Abstract
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.
| Original language | English (US) |
|---|---|
| Article number | 10508 |
| Journal | Scientific Reports |
| Volume | 9 |
| Issue number | 1 |
| DOIs | |
| State | Published - Dec 1 2019 |
Fingerprint
ASJC Scopus subject areas
- General
Cite this
A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses. / Andriani, Grasiella A.; Maggi, Elaine; Piqué, Daniel; Zimmerman, Samuel E.; Lee, Moonsook; Quispe-Tintaya, Wilber; Maslov, Alexander; Campisi, Judith; Vijg, Jan; Mar, Jessica C.; Montagna, Cristina.
In: Scientific Reports, Vol. 9, No. 1, 10508, 01.12.2019.Research output: Contribution to journal › Article
}
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
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.
UR - http://www.scopus.com/inward/record.url?scp=85069541814&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85069541814&partnerID=8YFLogxK
U2 - 10.1038/s41598-019-46606-w
DO - 10.1038/s41598-019-46606-w
M3 - Article
VL - 9
JO - Scientific Reports
JF - Scientific Reports
SN - 2045-2322
IS - 1
M1 - 10508
ER -