ACMG: A Look at Applying Genomic Data to Clinical Reports

The annual American College of Medical Geneticists (ACMG) conference meets this week (March 21-25, 2017) in Phoenix, Arizona, providing an outstanding forum to learn how genetics and genomics are being integrated into medical and clinical practice. Eric Venner, from the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine, will present the following poster (Abstract Number 368): Generating Clinical Reports from Genomic Data on the Cloud-based Neptune Platform  on Friday March 24th 10:30AM-12:00PM

In order to meet the demand for timely and cost-efficient clinical reporting, HGSC developed Neptune, an automated analytical platform to sign out and deliver clinical reports. The process starts when a clinical site uploads a test requisition to the HIPAA compliant environment on DNAnexus. Next, de-identified samples are analyzed with HGSC’s variant calling pipeline, Mercury, which feeds into the reporting pipeline, Neptune. Variants of putative clinical relevance are identified for manual review and possible addition to a VIP database of clinically relevant variation. The VIP database currently holds 20,872 SNPs and 3,946 indels, as well as a curated set of copy number variants.

Neptune’s manual review interface was designed with a clinical geneticist in mind. Users can login, curate variants in their samples, update the VIP database accordingly and create clinical reports. Early applications include reporting for the NIH Electronic Medical Records and Genomics (eMERGE) Network III where more than 14,500 samples and a panel of 109 genes will be processed over the course of three years.

eMERGE is a national network that combines DNA biorepositories with electronic medical record (EMR) systems for large scale, high-throughput genetic research to support investigating how personalized treatments impact patient care. Research so far has led to significant discoveries across a wide range of diseases, including prostate cancer, leukemia, and diabetes.  DNAnexus and the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine worked to build the eMERGE Commons, a data repository where genomic data are merged with patient electronic medical records (EMR), as well as analysis results and bioinformatics tools to be accessed and applied by eMERGE researchers.

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.

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.