potential applications for oxford nanopore sequnecing

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Problem: We Dont Know What Fish Were EatingThe problem is occurring at a variety of venues, though sushi restaurants are the worstThe mislabeling is happening for most fish and the true product is unpredictableThe problem is not just in NYC

Fish in the US is being mislabeled in alarming proportions

SEE FOOD: Genetic Verification for Proper Seafood Labeling Jacob Best

Solution: See Food See Food is a start up that genetically certifies restaurants that are correctly labeling fishTMWhat?Why?How?Where?Our company provides certification to restaurants that have correctly labeled their fish products

Certifications will be available online and displayed publically so consumers know its safe to eat there!Our goal is to provide transparency for fish consumption at the level closest to the consumer

We want people to know what they are eatingSee Food uses MinIon sequencing and alignment to the NR database

To make this cheap and effective See Food will collect only a handful of samples from a type of fish and at times unknown to the restaurant ownersWhile mislabeling is a problem at types of venues, the biggest violator is sushi restaurants

See Foods verification can be a big leg up in the sushi restaurant industry and this is where we plan to start

Feasibility and FutureGrowth Into New VenuesGrowth Into New Cities

Sushi restaurantsOther restaurants and super markets

Mobile Microbiome SequencingBenjamin Brittain

4

Why analyze your microbiome?

5

Why mobile sequencing?

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GenomcademyAdam Gayosoajg2188

Codecademy for GenomicsEmpower those wanting to join the ubiquitous genomics movement with interactive lessons in biology and programming (citizen science)Inspire people to discover new applications of mobile sequencing, which will only become more popular and cheaper in the next 5-10 years, by giving them the knowledge necessary to interact with genomic dataGeneral knowledge lessons on impact genomics has and can have on human health, as well as understanding ethical implicationsTargeted towards quantitatively inclined individuals, as well as those wanting a higher level overview of how genomics impacts their livesMonetize via advertising or freemium model

ChallengesOnly one mass-produced mobile sequencerExpensive cost of flow cell makes citizen science a bit harderApplications of knowledge limited to this one sequencer (MinION)Value to average person isnt currently very highFinding balance between interactivity and technicality given the many prerequisites necessary for interpreting genomic dataGoalsBring genomics education to masses, enabling better citizen science and potential for applications we havent thought ofBecome centralized knowledge resource for a wide-ranging field

Metagenomic Sequencing for Acute Febrile Illnesses Kimberly Hou

Key FeaturesOnline platform that analyzes nanopore sequenced data from patients saliva samples and makes preliminary diagnoses + treatment options for the patientKnowledge base of treatment options crowd-sourced from certified parties such as nurses and physiciansMobile sequencing advantageous over Illumina and other technology with Outputs

Technique Challenges: shorten the sequencing time (10 mins? Is it possible?)automate DNA extraction processassuming no reagents need to be added? Poretools and BLAST functions need to be included in the software package

BioTagsMobile sequencing to identify fallen soldiers

By: Jonathan Herman

The PremiseWhy do we need to identify fallen soldiers?To inform familiesReligious reasonsTactical reasonsWhat limitations are at play in a warzone?TimeLab resourcesBoth of these limitations are compounded if a soldier is on foreign soilWhat systems are currently in place?Dog tags but what if the complete body isnt found?

ProblemsEthical:Mandatory human reference databaseminION is not 100% accurate. Identifying the wrong body is BAD

Technical:$500-900/flow cellAcquiring DNA is not faster or cheaper than acquiring dog tags

HealixThe Future of Personalized MedicineEunice Kokor

The Post-Genome Era

Personalized medicine will provide the essential link between an individuals molecular and clinical profiles

risk algorithmsmolecular diagnosticstargeted therapiespharmacogenomics

There will be challenges!Cost of sequencing / each clinic might be unmanageableConvincing insurance companies to cover these costsCloud system that can manage lots of customer data

December 9, 2016

Max Mattioli

Ubiquitous Genomics | 1Stopping Outbreaks in their TracksFlySafe

http://www.clipartkid.com/images/158/cartoon-airplane-clipart-clipart-panda-free-clipart-images-QxR9SF-clipart.jpeghttps://jackcusumano.files.wordpress.com/2010/02/germ.png

