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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
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.
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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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