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Illumina

Illumina

Illumina is a biotechnology company founded in 1998 located in San Diego, California, developing and selling instruments, reagents, and services for DNA sequencing applications.

Illumina is headquartered in San Diego, California and was founded in 1998 by David Walt, John Stuelpnagel, Anthony Czarnik, Lawrence Bock, and Marck Chee, to develop, manufacture, and commercialize DNA sequencing technologies. The company is a global provider of DNA sequencing instruments, reagents, and services, that serve biotechnology markets such as DNA sequencing, genotyping, gene expression analysis, and proteomics. Illumina's customers are pharmaceutical companies, educational institutions, research scientists, biotechnology companies, and clinical research organizations.

Illumina has two distinct business units. The first focuses on life science related products and services such as DNA sequencing, bead arrays, vera-codes, and PCR technologies. The second unit focuses on the development and sale of technologies related to medical diagnostics.

According to Wired magazine, in 2016 Illumina's DNA sequencing machines perform 90% of global DNA sequencing. The director of global public relations for Illumina in 2016 told reporters, "We are at a tipping point in genomics, where a broad community of scientists and researchers continue to translate the potential of the genome from science to discoveries and applications" and believes DNA sequencing technologies made by Illumina will continue to be in high demand around the world well into the future.

DNA sequencing machines made by Illumina are based off DNA sequencing technologies developed by Solexa in the early to mid 2000's. Illumina acquired Solexa in 2007 for $600 million after Solexa successfully built a next generation sequencing machine that could sequence 1 gigabase (Gb) of data in a single run of the machine.

Illumina Accelerator

Illumina Accelerator is the investment arm of Illumina funding early stage genomics companies. They offer early stage companies financial support, mentorship and access to genomic technologies such as sequencing systems, reagents, and lab space.

Accelerator program

The Illumina Accelerator runs 2 six month funding cycles each year consisting of up to 5 companies per cycle with access to up to $100,000 in convertible notes from seed investors and a $20,000 unsecured line of credit. Chosen companies agree to give Illumina Accelerator 8% of common stock for participating in their accelerator program.

During each six month funding cycle selected companies are actively coached by mentors at the Illumina Accelerator to develop a custom curriculum for company building, business strategy, technology development, and pitch development. Credits are given to each company for access to Illumina sequencing technologies, and companies can hire scientists at illumina to help with experimental design. At the end of each funding cycle companies meet with venture capitalists affiliated with the Illumina Accelerator to pitch their business ideas and technologies.

Companies also have the opportunity to receive funding from a $40 million dollar pool of funding from the Illumina Accelerator Boost Capital fund. Illumina Accelerator Boost Capital has a deal with Viking Global Investors to match funding dollar-for-dollar for startups managing to raise in between $1 million and $5 million in funding.

Grant Competition

Illumina Accelerator's grant competition encourages entrepreneurs to create companies using next generation sequencing technologies. Grant winners are able to spend one week running sequencing experiments for proof-of-concept at Illumina Accelerator. When the grant is awarded it needs to be used within 6-months. The grant also gives entrepreneurs one business coaching session, and two sequencing experiment design meetings with a senior scientist at Illumina.

Partnerships
Helix

On August 17, 2017 Illumina Accelerator announced they will collaborating with a personal genomics company called Helix. The partnership seeks to help entrepreneurs develop DNA-driven products and services. Startups accepted into Illumina Accelerator's accelerator program will gain access to Helix's expertise and sequencing platform. The co-founder and senior vice president of Helix, Justin Kao, had the following to say about the partnership "We are proud to collaborate with Illumina Accelerator to stimulate innovation in personal genomics by helping selected startups harness their creativity and build best-in-class DNA-powered products for everyday use".

Investment portfolio

Timeline

April 22, 2021
Illumina and Kartos Therapeutics announce new oncology partnership to develop an NGS-based TP53 companion diagnostic.
May 2018
Illumina acquires Edico Genome for an undisclosed amount.
1998
Illumina was founded by Amanda Cashin.

