4 results
2278: Identifying causative mutations in Treacher Collins syndrome using iobio
- Alistair N. Ward, Matt Velinder, Chase Miller, Tony Di Sera, Yi Qiao, Dave Viskochil, Gabor Marth
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- Journal:
- Journal of Clinical and Translational Science / Volume 1 / Issue S1 / September 2017
- Published online by Cambridge University Press:
- 10 May 2018, pp. 13-14
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OBJECTIVES/SPECIFIC AIMS: The objective of the study was 2-fold; to identify potentially deleterious alleles in a child with Treacher Collins syndrome, and; to demonstrate the value of the iobio analysis platform for intuitively and rapidly analyzing genomic data. METHODS/STUDY POPULATION: We used the iobio suite of web-based applications to analyze quality metrics for the sequencing data and called variants for the proband and his parents. We then visually interrogated variants in genes potentially associated with the syndrome in real-time, using the intuitive gene.iobio application. We sought high impact variants that demonstrated a predicted impact on the protein function, and were simultaneously at low allele frequency in the general human population. Variants were also compared against the ClinVar database of known mutations to identify variants that have already been associated with this, or related syndromes in the literature or clinical studies. Finally, the gene.iobio tool allows users to interrogate the primary sequencing data to ensure that no variants had been missed by the primary variant calling pipeline. This analysis pipeline was performed using intuitive web-based apps in real time, and consequently represents a system that is available to users that traditionally are excluded from these analyses. RESULTS/ANTICIPATED RESULTS: The iobio suite was used to rapidly assess data quality and interrogate genetic variants for a child with Treacher Collins syndrome. A compound heterozygote consisting of 2 missense alleles in the TCOF1 gene was identified as a compelling pathogenic allele, necessitating further functional investigation. The study helped validate the use of the intuitive iobio tools in such analyses, strengthening the case for greater involvement of medical professionals in data analysis. DISCUSSION/SIGNIFICANCE OF IMPACT: The performed analyses demonstrated that the whole genome sequencing data for the family being studied was of a very high quality, although 1 gene demonstrated a local region of almost zero coverage. This ensured that study conclusions can be presented with confidence. A variant associated with Treacher Collins syndrome 1 in ClinVar was uncovered in the TCOF1 gene, however, given it’s benign rating, this variant was not considered further. The most interesting candidate was a compound heterozygote, consisting of 2 missense mutations, also in the TCOF1 gene. These mutations occurred with allele frequencies of 22% and 8% in the general population, and additional molecular and functional studies are currently being pursued.
2097: Aging-associated increases in platelet granzyme A regulate pro-inflammatory gene synthesis by monocytes
- Matthew Thomas Rondina, Robert A. Campbell, Anish Bhatnagar, Zechariah Franks, Jesse W. Rowley, Bhanu Kanth Manne, Mark A. Supiano, Alistair N. Ward
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- Journal:
- Journal of Clinical and Translational Science / Volume 1 / Issue S1 / September 2017
- Published online by Cambridge University Press:
- 10 May 2018, p. 56
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OBJECTIVES/SPECIFIC AIMS: Platelets govern signal-dependent inflammatory responses by leukocytes. Although dysregulated inflammation is common in older adults, platelet-leukocyte signaling events and downstream inflammatory gene synthesis in aging is not known. METHODS/STUDY POPULATION: Highly-purified platelets and monocytes were isolated from healthy older (age>60, n=27) and younger (age<45, n=36) adults and incubated together in autologous and nonautologous conditions. Inflammatory gene synthesis by monocytes, basally and in the presence of activated platelets, was examined. Next-generation RNA-sequencing allowed for unbiased profiling of the platelet transcriptome in older and younger adults. Differentially expressed candidates in aged platelets were validated and recombinant granzyme A (in the presence and absence of TLR4 and Caspase-1 inhibition) identified putative ligands controlling inflammatory gene synthesis. RESULTS/ANTICIPATED RESULTS: In unstimulated or activated conditions, monocyte chemoattractant protein 1 (MCP-1) and interleukin-8 (IL-8) synthesis by monocytes alone did not differ between older and younger adults. However, in the presence of autologous activated platelets, monocytes from older adults synthesized significantly greater MCP-1 (867.150 vs. 216.36 ng/mL, p<0.0001) and IL-8 (41.5 vs. 9.2 ng/mL, p<0.0001) than younger adults. Nonautologous, or switch experiments, demonstrated that aged platelets were sufficient for upregulating MCP-1 and IL-8 synthesis by monocytes. Surprisingly, classic platelet proteins known to signal to monocytes and induce MCP-1 synthesis (p-selectin, RANTES, and PF4) were not increased in platelets from older adults. Using RNA-seq followed by validation via RT-PCR and immunoblot, we identified candidate platelet molecules increased in aging that mediate platelet-monocyte signaling and pro-inflammatory gene synthesis. We confirmed that granzyme A (GrmA), a serine protease not previously identified in platelets, is present in human platelets at the mRNA and protein level. GrmA is secreted by activated platelets in signal-dependent fashion. Moreover, GrmA in platelets is significantly increased in aging (~9-fold vs. younger adults). Blocking GrmA inhibited MCP-1 and IL-8 synthesis in older adults. Finally, we uncovered that platelet GrmA signaling to monocytes is regulated through TLR4 and Caspase-1. DISCUSSION/SIGNIFICANCE OF IMPACT: Human aging is associated with reprogramming of the platelet transcriptome. A previously unrecognized protein in platelets, GrmA, is increased in aging and causes increased MCP-1 and IL-8 gene synthesis by target monocytes in a TLR4 and Caspase-1 dependent mechanism. Increased platelet GrmA in aging may contribute to injurious inflammatory responses common in older adults.
