Abstract:
BACKGROUND:Neoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, resulting in a vast total number, but only a small percentage of these peptides may achieve immune-dominant status with a given major histocompatibility complex (MHC) class I allele. Specific identification of immunogenic candidate neoantigens is consequently a major challenge. Currently almost all neoantigen prediction tools are based on genomics data. RESULTS:Here we report the construction of proteogenomics prediction of neoantigen (ProGeo-neo) pipeline, which incorporates the following modules: mining tumor specific antigens from next-generation sequencing genomic and mRNA expression data, predicting the binding mutant peptides to class I MHC molecules by latest netMHCpan (v.4.0), verifying MHC-peptides by MaxQuant with mass spectrometry proteomics data searched against customized protein database, and checking potential immunogenicity of T-cell-recognization by additional screening methods. ProGeo-neo pipeline achieves proteogenomics strategy and the neopeptides identified were of much higher quality as compared to those identified using genomic data only. CONCLUSIONS:The pipeline was constructed based on the genomics and proteomics data of Jurkat leukemia cell line but is generally applicable to other solid cancer research. With massively parallel sequencing and proteomics profiling increasing, this proteogenomics workflow should be useful for neoantigen oriented research and immunotherapy.
journal_name
BMC Med Genomicsjournal_title
BMC medical genomicsauthors
Li Y,Wang G,Tan X,Ouyang J,Zhang M,Song X,Liu Q,Leng Q,Chen L,Xie Ldoi
10.1186/s12920-020-0683-4subject
Has Abstractpub_date
2020-04-03 00:00:00pages
52issue
Suppl 5issn
1755-8794pii
10.1186/s12920-020-0683-4journal_volume
13pub_type
杂志文章abstract:BACKGROUND:A Mendelian transmission produces phenotypic and genetic relatedness between family members, giving family-based analytical methods an important role in genetic epidemiological studies-from heritability estimations to genetic association analyses. With the advance in genotyping technologies, whole-genome seq...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0345-y
更新日期:2018-04-20 00:00:00
abstract:BACKGROUND:Type 1 diabetes (T1D) is a complex disease and harmful to human health, and most of the existing biomarkers are mainly to measure the disease phenotype after the disease onset (or drastic deterioration). Until now, there is no effective biomarker which can predict the upcoming disease (or pre-disease state) ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-S2-S8
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Detection of copy number variants (CNVs) is an important aspect of clinical testing for several disorders, including Duchenne muscular dystrophy, and is often performed using multiplex ligation-dependent probe amplification (MLPA). However, since many genetic carrier screens depend instead on next-generation...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0404-4
更新日期:2018-10-20 00:00:00
abstract:BACKGROUND:Genes do not act in isolation but instead as part of complex regulatory networks. To understand how breast tumors adapt to the presence of the drug letrozole, at the molecular level, it is necessary to consider how the expression levels of genes in these networks change relative to one another. METHODS:Usin...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-S2-S2
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Prostate cancer is one of the most common complex diseases with high leading cause of death in men. Identifications of prostate cancer associated genes and biomarkers are thus essential as they can gain insights into the mechanisms underlying disease progression and advancing for early diagnosis and developi...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-S1-S3
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:12q14 microdeletion syndrome is characterized by low birth weight and failure to thrive, proportionate short stature and developmental delay. The opposite syndrome (microduplication) has not yet been characterized. Our main objective is the recognition of a new clinical entity - 12q14 microduplication syndro...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0653-x
更新日期:2020-01-03 00:00:00
abstract:BACKGROUND:Primary microcephaly represents an example of clinically and genetically heterogeneous condition. Here we describe a case of primary microcephaly from the Karachay-Cherkess Republic, which was initially diagnosed with Seckel syndrome. CASE PRESENTATION:Clinical exome sequencing of the proband revealed a nov...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0326-1
更新日期:2018-02-13 00:00:00
abstract:BACKGROUND:The rapid adoption of next-generation sequencing provides an efficient system for detecting somatic alterations in neoplasms. The detection of such alterations requires a matched non-neoplastic sample for adequate filtering of non-somatic events such as germline polymorphisms. Non-neoplastic tissue adjacent ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0226-1
更新日期:2016-10-19 00:00:00
abstract:BACKGROUND:Glaucoma is the largest cause of irreversible blindness affecting more than 60 million people globally. The disease is defined as a gradual loss of peripheral vision due to death of Retinal Ganglion Cells (RGC). The RGC death is largely influenced by the rate of aqueous humor production by ciliary processes ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-016-0177-6
更新日期:2016-03-22 00:00:00
abstract:BACKGROUND:Neuroblastoma (NB) tumors are well known for their pronounced clinical and molecular heterogeneity. The global gene expression and DNA copy number alterations have been shown to have profound differences in tumors of low or high stage and those with or without MYCN amplification. RNA splicing is an important...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-35
更新日期:2011-04-18 00:00:00
abstract:BACKGROUND:Glioblastoma multiforme (GBM) tends to occur between the ages of 45 and 70. This relatively early onset and its poor prognosis make the impact of GBM on public health far greater than would be suggested by its relatively low frequency. Tissue and blood samples have now been collected for a number of populati...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-63
更新日期:2011-08-09 00:00:00
abstract:BACKGROUND:Currently, diagnosis of affected individuals with rare genetic disorders can be lengthy and costly, resulting in a diagnostic odyssey and in many patients a definitive molecular diagnosis is never achieved despite extensive clinical investigation. The recent advent and use of genomic medicine has resulted in...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-32
更新日期:2013-09-17 00:00:00
