A typical human cell consists of about 2 x 3.3 billion base pairs of DNA and 600 million bases of mRNA. Usually a mix of millions of cells are used in sequencing the DNA or RNA using traditional methods like Sanger sequencing or Illumina sequencing. By using deep sequencing of DNA and RNA from a single cell, cellular functions can be investigated extensively.
Single-cell Seq: Single-cell DNA genome sequencing involves isolating a single cell, amplifying the whole genome or region of interest, constructing sequencing libraries, and then applying next-generation DNA sequencing (ex. Illumina, Ion Torrent). In mammalian systems, single-cell DNA sequencing has been widely applied to study normal physiology and disease. Single-cell resolution can uncover the roles of genetic mosaicism or intra-tumor genetic heterogeneity in cancer development or treatment response.
Single-cell RNA-Seq: Single-Cell RNA sequencing aims to uncover the transcriptome diversity in heterogeneous cell populations. Cell populations are rarely homogeneous and synchronized in their characteristics. When researchers trying to evaluate the response of cells to internal or external stimuli, standard RNA-Seq won’t help much due to averaging of expression levels between thousands of cells. Using the 10x Genomics@ ChromiumTM platform, we could help the researchers perform transcriptome analysis of tens of thousands of individual cells in a cost-effective way.
Data analysis, including data validation, visualization and quantification, are performed with commercial softwares and Complete Omics’ unique R packages and scripts. Report will be sent to you in Excel format as well as a summary in PDF format. We will also provide you any details you need for your papers’ MATERIALS AND METHODS section. We will make sure you understand your result and help you with your paper writing with free follow-up services.
All Single Cell Omics assays are conducted through our Department of Single Cell, please visit singlecell.com for further details.
Sample types we accept:
1, Cultured cell
2, Primary cell
3, Wet / Frozen tissue
4, Customized sample types (please contact us to discuss)
Detecting and Absolutely Quantifying Patient-specific Neoantigens from Limited Input of Biopsy Sample — An Integrated Pipeline for Neoantigen-targeted Cancer Treatments
Neoantigens derived from HERVs represent a new group of cancer therapeutic targets. In a collaborating project, Complete Omics identified and quantified HERVs derived neoantigens and provided solid evidence for developing…
Some of our impacts
2022–Direct Identification and Quantification of Neoantigens from Minute Amount of Clinical Biopsy Sample — published on CancersIn recent years, neoantigens are becoming popular cancer therapeutic targets under intensive studies by almost all major oncology pharmaceuticals. However, who are the target patients? Does the patient with a “correct” mutation and a “correct” HLA allele indeed present the “correct” neoantigen? Is this individual’s neoantigen copy number high enough for immunotherapy? AI predictions based on NGS genomic information have been proven incapable of answering these questions. Immunopeptidome through mass spectrometry is dominated by disease-irrelevant peptide sequences. There is no existing way to identify and quantify neoantigens from a minute amount of clinical biopsy sample, such as 50 mg tissue or less. Valid-NEO is developed to fit this demanding clinical need through combining our proprietary multi-omics platforms including NGS-based ultra-rare mutation calling technique, DEEPER-SeqS, and our unique clinical proteomics platform, Complete360®, with additional hardware innovations (Ref. 1).Valid-NEO: Multi-omics Pipeline for Neoantigen Assays
2022–Identify and Quantify Neoantigens derived from Human endogenous retroviruses (HERVs) — published on Science AdvancesHuman endogenous retroviruses (HERVs) represent 8% of the human genome. Working with, ErVaccine Technologies, our scientists identified neoantigens encoded by HERVs across a broad spectrum of cancers, and this finding may help enable next-generation therapeutic vaccines and cellular immunotherapies targeting these so-called “unconventional” tumor antigens (Ref 1). These antigens are shared by different tumor types. They would prove useful as personalized cancer therapeutic targets for a large number of patients. Along the side when we are keep on improving and developing our own disease detection and companion diagnostic pipelines, we are excited to be working with a large number of collaborators to implement our multi-omics platforms in their different clinical and basic research projects.Identify and Quantify Neoantigens derived from Human endogenous retroviruses (HERVs) — A new class of cancer therapeutic targets
2021–Therapeutic Neoantigens Encoded by Oncogene K-Ras — published on Science ImmunologyK-Ras is one of the most highly mutated oncogenes in cancers. The neoantigens encoded by K-Ras can be presented by many different types of cancer cells. Here we utilized our multi-omics neoantigen validation pipeline to detect and quantify K-Ras neoantigens from a variety of cancer samples (Ref 1.). We found that the K-Ras as well as several other oncogenes can be presented on cancer cell surface, but at extremely low copy numbers. We adopted a variety of internal control system to measure their abundance down to <1 copy per cell level. To come up with an actionable strategy, the therapeutic team at JHU developed bispecific antibodies that can target the neoantigens we identified, and deliver dramatic therapeutic effects to mice. These findings are significant in the way that it opens a gate to developing pan-cancer immunotherapeutic agents that can treat a large number of patients sharing cancer hotspot mutations. Identifying such neoantigens is the first step in this campaign and is being accomplished by Complete Omics Inc.K-Ras Neoantigen Identified for Personalized Cancer Therapeutics
2021–Direct Quantification of Neoantigens Like Never Before — published on ScienceGenetic changes in human genome are the driving force for all cancers. Different patients have different sets of mutation profiles even for the patients who all have the same disease. For decades, doctors, cancer researchers, and pharmaceutical companies have been working tirelessly trying to find a way to treat each person’s unique disease in a highly personalized way that will reach the maximum treatment efficacy with the lowest side effects. Complete Omics, working with leaders in cancer therapeutics, has developed pipelines based on our multi-omics techniques through which we clearly observe and quantify personalized therapeutic targets encoded by the most frequently mutated tumor suppressor gene TP53. We validated and quantified the TP53 neoantigens on the surfaces of cancers and provided information to healthcare providers to support their decision on if or not to adopt a highly personalized cancer treatment targeting these neoantigens and when to use it (Ref 1). These findings provided the 1st-hand evidence for cancer therapeutics without the uncertainty that comes with predictions.Prediction-FREE Neoantigen Validation Enables TP53-targeted Personalized Cancer Therapeutics
2019–First Pipeline for Direct Detection and Quantification of Neoantigens — published on Cancer Immunology ResearchCancer-linked genetic mutations can code for mutant proteins, which can then be processed by proteasomes into peptides that are presented by human leukocyte antigen (HLA) molecules, triggering the body’s immune response. The idea that such mutant peptides can trigger an immune response is fundamental to immunotherapies like checkpoint inhibitors as well as cancer vaccines that present the body with these peptides to generate an immune reaction. However, while the rise of next-generation sequencing has allowed researchers to identify a large number of cancer-linked mutations, actually detecting these mutation-associated neo-antigens, or MANAs, at the peptide level remains difficult. The fact that a mutant is present at the genetic level does not mean it will be produced at the protein level, and, even if it is, that is no guarantee that it will be processed and presented by HLA molecules. This has proved a challenge for, for instance, personalized cancer vaccine development. Our technology (Ref. 1) provide the 1st pipeline for detecting personalized cancer therapeutic targets. Our method has been reported by public media and has a significant impact in cancer research (Ref. 2).Direct Detection and Quantification of Neoantigens