G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Analysis of the Mutation Context around Tumor Mutation Sites
2.2. Mutational Signatures Found in the Tumors of the Patients Studied
2.3. Classification of Somatic Mutations according to the Type of Substitutions and Their Predicted Consequence
2.4. Germline Variants Found in Patients
2.5. Identification of the Germline SNPs Common to the Patients with the G4 Strong Context Enrichment in Tumors
3. Discussion
4. Materials and Methods
4.1. Patients
4.2. Sequencing of the DNA from Tumor and Normal Samples
4.3. Data Processing and Somatic Variant Calling
4.4. Mutational Signatures
4.5. Identification of G4-Forming Motifs around the Somatic Variants
- (1)
- Weak G4 consisting of stretches of two consecutive guanines:
- (2)
- Strong G4 consisting of stretches of three to four consecutive guanines:
4.6. Statistical Evaluation
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Patient | Sex | Age | Paraprotein | R-ISS | Performance Status |
---|---|---|---|---|---|
S7 | M | 81 | IgG k | I | ECOG II |
S12 | F | 61 | IgG λ | II | ECOG II |
P1 | F | 74 | IgG k | II | ECOG II |
P14 | F | 58 | IgA k | I | ECOG I |
P20 | M | 74 | IgG k | III | ECOG III |
P22 | F | 71 | IgA λ | I | ECOG I |
P23 | F | 73 | IgG k | I | ECOG I |
P30 | M | 69 | IgG k | III | ECOG II |
P34 | M | 83 | IgG k | II | ECOG II |
P37 | M | 64 | IgA λ | II | ECOG III |
P48 | F | 56 | IgG k | III | ECOG III |
Patient | Number of Somatic Mutations Identified in Tumor | G4 Enrichment in the Regions of Somatic Mutations |
---|---|---|
S7 | 115 | No |
S12 | 63 | G4 strong |
P1 | 87 | No |
P14 | 234 | No |
P20 | 182 | No |
P22 | 191 | No |
P23 | 119 | G4 strong |
P30 | 662 | No |
P34 | 267 | No |
P37 | 82 | G4 strong |
P48 | 227 | G4 weak + G4 strong $ |
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Zhuk, A.S.; Stepchenkova, E.I.; Zotova, I.V.; Belopolskaya, O.B.; Pavlov, Y.I.; Kostroma, I.I.; Gritsaev, S.V.; Aksenova, A.Y. G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients. Int. J. Mol. Sci. 2024, 25, 5269. https://doi.org/10.3390/ijms25105269
Zhuk AS, Stepchenkova EI, Zotova IV, Belopolskaya OB, Pavlov YI, Kostroma II, Gritsaev SV, Aksenova AY. G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients. International Journal of Molecular Sciences. 2024; 25(10):5269. https://doi.org/10.3390/ijms25105269
Chicago/Turabian StyleZhuk, Anna S., Elena I. Stepchenkova, Irina V. Zotova, Olesya B. Belopolskaya, Youri I. Pavlov, Ivan I. Kostroma, Sergey V. Gritsaev, and Anna Y. Aksenova. 2024. "G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients" International Journal of Molecular Sciences 25, no. 10: 5269. https://doi.org/10.3390/ijms25105269