Impact of allele‐specific peptides in proteome quantification

Wu, Linfeng; Snyder, M

doi:10.1002/prca.201400126

Cited by 4 publications

(5 citation statements)

References 32 publications

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“…S2.3). Finally, for proteomics we mapped peptides directly to the personal genomes, calling AS peptides in consistent fashion to the processing for AS RNA-seq (contrasting to other approaches (28)(29)(30)); in total, we found 2,028 potential AS peptides (Fig. S4.4c and Supplement).…”

Section: Measuring As Activity In Diverse Assaysmentioning

confidence: 99%

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Rozowsky¹,

Moore²,

Pratt³

et al. 2021

Preprint

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Evaluating the impact of genetic variants on transcriptional regulation is a central goal in biological science that has been constrained by reliance on a single reference genome. To address this, we constructed phased, diploid genomes for four cadaveric donors (using longread sequencing) and systematically charted noncoding regulatory elements and transcriptional activity across more than 25 tissues from these donors. Integrative analysis revealed over a million variants with allele-specific activity, coordinated, locus-scale allelic imbalances, and structural variants impacting proximal chromatin structure. We relate the personal genome analysis to the ENCODE encyclopedia, annotating allele- and tissue-specific elements that are strongly enriched for variants impacting expression and disease phenotypes. These experimental and statistical approaches, and the corresponding EN-TEx resource, provide a framework for personalized functional genomics.

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Section: Measuring As Activity In Diverse Assaysmentioning

confidence: 99%

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Rozowsky¹,

Moore²,

Pratt³

et al. 2021

Preprint

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“…Protein variants can modify binding surfaces and lead to alterations in peptides encompassing variant regions, potentially introducing biases in proteomic studies 11,17,37 . We developed a framework to thoroughly examine peptide-level information for indications of artefactual pQTLs (Extended Data Fig.…”

Section: Eliminating Artefactual Pqtlsmentioning

confidence: 99%

Plasma Proteome Variation and its Genetic Determinants in Children and Adolescents

Niu

Stinson

Holm

et al. 2023

Preprint

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The levels of specific proteins in human blood are the most commonly used indicators of potential health-related problems. Understanding the genetic and other determinants of the human plasma proteome can aid in biomarker research and drug development. Diverse factors including genetics, age, sex, body mass index (BMI), growth and development including puberty can affect the circulating levels of proteins. Affinity-based proteomics can infer the relationship between blood protein levels and these factors at a large scale. Compared to these methods, mass spectrometry (MS)-based proteomics provides much higher specificity of identification and quantification, but existing studies are limited by small sample sizes or low numbers of quantified proteins. Here we aim to elucidate to which extent genomic variation affects plasma protein levels across diverse age ranges and cohort characteristics. Employing a streamlined and highly quantitative MS-based plasma proteomics workflow, we measured the plasma proteome of 2,147 children and adolescents. Levels of 90% of these proteins were significantly associated with age, sex, BMI or genetics. More than 1,000 protein quantitative trait loci (pQTLs) - a third of which were novel - regulated protein levels between a few percent and up to 30-fold. These replicated excellently in an independent cohort of 558 adults, with highly concordant effect sizes (Pearson r > 0.97). We developed a framework to eliminate artefactual pQTLs due to protein-altering variants, paving the way for large-scale interrogation of pQTLs using MS-based proteomics. Our data reveal unexpectedly extensive genetic impacts on plasma protein levels, consistent from childhood into adulthood. These findings have implications for biomarker research and drug development.

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“…A FNAB biopsy hence becomes an important marker for the management of the cancer patients. iii Moreover, studying the tumor microenvironment at protein level is more important than the RNA studies due to the discrepancy between the protein and the RNA expression [4].…”

Section: The Importance Of Tumor Microenvironmentmentioning

confidence: 99%

Recent Advances and Researches in the Field of Fine Needle Aspiration Cytopathology

Goyal¹

2023

Advances in Fine Needle Aspiration Cytopathology

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Fine needle aspiration cytology/biopsy (FNAB) is quite often one of the first tests for the initial evaluation of lesions/swellings which are accessible to the needle tracts. The technique has its limitations in certain cases owing to the non-representative or inadequate material aspirated or due to the confusion arising from the lack of histologic pattern as observed on a biopsy. An immediate rapid on-site evaluation (ROSE) is valuable in minimizing the limitations arising from the non-representative/inadequate material. The introduction and application of several ancillary modalities, like immunocytochemistry, molecular tests and the advancements in interventional radiology, has further revolutionized the diagnostic scope of FNA biopsy. Molecular tests on the FNAC samples can aid in the distinction of benign from malignant lesions, in determining the genetic abnormalities and genetic makeup of tumors that can be useful not only for making a more specific diagnosis but also for determining prognosis, response to therapy and for the selection of patients for targeted therapy. FNAB biopsies have an added advantage in comparison with the core needle biopsies for molecular analysis since they have a much lower contamination of stroma. The chapter will be discussing the advancements and the uses of these ancillary techniques in the field of FNAC.

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Impact of allele‐specific peptides in proteome quantification

Cited by 4 publications

References 32 publications

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

Plasma Proteome Variation and its Genetic Determinants in Children and Adolescents

Recent Advances and Researches in the Field of Fine Needle Aspiration Cytopathology

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