TY - JOUR
T1 - A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses
AU - Andriani, Grasiella A.
AU - Maggi, Elaine
AU - Piqué, Daniel
AU - Zimmerman, Samuel E.
AU - Lee, Moonsook
AU - Quispe-Tintaya, Wilber
AU - Maslov, Alexander
AU - Campisi, Judith
AU - Vijg, Jan
AU - Mar, Jessica C.
AU - Montagna, Cristina
N1 - Funding Information:
We would like to thank the Molecular Cytogenetic Core at Albert Einstein College of Medicine and in particular Dr. Jidong Shan and Dr. Yinghui Song for assisting with the FISH studies. Research reported in this publication was supported by the Albert Einstein Cancer Center Support Grant of the National Institutes of Health under award number P30CA013330. Part of this work was also supported by a grant from the National Institutes of Health [P01AG17242 to J.V., in which J.C. and C.M. participate].
Publisher Copyright:
© 2019, The Author(s).
PY - 2019/12/1
Y1 - 2019/12/1
N2 - Aneuploidy has been reported to occur at remarkably high levels in normal somatic tissues using Fluorescence In Situ Hybridization (FISH). Recently, these reports were contradicted by single-cell low-coverage whole genome sequencing (scL-WGS) analyses, which showed aneuploidy frequencies at least an order of magnitude lower. To explain these seemingly contradictory findings, we used both techniques to analyze artificially generated mock aneuploid cells and cells with natural random aneuploidy. Our data indicate that while FISH tended to over-report aneuploidies, a modified 2-probe approach can accurately detect low levels of aneuploidy. Further, scL-WGS tends to underestimate aneuploidy levels, especially in a polyploid background.
AB - Aneuploidy has been reported to occur at remarkably high levels in normal somatic tissues using Fluorescence In Situ Hybridization (FISH). Recently, these reports were contradicted by single-cell low-coverage whole genome sequencing (scL-WGS) analyses, which showed aneuploidy frequencies at least an order of magnitude lower. To explain these seemingly contradictory findings, we used both techniques to analyze artificially generated mock aneuploid cells and cells with natural random aneuploidy. Our data indicate that while FISH tended to over-report aneuploidies, a modified 2-probe approach can accurately detect low levels of aneuploidy. Further, scL-WGS tends to underestimate aneuploidy levels, especially in a polyploid background.
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U2 - 10.1038/s41598-019-46606-w
DO - 10.1038/s41598-019-46606-w
M3 - Article
C2 - 31324840
AN - SCOPUS:85069541814
SN - 2045-2322
VL - 9
JO - Scientific Reports
JF - Scientific Reports
IS - 1
M1 - 10508
ER -