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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...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9026980/ https://www.ncbi.nlm.nih.gov/pubmed/35456449 http://dx.doi.org/10.3390/genes13040643 |
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author | Sahajpal, Nikhil Shri Mondal, Ashis K. Ananth, Sudha Pundkar, Chetan Jones, Kimya Williams, Colin Fee, Timothy Weissman, Amanda Tripodi, Giuseppe Oza, Eesha Gavrilova-Jordan, Larisa Omar, Nivin Hastie, Alex R. DuPont, Barbara R. Layman, Lawrence Chaubey, Alka Kolhe, Ravindra |
author_facet | Sahajpal, Nikhil Shri Mondal, Ashis K. Ananth, Sudha Pundkar, Chetan Jones, Kimya Williams, Colin Fee, Timothy Weissman, Amanda Tripodi, Giuseppe Oza, Eesha Gavrilova-Jordan, Larisa Omar, Nivin Hastie, Alex R. DuPont, Barbara R. Layman, Lawrence Chaubey, Alka Kolhe, Ravindra |
author_sort | Sahajpal, Nikhil Shri |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-9026980 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-90269802022-04-23 Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating Products of Conception Sahajpal, Nikhil Shri Mondal, Ashis K. Ananth, Sudha Pundkar, Chetan Jones, Kimya Williams, Colin Fee, Timothy Weissman, Amanda Tripodi, Giuseppe Oza, Eesha Gavrilova-Jordan, Larisa Omar, Nivin Hastie, Alex R. DuPont, Barbara R. Layman, Lawrence Chaubey, Alka Kolhe, Ravindra Genes (Basel) Article 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. MDPI 2022-04-03 /pmc/articles/PMC9026980/ /pubmed/35456449 http://dx.doi.org/10.3390/genes13040643 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Sahajpal, Nikhil Shri Mondal, Ashis K. Ananth, Sudha Pundkar, Chetan Jones, Kimya Williams, Colin Fee, Timothy Weissman, Amanda Tripodi, Giuseppe Oza, Eesha Gavrilova-Jordan, Larisa Omar, Nivin Hastie, Alex R. DuPont, Barbara R. Layman, Lawrence Chaubey, Alka Kolhe, Ravindra Optical Genome Mapping and Single Nucleotide Polymorphism Microarray: An Integrated Approach for Investigating 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 | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9026980/ https://www.ncbi.nlm.nih.gov/pubmed/35456449 http://dx.doi.org/10.3390/genes13040643 |
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