potential applications for oxford nanopore sequnecing

Problem: We Don’t Know What Fish We’re Eating

The problem is occurring at a variety of venues, though sushi restaurants are the worst

The mislabeling is happening for most fish and the true product is unpredictable

The 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 fish

TM

What? 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 it’s 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 eating

● See 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 owners

● While mislabeling is a problem at types of venues, the biggest violator is sushi restaurants

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

Feasibility and Future

Random Samplings

• See food will only collect a handful of samples (say 5-8 a month)

• But it will do so on random days at random times and to random fish so as to avoid fraud

Cost Effective

• Because there are only a limited number of samples it will not be too expensive

• The variable costs are roughly $2,500 to $4,000 per restaurant

Competitive Advantage

• In an industry plagued by uncertainty, genetic verification of fish labeling will provide businesses the opportunity to capture market share very quickly

Growth Into New Venues

Growth Into New Cities

Sushi restaurants Other restaurants and super markets

Mobile Microbiome Sequencing

Benjamin Brittain

Why analyze your microbiome?

Why mobile sequencing?

GenomcademyAdam Gayoso

ajg2188

Codecademy for Genomics

• Empower 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 data

• General knowledge lessons on impact genomics has and can have on human health, as well as understanding ethical implications

• Targeted towards quantitatively inclined individuals, as well as those wanting a higher level overview of how genomics impacts their lives

• Monetize via advertising or freemium model

Challenges

• Only one mass-produced mobile sequencer

• Expensive cost of flow cell makes citizen science a bit harder

• Applications of knowledge limited to this one sequencer (MinION)

• Value to average person isn’t currently very high

• Finding balance between interactivity and technicality given the many prerequisites necessary for interpreting genomic data

Goals• Bring genomics education to masses, enabling better citizen science and potential for

applications we haven’t thought of• Become centralized knowledge resource for a wide-ranging field

Metagenomic Sequencing for Acute Febrile Illnesses Kimberly Hou

Key Features

Online platform that analyzes nanopore sequenced data from patients’ saliva samples and makes preliminary diagnoses + treatment options for the patient

Knowledge base of treatment options crowd-sourced from certified parties such as nurses and physicians

Mobile sequencing advantageous over Illumina and other technology with <6hr sample-to-answer turnaround time and longer read lengths

Tracks metadata such as location of patient, patient ID, etc. as part of data processing to look out for trends

Considerations

Advantages❏ Big Picture❏ Comprehensiv

e❏ Universal

Challenges❏ HIPAA

Compliance❏ Data Storage❏ minION Sales

MOBILE SEQUENCER FOR MISSING PERSONS

IDENTIFICATION SIKAI HUANG

Help me back home!!!

BACKGROUND• 797,500 children reported missing in a one-year.• About 64.34% of missing children can be found.• Difficulties in bringing the missing children back home

• Advantages of MOBILE SEQUENCER:

1. Some children were kidnapped at a really young age. 2. Some are disabled 3. International child-trafficking …..

1. Portable and efficient2. Solve the difficulties above

• Process：

• Doubt:

DNA info

Basic info

Basic Info

DNA info

1. Profitability?? It is a VC pitch !!! 2. Accuracy ??

Nascent:Making Mothers Aware

Stephanie Huang

Changing the prenatal experience once mother at a time

We provide the kit and software needed for OB/GYNs to help expecting mothers do on-the-spot genetic screenings and analysis.

High-risk pregnancy rates are on the rise.

Prenatal screening is time-sensitive: current tests require ~1 week for results. Amniocentesis results take 2-3 weeks.

Challenges & Potential

Challenges:● Error rate: false positives and false negatives are both dangerous.● Sequencing mixed samples -- but we saw that it’s possible differentiate a mixed sample.● Training doctors/nurses to use the device and software -- but we were able to learn how

to use the MinION quickly.● Developing a primer mix and easy sample prep protocol.

Potential:● Expand to on-site doctor’s screenings for general patients.

Mobile Sequencer for Food Safety Inspection

Wenrui HuangDec. 9th, 2016

Have you ever wondering….

Meanwhile, 40% of food were trashed by grocery stores each year, which is equivalent to 165 billion dollars*!!! Huge waste!!!*data according to USDA reports

Half empty milk just expired

Leftover food kept in fridge for a few days

A partially rotten apple

Use them or throw away???

Are they still safe to eat???

Mobile Sequencer can provide the answer!!

UNSAFE

SAFE

tiny bite of the food

DNA extraction

MobileSequencing

HMP BLAST Macbook App

Mobile Sequencer directly linked to laptop

Black Box scheme for Food Safety Inspection with mobile sequencer

• Proposed Scheme will work: E. coli DNAs were prominent even at the first hour of sequencing, enough resolution for identifying subspecies

• Save millions $$$: for both families and grocery stores nationwide• Easy to equip and operate on: three simple steps: Load Plug in -> 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 Premise• Why do we need to identify fallen soldiers?

• To inform families• Religious reasons• Tactical reasons

• What limitations are at play in a warzone?• Time• Lab resources• Both of these limitations are compounded if a soldier is on foreign soil

• What systems are currently in place?• Dog tags – but what if the complete body isn’t found?

Problems

• Ethical:• Mandatory human reference database• minION is not 100% accurate. Identifying the wrong body is

BAD

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

Healix

The Future of Personalized Medicine

Eunice Kokor

The Post-Genome Era

Personalized medicine will provide the essential link between an individual’s molecular and clinical

profilesrisk algorithmsmolecular diagnostics

targeted therapiespharmacogenomics

There will be challenges!

