Come visit us at the MIT Techfair 2012 on Monday, February 6 from 9am to 3pm in Rockwell Cage.

Techfair is an annual student-run technology expo dedicated to innovation. Visit us and experience Techfair’s unique blend of cutting-edge technology and innovation from visionary companies, MIT research groups, and student projects.

Techfair will be conducted “trade-show” style. Attendees will be able to walk around to different booths and learn about the presenters, how the science and technologies work, and careers in the company and field of research.

CAMBRIDGE, MA – January 9, 2012 – Knome, Inc., the human genome interpretation company, today announced that it has appointed Martin Tolar, MD, PhD, as the company’s Chief Executive Officer. In addition, Knome has expanded the management team as the company pursues new growth opportunities to interpret and apply genomic information across the healthcare community—including academic researchers, drug companies, physicians, and consumers.

“We are very pleased to appoint an outstanding, seasoned life sciences executive to lead Knome as we seek to partner with pharmaceutical and biotechnology companies and expand our products and services into the clinic and beyond,” said Sundar Subramaniam, Chairman of the Board of Directors of Knome. “Martin has the ideal skills and experience we need to accelerate our growth and extend our leadership in the interpretation and application of genomic data.”

Dr. Tolar has served in several senior positions in pharmaceutical and biotechnology companies. Before joining Knome, he was Chief Executive Officer of Normoxys, Inc., where he established the foundation for the business—including building a professional management team, securing venture financings, and successfully advancing the company’s novel cancer therapeutics from a research project into clinical development. Prior to Normoxys, he was Chief Scientific Officer and then Chief Business Officer at CoMentis, Inc., where he led the company’s scientific and business growth and negotiated a landmark collaboration agreement with Astellas Pharma. Prior to CoMentis, Dr. Tolar held a variety of leadership positions at Pfizer in the Clinical Development, Strategic Partnerships and Business Development divisions. At Pfizer, he directed programs through all stages of clinical development and NDA submissions, and was instrumental in a wide range of business development transactions, including the record-breaking acquisition of Rinat Neurosciences.

Prior to entering the private sector, Dr. Tolar served as an Assistant Professor in the Department of Neurology at Yale University School of Medicine. He trained in Neurology at the Boston Medical Center, where he served as a Teaching Fellow in Neurology at the Boston University School of Medicine and as a Research Fellow at the Massachusetts General Hospital. Dr. Tolar received a PhD in Neuroscience and has published a number of scientific publications in the area of Neuroscience and Alzheimer’s disease.

“I am delighted to join Knome. The company has superior technology and world-class genome interpretation capabilities that I believe will make a major impact on the way we diagnose and treat diseases, develop drugs, and make lifestyle decisions. We are on the cusp of the genomic and personalized medicine revolution—right when the cost of sequencing has reached a point where the application of genetic information is feasible across a host of opportunities. I expect that Knome will be a leader in this transformation as we broaden our business from academic research into expanded applications for drug development at pharmaceutical and biotechnology companies; the treatment of individual patients at hospitals and clinics; and a wide range of consumer applications,” said Martin Tolar, Chief Executive Officer of Knome.

In addition to Martin Tolar’s appointment as CEO, new executive positions were announced by Knome:

• Jorge Conde, the company’s founding CEO, will become Chief Strategy Officer and continue to serve on the board of directors for Knome. In his new role, he will lead the development of Knome’s genome interpretation software and services. Mr. Conde has spent his professional career in the biotechnology industry. Prior to Knome, he worked in strategic marketing and operations at MedImmune, Inc., in business development at Helicos Biosciences Corporation, and in the life sciences group at Flagship Ventures. Earlier in his career, Mr. Conde was an investment banker at Morgan Stanley & Co., specializing in the biotechnology and genomics industries. He holds an MBA from Harvard Business School, an MS from the Harvard-MIT Division of Health Sciences and Technology (HST) and a Bachelor’s degree in Biology from The Johns Hopkins University.

• Jonas Lee, a founding member of Knome’s board of directors, will become Chief Marketing Officer and Head of Consumer Genomics. Prior to Knome, Mr. Lee founded and managed several finance, internet, and high technology ventures that pioneered new markets and technologies, including Redbrick Partners, Poindexter Systems, GiftCertificates.com, and Integrated Computing Engines. Earlier in his career, Mr. Lee served as a management consultant with Bain & Company. He holds an MBA from Harvard Business School and a Bachelor’s degree from Brandeis University.