Funding rounds

Funding round
Funding type
Funding round amount (USD)
Funding round date
Investment
Illumina Venture Funding Round January 2000
28,000,000
1 Result
Results per page:
Page 1 of 1

Acquisitions

Acquisition
Acquired company
Acquisition amount (USD)
Date announced
96,000,000
July 24, 2013
2 Results
Results per page:
Page 1 of 1

SBA Awards

SBA Award
Agency
Award Type
Amount (USD)
Date Awarded
24 Results
Results per page:
Page 1 of 1

People

Name
Role
LinkedIn

Amanda Cashin

Head of Illumina Accelerator & Co-Founder

Anthony Czarnik

Co-Founder

Charles Dadswell

Senior Vice President & General Counsel

Dave Grimm

Digital Experience Director

David Walt

Co-Founder, Board Director

Francis deSouza

President

Francis deSouza

Chief Executive Officer

Jay Flatley

President, Chief Executive Officer

John Liebig

Vice President of Customer Solutions

John Stuelpnagel

Co-Founder, Senior Vice President

Larry Bock

Co-Founder

Licen Xu

Vice President Product Management, Strategic Marketing

Marc Stapey

Executive Vice President, Chief Administrative Officer, & Chief Financial Officer

Mark Chee

Co-Founder

Mostafa Ronaghi

Chief Technical Officer & Co-Founder

Mostafa Ronaghi

Senior Vice President, Chief Technology Officer

Nick Naclerio

Senior Vice President Corporate Development and General Manager Enterprise Informatics

