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Depth of Sequencing Plays a Determining Role in the Characterization of Phage Display Peptide Libraries by NGS.

التفاصيل البيبلوغرافية
العنوان: Depth of Sequencing Plays a Determining Role in the Characterization of Phage Display Peptide Libraries by NGS.
المؤلفون: Sloth AB; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Bakhshinejad B; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Stavnsbjerg C; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Rossing M; Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, 2100 Copenhagen, Denmark.; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark., Kjaer A; Department of Clinical Physiology and Nuclear Medicine & Cluster for Molecular Imaging, Copenhagen University Hospital-Rigshospitalet & Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
المصدر: International journal of molecular sciences [Int J Mol Sci] 2023 Mar 11; Vol. 24 (6). Date of Electronic Publication: 2023 Mar 11.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Basel, Switzerland : MDPI, [2000-
مواضيع طبية MeSH: Peptide Library* , Bacteriophages*/genetics, High-Throughput Nucleotide Sequencing/methods ; Cell Surface Display Techniques ; Peptides/genetics
مستخلص: Next-generation sequencing (NGS) has raised a growing interest in phage display research. Sequencing depth is a pivotal parameter for using NGS. In the current study, we made a side-by-side comparison of two NGS platforms with different sequencing depths, denoted as lower-throughput (LTP) and higher-throughput (HTP). The capacity of these platforms for characterization of the composition, quality, and diversity of the unselected Ph.D. TM -12 Phage Display Peptide Library was investigated. Our results indicated that HTP sequencing detects a considerably higher number of unique sequences compared to the LTP platform, thus covering a broader diversity of the library. We found a larger percentage of singletons, a smaller percentage of repeated sequences, and a greater percentage of distinct sequences in the LTP datasets. These parameters suggest a higher library quality, resulting in potentially misleading information when using LTP sequencing for such assessment. Our observations showed that HTP reveals a broader distribution of peptide frequencies, thus revealing increased heterogeneity of the library by the HTP approach and offering a comparatively higher capacity for distinguishing peptides from each other. Our analyses suggested that LTP and HTP datasets show discrepancies in their peptide composition and position-specific distribution of amino acids within the library. Taken together, these findings lead us to the conclusion that a higher sequencing depth can yield more in-depth insights into the composition of the library and provide a more complete picture of the quality and diversity of phage display peptide libraries.
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معلومات مُعتمدة: 670261 European Union's Horizon 2020 research and innovation programme (ERC Advanced Grant); 668532 European Union's Horizon 2020 research and innovation programme (Click-It); 126 The Danish National Research Foundation - PERSIMUNE
فهرسة مساهمة: Keywords: Ph.D.TM-12 peptide library; composition; deep sequencing; distinguishing capacity; diversity; illumina sequencing; next-generation sequencing; phage display peptide library; quality; sequencing depth
المشرفين على المادة: 0 (Peptide Library)
0 (Peptides)
تواريخ الأحداث: Date Created: 20230329 Date Completed: 20230330 Latest Revision: 20230331
رمز التحديث: 20230331
مُعرف محوري في PubMed: PMC10049078
DOI: 10.3390/ijms24065396
PMID: 36982469
قاعدة البيانات: MEDLINE
الوصف
تدمد:1422-0067
DOI:10.3390/ijms24065396