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Validation of fetus aneuploidy in 221 Korean clinical samples using noninvasive chromosome examination: Clinical laboratory improvement amendments-certified noninvasive prenatal test
J Genet Med 2015;12:79-84
Published online December 31, 2015;
© 2015 Korean Society of Medical Genetics.

Min-Jeong Kim, Chang Hyuk Kwon, Dong-In Kim, Hee Su Im, Sungil Park, Ji Ho Kim, Jin-Sik Bae, Myunghee Lee, and Min Seob Lee*

Eone-Diagnomics Genome Center (EDGC), Inc., Incheon, Korea
Min Seob Lee, Ph.D. Eone-Diagnomics Genome Center (EDGC), Inc., 291 Harmony-ro, Yeonsu-gu, Incheon 22014, Korea. Tel: +82-32-210-2341, Fax: +82-32-210-2349, E-mail:
Received November 11, 2015; Revised December 14, 2015; Accepted December 24, 2015.
cc This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.


We developed and validated a fetal trisomy detection method for use as a noninvasive prenatal test (NIPT) including a Clinical Laboratory Improvement Amendments (CLIA)-certified bioinformatics pipeline on a cloud-based computing system using both Illumina and Life Technology sequencing platforms for 221 Korean clinical samples. We determined the necessary proportions of the fetal fraction in the cell-free DNA (cfDNA) sample for NIPT of trisomies 13, 18, and 21 through a limit of quantification (LOQ) test.

Materials and Methods:

Next-generation sequencing libraries from 221 clinical samples and three positive controls were generated using Illumina and Life Technology chemistries. Sequencing results were uploaded to a cloud and mapped on the human reference genome (GRCh37/hg19) using bioinformatics tools. Based on Z-scores calculated by normalization of the mapped read counts, final aneuploidy reports were automatically generated for fetal aneuploidy determination.


We identified in total 29 aneuploid samples, and additional analytical methods performed to confirm the results showed that one of these was a false-positive. The LOQ test showed that the proportion of fetal fraction in the cfDNA sample would affect the interpretation of the aneuploidy results.


Noninvasive chromosome examination (NICE), a CLIA-certified NIPT with a cloud-based bioinformatics platform, showed unambiguous success in fetus aneuploidy detection.

Keywords : Prenatal diagnosis, High-throughput nucleotide sequencing, Computational biology, Cell-free DNA, Trisomy, Aneuploidy

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