Omead Ostadan

Executive Vice President. Operations, Products & Strategy

Ray Alley

Senior System Engineer

Richard Klausner

Senior VIce President, Chief Medical Officer

Richard Klausner

Chief Medical Officer & Interim General Manager

Sanjay Chikarmane

Senior Vice President & General Manager of Enterprise Informatics

Seems Rego

Associate Director, Global Clinical Operations

Simon Valentine

Global Head of Sales, Enterprise Informatics

Tristan Orpin

Senior Vice President, Chief Commercial Officer

Further reading

Title
Author
Link
Type
Date

$40 million genomics accelerator introduced by Helix and Illumina

Richard Harris

News article

Illumina Accelerator explores genomic innovation in Ontario - Ontario Genomics

Ontario Genomics

News article

Illumina Might Be Overlooking Its Top Competitor; Here's Why Investors Shouldn't

Maxx Chatsko

Web article

Illumina, the Google of Genetic Testing, Has Plans for World Domination

Sarah Zhang

Web article

The genomics-focused Illumina Accelerator backs five new companies

Jonathan Shieber

News article

Documentaries, videos and podcasts

Title
Date
Link

News

Title
Author
Date
Publisher
Description
Jesse Lennox
May 5, 2021
Digital Trends
Some of the best pictures can't be taken until you've finished the game. Here's where you can snap a pic of all 10 of the Legendary Pokémon in New Pokémon Snap.
Conor Hale
April 29, 2021
FierceBiotech
To avoid fighting a two-front, international legal battle over its pursuit of the cancer tester Grail, Illumina has asked judges to step in and halt the European Commission's review of the proposed $8 billion deal.
Andrea Park
April 28, 2021
FierceBiotech
Amid the havoc wreaked around the world by the COVID-19 pandemic, the race is on to build better protections against future outbreaks. After dipping its toe in these waters with the launch of a pathogen-tracking initiative in Africa, Illumina is now fully diving in with a five-year commitment to a global version.
BioSpace
April 28, 2021
BioSpace
Illumina, Inc. (NASDAQ: ILMN) has committed US $60 million in sequencing capabilities to a global pathogen genomics initiative, in partnership with the Bill & Melinda Gates Foundation and other public and private entities
Conor Hale
April 23, 2021
FierceBiotech
Following the launch of multiple tumor diagnostic partnerships with Big Pharma earlier this year for its TruSight Oncology 500 assay, Illumina now aims to expand the use of its genomic profiling test to blood-based cancers.
April 22, 2021
BioSpace
Illumina and Kartos Therapeutics Announce New Oncology Partnership to Develop an NGS-Based TP53 Companion Diagnostic - read this article along with other careers information, tips and advice on BioSpace
April 22, 2021
BioSpace
Illumina and Kartos Therapeutics Announce New Oncology Partnership to Develop an NGS-Based TP53 Companion Diagnostic - read this article along with other careers information, tips and advice on BioSpace
Lythgoe, K. A., Hall, M., Ferretti, L., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., Andersson, M., Otecko, N., Wise, E. L., Moore, N., Lynch, J., Kidd, S., Cortes, N., Mori, M., Williams, R., Vernet, G., Justice, A., Green, A., Nicholls, S. M., Ansari, M. A., Abeler-Dörner, L., Moore, C. E., Peto, T. E. A., Eyre, D. W., Shaw, R., Simmonds, P., Buck, D., Todd, J. A., on behalf of the Oxford Virus Sequencing Analysis Group (OVSG), Connor, T. R., Ashraf, S., da Silva Filipe, A., Shepherd, J., Thomson, E. C., The COVID-19 Genomics UK (COG-UK) Consortium, Bonsall, D., Fraser, C., Golubchik, T.
April 16, 2021
Science
A year into the severe acute respiratory syndrome coronavirus 2 pandemic, we are experiencing waves of new variants emerging. Some of these variants have worrying functional implications, such as increased transmissibility or antibody treatment escape. Lythgoe et al. have undertaken in-depth sequencing of more than 1000 hospital patients' isolates to find out how the virus is mutating within individuals. Overall, there seem to be consistent and reproducible patterns of within-host virus diversity. The authors observed only one or two variants in most samples, but a few carried many variants. Although the evidence indicates strong purifying selection, including in the spike protein responsible for viral entry, the authors also saw evidence for transmission clusters associated with households and other possible superspreader events. After transmission, most variants fizzled out, but occasionally some initiated ongoing transmission and wider dissemination. Science , this issue p. [eabg0821][1] ### INTRODUCTION Genome sequencing at an unprecedented scale during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is helping to track spread of the virus and to identify new variants. Most of this work considers a single consensus sequence for each infected person. Here, we looked beneath the consensus to analyze genetic variation within viral populations making up an infection and studied the fate of within-host mutations when an infection is transmitted to a new individual. Within - host diversity offers the means to help confirm direct transmission and identify new variants of concern. ### RATIONALE We sequenced 1313 SARS-CoV-2 samples from the first wave of infection in the United Kingdom. We characterized within-host diversity and dynamics in the context of transmission and ongoing viral evolution. ### RESULTS Within-host diversity can be described by the number of intrahost single nucleotide variants (iSNVs) occurring above a given minor allele frequency (MAF) threshold. We found that in lower-viral-load samples, stochastic sampling effects resulted in a higher variance in MAFs, leading to more iSNVs being detected at any threshold. Based on a subset of 27 pairs of high-viral-load replicate RNA samples (>50,000 uniquely mapped veSEQ reads, corresponding to a cycle threshold of ~22), iSNVs with a minimum 3% MAF were highly reproducible. Comparing samples from two time points from 41 individuals, taken on average 6 days apart (interquartile ratio 2 to 10), we observed a dynamic process of iSNV generation and loss. Comparing iSNVs among 14 household contact pairs, we estimated transmission bottleneck