Harvard Personal Genome Project: lessons from participatory public research

Background: Since its initiation in 2005, the Harvard Personal Genome Project has enrolled thousands of volunteers interested in publicly sharing their genome, health and trait data. Because these data are highly identifiable, we use an ‘open consent’ framework that purposefully excludes promises about privacy and requires participants to demonstrate comprehension prior to enrollment. Discussion Our model of non-anonymous, public genomes has led us to a highly participatory model of researcher-participant communication and interaction. The participants, who are highly committed volunteers, self-pursue and donate research-relevant datasets, and are actively engaged in conversations with both our staff and other Personal Genome Project participants. We have quantitatively assessed these communications and donations, and report our experiences with returning research-grade whole genome data to participants. We also observe some of the community growth and discussion that has occurred related to our project. Summary We find that public non-anonymous data is valuable and leads to a participatory research model, which we encourage others to consider. The implementation of this model is greatly facilitated by web-based tools and methods and participant education. Project results are long-term proactive participant involvement and the growth of a community that benefits both researchers and participants

Antiandrogens Act as Selective Androgen Receptor Modulators at the Proteome Level in Prostate Cancer Cells*

Current therapies for prostate cancer include antiandrogens, inhibitory ligands of the androgen receptor, which repress androgen-stimulated growth. These include the selective androgen receptor modulators cyproterone acetate and hydroxyflutamide and the complete antagonist bicalutamide. Their activity is partly dictated by the presence of androgen receptor mutations, which are commonly detected in patients who relapse while receiving antiandrogens, i.e. in castrate-resistant prostate cancer. To characterize the early proteomic response to these antiandrogens we used the LNCaP prostate cancer cell line, which harbors the androgen receptor mutation most commonly detected in castrate-resistant tumors (T877A), analyzing alterations in the proteome, and comparing these to the effect of these therapeutics upon androgen receptor activity and cell proliferation. The majority are regulated post-transcriptionally, possibly via nongenomic androgen receptor signaling. Differences detected between the exposure groups demonstrate subtle changes in the biological response to each specific ligand, suggesting a spectrum of agonistic and antagonistic effects dependent on the ligand used. Analysis of the crystal structures of the AR in the presence of cyproterone acetate, hydroxyflutamide, and DHT identified important differences in the orientation of key residues located in the AF-2 and BF-3 protein interaction surfaces. This further implies that although there is commonality in the growth responses between androgens and those antiandrogens that stimulate growth in the presence of a mutation, there may also be influential differences in the growth pathways stimulated by the different ligands. This therefore has implications for prostate cancer treatment because tumors may respond differently dependent upon which mutation is present and which ligand is activating growth, also for the design of selective androgen receptor modulators, which aim to elicit differential proteomic responses dependent upon cellular context

Accurate Whole-Genome Sequencing and Haplotyping from 10 to 20 Human Cells

Recent advances in whole genome sequencing have brought the vision of personal genomics and genomic medicine closer to reality. However, current methods lack clinical accuracy and the ability to describe the context (haplotypes) in which genome variants co-occur in a cost-effective manner. Here we describe a low-cost DNA sequencing and haplotyping process, Long Fragment Read (LFR) technology, similar to sequencing long single DNA molecules without cloning or separation of metaphase chromosomes. In this study, ten LFR libraries were made using only ~100 pg of human DNA per sample. Up to 97% of the heterozygous single nucleotide variants (SNVs) were assembled into long haplotype contigs. Removal of false positive SNVs not phased by multiple LFR haplotypes resulted in a final genome error rate of 1 in 10 Mb. Cost-effective and accurate genome sequencing and haplotyping from 10-20 human cells, as demonstrated here, will enable comprehensive genetic studies and diverse clinical applications

Three plasma biomarkers of HTLV-1-associated myelopathy/tropical spastic paraparesis

The pathogenesis of HAM remains uncertain: the disease is thought to be caused by the immune response to HTLV-1, possibly by bystander damage to neurons in the spinal cord. The strongest correlate of HAM in HTLV-1-infected individuals is the proviral load of HTLV-1, i.e. the percentage of peripheral blood mononuclear cells that carry the provirus. To aid in the differential diagnosis of HAM, and to search for clues as to the pathogenetic mechanisms of the disease, we carried out SELDI mass spectrometry on plasma samples from 68 HTLV-1-positive individuals, 16 uninfected controls and 11 patients with secondary progressive MS. We identified three plasma protein biomarkers that are specifically associated with HAM, independently of proviral load. The three proteins were identified by tandem mass spectrometry as b2-microglobulin, calgranulin B, and apolipoprotein A2. Using the two most strongly associated biomarkers, b2-microglobulin and calgranulin B, we derive a simple algorithm that correctly classified the disease status (presence or absence of HAM) in 81% of HTLV-1-infected subjects in the cohort

A singular finite element for Stokes flow: The stick–slip problem

Abrupt changes in boundary conditions in viscous flow problems give rise to stress singularities. Ordinary finite element methods account effectively for the global solution but perform poorly near the singularity. In this paper we develop singular finite elements, similar in principle to the crack tip elements used in fracture mechanics, to improve the solution accuracy in the vicinity of the singular point and to speed up the rate of convergence. These special elements surround the singular point, and the corresponding field shape functions embody the form of the singularity. Because the pressure is singular, there is no pressure node at the singular point. The method performs well when applied to the stick–slip problem and gives more accurate results than those from refined ordinary finite element meshes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/50199/1/1650091105_ftp.pd

Emission of non‐thermal microwave radiation by a Martian dust storm

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94934/1/grl26053.pd