Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patient Specimen and Study Design
2.2. Maternal Cell Contamination
2.3. Optical Genome Mapping
2.4. Histological Assessment and SNPM Analysis
2.5. Data Analysis
3. Results
3.1. Patient Characteristics
3.2. Prospective Sample Processing with Current and Proposed Workflow
3.3. Optical Genome Mapping Analysis
3.4. Histological Assessment and SNPM Analysis
3.5. Proposed Workflow Compared to Conventional Cytogenetic Testing
3.6. Selected, Interesting Clinical Cases
4. Discussion
5. Limitations of the Study
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Ethics Approval
References
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Patient Characteristic | Classification | No. |
---|---|---|
Anamnestic data | ||
Age (Mean ± SD) | 33.4 ± 5.1 | |
No. of previous losses | 2 | 4 |
3 | 4 | |
4 | 0 | |
5 | 1 | |
6 | 1 | |
7 | 1 | |
No. of previous live births | 0 | 16 |
1 | 8 | |
2 | 4 | |
3 | 3 | |
Miscarriage | <20 weeks | 27 |
Intra-uterine fetal demise | 3 | |
Stillbirths | 1 | |
Current Material | ||
Sporadic miscarriage | 22 | |
Recurrent pregnancy loss | 9 |
S.No. | Trimester | ISCN Nomenclature | Size |
---|---|---|---|
OncoScan Analysis | |||
1 | 9 weeks, 1st | arr[hg19] (22) × 3 | Entire chromosome 22 |
2 | 10 weeks, 1st | arr[hg19] 4q34.3(178,112,003-182,153,124)×3, (21,22) × 2~3 | 4.0 Mb Gain of chr 4 and Gain of entire chromosomes 21 and 22 |
3 | 8 weeks, 1st | arr[hg19] (8) × 2~3 | Entire chromosome 8 |
4 | 9 weeks, 1st | arr[hg19] (8) × 3 | 146.1Mb |
5 | 10 weeks, 1st | arr[hg19] (14) × 2~3 | Entire chromosome 14 |
6 | 10 weeks, 1st | arr[hg19] (X) × 1~2 | Entire chromosome X |
7 | 14 weeks, 2nd | arr[hg19]2q34q37.2(214027641-236628038) ×3, 2q37.2q37.3(236228142-243052331) × 1 | 22.6Mb gain and 6.4Mb loss |
8 | 11 weeks, 1st | arr [hg19] (1-21,X) × 2, (22)×2~3 | Entire chromosome 22 |
9 | 8 weeks 5 days, 1st | arr[hg19] (15) × 2~3 | Entire chromosome 15 |
10 | 6 weeks, 6 days, 1st | arr[hg19] (18) × 3 | Entire chromosome 18 |
11 | 26 weeks 1 day, 2nd | arr[hg19] 2p21(43411752-44710936) × 3, 21q21.1(18762223-19136546) ×1 | 1.29 Mb Gain and 374 Kb Loss |
12 | Less than 3 weeks, 1st | arr[hg19] 13q14.11(42311546_42413745) × 1 | 102 Kb Loss |
Optical Genome Mapping | |||
13 | 6 weeks, 1st | ogm[GrCh38](15) × 3 | Entire chromosome 15 |
14 | 8 weeks, 1st | ogm[GrCh38](20) × 3 | Entire chromosome 20 |
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Sahajpal, N.S.; Mondal, A.K.; Ananth, S.; Pundkar, C.; Jones, K.; Williams, C.; Fee, T.; Weissman, A.; Tripodi, G.; Oza, E.; et al. Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception. Genes 2022, 13, 643. https://doi.org/10.3390/genes13040643
Sahajpal NS, Mondal AK, Ananth S, Pundkar C, Jones K, Williams C, Fee T, Weissman A, Tripodi G, Oza E, et al. Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception. Genes. 2022; 13(4):643. https://doi.org/10.3390/genes13040643
Chicago/Turabian StyleSahajpal, Nikhil Shri, Ashis K. Mondal, Sudha Ananth, Chetan Pundkar, Kimya Jones, Colin Williams, Timothy Fee, Amanda Weissman, Giuseppe Tripodi, Eesha Oza, and et al. 2022. "Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception" Genes 13, no. 4: 643. https://doi.org/10.3390/genes13040643
APA StyleSahajpal, N. S., Mondal, A. K., Ananth, S., Pundkar, C., Jones, K., Williams, C., Fee, T., Weissman, A., Tripodi, G., Oza, E., Gavrilova-Jordan, L., Omar, N., Hastie, A. R., DuPont, B. R., Layman, L., Chaubey, A., & Kolhe, R. (2022). Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception. Genes, 13(4), 643. https://doi.org/10.3390/genes13040643