2254: iobio: From academic project to commercial enterprise
- Alistair N. Ward, Chase Miller, Gabor Marth
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- Journal:
- Journal of Clinical and Translational Science / Volume 1 / Issue S1 / September 2017
- Published online by Cambridge University Press:
- 10 May 2018, p. 38
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OBJECTIVES/SPECIFIC AIMS: The iobio project enables anyone (eg, diagnosticians, MDs, genetic counselors, citizen scientists) to perform useful analysis of genomic data, without a need to rely on bioinformaticians. iobio uses a novel real-time analysis framework, coupled with powerful visualizations delivered in a standard web browser. The project successfully supports free academic/nonprofit users, but occasions exist where it is more applicable for the project to be delivered commercially. Frameshift Genomics is developing commercial applications and functionality, which will exist alongside and in coordination with the academic project. These products will be marketed to large institutions including genome institutes, hospitals, diagnostic labs etc., but also to individual users who do not have access to large compute resources, or bioinformatic analysts, and everything in between. METHODS/STUDY POPULATION: The commercial iobio project under Frameshift Genomics aims to develop applications and features that cannot be successfully supported by an academic model. For example, when analyses are scaled up to processing of extremely large data sets, a commercial product with access to compute resources makes more sense than an academic tool. Bam.iobio is an application that samples data from sequencing alignment files, taking seconds to generate and visualize statistics representative of the entire file. This app is offered for free academically. When analysis involves thousands of such files, however, the commercial application, multibam.iobio, is more suitable. Other examples, including support for licensed third-party software and permitting extensive computation via cloud platforms, can also only be reasonably be supported via commercial software. Finally, development of commercial applications is driving adoption of more rigorous testing platforms, delivering more robust products. A particular strength of the iobio platform is allowing non-bioinformaticians to understand their data, for example providing quality control functionality providing confidence in data sets and the conclusions drawn from them. Such analyses are critical to all users of genomic data, and the iobio platform is ideally suited to provide an intuitive, integrated framework for performing them. RESULTS/ANTICIPATED RESULTS: The iobio project has been readily adopted by many in the community and shows significant promise for democratizing genomic analysis. Work is ongoing, supported by NIH small business grants, to develop commercial applications that will be marketed to analysts and medical professionals from large genome institutes and universities, to individual project users and citizen scientists. DISCUSSION/SIGNIFICANCE OF IMPACT: There are currently a number of iobio tools available academically, and they have been embraced by many in the genomics community. In fact, a number of popular platforms (eg, Galaxy, the International Cancer Genome Consortium (ICGC) data portal, mygene2 at the University of Washington) have incorporated iobio tools into their own platforms. To date, the gene.iobio variant interrogation tool has been used in a number of diagnostic projects, aiding identification of putative causative variants, and the pre-release version of the commercial multibam.iobio tool has been critical in unearthing data quality problems in project level data.
Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools
- Alistair Ward, Mary A. Karren, Tonya Di Sera, Chase Miller, Matt Velinder, Yi Qiao, Francis M. Filloux, Betsy Ostrander, Russell Butterfield, Joshua L. Bonkowsky, Willard Dere, Gabor T. Marth
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- Journal:
- Journal of Clinical and Translational Science / Volume 1 / Issue 6 / December 2017
- Published online by Cambridge University Press:
- 23 April 2018, pp. 381-386
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Introduction
Computational analysis of genome or exome sequences may improve inherited disease diagnosis, but is costly and time-consuming.
MethodsWe describe the use of iobio, a web-based tool suite for intuitive, real-time genome diagnostic analyses.
ResultsWe used iobio to identify the disease-causing variant in a patient with early infantile epileptic encephalopathy with prior nondiagnostic genetic testing.
ConclusionsIobio tools can be used by clinicians to rapidly identify disease-causing variants from genomic patient sequencing data.