A rapid and reliable chromosome analysis method for products of conception using interphase nuclei

Ramesh Babu, Daniel L. Van Dyke, Saurabh Bhattacharya, Vaithilingam G. Dev, Mingya Liu, Minjae Kwon, Guangyu Gu, Prasad Koduru, Nagesh Rao, Cynthia Williamson, Ernesto Fuentes, Sarah Fuentes, Stephen Papa, Srikanthi Kopuri, Vandana Lal

Research output: Contribution to journalArticle

Abstract

Background: Karyotype determination has a central role in the genetic workup of pregnancy loss, as aneuploidy (trisomy and monosomy) and polyploidy (triploidy and tetraploidy) are the cause in at least 50% of first trimester, 25% of second trimester, and 11% of third trimester miscarriages. There are several limitations with the current approaches of obtaining a karyotype using traditional cytogenetics, fluorescence in situ hybridization with a limited number of probes, and chromosomal microarray. These include culture failure, incomplete results, lower sensitivity, and longer reporting time. Methods: To overcome current limitations, a novel molecular assay is developed with a Standard Resolution Interphase Chromosome Profiling probe set which is a variation of the recently developed High Resolution probe set. It generates a molecular karyotype that can detect all major changes commonly associated with pregnancy loss. Initial familiarization of signal patterns from the probe set was used, followed by validation of the method using 83 samples from miscarriages in a blind study from three different laboratories. Finally, the clinical utility of the method was tested on 291 clinical samples in two commercial reference laboratory settings on two different continents. Results: The new molecular approach not only identified all the chromosome changes observed by current methods, but also significantly improved abnormality detection by characterizing derivative chromosomes and finding subtle subtelomeric rearrangements, balanced and unbalanced. All Robertsonian translocations were also detected. The abnormality rate was 54% on clinical samples from commercial laboratory 1 and 63% from laboratory 2. Conclusion: The attributes of this method make it an ideal choice for the genetic workup of miscarriages, namely (1) near 100% successful results, (2) greater sensitivity than conventional chromosome analysis or FISH panels, (3) rapid reporting time, and (4) favorable comparisons with chromosomal microarray.

Original languageEnglish (US)
Pages (from-to)370-381
Number of pages12
JournalMolecular Genetics and Genomic Medicine
Volume6
Issue number3
DOIs
StatePublished - May 1 2018

Fingerprint

Interphase
Chromosomes
Spontaneous Abortion
Karyotype
Monosomy
Triploidy
Pregnancy
Polyploidy
Tetraploidy
Trisomy
DNA Probes
Third Pregnancy Trimester
Second Pregnancy Trimester
Aneuploidy
First Pregnancy Trimester
Cytogenetics
Fluorescence

Keywords

  • abortion
  • fluorescence
  • in situ hybridization
  • karyotype
  • spontaneous

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)

Cite this

Babu, R., Van Dyke, D. L., Bhattacharya, S., Dev, V. G., Liu, M., Kwon, M., ... Lal, V. (2018). A rapid and reliable chromosome analysis method for products of conception using interphase nuclei. Molecular Genetics and Genomic Medicine, 6(3), 370-381. https://doi.org/10.1002/mgg3.381

A rapid and reliable chromosome analysis method for products of conception using interphase nuclei. / Babu, Ramesh; Van Dyke, Daniel L.; Bhattacharya, Saurabh; Dev, Vaithilingam G.; Liu, Mingya; Kwon, Minjae; Gu, Guangyu; Koduru, Prasad; Rao, Nagesh; Williamson, Cynthia; Fuentes, Ernesto; Fuentes, Sarah; Papa, Stephen; Kopuri, Srikanthi; Lal, Vandana.

In: Molecular Genetics and Genomic Medicine, Vol. 6, No. 3, 01.05.2018, p. 370-381.

Research output: Contribution to journalArticle

Babu, R, Van Dyke, DL, Bhattacharya, S, Dev, VG, Liu, M, Kwon, M, Gu, G, Koduru, P, Rao, N, Williamson, C, Fuentes, E, Fuentes, S, Papa, S, Kopuri, S & Lal, V 2018, 'A rapid and reliable chromosome analysis method for products of conception using interphase nuclei', Molecular Genetics and Genomic Medicine, vol. 6, no. 3, pp. 370-381. https://doi.org/10.1002/mgg3.381
Babu, Ramesh ; Van Dyke, Daniel L. ; Bhattacharya, Saurabh ; Dev, Vaithilingam G. ; Liu, Mingya ; Kwon, Minjae ; Gu, Guangyu ; Koduru, Prasad ; Rao, Nagesh ; Williamson, Cynthia ; Fuentes, Ernesto ; Fuentes, Sarah ; Papa, Stephen ; Kopuri, Srikanthi ; Lal, Vandana. / A rapid and reliable chromosome analysis method for products of conception using interphase nuclei. In: Molecular Genetics and Genomic Medicine. 2018 ; Vol. 6, No. 3. pp. 370-381.
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abstract = "Background: Karyotype determination has a central role in the genetic workup of pregnancy loss, as aneuploidy (trisomy and monosomy) and polyploidy (triploidy and tetraploidy) are the cause in at least 50{\%} of first trimester, 25{\%} of second trimester, and 11{\%} of third trimester miscarriages. There are several limitations with the current approaches of obtaining a karyotype using traditional cytogenetics, fluorescence in situ hybridization with a limited number of probes, and chromosomal microarray. These include culture failure, incomplete results, lower sensitivity, and longer reporting time. Methods: To overcome current limitations, a novel molecular assay is developed with a Standard Resolution Interphase Chromosome Profiling probe set which is a variation of the recently developed High Resolution probe set. It generates a molecular karyotype that can detect all major changes commonly associated with pregnancy loss. Initial familiarization of signal patterns from the probe set was used, followed by validation of the method using 83 samples from miscarriages in a blind study from three different laboratories. Finally, the clinical utility of the method was tested on 291 clinical samples in two commercial reference laboratory settings on two different continents. Results: The new molecular approach not only identified all the chromosome changes observed by current methods, but also significantly improved abnormality detection by characterizing derivative chromosomes and finding subtle subtelomeric rearrangements, balanced and unbalanced. All Robertsonian translocations were also detected. The abnormality rate was 54{\%} on clinical samples from commercial laboratory 1 and 63{\%} from laboratory 2. Conclusion: The attributes of this method make it an ideal choice for the genetic workup of miscarriages, namely (1) near 100{\%} successful results, (2) greater sensitivity than conventional chromosome analysis or FISH panels, (3) rapid reporting time, and (4) favorable comparisons with chromosomal microarray.",
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AU - Liu, Mingya

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AU - Gu, Guangyu

AU - Koduru, Prasad

AU - Rao, Nagesh

AU - Williamson, Cynthia

AU - Fuentes, Ernesto

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AU - Kopuri, Srikanthi

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