus callosum caused by a mitochondrial citrate carrier deficiency. The team performed exome sequencing and used DNAnexus for read alignment and variant calling. Two pathogenic variants were found in a gene responsible for the mitochondrial citrate transporter, and functional studies in yeast validated the findings by displaying the same biomolecular effects of the mutated proteins.

 

In the January issue of Antimicrobial Agents and Chemotherapy, a journal from the American Society for Microbiology, a research team from Georgetown University Medical Center and the Institute of Microbiology in Beijing released a paper called “Azole Susceptibility and Transcriptome Profiling in Candida albicans Mitochondrial Electron Transport Chain Complex I Mutants.” In the study, the authors looked at how mitochondrial changes in yeast alter susceptibility to certain azole compounds commonly used as antifungal agents. As part of the effort, the team used RNA-seq to generate a transcriptome profile of two mutants known to increase susceptibility to azoles. Data analysis was conducted through DNAnexus. The scientists found that both mutants showed downregulation of transporter genes that encode efflux proteins, a mechanism thought to be linked to the cell energy required for azole susceptibility.

 

In the journal Human Mutation, a paper entitled “A Deletion Mutation in TMEM38B Associated with Autosomal Recessive Osteogenesis Imperfecta” (published online in January) comes from a research group at Ben Gurion University and the Soroka Medical Center, both in Israel. The scientists studied patients with autosomal recessive osteogenesis imperfecta, or brittle bone disease, which could not be explained by any previously known mutation. The team used genome-wide linkage analysis and whole exome sequencing to identify a single mutation common to all three patients: a homozygous deletion mutation of an exon in TMEM38B. Sequence read alignment, variant calling, and annotation were done with DNAnexus tools.

 

Finally, a paper published early online in February in the journal Case Reports in Genetics called “Targeted Next-generation Re-sequencing of F5 gene Identifies Novel Multiple Variants Pattern in Severe Hereditary Factor V Deficiency“ comes from a group that used DNAnexus for data quality, exome coverage, and exome-wide SNP/indel analysis. The authors — scientists from Pennsylvania State University and MS Hershey Medical Center — present a study of four people with severe factor V deficiency in which they used next-gen sequencing to study the factor V gene locus. They found five coding mutations and 75 noncoding variants, including three missense mutations previously associated with other factor V phenotypes.