sizes of one to eight viruses. Consensus differences between individuals in the same household, where sample depth allowed iSNV detection, were explained by the presence of an iSNV at the same site in the paired individual, consistent with direct transmission leading to fixation. We next focused on a set of 563 high-confidence iSNV sites that were variant in at least one high-viral-load sample (>50,000 uniquely mapped); low-confidence iSNVs unlikely to represent genomic diversity were excluded. Within-host diversity was limited in high-viral-load samples (mean 1.4 iSNVs per sample). Two exceptions, each with >14 iSNVs, showed variant frequencies consistent with coinfection or contamination. Overall, we estimated that 1 to 2% of samples in our dataset were coinfected and/or contaminated. Additionally, one sample was coinfected with another coronavirus (OC43), with no detectable impact on diversity. The ratio of nonsynonymous to synonymous ( dN/dS ) iSNVs was consistent with within-host purifying selection when estimated across the whole genome [ dN/dS = 0.55, 95% confidence interval (95% CI) = 0.49 to 0.61] and for the Spike gene ( dN/dS = 0.60, 95% CI = 0.45 to 0.82). Nevertheless, we observed Spike variants in multiple samples that have been shown to increase viral infectivity (L5F) or resistance to antibodies (G446V and A879V). We observed a strong association between high-confidence iSNVs and a consensus change on the phylogeny (153 cases), consistent with fixation after transmission or de novo mutations reaching consensus. Shared variants that never reached consensus (261 cases) were not phylogenetically associated. ### CONCLUSION Using robust methods to call within-host variants, we uncovered a consistent pattern of low within-host diversity, purifying selection, and narrow transmission bottlenecks. Within-host emergence of vaccine and therapeutic escape mutations is likely to be relatively rare, at least during early infection, when viral loads are high, but the observation of immune-escape variants in high-viral-load samples underlines the need for continued vigilance. ![Figure][2] Diagram showing low SARS-CoV-2 within-host genetic diversity and narrow transmission bottleneck. Individuals with high viral load typically have few, if any, within-host variants. Narrow transmission bottlenecks mean that the major variant in the source individual was typically transmitted and the minor variants lost. Occasionally, the minor variant was transmitted, leading to a consensus change, or multiple variants were transmitted, resulting in a mixed infection. Credit: FontAwesome, licensed under CC BY 4.0. Extensive global sampling and sequencing of the pandemic virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have enabled researchers to monitor its spread and to identify concerning new variants. Two important determinants of variant spread are how frequently they arise within individuals and how likely they are to be transmitted. To characterize within-host diversity and transmission, we deep-sequenced 1313 clinical samples from the United Kingdom. SARS-CoV-2 infections are characterized by low levels of within-host diversity when viral loads are high and by a narrow bottleneck at transmission. Most variants are either lost or occasionally fixed at the point of transmission, with minimal persistence of shared diversity, patterns that are readily observable on the phylogenetic tree. Our results suggest that transmission-enhancing and/or immune-escape SARS-CoV-2 variants are likely to arise infrequently but could spread rapidly if successfully transmitted. [1]: /lookup/doi/10.1126/science.abg0821 [2]: pending:yes
Grand View Research, Inc.
April 13, 2021
www.prnewswire.com:443
/PRNewswire/ -- The global biotechnology market size is expected to reach USD 2.44 trillion by 2028, according to a new report by Grand View Research, Inc. It...
Conor Hale
March 31, 2021
FierceBiotech
Guess you can't always go home again. The FTC said it would intervene in Illumina's $8 billion acquisition plans for its former spinout, the multi-cancer blood test developer Grail.
New England Biolabs
February 25, 2021
www.prnewswire.com:443
/PRNewswire/ -- New England Biolabs (NEB®) today released three kits based on the ARTIC Network protocols for multiplexed amplicon-based sequencing of viral...
Christina Jewett, Kaiser Health News and JoNel Aleccia, Kaiser Health News and Rachana Pradhan
February 24, 2021
NBC News
Covid variants in the U.S.: Have a case of Covid variant? No one is going to tell you.
INOVIO Pharmaceuticals, Inc.
February 24, 2021
www.prnewswire.com:443
/PRNewswire/ -- QIAGEN (NYSE: QGEN; Frankfurt Prime Standard: QIA) and INOVIO Pharmaceuticals (NASDAQ: INO) today announced an extension of their partnership...
MGI Tech Co., Ltd.
February 23, 2021
www.prnewswire.com:443
/PRNewswire/ -- A judge in the U.S. District Court for the Northern District of California has granted MGI's motion for leave to amend to add a new inequitable...
Zymo Research Corp.
February 13, 2021
www.prnewswire.com:443
/PRNewswire/ -- Společnost Zymo Research dnes představila svou novou službu pro diagnostiku mutací viru COVID 19 COVID-19 Variant Sequencing Service. Tato nová...
Zymo Research Corp.
February 12, 2021
www.prnewswire.com:443
/PRNewswire/ -- Zymo Research hat heute seinen neuen COVID-19 Variant Sequencing Service bekannt gegeben. Dieser neue globale Service erweitert die...
Zymo Research Corp.
February 11, 2021
www.prnewswire.com:443
/PRNewswire/ -- Zymo Research anunció hoy su servicio de secuenciación de variantes de COVID-19. Este nuevo servicio global amplía las soluciones de extremo a...
Zymo Research Corp.
February 11, 2021
www.prnewswire.com:443
/PRNewswire/ -- A Zymo Research anunciou hoje seu serviço de sequenciamento de variantes da covid-19. Este novo serviço global amplia as soluções de ponta a...
Zymo Research Corp.
February 11, 2021
www.prnewswire.com:443
/PRNewswire/ -- Zymo Research ogłosiło dziś uruchomienie autorskiej Usługi Sekwencjonowania Genomu Mutacji COVID-19. Ta nowa, globalna usługa rozszerza ofertę...
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References

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