DNAnexus in the Literature: A Look at Recent Papers Using Our Platform

It’s great to find that several papers published recently have used DNAnexus in their research — and even more interesting to see the broad range of applications presented in these papers, from cross-species analyses to novel disease polymorphisms, and from single genes to whole genomes. We thought it would be informative to take a look at a few of these publications and discuss how the DNAnexus tools contributed to them.

academic papers citing dnanexusFirst we have a paper in Genome Biology from Eric Vallender at Harvard Medical School. He reports using human exome enrichment methods on chimpanzee and rhesus macaque samples. The chimpanzee sample showed similar coverage levels and distributions following exome capture as the human sample, whereas the rhesus macaque sample showed significant coverage in protein-coding sequence but much less in untranslated regions. In both cases, the primates showed significant numbers of frameshift mutations compared to self-genomes. Vallender used DNAnexus for “initial data analysis, including alignment to genome, coverage analysis, and Nucleotide-Level Variation analysis,” according to the paper.

Next up, we have three papers from scientists at the Cleveland Clinic focusing on myeloid disorders. In a paper from the journal Leukemia, researchers screened samples from patients with RARS (Refractory Anemia with Ring Sideroblasts) and RARS-T (RARS with refractory thrombosis), two distinct subtypes of MDS (myelodysplastic syndromes) and MDS/myeloproliferative neoplasms (MDSs/MPNs). They used Exome and Nucleotide-Level Variation analyses to identify variants associated with the conditions, finding somatic mutation in SF3B1, a gene located in chromosome 2q in several of the patients with RARS or RARS-T. Another paper, this one published in Blood, used DNAnexus to perform mapping, variant analysis, and RNA-seq in a project that used exome sequencing of 15 patients with myeloid neoplasms to find somatic mutations. Mutations were found that affect spliceosomal genes, resulting in defective splicing and suggesting a new leukemogenic pathway. Analysis of the mutations may serve as useful diagnostic markers, or potentially even therapeutic targets. In the third paper, also in Blood, they used SNP chips, gene expression arrays, and next-gen sequencing to look at loss of heterozygosity affecting chromosome 7q, which is common in AML and MDSs. Using direct and parallel sequencing, they found no recurrent mutations in typically large deletion 7q and monosomy 7 patients, but they did find decreased expression of genes included in SNP-A defined minimally deleted regions.

A Nature paper from Stanford scientists Rada-Iglesias et al. employed ChIP-seq and RNA-seq analyses of human embryonic stem cells to find unique chromatin signatures that identified two distinct classes of genomic elements. The study also identified more than 2,000 putative regulatory sequences, providing an invaluable resource for lineage tracking and isolation of transient cell populations representing early steps of human development. In a second paper, the same group identified a new member of the mESC (mouse embryonic stem cell) transcriptional network, Prdm14, which plays a dual role as a context-dependent transcriptional repressor or activator.

Scientists at the Hadassah-Hebrew University Medical Center in Israel have made use of DNAnexus in four of their recently published papers that used our Exome and Nucleotide-level Variation analysis to look at polymorphic changes associated with various clinical conditions. The first of these came out in Molecular Genetics and Metabolism, providing a study of three siblings with ventriculomegaly at early gestation. The group used linkage analysis and exome sequencing to identify a hemizygous mutation in the mitochondrial X-linked AIFM1 gene which encodes Apoptosis Induced Factor (AIF), a 613 amino acid flavoprotein. In the Annals of Neurology, the team reports homozygosity mapping followed by exome sequencing to find a deleterious mutation in the DST gene in four infants with a new lethal autonomic sensory neuropathy. In PLoS ONE, they studied two patients with juvenile parkinsonism and used homozygosity mapping and whole exome sequencing to identify a deleterious mutation in DNAJC6, which encodes the HSP40 Auxilin, a protein selectively expressed in neurons. The paper underscores a key role of the endocytic/lysosomal pathway in the pathogenesis of Parkinson disease and other forms of parkinsonism. In their most recent paper, the group studied the molecular basis of childhood familial chronic Coombs’ negative hemolysis and relapsing polyneuropathy in infants of North-African Jewish origin from four unrelated families using homozygosity mapping and exome sequencing. A homozygous missense mutation, p.Cys89Tyr in CD59, was identified in all the patients. The mutated protein was expressed at lower levels and failed to localize properly on the cell surface.

It’s really rewarding to see that DNAnexus is making a difference for scientists. We’ll continue to keep an eye on the literature and offer updates as other publications using DNAnexus are released.

At NGS Meeting: Epigenetics & “Dark Matter” Were Major Themes

next generation sequencing congress 2012It was with great enthusiasm that I attended Oxford Global’s recent 4th Next Generation Sequencing meeting in London, where some 500 delegates from more than 20 different countries gathered to discuss sequencing technology and research innovations. There were more than 60 presentations, ranging from vendors showcasing their wares to ground breaking new science from academic research labs. Three themes stood out as I listened: the scale of the technologies being applied to studying genomes, the ever-increasing studies on epigenetics, and studies on the so-called ‘dark matter’ in the genome.

Here are several highlights from some of the talks I attended:

Joakim Sandeberg (SciLifeLab, Stockholm) opened the meeting describing a method his group has been using to measure localized RNA expression changes in thousands of cells simultaneously from tissue slices using next generation sequencing, showing examples from olfactory bulb and tumor samples.

Neil Ward (Illumina) discussed the increase in HiSeq throughput and new data compression (CRAM) and alignment (ISAAC) tools, and Kevin Corcoran (Pacific Biosciences) described their new Quiver algorithm, which can convert raw single read accuracy of 87% in 4-10kb reads, to 99.99964% at QV54 over 3Mb of Meiothermus ruber. A talk by Lex Nederbragt (Norwegian Sequencing Centre) showed data from the Cod genome using the Pacific Bioscience instrument giving an N50 of 6kb, with maximum read length at 25kb.