abstract:BACKGROUND:Urothelial carcinoma (UC) can arise at any location along the urothelial tract, including the urethra, bladder, ureter, or renal pelvis. Although tumors arising in these various locations have similar morphology, it is unclear whether the gene expression profiles are similar between the upper-tract (ureter a...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-58
更新日期:2010-12-15 00:00:00
abstract:BACKGROUNDS:Recent large-scale genetic studies often involve clustered phenotypes such as repeated measurements. Compared to a series of univariate analyses of single phenotypes, an analysis of clustered phenotypes can be useful for substantially increasing statistical power to detect more genetic associations. Moreove...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0517-4
更新日期:2019-07-11 00:00:00
abstract:BACKGROUND:Preeclampsia (PE) is a pregnancy-related condition that affects both the infant and the mother. Although the role of various inflammatory molecules in PE has been demonstrated, the importance of pro-inflammatory molecules such as IL-17A, IL-23 is not well understood. In the present investigation, a potential...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00840-8
更新日期:2021-01-06 00:00:00
abstract:BACKGROUND:Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patien...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-3-11
更新日期:2010-04-09 00:00:00
abstract:BACKGROUND:Childhood asthma is a syndrome composed of heterogeneous phenotypes; furthermore, intrinsic biologic variation among racial/ethnic populations suggests possible genetic ancestry variation in childhood asthma. The objective of the study is to identify clinically homogeneous asthma subphenotypes in a diverse s...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0367-5
更新日期:2018-05-31 00:00:00
abstract:BACKGROUND:Cancer shows a great diversity in its clinical behavior which cannot be easily predicted using the currently available clinical or pathological markers. The identification of pathways associated with lymph node metastasis (N+) and recurrent head and neck squamous cell carcinoma (HNSCC) may increase our under...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-4-33
更新日期:2011-04-13 00:00:00
abstract:BACKGROUND:Methotrexate is one of the earliest cytotoxic drugs used in cancer therapy, and despite the isolation of multiple other folate antagonists, methotrexate maintains its significant role as a treatment for different types of cancer and other disorders. The usefulness of treatment with methotrexate is limited by...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-35
更新日期:2008-08-11 00:00:00
abstract:BACKGROUND:Microtia-atresia is characterized by abnormalities of the auricle (microtia) and aplasia or hypoplasia of the external auditory canal, often associated with middle ear abnormalities. To date, no causal genetic mutations or genes have been identified in microtia-atresia patients. METHODS:We designed a panel ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0475-x
更新日期:2019-01-28 00:00:00
abstract:BACKGROUND:Gene expression profiling has shown its ability to identify with high accuracy low cytogenetic risk acute myeloid leukemia such as acute promyelocytic leukemia and leukemias with t(8;21) or inv(16). The aim of this gene expression profiling study was to evaluate to what extent suboptimal samples with low leu...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-6
更新日期:2012-01-30 00:00:00
abstract:BACKGROUND:Preterm birth (PTB), defined as infant delivery before 37 weeks of completed gestation, results from the interaction of both genetic and environmental components and constitutes a complex multifactorial syndrome. Transcriptome analysis of PTB has proven challenging because of the multiple causes of PTB and t...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-019-0498-3
更新日期:2019-04-01 00:00:00
abstract:BACKGROUND:Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exact underlying mechanisms of COAD pathogenesis are clearly not known yet. In this regard, there is an...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-020-00757-2
更新日期:2020-07-29 00:00:00
abstract:BACKGROUND:We explored the imputation performance of the program IMPUTE in an admixed sample from Mexico City. The following issues were evaluated: (a) the impact of different reference panels (HapMap vs. 1000 Genomes) on imputation; (b) potential differences in imputation performance between single-step vs. two-step (...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-12
更新日期:2012-05-01 00:00:00
abstract:BACKGROUND:One of the tasks in the 2017 iDASH secure genome analysis competition was to enable training of logistic regression models over encrypted genomic data. More precisely, given a list of approximately 1500 patient records, each with 18 binary features containing information on specific mutations, the idea was f...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/s12920-018-0397-z
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:To get insight into molecular mechanisms underlying insulin resistance, we compared acute in vivo effects of insulin on adipose tissue transcriptional profiles between obese insulin-resistant and lean insulin-sensitive women. METHODS:Subcutaneous adipose tissue biopsies were obtained before and after 3 and ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-5-9
更新日期:2012-04-03 00:00:00
abstract:BACKGROUND:In addition to their well-documented ocular therapeutic effects, glucocorticoids (GCs) can cause sight-threatening side-effects including ocular hypertension presumably via morphological and biochemical changes in trabecular meshwork (TM) cells. In the present study, we directly compared the glucocorticoid r...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-2-58
更新日期:2009-09-10 00:00:00
abstract:BACKGROUND:Images embedded in biomedical publications carry rich information that often concisely summarize key hypotheses adopted, methods employed, or results obtained in a published study. Therefore, they offer valuable clues for understanding main content in a biomedical publication. Prior studies have pointed out ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-6-S3-S8
更新日期:2013-01-01 00:00:00
abstract:BACKGROUND:Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metast...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-1-56
更新日期:2008-11-11 00:00:00
abstract:BACKGROUND:2q37 deletion syndrome is a rare congenital disorder that is characterized by facial dysmorphism, obesity, vascular and skeletal malformations, and a variable degree of intellectual disability. To date, common but variable phenotypes, such as skeletal or digit malformations and obesity, have been associated ...
journal_title:BMC medical genomics
pub_type: 杂志文章
doi:10.1186/1755-8794-7-19
更新日期:2014-04-22 00:00:00