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Ball, Madeleine

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Madeleine

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Ball, Madeleine

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Author's Publications: search.filters.isAuthorOfPublication.84baa0fa-e53a-4208-b32f-626f2f606e70

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    Meeting report for the 1st skin microbiota workshop, boulder, CO October 15-16 2012
    (BioMed Central, 2014) Gilbert, Jack A; Ball, Madeleine; Blainey, Paul; Blaser, Martin J; Bohannan, Brendan JM; Bateman, Ashley; Bunge, John; Dominguez-Bello, Maria Gloria; Epstein, Slava; Fierer, Noah; Gevers, Dirk; Grikscheit, Tracy; Hamdan, Leila J; Harvey, James; Huttenhower, Curtis; Kirkup, Benjamin; Kong, Heidi H; Lauber, Christian; Lemon, Katherine P; Lynch, Susan V; Martin, Lance; Mello, Charlene; Palma, Joseph; Parker, Roy; Petrosino, Joseph; Segre, Julia A; Vosshall, Leslie; Yi, Rui; Knight, Rob
    This report details the outcome of the 1st Skin Microbiota Workshop, Boulder, CO, held on October 15th-16th 2012. The workshop was arranged to bring Department of Defense personnel together with experts in microbial ecology, human skin physiology and anatomy, and computational techniques for interrogating the microbiome to define research frontiers at the intersection of these important areas. The workshop outlined a series of questions and created several working groups to address those questions, specifically to promote interdisciplinary activity and potential future collaboration. The US Army provided generous grant support and the meeting was organized and hosted by the University of Colorado at Boulder. A primary forward vision of the meeting was the importance of understanding skin microbial communities to improve the health and stealth of US Army warfighters.
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    Our genomes today: time to be clear
    (BioMed Central, 2013) Lunshof, Jeantine; Ball, Madeleine
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    Harvard Personal Genome Project: lessons from participatory public research
    (BioMed Central, 2014) Ball, Madeleine; Bobe, Jason R; Chou, Michael; Clegg, Tom; Estep, Preston W; Lunshof, Jeantine; Vandewege, Ward; Zaranek, Alexander Wait; Church, George
    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.
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    Accurate Whole-Genome Sequencing and Haplotyping from 10 to 20 Human Cells
    (Nature Publishing Group, 2012) Peters, Brock A.; Kermani, Bahram G.; Sparks, Andrew B.; Alferov, Oleg; Hong, Peter; Alexeev, Andrei; Jiang, Yuan; Dahl, Fredrik; Tang, Y. Tom; Haas, Juergen; Robasky, Kimberly; Lee, Je-Hyuk; Peterson, Joseph E.; Perazich, Helena; Yeung, George; Liu, Jia; Chen, Linsu; Kennemer, Michael I.; Pothuraju, Kaliprasad; Konvicka, Karel; Tsoupko-Sitnikov, Mike; Pant, Krishna P.; Ebert, Jessica C.; Nilsen, Geoffrey B.; Baccash, Jonathan; Halpern, Aaron L.; Church, George; Drmanac, Radoje; Wait, Alexander; Ball, Madeleine
    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.
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    Targeted and Genome-Scale Methylomics Reveals Gene Body Signatures in Human Cell Lines
    (Nature Publishing Group, 2009) Ball, Madeleine; Li, Jin Billy; Gao, Yuan; Lee, Je-Hyuk; LeProust, Emily; Park, In-Hyun; Xie, Bin; Daley, George; Church, George
    Cytosine methylation, an epigenetic modification of DNA, is a target of growing interest for developing high throughput profiling technologies. Here we introduce two new, complementary techniques for cytosine methylation profiling utilizing next generation sequencing technology: bisulfite padlock probes (BSPPs) and methyl sensitive cut counting (MSCC). In the first method, we designed a set of ~10,000 BSPPs distributed over the ENCODE pilot project regions to take advantage of existing expression and chromatin immunoprecipitation data. We observed a pattern of low promoter methylation coupled with high gene body methylation in highly expressed genes. Using the second method, MSCC, we gathered genome-scale data for 1.4 million HpaII sites and confirmed that gene body methylation in highly expressed genes is a consistent phenomenon over the entire genome. Our observations highlight the usefulness of techniques which are not inherently or intentionally biased in favor of only profiling particular subsets like CpG islands or promoter regions.