Phase Genomics

Last updated

Phase Genomics
Type Startup company
Industry Biotechnology
Founded2015
FoundersIvan Liachko, Shawn Sullivan
Headquarters
Seattle, Washington, US
Key people
Ivan Liachko (CEO, president), Shawn Sullivan (CTO)
Website phasegenomics.com OOjs UI icon edit-ltr-progressive.svg

Phase Genomics is an American biotechnology company based in Seattle, Washington. The company develops proximity ligation kits and Hi-C sequencing technology used to analyze chromosomes. Phase Genomics sells proximity ligation kits, scientific services, and computational analyses.

Contents

History

The company was founded by Ivan Liachko and Shawn Sullivan in 2015. It was originally housed in the CoMotion biotech incubator at University of Washington before relocating to a separate facility. It develops proximity ligation kits and Hi-C sequencing technology used to analyze chromosomes. The company sells proximity ligation kits, scientific services, and computational analyses. [1]

Research

Phase Genomics developed a library preparation kit for the Hi-C sequencing method previously developed by researchers Job Dekker and Eric Lander. The kits are used to study the architecture of genomes. [2] In 2018, Phase Genomics received a $1.5 million SBIR grant from the National Institute of Allergy and Infectious Diseases (NIAID) to research antimicrobial resistance using Hi-C technology. In January 2020, it was awarded an additional $1.5 million from NIAID for phase 2 SBIR funding. [3] In 2019, Phase Genomics received $200,000 from the Bill & Melinda Gates Foundation to improve computational methods of extracting genomic data in microbiome samples. [3] [4] Later in 2019, the company was awarded $325,000 from the U.S. Department of Energy to research algae biofuels using proximity litigation technology for metagenome assembly. [4] In 2020, Phase Genomics received 2 grants totaling $3.9 million from the National Human Genome Research Institute and the Eunice Kennedy Shriver National Institute of Child Health and Human Development. The 3-year grants fund research on chromosomal abnormalities causing cancer, infertility, and reproductive issues. [1]

In June 2021, the company released a platform for discovering new viruses in microbiome samples. [5] [6]

Related Research Articles

In genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun.

<span class="mw-page-title-main">Genomics</span> Discipline in genetics

Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dimensional structural configuration. In contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism's genes, their interrelations and influence on the organism. Genes may direct the production of proteins with the assistance of enzymes and messenger molecules. In turn, proteins make up body structures such as organs and tissues as well as control chemical reactions and carry signals between cells. Genomics also involves the sequencing and analysis of genomes through uses of high throughput DNA sequencing and bioinformatics to assemble and analyze the function and structure of entire genomes. Advances in genomics have triggered a revolution in discovery-based research and systems biology to facilitate understanding of even the most complex biological systems such as the brain.

<span class="mw-page-title-main">Omics</span> Suffix in biology

The branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collective characterization and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms.

<span class="mw-page-title-main">DNA sequencing</span> Process of determining the nucleic acid sequence

DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.

<span class="mw-page-title-main">Metagenomics</span> Study of genes found in the environment

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.

Computational genomics refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, including both DNA and RNA sequence as well as other "post-genomic" data. These, in combination with computational and statistical approaches to understanding the function of the genes and statistical association analysis, this field is also often referred to as Computational and Statistical Genetics/genomics. As such, computational genomics may be regarded as a subset of bioinformatics and computational biology, but with a focus on using whole genomes to understand the principles of how the DNA of a species controls its biology at the molecular level and beyond. With the current abundance of massive biological datasets, computational studies have become one of the most important means to biological discovery.

<span class="mw-page-title-main">Joint Genome Institute</span>

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), first located in Walnut Creek then Berkeley, California, was created in 1997 to unite the expertise and resources in genome mapping, DNA sequencing, technology development, and information sciences pioneered at the DOE genome centers at Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL). As a DOE Office of Science User Facility of Berkeley Lab, the JGI staff is composed of employees from Berkeley Lab, LLNL and the HudsonAlpha Institute for Biotechnology. The JGI also collaborates with other DOE-supported programs and facilities, such as the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory (PNNL), the National Energy Research Scientific Computing Center, or NERSC, and the DOE Bioenergy Research Centers.

<span class="mw-page-title-main">Human Genome Project</span> Human genome sequencing programme

The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a physical and a functional standpoint. It started in 1990 and was completed in 2003. It remains the world's largest collaborative biological project. Planning started after the idea was picked up in 1984 by the US government, the project formally launched in 1990, and was declared essentially complete on April 14, 2003, but included only about 85% of the genome. Level "complete genome" was achieved in May 2021, with a remaining only 0.3% bases covered by potential issues. The final gapless assembly was finished in January 2022.