• Marc Rubenfield will become Vice President of Operations for Knome. Mr. Rubenfield has more 20 years of experience in genomics and genomic services. Prior to joining Knome, he was responsible for the sequencing services product line at Beckman Coulter Genomics, including the introduction of next-generation sequencing. Previously, he worked with Agencourt Biosciences, where he led many of the company’s largest sequencing and genomics projects, and with Genome Therapeutics Corporation (GTC), where he helped establish and build one of the first commercial DNA sequencing services. Earlier in his career, he was also involved in several pioneering genomic developments, including the early development and application of multiplex sequencing.

About Knome
Knome is a commercial stage life sciences company that specializes in the interpretation of human genomes. Knome supports researchers with the informatics and software tools they need to investigate the genetic basis of human disease and drug response. In addition, the company provides researchers, drug developers and clinics with end-to-end genome interpretation solutions.

CAMBRIDGE, MA – January 9, 2012 – Knome, Inc., the human genome interpretation company, today announced that it has been awarded a contract by the Johns Hopkins University School of Medicine. Under the agreement, Knome will supply its informatics services and software tools to Johns Hopkins’ landmark study to uncover genetic variants that contribute to asthma in African American and African Caribbean populations. The 1,000 genomes in the study will come from participants of African descent from 15 academic research centers across the United States, the Caribbean, and South America—as well as from four additional research sites in Western Africa.

In addition to annotating the genomes in the study, Knome’s informatics platform will transform each genome’s raw sequence information into a dataset suitable for comparative interpretation. Knome’s advanced software tools, including knomeVARIANTS and knomePATHWAYS, will then be used by Johns Hopkins researchers to shortlist candidate causal variants, genes, and gene networks.

“We are delighted to be working with Johns Hopkins,” said Martin Tolar, MD, PhD, Chief Executive Officer of Knome. “The Johns Hopkins team has always been on the cutting-edge of genomics. The fact that they have selected us for a project of this magnitude validates the superior quality of our whole genome informatics platform and interpretation tools.”

About Knome
Knome is a commercial stage life sciences company that specializes in the interpretation of human genomes. Knome supports researchers with the informatics and software tools they need to investigate the genetic basis of human disease and drug response. In addition, the company provides researchers, drug developers and clinics with end-to-end genome interpretation solutions.

CAMBRIDGE, MA – January 9, 2012 – Knome, Inc., the human genome interpretation company, today announced that it has expanded its scientific advisory board to include two respected experts in genomics, Dr. David Goldstein of Duke University and Dr. Yaniv Erlich of the Whitehead Institute for Biomedical Research.

“We are very pleased to appoint two highly talented genomics experts to our scientific advisory board as we continue to pursue Knome’s mission of improving lives by applying the scientific insights gained from the interpretation of human genomes,” said Martin Tolar, Chief Executive Officer of Knome. “Drs. Goldstein and Erlich each offer incredibly valuable expertise as we pursue new opportunities in drug development and medicine. We look forward to their contributions this year and into the future.”

Dr. David Goldstein is Professor of Molecular Genetics & Microbiology, Professor of Biology and Director of the Center for Human Genome Variation at Duke University. His work focuses on the use of modern genomics to help understand how human genetic variation influences disease. He received his PhD in Biological Sciences from Stanford University and was previously a professor of Genetics at University College London. In 2007, he was also appointed Honorary Professor at the Institute of Neurology at University College London in the UK.

Dr. Goldstein is the author of more than 175 scholarly publications in the areas of population and medical genetics. He is the recipient of one of the first seven nationally awarded Royal Society/Wolfson research merit awards in the UK for his work in human population genetics. Dr. Goldstein was awarded the Triangle Business Journal Health Care Heroes Award for Innovator/Researcher in March 2008.

“Knome has been visionary in its early anticipation of the importance of complete human sequence information and is poised to play a key role in helping to advance new ways to interpret genomic data and to assess the implications for diagnostics, drug response, and our understanding of the biology of disease,” said Dr. Goldstein.

Dr. Yaniv Erlich is Andria and Paul Heady Family Fellow and Principal Investigator at the Whitehead Institute for Biomedical Research at the Massachusetts Institute of Technology. He received a bachelor’s degree from Tel-Aviv University at Israel and his PhD from the Watson School of Biological Sciences at Cold Spring Harbor Laboratory. Dr. Erlich’s research interests are computational human genetics. He has extensive experience in developing new algorithms for high throughputs sequencing and to detect disease genes. In two of his studies, he identified the genetic basis of devastating genetic disorders. His lab works on a wide range of topics including developing compressed sensing approach to identify rare genetic variations, devising new algorithms for personal genomics, and using Web 2.0 information for genetic studies.

