Paperfuge An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy, bioRxiv, 2016-09-01
AbstractSample preparation, including separation of plasma from whole blood or isolation of parasites, is an unmet challenge in many point of care (POC) diagnostics and requires centrifugation as the first key step. From the context of global health applications, commercial centrifuges are expensive, bulky and electricity-powered, leading to a critical bottle-neck in the development of decentralized, electricity-free POC diagnostic devices. By uncovering the fundamental mechanics of an ancient whirligig toy (3300 B.C.E), we design an ultra-low cost (20 cents), light-weight (2 g), human-powered centrifuge that is made out of paper (“paperfuge”). To push the operating limits of this unconventional centrifuge, we present an experimentally-validated theoretical model that describes the paperfuge as a non-linear, non-conservative oscillator system. We use this model to inform our design process, achieving speeds of 125,000 rpm and equivalent centrifugal forces of 30,000 g, with theoretical limits predicting one million rpm. We harness these speeds to separate pure plasma in less than 1.5 minutes and isolate malaria parasites in 15 minutes from whole human blood. By expanding the materials used, we implement centrifugal microfluidics using PDMS, plastic and 3D-printed devices, ultimately opening up new opportunities for electricity-free POC diagnostics, especially in resource-poor settings.
biorxiv bioengineering 200-500-users 2016A tutorial on how (not) to over-interpret STRUCTUREADMIXTURE bar plots, bioRxiv, 2016-07-29
AbstractGenetic clustering algorithms, implemented in popular programs such as STRUCTURE and ADMIXTURE, have been used extensively in the characterisation of individuals and populations based on genetic data. A successful example is the reconstruction of the genetic history of African Americans who are a product of recent admixture between highly differentiated populations. Histories can also be reconstructed using the same procedure for groups which do not have admixture in their recent history, where recent genetic drift is strong or that deviate in other ways from the underlying inference model. Unfortunately, such histories can be misleading. We have implemented an approach (badMIXTURE, available at github.comdanjlawsonbadMIXTURE) to assess the goodness of fit of the model using the ancestry “palettes” estimated by CHROMOPAINTER and apply it to both simulated data and real case studies. Combining these complementary analyses with additional methods that are designed to test specific hypotheses allows a richer and more robust analysis of recent demographic history based on genetic data.
biorxiv genetics 200-500-users 2016Deep Sequencing of 10,000 Human Genomes, bioRxiv, 2016-07-02
AbstractWe report on the sequencing of 10,545 human genomes at 30-40x coverage with an emphasis on quality metrics and novel variant and sequence discovery. We find that 84% of an individual human genome can be sequenced confidently. This high confidence region includes 91.5% of exon sequence and 95.2% of known pathogenic variant positions. We present thedistribution of over 150 million single nucleotide variants in the coding and non-coding genome. Each newly sequenced genome contributes an average of 8,579 novel variants. In addition, each genome carries in average 0.7 Mb of sequence that is not found in the main build of the hg38 reference genome. The density of this catalog of variation allowed us to construct highresolution profiles that define genomic sites that are highly intolerant of genetic variation. These results indicate that the data generated by deep genome sequencing is of the quality necessary for clinical use.Significance statementDeclining sequencing costs and new large-scale initiatives towards personalized medicine are driving a massive expansion in the number of human genomes being sequenced. Therefore, there is an urgent need to define quality standards for clinical use. This includes deep coverage and sequencing accuracy of an individual’s genome, rather than aggregated coverage of data across a cohort or population. Our work represents the largest effort to date in sequencing human genomes at deep coverage with these new standards. This study identifies over 150 million human variants, a majority of them rare and unknown. Moreover, these data identify sites in the genome that are highly intolerant to variation - possibly essential for life or health. We conclude that high coverage genome sequencing provides accurate detail on human variation for discovery and for clinical applications.
biorxiv genomics 200-500-users 2016Suite2p beyond 10,000 neurons with standard two-photon microscopy, bioRxiv, 2016-07-01
AbstractTwo-photon microscopy of calcium-dependent sensors has enabled unprecedented recordings from vast populations of neurons. While the sensors and microscopes have matured over several generations of development, computational methods to process the resulting movies remain inefficient and can give results that are hard to interpret. Here we introduce Suite2p a fast, accurate and complete pipeline that registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. Suite2p runs on standard workstations, operates faster than real time, and recovers ~2 times more cells than the previous state-of-the-art method. Its low computational load allows routine detection of ~10,000 cells simultaneously with standard two-photon resonant-scanning microscopes. Recordings at this scale promise to reveal the fine structure of activity in large populations of neurons or large populations of subcellular structures such as synaptic boutons.
biorxiv neuroscience 200-500-users 2016The genetic structure of the world’s first farmers, bioRxiv, 2016-06-17
We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000-1,400 BCE, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a ‘Basal Eurasian’ lineage that had little if any Neanderthal admixture and that separated from other non-African lineages prior to their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to drastically reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those from Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
biorxiv genetics 200-500-users 2016A natural encoding of genetic variation in a Burrows-Wheeler Transform to enable mapping and genome inference, bioRxiv, 2016-06-16
AbstractWe show how positional markers can be used to encode genetic variation within aBurrows-Wheeler Transform (BWT), and use this to construct a generalisation ofthe traditional “reference genome”, incorporating known variation within aspecies. Our goal is to support the inference of the closest mosaic of previouslyknown sequences to the genome(s) under analysis.Our scheme results in an increased alphabet size, and by using a wavelet tree encoding of the BWT we reduce the performance impact on rank operations. We give a specialised form of the backward search that allows variation-aware exact matching. We implement this, and demonstrate the cost of constructing an index of the whole human genome with 8 million genetic variants is 25GB of RAM. We also show that inferring a closer reference can close large kilobase-scale coverage gaps in P. falciparum.
biorxiv bioinformatics 200-500-users 2016