<span class="mw-page-title-main">Molecular cytogenetics</span>

Molecular cytogenetics combines two disciplines, molecular biology and cytogenetics, and involves the analysis of chromosome structure to help distinguish normal and cancer-causing cells. Human cytogenetics began in 1956 when it was discovered that normal human cells contain 46 chromosomes. However, the first microscopic observations of chromosomes were reported by Arnold, Flemming, and Hansemann in the late 1800s. Their work was ignored for decades until the actual chromosome number in humans was discovered as 46. In 1879, Arnold examined sarcoma and carcinoma cells having very large nuclei. Today, the study of molecular cytogenetics can be useful in diagnosing and treating various malignancies such as hematological malignancies, brain tumors, and other precursors of cancer. The field is overall focused on studying the evolution of chromosomes, more specifically the number, structure, function, and origin of chromosome abnormalities. It includes a series of techniques referred to as fluorescence in situ hybridization, or FISH, in which DNA probes are labeled with different colored fluorescent tags to visualize one or more specific regions of the genome. Introduced in the 1980s, FISH uses probes with complementary base sequences to locate the presence or absence of the specific DNA regions you are looking for. FISH can either be performed as a direct approach to metaphase chromosomes or interphase nuclei. Alternatively, an indirect approach can be taken in which the entire genome can be assessed for copy number changes using virtual karyotyping. Virtual karyotypes are generated from arrays made of thousands to millions of probes, and computational tools are used to recreate the genome in silico.

<span class="mw-page-title-main">New England Biolabs</span>

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<span class="mw-page-title-main">Chromosome conformation capture</span>

Chromosome conformation capture techniques are a set of molecular biology methods used to analyze the spatial organization of chromatin in a cell. These methods quantify the number of interactions between genomic loci that are nearby in 3-D space, but may be separated by many nucleotides in the linear genome. Such interactions may result from biological functions, such as promoter-enhancer interactions, or from random polymer looping, where undirected physical motion of chromatin causes loci to collide. Interaction frequencies may be analyzed directly, or they may be converted to distances and used to reconstruct 3-D structures.

<span class="mw-page-title-main">Human Microbiome Project</span> Former research initiative

The Human Microbiome Project (HMP) was a United States National Institutes of Health (NIH) research initiative to improve understanding of the microbiota involved in human health and disease. Launched in 2007, the first phase (HMP1) focused on identifying and characterizing human microbiota. The second phase, known as the Integrative Human Microbiome Project (iHMP) launched in 2014 with the aim of generating resources to characterize the microbiome and elucidating the roles of microbes in health and disease states. The program received $170 million in funding by the NIH Common Fund from 2007 to 2016.

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<span class="mw-page-title-main">Earth Microbiome Project</span>

The Earth Microbiome Project (EMP) is an initiative founded by Janet Jansson, Jack Gilbert and Rob Knight in 2010 to collect natural samples and to analyze the microbial community around the globe.

<span class="mw-page-title-main">Single cell epigenomics</span> Study of epigenomics in individual cells by single cell sequencing

Single cell epigenomics is the study of epigenomics in individual cells by single cell sequencing. Since 2013, methods have been created including whole-genome single-cell bisulfite sequencing to measure DNA methylation, whole-genome ChIP-sequencing to measure histone modifications, whole-genome ATAC-seq to measure chromatin accessibility and chromosome conformation capture.

Second Genome is a venture capital funded, life sciences research company based in South San Francisco. The company's focus is on the development and exploitation of a research platform which facilitates the identification and elucidation of relationships between human physiology and the human microbiota, and it has a long term goal of becoming a drug development company. The name "second genome" comes from the notion that humans have, effectively, two genomes: the native human genome, and the more diverse set of genomes carried by the human microbiota.

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<span class="mw-page-title-main">Hi-C (genomic analysis technique)</span> Genomic analysis technique

Hi-C is a high-throughput genomic and epigenomic technique first described in 2009 by Lieberman-Aiden et al. to capture chromatin conformation. In general, Hi-C is considered as a derivative of a series of chromosome conformation capture technologies, including but not limited to 3C, 4C, and 5C. Hi-C comprehensively detects genome-wide chromatin interactions in the cell nucleus by combining 3C and next-generation sequencing (NGS) approaches and has been considered as a qualitative leap in C-technology development and the beginning of 3D genomics.

References

  1. 1 2 Stiffler, Lisa (September 30, 2020). "Phase Genomics lands $3.9M in grants to improve testing for chromosomal abnormalities". GeekWire . Retrieved January 31, 2021.{{cite web}}: CS1 maint: url-status (link)
  2. LeMieux, Julianna (November 15, 2018). "Precision Medicine Looks beyond DNA Sequences". Genetic Engineering & Biotechnology News. 38 (20): 1, 22, 24–25. doi:10.1089/gen.38.20.02. ISSN   1935-472X. S2CID   239781336.
  3. 1 2 "Phase Genomics Wins $1.5M for Proximity Ligation-Based AMR Tracking". GenomeWeb . January 7, 2020. Retrieved January 31, 2021.{{cite web}}: CS1 maint: url-status (link)
  4. 1 2 Kotrba, Ron (October 22, 2019). "Phase Genomics awarded DOE grant for algae biofuel research". Biodiesel Magazine. Retrieved January 31, 2021.{{cite web}}: CS1 maint: url-status (link)
  5. Gounot, Jean-Sebastien; Chia, Minghao; Bertrand, Denis; Saw, Woei-Yuh; Ravikrishnan, Aarthi; Low, Adrian; Ding, Yichen; Ng, Amanda Hui Qi; Tan, Linda Wei Lin; Teo, Yik-Ying; Seedorf, Henning; Nagarajan, Niranjan (October 13, 2022). "Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians". Nature Communications. 13 (1): 6044. Bibcode:2022NatCo..13.6044G. doi:10.1038/s41467-022-33782-z. ISSN   2041-1723. PMC   9561172 . PMID   36229545.
  6. "Phase Genomics Releases Platform for Discovering New Viruses in Microbiome Samples". www.businesswire.com. June 15, 2021. Retrieved December 7, 2022.