Hubert Rehrauer (Functional Genomics Center Zurich) gave a good overview of optimizing sequence data analysis by monitoring data QC and the parameters used in analyses, and Sarah Ennis (Southampton Hospital) described a range of simple QC checks in addition to data QC. These include checking familial relationships and gender of the samples received from sequencing services and that they correlate with the expected data sent, showing examples of cross-contamination and mixed up samples.

Seth Crosby (Genome Technology Access Center, Washington University St. Louis) is running CAP and CLIA compliant sequencing for clinicians. He described the challenges of clinical sequencing and analysis. They use validated gene panels, which are reimbursable from medical insurers, and have generated a library of around 5,000 annotated publications. As a result clinicians are now provided with a rating from 1 (medically actionable) to 8 (SNP only) for the patient’s samples.

James Flanagan (Imperial College) showed data using epigenetics and EWAS on breast cancer patients’ peripheral blood. They switched from exome arrays to bisulphite sequencing as exome arrays do not cover promoter sites, which show an enormous variation in methylation states.

Tim Aitman’s group (Imperial College) has sequenced the whole genomes of 27 different rat strains and used bisulphite sequencing to look at epigenetic change between normal and hypertensive rat left ventricles. They found 55,000 differentially methylated CpG islands at >5% difference, of which, more than 3,200 showed >50% difference.

Gil Atzman (Albert Einstein College of Medicine) described the LonGenity study looking at 540 centenarians, 750 of their offspring against 750 controls. They found an age-related accumulation of methylation that followed a predictable pattern up to 60, and then continued in a less predictable way as individuals aged further.

Gareth Wilson (UCL, Cancer Institute, London) described the work in the Beck lab, using the MeDUSA pipeline to analyse methylation during cellular differentiation by comparing ESC, NPC and MEF cells. The more differentiated the cells were, the lower the global methylation and the higher the variation in methylation around CpG islands. They also looked at methylation in HPV16 virus and saw most of the methylation around the L1/L2 boundary region of the virus genome.

Ellen Li’s group (Stonybrook) studied Crohn’s Disease (CD) using RNA expression analyses and DNA analyses for host and microbiome (16S analyses). They found different expression patterns for ileal CD, colitis and normal lieum and are now using 16S profiling on all patients to identify possible roles for gut microbial in Crohn’s Disease. Meanwhile, Mick Watson’s group (ARK Genomics) has been working on re-sequenced sheep, cattle, deer, and reindeer genomes, and individual samples, they were able to identify between 10,000-80,000 unique hits to 16S RNAs.

ASHG: With Great Science Comes Great Responsibility

ASHG Conference 2012The American Society of Human Genetics annual meeting was held at the Moscone Center in San Francisco, not far from DNAnexus headquarters in Mountain View, Calif. Several of us were lucky enough to make the short trip and check out what is widely considered the biggest genomics conference of the year, this time with almost 7,000 scientists in attendance.

The conference kicked off with a plenary talk from the University of Washington’s Mary-Claire King, 2012 President of ASHG. Her focus, “The Scientist as a Citizen of the World,” really resonated with attendees — as evidenced not only by the energy in the room, but by how many people were tweeting from King’s address. She told attendees that scientists have a responsibility to put their knowledge and common sense to use, not just in the lab but as world citizens. She also urged researchers to remember that no question is too large or too daunting to be asked.

Another session that really stirred interest centered on gene patents. Panelists, including Mark Lemley from Stanford and Lori Andrews from the Hastings Institute, discussed the Myriad BRCA gene patents in depth, adding context from other cases, such as Prometheus and a GlaxoSmithKline patent related to asthma. Regardless of your view on the patentability of genes, this was a fascinating discussion that highlighted the importance — both in the commercial market and in academic research — of linking genes to particular traits.

The ASHG meeting is known as the place to give out major genetics awards, and this year’s event did not disappoint. Some leading names in the field went home with new recognition, including: Uta Francke, formerly at Stanford and now Senior Medical Director at 23&Me (ASHG William Allan Award); Jay Shendure at the University of Washington (ASHG Curt Stern Award); Alan Emery of the University of Edinburgh (ASHG Award for Excellence in Human Genetics Education); and Douglas Wallace at the Children’s Hospital of Philadelphia (Gruber Genetics Prize).

One award winner offered a particularly popular talk: NIH Director Francis Collins was on site to give the ASHG Victor A. McKusick Leadership Award Presentation. Collins, a longtime ASHG champion, bemoaned the state of funding for life sciences, noting that his agency’s budget is now 20 percent lower in constant dollars than it was in 2003. He encouraged scientists to promote the value of research in their communities, helping the public understand why it is so important to continue strong funding levels for scientific research.

We were proud to be active participants at ASHG, with our exhibit hall booth and our luncheon workshop featuring a customer story from Anshul Kundaje, presenting his latest Encode paper, along with the latest information about DNAnexus from our CEO Andreas Sundquist. It was an honor to have so many attendees take part in our workshop — thanks to everyone for taking the time to learn more about DNAnexus.

We raffled off an iPod to one of our luncheon or booth visitors, and the winner was Suleyman Gulsuner from the University of Washington. Congratulations, Suleyman!

A lot of what we learned at ASHG this year was related to responsibility: our collective responsibility to promote science and the scientific approach in the world, as well as the responsibility for enabling research with or without gene patents. At DNAnexus, our responsibility is to provide an easy-to-use, secure, and convenient platform to facilitate research and to help scientists make connections that are important enough to share with the broader world. We consider it a privilege to be entrusted with your data, and we take that responsibility very seriously.