Introduction:
NGS using FFPE slide is proven to be a very valuable resource for retrospective studies across long period of time and providing opportunity to correlate disease state, outcome and tissue morphology to genotype (DNA) and/or expression (RNA). However, it is challenging to get intact information from FFPE samples because of the severe degradation, damage and biological modification occured within such samples during years of storage in the air at variable ambient temperatures. With Complete Omics’ unique MyGene™-UltimateSens™ FFPE NGS service, NGS sequencing can be accomplished with as few as one FFPE slide.
The quest to trace the roots of the human race has long motivated scientists into the sequences of ancient DNA extracted from skeletal remains unearthed by archaeologists. However, ancient DNA typically bears signs of fraying and fragmentation inflicted by exposure to the elements over great gulfs of time, posing challenges to a successful NGS sequencing. Complete Omics’ MyGene™-UltimateSens™ was initially invented to concstuct NGS libraries with human remains 30,000 years old. Our genomics team is specialized in handling toughest ancient and damaged DNA samples and provide you best result in the field of NGS sequencing.
In a NGS seqeuncing project, it is very common to fall into the situation of being lack of enough materials for sequencing. Samples that are collected for deep study, such as NGS sequencing, are usually precious with very limited amount available. Sometimes, you have enough materials to start with, however, after several rounds of library preparations, you still can not get NGS datasets with desired quality, and now only very few samples are left for further test. It is the time to contact Complete Omics and learn more about our MyGene™-UltimateSens™ NGS technology, a NGS library construction method WITHOUT EXCESSIVE PCR AMPLIFICATION.
Sample types we accept:
1, Purified DNA / RNA samples
2, Cell Lysates and Tissue Lysates
3, Biofluids, such as plasma*, serum*, saliva, tear, etc.
4, FFPE slide/ FFPE extract
5, Fossil
6, Customized sample types (please contact us to discuss)
Collaboration with Columbia University
Mar 30, 2022 | BALTIMORE – Complete Omics’ Clinical Proteomics team announced a collaboration with Professor Kam W. Leong, Samuel Y. Sheng professor of Biomedical Engineering, and his team from…
Collaboration with Tel Aviv University
Mar 20, 2022 | BALTIMORE – Complete Omics’ Clinical Proteomics team announced a collaboration with Professor Miguel Weil from Department of Cell Research and Immunology at the Tel Aviv University…
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 Cancers
In 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 Assays2022--Identify and Quantify Neoantigens derived from Human endogenous retroviruses (HERVs) --- published on Science Advances
Human 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 targets2021--Therapeutic Neoantigens Encoded by Oncogene K-Ras --- published on Science Immunology
K-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 Therapeutics2021--Direct Quantification of Neoantigens Like Never Before --- published on Science
Genetic 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 Therapeutics2019--First Pipeline for Direct Detection and Quantification of Neoantigens --- published on Cancer Immunology Research
Cancer-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
