Genomic Insights into Idiopathic Granulomatous Mastitis through Whole-Exome Sequencing: A Case Report of Eight Patients
Abstract
:1. Introduction
2. Results
2.1. Patient Demographics and Clinical Characteristics
2.2. DNA Quality and Sequencing Metrics
2.3. Somatic Variants Identified from WES
- Variants called from blood samples: variants identified in blood samples (Supplementary Table S4);
- Variants called from paired blood/tissue samples: variants identified in the tissue sample that were not present in the corresponding blood sample (Table 2).
Case | Somatic Variants | SNVs 1 | Indels 2 | PTVs 3 | Pathogenic 4 | Pathogenic/Likely Pathogenic 4 | Likely Pathogenic 4 | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Strelka2 | Mutect2 | Strelka2 | Mutect2 | Strelka2 | Mutect2 | Strelka2 | Mutect2 | Strelka2 | Mutect2 | Strelka2 | Mutect2 | Strelka2 | Mutect2 | |
1 | 57 | 224 | 56 | 219 | 1 | 1 | 1 | 13 | 0 | 0 | 0 | 0 | 0 | 0 |
2 | 50 | 46 | 48 | 38 | 2 | 7 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 0 |
3 | 57 | 72 | 56 | 69 | 1 | 2 | 1 | 4 | 0 | 0 | 0 | 0 | 0 | 0 |
4 | 53 | 52 | 51 | 48 | 2 | 4 | 3 | 5 | 0 | 0 | 0 | 0 | 0 | 0 |
5 | 56 | 33 | 54 | 28 | 2 | 5 | 2 | 6 | 0 | 0 | 0 | 0 | 0 | 0 |
6 | 80 | 35 | 79 | 26 | 1 | 8 | 0 | 4 | 0 | 0 | 0 | 0 | 0 | 0 |
7 | 65 | 39 | 65 | 32 | 0 | 6 | 0 | 5 | 0 | 0 | 0 | 0 | 0 | 0 |
8 | 53 | 52 | 52 | 39 | 1 | 11 | 0 | 8 | 0 | 0 | 0 | 0 | 0 | 0 |
Median (range) | 56.5 (50–80) | 49 (23–224) | 55 (48–79) | 38.5 (26–219) | 1 (0–2) | 5.5 (1–11) | 0.5 (0–3) | 5 (4–13) | 0 (0–0) | 0 (0–0) | 0 (0–0) | 0 (0–0) | 0 (0–0) | 0 (0–0) |
- CHIT1, altered in Cases 3, 4 and 5, nonsense mutations;
- CEP170, altered in Cases 4 and 5, nonsense mutations;
- CTR9, altered in Cases 7 and 8, nonsense mutation and frameshift deletion, respectively.
2.4. Validation of Somatic Variants with Sanger Sequencing
3. Discussion
4. Materials and Methods
4.1. Patient Recruitment
4.2. Sample Collection
4.3. DNA Extraction and Sequencing
4.4. Quality Control and Somatic Variant Calling
- Catalogue of Somatic Mutations in Cancer (COSMIC) Cancer Gene Census (CGC) (data source dated 15 March 2012) [77];
- NCBI dbSNP (data source dated 18 April 2018) [80];
- Human DNA repair genes (data source dated 24 May 2018) [81];
- GENCODE (v34) [84];
- Genome Aggregation Database (gnomAD) (v3.1.2) [85];
- Human Genome Organisation (HUGO) Gene Nomenclature Committee (HGNC) Database (data source dated 30 November 2017) [86].
4.5. Validating Called Variants with Sanger Sequencing
4.6. Gene Set Analysis
4.7. Data and Sample Availability Statement
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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Demographic and Clinical Parameters | IGM n = 8 |
---|---|
Demographics | |
Median age at diagnosis (years, IQR) | 33.0 (27.3–34.5) |
Ethnicity (n, %) | |
Chinese | 4 (50) |
Malay | 3 (38) |
Others | 1 (12) |
Body mass index (kg/m2, IQR) | 27.770 (23.460–33.454) |
Education level (n, %) | |
Up to secondary school | 3 (38) |
Secondary school to pre-university | 3 (38) |
Tertiary education | 2 (25) |
Patient characteristics | |
Parity (n, %) | |
Yes | 6 (75) |
No | 2 (25) |
Number of children (n, %) | |
No children | 2 (25) |
1–2 children | 5 (62) |
More than 2 children | 1 (12) |
Smoking (n, %) | |
Yes | 2 (25) |
No | 6 (75) |
Chronic illness 1 diagnosis (n, %) | |
Yes | 2 (25) |
No | 6 (75) |
Family history 2 of breast cancer (n, %) | |
Yes | 1 (12) |
No | 7 (88) |
Case | Somatic Variants | SNVs 1 | Indels 2 | PTVs 3 | Pathogenic 4 | Pathogenic/Likely Pathogenic4 | Likely Pathogenic4 |
---|---|---|---|---|---|---|---|
1 | 3 | 3 | 0 | 0 | 0 | 0 | 0 |
2 | 2 | 2 | 0 | 0 | 0 | 0 | 0 |
3 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
4 | 1 | 1 | 0 | 0 | 0 | 0 | 0 |
5 | 2 | 2 | 0 | 0 | 0 | 0 | 0 |
6 | 2 | 2 | 0 | 0 | 0 | 0 | 0 |
7 | 3 | 3 | 0 | 0 | 0 | 0 | 0 |
8 | 2 | 2 | 0 | 0 | 0 | 0 | 0 |
Median (range) | 2 (1–3) | 2 (1–3) | 0 (0–0) | 0 (0–0) | 0 (0–0) | 0 (0–0) | 0 (0–0) |
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Ong, S.S.; Ho, P.J.; Khng, A.J.; Tan, B.K.T.; Tan, Q.T.; Tan, E.Y.; Tan, S.-M.; Putti, T.C.; Lim, S.H.; Tang, E.L.S.; et al. Genomic Insights into Idiopathic Granulomatous Mastitis through Whole-Exome Sequencing: A Case Report of Eight Patients. Int. J. Mol. Sci. 2024, 25, 9058. https://doi.org/10.3390/ijms25169058
Ong SS, Ho PJ, Khng AJ, Tan BKT, Tan QT, Tan EY, Tan S-M, Putti TC, Lim SH, Tang ELS, et al. Genomic Insights into Idiopathic Granulomatous Mastitis through Whole-Exome Sequencing: A Case Report of Eight Patients. International Journal of Molecular Sciences. 2024; 25(16):9058. https://doi.org/10.3390/ijms25169058
Chicago/Turabian StyleOng, Seeu Si, Peh Joo Ho, Alexis Jiaying Khng, Benita Kiat Tee Tan, Qing Ting Tan, Ern Yu Tan, Su-Ming Tan, Thomas Choudary Putti, Swee Ho Lim, Ee Ling Serene Tang, and et al. 2024. "Genomic Insights into Idiopathic Granulomatous Mastitis through Whole-Exome Sequencing: A Case Report of Eight Patients" International Journal of Molecular Sciences 25, no. 16: 9058. https://doi.org/10.3390/ijms25169058