Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception
Conventional cytogenetic analysis of products of conception (POC) is of limited utility because of failed cultures, as well as microbial and maternal cell contamination (MCC). Optical genome mapping (OGM) is an emerging technology that has the potential to replace conventional cytogenetic methods. T...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-04-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/13/4/643 |
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| author | Nikhil Shri Sahajpal Ashis K. Mondal Sudha Ananth Chetan Pundkar Kimya Jones Colin Williams Timothy Fee Amanda Weissman Giuseppe Tripodi Eesha Oza Larisa Gavrilova-Jordan Nivin Omar Alex R. Hastie Barbara R. DuPont Lawrence Layman Alka Chaubey Ravindra Kolhe |
| author_facet | Nikhil Shri Sahajpal Ashis K. Mondal Sudha Ananth Chetan Pundkar Kimya Jones Colin Williams Timothy Fee Amanda Weissman Giuseppe Tripodi Eesha Oza Larisa Gavrilova-Jordan Nivin Omar Alex R. Hastie Barbara R. DuPont Lawrence Layman Alka Chaubey Ravindra Kolhe |
| author_sort | Nikhil Shri Sahajpal |
| collection | DOAJ |
| description | Conventional cytogenetic analysis of products of conception (POC) is of limited utility because of failed cultures, as well as microbial and maternal cell contamination (MCC). Optical genome mapping (OGM) is an emerging technology that has the potential to replace conventional cytogenetic methods. The use of OGM precludes the requirement for culturing (and related microbial contamination). However, a high percentage of MCC impedes a definitive diagnosis, which can be addressed by an additional pre-analytical quality control step that includes histological assessment of H&E stained slides from formalin-fixed paraffin embedded (FFPE) tissue with macro-dissection for chorionic villi to enrich fetal tissue component for single nucleotide polymorphism microarray (SNPM) analysis. To improve the diagnostic yield, an integrated workflow was devised that included MCC characterization of POC tissue, followed by OGM for MCC-negative cases or SNPM with histological assessment for MCC-positive cases. A result was obtained in 93% (29/31) of cases with a diagnostic yield of 45.1% (14/31) with the proposed workflow, compared to 9.6% (3/31) and 6.4% (2/31) with routine workflow, respectively. The integrated workflow with these technologies demonstrates the clinical utility and higher diagnostic yield in evaluating POC specimens. |
| first_indexed | 2024-03-09T13:38:00Z |
| format | Article |
| id | doaj.art-5021256192b24655918971fc27650b6a |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T13:38:00Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-5021256192b24655918971fc27650b6a2023-11-30T21:10:01ZengMDPI AGGenes2073-44252022-04-0113464310.3390/genes13040643Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of ConceptionNikhil Shri Sahajpal0Ashis K. Mondal1Sudha Ananth2Chetan Pundkar3Kimya Jones4Colin Williams5Timothy Fee6Amanda Weissman7Giuseppe Tripodi8Eesha Oza9Larisa Gavrilova-Jordan10Nivin Omar11Alex R. Hastie12Barbara R. DuPont13Lawrence Layman14Alka Chaubey15Ravindra Kolhe16Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USADepartment of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USADepartment of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USADepartment of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL 36849, USADepartment of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USADepartment of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USACytogenetics Laboratory, Greenwood Genetic Center, Greenwood, SC 29646, USAMedical College of Georgia, Augusta University, Augusta, GA 30912, USAMedical College of Georgia, Augusta University, Augusta, GA 30912, USADepartment of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USADepartment of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USADepartment of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USABionano Genomics Inc., San Diego, CA 92121, USACytogenetics Laboratory, Greenwood Genetic Center, Greenwood, SC 29646, USADepartment of Obstetrics and Gynecology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USABionano Genomics Inc., San Diego, CA 92121, USADepartment of Pathology, Medical College of Georgia, Augusta University, Augusta, GA 30912, USAConventional cytogenetic analysis of products of conception (POC) is of limited utility because of failed cultures, as well as microbial and maternal cell contamination (MCC). Optical genome mapping (OGM) is an emerging technology that has the potential to replace conventional cytogenetic methods. The use of OGM precludes the requirement for culturing (and related microbial contamination). However, a high percentage of MCC impedes a definitive diagnosis, which can be addressed by an additional pre-analytical quality control step that includes histological assessment of H&E stained slides from formalin-fixed paraffin embedded (FFPE) tissue with macro-dissection for chorionic villi to enrich fetal tissue component for single nucleotide polymorphism microarray (SNPM) analysis. To improve the diagnostic yield, an integrated workflow was devised that included MCC characterization of POC tissue, followed by OGM for MCC-negative cases or SNPM with histological assessment for MCC-positive cases. A result was obtained in 93% (29/31) of cases with a diagnostic yield of 45.1% (14/31) with the proposed workflow, compared to 9.6% (3/31) and 6.4% (2/31) with routine workflow, respectively. The integrated workflow with these technologies demonstrates the clinical utility and higher diagnostic yield in evaluating POC specimens.https://www.mdpi.com/2073-4425/13/4/643optical genome mappingmicroarrayproducts of conception |
| spellingShingle | Nikhil Shri Sahajpal Ashis K. Mondal Sudha Ananth Chetan Pundkar Kimya Jones Colin Williams Timothy Fee Amanda Weissman Giuseppe Tripodi Eesha Oza Larisa Gavrilova-Jordan Nivin Omar Alex R. Hastie Barbara R. DuPont Lawrence Layman Alka Chaubey Ravindra Kolhe Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception Genes optical genome mapping microarray products of conception |
| title | Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception |
| title_full | Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception |
| title_fullStr | Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception |
| title_full_unstemmed | Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception |
| title_short | Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception |
| title_sort | optical genome mapping and single nucleotide polymorphism microarray an integrated approach for investigating products of conception |
| topic | optical genome mapping microarray products of conception |
| url | https://www.mdpi.com/2073-4425/13/4/643 |
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