Dr. Erlich is the recipient of the Harold M. Weintraub award, the IEEE/ACM-CS HPC award, Goldberg-Lindsay Fellowship, Wolf foundation scholarship for Excellence in exact science, and Emmanuel Ax scholarship, and he was selected as one of 2010 Tomorrow’s PIs team of Genome Technology.

“The potential to apply genomic findings to clinical care represents an enormous opportunity. The challenge will be how best to interpret and deliver that information. I am extremely pleased to join the Knome advisory team to help guide and shape the company’s role in the ongoing discovery of solutions to interpret human genomic information,” said Dr. Erlich.

Knome’s scientific advisory board is currently chaired by Dr. George Church, PhD, Professor of Genetics at Harvard Medical School and Director of the Center for Computational Genetics, and co-founder of Knome. Other members of the board include Lincoln Stein, MD/PhD, Professor at Cold Spring Harbor Laboratory and Platform Leader of Informatics and Biocomputing at the Ontario Institute for Cancer Research, and Anthony Sinskey, ScD, Professor of Microbiology and Health Sciences and Technology at the Massachusetts Institute of Technology.

About Knome
Knome is a commercial stage life sciences company that specializes in the interpretation of human genomes. Knome supports researchers with the informatics and software tools they need to investigate the genetic basis of human disease and drug response. In addition, the company provides researchers, drug developers and clinics with end-to-end genome interpretation solutions.

As part of the knomeBASE service, clients receive a genome discovery kit (knomeGDK™)—a suite of software tools, scripts and libraries that give geneticists unprecedented flexibility to query multiple genomes and visualize gene interaction networks across multiple genomes.

“Our geneticists have been interpreting whole human genomes since early 2008,” said Jorge Conde, Knome’s CEO. “Since then, we’ve engaged in multi-genome interpretation projects for researchers in 18 countries—primarily for cancer, drug response, rare disease and common disease. In the process, we’ve had a team of top software engineers creating the industrial-strength informatics pipeline and applications needed to solve real-world genome interpretation problems. With knomeBASE, we are making the battle-tested pipeline and tools we’ve used internally available to all geneticists.”

knomeBASE addresses many of the bioinformatics challenges facing geneticists engaged in whole genome studies. These challenges generally fall into three categories: annotation, comparison and distillation.

Annotation: to annotate variants, Knome has invested thousands of hours in curating and harmonizing reference data from more than a dozen sources, including dbSNP, PubMed, 1000 Genomes, ENSEMBL, RefGene, HGMD, SIFT, HPRD, KEGG and Reactome— yielding a deep database of functionally relevant information on human sequence variants.

Comparison: to enable robust, simultaneous comparisons between many genomes, knomeBASE first converts raw sequence data into a standard genome format that thoroughly captures simple and complex variants. This allows genomes or exomes sequenced at different times, under different methods, and by different platforms (such as Illumina (ILMN) and Complete Genomics (GNOM)) to be compared to one another.

In addition, for all genomes in a study, knomeBASE creates a compact database that summarizes the distribution of variants among all studied genomes—allowing users to quickly and flexibly query multiple genomes in order to shortlist candidate causal variants, genes and gene networks.

Distillation: to allow desktop interpretation, knomeBASE distills raw whole genome sequence data (typically ~200 GB) into a compact, easily queriable database (~9 GB) that details:

o Genotypes at known and novel variable sites in the human genome, including base substitutions and short indels;

o Call confidence, including reference matching and no-calls;

o Variant frequencies in appropriate populations;

o Gene IDs and associated phenotypes; site-associated phenotypes, with estimated odds ratio ranges and p-values;

o Variant specific effects on protein sequence and function (predicted); and

o Gene-to-gene interactions.

These databases are small enough to be managed on a desktop computer, yet robust enough to provide all of the information needed for interpretation. Further, they are easily accessed through a published API and set of libraries, allowing geneticists to create their own domain-specific applications and scripts.

The software tools delivered with knomeBASE include knomeVARIANTS™—a GUI-based query interface that lets geneticists quickly and flexibly find suspect variants among many genomes, and knomePATHWAYS™, a gene interaction visualization tool that lets users find sets of genes enriched for suspect variants in one set of genomes versus another.

