TY - JOUR
T1 - Optical Genome Mapping and Single Nucleotide Polymorphism Microarray
T2 - An Integrated Approach for Investigating Products of Conception
AU - Sahajpal, Nikhil Shri
AU - Mondal, Ashis K.
AU - Ananth, Sudha
AU - Pundkar, Chetan
AU - Jones, Kimya
AU - Williams, Colin
AU - Fee, Timothy
AU - Weissman, Amanda
AU - Tripodi, Giuseppe
AU - Oza, Eesha
AU - Gavrilova-Jordan, Larisa
AU - Omar, Nivin
AU - Hastie, Alex R.
AU - Dupont, Barbara R.
AU - Layman, Lawrence
AU - Chaubey, Alka
AU - Kolhe, Ravindra
N1 - Funding Information:
Funding: R.K. has received honoraria, and/or travel funding, and/or research support from Illumina, San Diego, CA, USA; Asuragen, Austin, TX, USA; QIAGEN, Germantown, MD, USA; Perkin Elmer Inc., Waltham, MA, USA; Bionano Genomics, San Diego, CA, USA; Agena, San Diego, CA, USA; Agendia, Irvine, CA, USA; PGDx, Baltimore, MD, USA; Thermo Fisher Scientific, Waltham, MA, USA; Cepheid, Sunnyvale, CA, USA; and BMS, Brookhaven, GA, USA. A.R.H. and A.C. are salaried employee at Bionano Genomics Inc., CA, USA.
Publisher Copyright:
© 2022 by the authors. Licensee MDPI, Basel, Switzerland.
PY - 2022/4
Y1 - 2022/4
N2 - 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.
AB - 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.
KW - microarray
KW - optical genome mapping
KW - products of conception
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U2 - 10.3390/genes13040643
DO - 10.3390/genes13040643
M3 - Article
C2 - 35456449
AN - SCOPUS:85128657985
SN - 2073-4425
VL - 13
JO - Genes
JF - Genes
IS - 4
M1 - 643
ER -