Validation of fetus aneuploidy in 221 Korean clinical samples using noninvasive chromosome examination: Clinical laboratory improvement amendments-certified noninvasive prenatal test

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

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자료유형: 학술저널

저자정보: Kim, Min-Jeong (Eone-Diagnomics Genome Center [EDGC], Inc.) Kwon, Chang Hyuk (Eone-Diagnomics Genome Center [EDGC], Inc.) Kim, Dong-In (Eone-Diagnomics Genome Center [EDGC], Inc.) Im, Hee Su (Eone-Diagnomics Genome Center [EDGC], Inc.) Park, Sungil (Eone-Diagnomics Genome Center [EDGC], Inc.) Kim, Ji Ho (Eone-Diagnomics Genome Center [EDGC], Inc.) Bae, Jin-Sik (Eone-Diagnomics Genome Center [EDGC], Inc.) Lee, Myunghee (Eone-Diagnomics Genome Center [EDGC], Inc.) Lee, Min Seob (Eone-Diagnomics Genome Center [EDGC], Inc.)

저널정보: 대한의학유전학회 Journal of genetic medicine Journal of genetic medicine 제12권 제2호

발행연도: 2015.1

수록면: 79 - 84 (6page)

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

#Prenatal diagnosis #High-throughput nucleotide sequencing #Computational biology #Cell-free DNA #Trisomy #Aneuploidy

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