“The genomics revolution has been slowed by a dearth of downstream analysis tools and services,” said James D’Augustine, chief technology officer of Knome. “Researchers are flooded with sequence data and need help making sense of it all. knomeBASE breaks new ground by transforming raw sequence data into an interpretation-ready format that lets geneticists leverage their domain expertise to make sophisticated queries of many whole genomes at once without requiring a supporting team of bioinformaticians and software engineers.”

About knomeBASE
knomeBASE is an informatics service that transforms raw sequence data from human genomes into a format optimized for comparison and interpretation. The service accepts whole genome data from all major platforms, including Illumina and Complete Genomics—automatically standardizing, distilling, annotating, and comparing genome data so that geneticists can quickly identify the variants, genes and pathways that govern the phenotype of interest. As part of knomeBASE, clients also receive easy-to-use genome interpretation tools, libraries, and scripts that enable flexible querying, rapid hypothesis generation, data visualization, and custom software development. knomeBASE is priced at $750 per whole genome or exome, with academic and volume discounts available.

About Knome Inc.
Knome is a life sciences company that specializes in the interpretation of human genomes. Knome supports researchers with the informatics and software tools they need to investigate the genetic basis of human disease and drug response. In addition, the company provides researchers, drug developers and clinics with end-to-end genome interpretation solutions.

Click here to read the full article.

Knome worked with PBS’s “Faces of America with Henry Louis Gates, Jr.” to sequence and interpret the genome of Henry Louis Gates, Jr., the Alphonse Fletcher University Professor and the Director of the W. E. B. Du Bois Institute for African and African American Research at Harvard University.

Here’s a quote from the episode’s description:

“Interwoven with these stories and others is the journey of the host, Henry Louis Gates, Jr. as he and his father and brother undertake an historic project to have their entire genomes mapped, and thereby to learn everything they possibly can about their own family.”

This was an exciting (and emotional) project for all involved. The section featuring Knome is now available online. To see it, click here.

CAMBRIDGE, MASS. – July 14, 2011 – Knome, a life sciences company that interprets human genomes to identify the genetic factors that influence disease risk, today announced that its services aided in the discovery of a mutation associated with an inherited form of Parkinson’s disease (PD). The research, led by investigators from the University of British Columbia (UBC), leveraged recent advances in human exome sequencing and bioinformatics analysis to identify a mutation in vacuolar protein-sorting associated protein 35 (VPS35) as a genetic determinant of late-onset PD. Their findings were published online on July 14 and in the July 15 issue of the American Journal of Human Genetics.
“Knome thoroughly characterized both known and novel variants in these genomes. Their analysis helped clarify which variants were most important, greatly accelerating our discovery,” said Carles Vilariño-Güell, Ph.D., of the Brain Research Center at UBC and lead author of the paper. “Overall, the findings support a new scientific understanding that common and serious diseases like PD can be due to rare genetic variants.”

To help Vilariño-Güell find the novel variant that predisposes to late-onset PD in a Swiss family, Knome thoroughly sequenced and interpreted more than 20,000 genes in two first cousins. After richly annotating genetic spelling variants in these genes and comparing these differences to those found in other genomes, Knome helped the researchers home in on a shortlist of suspect variants. The study’s investigators found that seven other PD-stricken family members shared a variant that alters the VPS35 protein, part of the retromer complex that helps nerve cells recycle worn-out proteins. Subsequent screening showed that the newly found VPS35 variant is also found in other PD patients – but not in thousands of healthy controls – from Israel, North America, Taiwan and Tunisia. The findings strongly implicate the VPS35 variant in some familial cases of PD and should boost interest in the retromer complex as a potential target for nerve disease treatments.

“The findings further validate Knome’s genome interpretation technology, highlighting how researchers are using it to make key discoveries in medical genetics,” said Jorge Conde, co-CEO of Knome. “Such work heralds a new era of whole genome and exome studies that leverage powerful comparative analysis to genetically dissect diseases like Parkinson’s, helping to understand their causes and sparking new ideas for treatments.”

The study, titled “VPS35 Mutations in Parkinson’s Disease,” is available online at http://www.cell.com/AJHG/.

About Knome Inc.
Knome is a life sciences company that specializes in the interpretation of human genomes. Knome supports researchers with the informatics and software tools they need to investigate the genetic basis of human disease and drug response. In addition, the company provides researchers, drug developers and clinics with end-to-end genome interpretation solutions.