Cost of sequencing / each clinic might be unmanageable

Convincing insurance companies to cover these costs

Cloud system that can manage lots of customer data

December 9, 2016Max Mattioli

Ubiquitous Genomics | 1

Stopping Outbreaks in their Tracks

We Need FlySafe

● Serious Recent Outbreaks:○ Zika, Ebola, MERS etc.

● Growing Antibiotic Resistance○ UN declared “greatest and most urgent global risk”-Fall 20161

● No formal system of outbreak surveillance exists in U.S. Airports2

○ Current systems ask patients to monitor outbreak symptoms - wait until someone is sick then report back to CDC

○ In the days between flight arrival and confirmed illness, many more infections could occur

FlySafe | 2

Our Solution Pipeline

● Use time-separated multi-sample sequencing across spatial locations in airports to localize pathogen source○ When 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-00

T-15T-30

T-45

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

• Evolution

• History

Bringing minIONs on site

Archaeological 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 sample

Computation and database storage done on cloud, accessed through mobile application

Fun, pokedex style way to grow a global database and identify species on the fly

Applications and Challenges

For scientists: way to identify or add genomic data of new samples while on the field

For nature hobbyists: way to identify curious flora and fauna while exploring

For everybody: fun way to explore environment in a game-like environment

Challenges: 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 Romano

Ubiquitous 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/Medicaid

• 42.8% w/ malignant cancer

• Precision medicine: target healthcare to an individual’s genetics and exposures

• Cost of WGS service: ~$1,500 per person (July 2016)

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

Making precision medicine portable• Provide 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 home

• Dataset analysis can be performed off-site, at central location• Nurses only need training in library prep and MinION use

• Treat the disease rather than just manage the symptoms• ONT estimates ~$1,000 WGS; not infeasible for Medicare/Medicaid

• Initial 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 Nanopore

Ubiquitous Genomics9 December 2016

Dinara 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 identification• Difficult to sequence many samples on one MinION flow cells

Goals and problems

Technological solution

fragmentation

adapter ligation

hybridization with target specific beads

denaturation

UBISeq Kanika Verma

THE IDEAo The future: Mobile genomic

sequencing as a vital aspect of everyday primary care• Preventative for predisposed

conditions• Bacterial/Viral diagnostics

o An app that makes it as simple as:Connect

MinION to iPad

Obtain and load

sampleShare results

ADVANTAGES AND CHALLENGESo Portable, accessible,

and efficient o Process and share

genomic data via app directly

o Consider ethical implications of easily obtainable genomic data

o Basic training necessary to operate

o Technical challenges

Healthy Skin TesterShengtong Zhang

UNI: sz2539

Your beard = Toilet

• Normal: 100,000,000,000 bacteria on your face. 200-1000 species.

• But if you do not clean your beard often, it can be like a toilet.

• Do you want to know the condition of your skin everyday and get a right advice?

=

Thanks to our new product: Healthy Skin Tester• Using latest mobile sequencing technique

• Based on MinION

• Test your skin everyday

• Pick up the sample

• Get the sequence

• Analyze the species of bacteria

• Compare with our library and give you a professional suggestion

StoolTrakMicroBiome Mapping Device

Noah Zweben

RationaleAntibiotic associated diarrhea due to C.diff incurs average additional costs of $3,669 and has a mortality rate of 6% [3]

Directly linked to makeup of gut microbiome, probiotics can prevent [2,4]

H. pylori, a common gut microbe is responsible for many cases of gastritis and most stomach ulcers, and is a strong risk factor for stomach cancer [5]

In mice with colon cancer, number of tumors corresponded to the unique ways that different antibiotic cocktail modulated the microbiome [5]

Prohep, a probiotic mixture reduced liver tumor size by 40% in mice, likely by promoting an anti-inflammatory environment in the gut [5]

Cancer drugs, such as oxaliplatin chemotherapy and CpG-oligonucleotide immunotherapy, work by boosting inflammation. If the microbiome is altered in such a way that inflammation is reduced, these therapeutic agents are less effective [5]

Looking Forward

As research uncovers more and more links between our health and our microbiome, the advantages and rationale behind a technology

which can track and quantify our biome will grow

[1] http://www.theatlantic.com/science/archive/2016/05/white-house-launches-the-national-microbiome-initiative/482598/[2] https://www.sciencedaily.com/releases/2015/07/150723092123.htm

[3] https://www.ncbi.nlm.nih.gov/pubmed/16633131[4] http://cid.oxfordjournals.org/content/34/3/346.long

[5] http://www.the-scientist.com/?articles.view/articleNo/45616/title/Microbes-Meet-Cancer/

Installed in hospital toilets to monitor patients’ BMTest for microbiome environment conducive for certain cancer drugsExpose risk factors for certain conditions, early warning for C.diffMeasure efficacy of probiotics on microbiome

Use seed money to develop a quick automated stool-DNA pipeline to be delivered to the mobile sequencer based off nanopore technology.Results linked to patient profile

Launch of the White House’s National Microbiome Initiative in May [1]~$500 million from pledged from WH and Universities over next 2 years

Late session

By James Xue (jx2218)

FoodSeq: Eat With Confidence

By James Xue (jx2218)

Problem: Foodborne illness and quality- Estimated 48 million get sick, 128k are hospitalized, and 3k die each year

- Market size and potential: $782.7 billion restaurant industry sales

- Restaurants lose a significant amount of sales every year from customers who get sick from their food / do not trust their cleanliness

- Customers demand more reliable food quality

Solution: Mobile sequencer for restaurants

- Restaurants would use our sequencers for their food to determine sufficiently high quantities of dangerous viruses or bacteria

- Empowers restaurants and empowers customers

- Both budget and luxury restaurants

- Mobile (Yelp-like) application + data processing platform

- Asking for $2 million: research and development (improving accuracy of sequencer), server space