We Need FlySafeSerious Recent Outbreaks:Zika, Ebola, MERS etc.Growing Antibiotic ResistanceUN declared greatest and most urgent global risk-Fall 20161No formal system of outbreak surveillance exists in U.S. Airports2Current systems ask patients to monitor outbreak symptoms - wait until someone is sick then report back to CDCIn the days between flight arrival and confirmed illness, many more infections could occurFlySafe | 2

1. http://www.cdc.gov/vhf/ebola/outbreaks/2014-west-africa/qa.html2. http://news.nationalgeographic.com/2016/09/antibiotic-resistance-bacteria-disease-united-nations-health/?linkId=29137110

Recent Serious Outbreaks:Zika VirusEbola Middle East Respiratory SyndromeAntibiotic-resistant strains There is no formal system of outbreak surveillance in U.S. Travel SystemsCurrent systems essentially monitor outbreak symptoms - waiting until someone is sick then reporting back to CDCIn the days between flight arrival and confirmed illness, many more infections could occur

Our Solution PipelineUse time-separated multi-sample sequencing across spatial locations in airports to localize pathogen sourceWhen FlySafe is used in multiple airports, network analysis can offer granularity in determining infection pathways.FlySafe | 3

Align in real-time: BLAST and mash

T-00T-15T-30T-45

http://www.airport-new-york.com/airport/laguardia-airport-map.jpg

http://mash.readthedocs.io/en/latest/_images/logo_med.pnghttps://blast.ncbi.nlm.nih.gov/images/nucleutide-blast-cover.png

Using the future to uncover the pastJordana Aviva Mael,B.A. in Mathematics/Computer Science

There have been numerous breakthroughs in a vast array of disciplines by sequencing DNA from archaeological sites

EvolutionHistory

32

Bringing minIONs on siteArchaeological expeditions can last for extended periods of timeArchaeological expeditions may occur in remote locationsImportance of knowing the context of the archaeological site while excavatingPotential Difficulties:Not being able to extract and or purify the DNA on site, outside of a laboratory

Darwin+: Exploring our biosphere like never before

Aalhad Patankar

SEAS 17 CS MS

Darwin+: The real animal pokedex Mobile sequencer that interfaces with smartphone application to provide information on a DNA sample, such as most likely species, species ancestry or distribution of species in a sampleComputation and database storage done on cloud, accessed through mobile applicationFun, pokedex style way to grow a global database and identify species on the fly

Applications and ChallengesFor scientists: way to identify or add genomic data of new samples while on the fieldFor nature hobbyists: way to identify curious flora and fauna while exploringFor everybody: fun way to explore environment in a game-like environmentChallenges: purification + preprocessing of sample, using the application on the fly without connection to a cloud, speedy computation

Enabling precision medicine in home hospice care using portable sequencingJoseph RomanoUbiquitous Genomics; Fall 2016Presented Dec. 9, 2016

Hospice care & Precision medicine>1.5 million home health care patients per day in US[1]79.1% covered by Medicare/Medicaid42.8% w/ malignant cancer

Precision medicine: target healthcare to an individuals genetics and exposuresCost of WGS service: ~$1,500 per person (July 2016)

[1] doi:10.1097/01.nhh.0000263436.08062.85

Making precision medicine portableProvide sample collection and sequencing at point-of-care (in home)With improving quality and throughput of MinION, soon obtain >1X coverage with reasonable accuracy[2]Identify variants corresponding to patient symptoms without the patient having to leave homeDataset analysis can be performed off-site, at central locationNurses only need training in library prep and MinION useTreat the disease rather than just manage the symptomsONT estimates ~$1,000 WGS; not infeasible for Medicare/MedicaidInitial funding use: purchase MinIONs and reagent stock, build infrastructure for training, and hire technicians/bioinformaticians for data analysis

[2] https://nanoporetech.com/about-us/news/human-genome-minion

Targeted Sequencing with Oxford NanoporeUbiquitous Genomics9 December 2016Dinara Usmanova

We want to know exactly which bacteria/virus/fungi causes the disease Problems:Quality of sequencing data is not good enough for reliable species identificationDifficult to sequence many samples on one MinION flow cellsGoals and problems

Technological solutionfragmentation

adapter ligation

hybridization with target specific beadsdenaturation

UBISeq

Kanika Verma

The Idea

The future: Mobile genomic sequencing as a vital aspect of everyday primary carePreventative for predisposed conditionsBacterial/Viral diagnostics

An app that make

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