title: Improved assay performance of single nucleotide polymorphism array over conventional karyotyping in analyzing products of conception.
abstract: BACKGROUND
  Conventional karyotyping has been a routine method to identify chromosome abnormalities in products of conception. However, this process is being transformed by single nucleotide polymorphism (SNP) array, which has advantages over karyotyping, including higher resolution and dispensing with cell culture. Therefore, the purpose of this study was to evaluate the advantage of high-resolution SNP array in identifying genetic aberrations in products of conception.
  
  
  METHODS
  We consecutively collected 155 products of conception specimens, including 139 from first-trimester miscarriage and 16 from second-trimester miscarriage. SNP array was performed on these samples in parallel with G-banded karyotyping.
  
  
  RESULTS
  The test success rate was 98.1% (152/155) using SNP array, which was higher than that using karyotyping (133/155, 85.8%). It yielded a 63.8% (97/152) abnormality rate, and the frequency of various chromosome abnormalities was in agreement with other previous studies. The results between array and karyotyping demonstrated a 94.0% (125/133) concordance. SNP array obtained additional aberrations in 3.8% (5/133) of those cases unidentified by karyotyping, which included three cases with whole-genome uniparental disomy, one with pathogenic copy number variation, and one with del(4)(q35.1q35.2) and dup(12)(q24.31q24.33). However, chromosome translocations presented in two cases and tetraploidy presented in one case were detected by karyotyping instead of array. Additionally, two out of three cases with mosaic trisomy were revealed by array but recognized as pure trisomy by karyotyping.
  
  
  CONCLUSIONS
  This study demonstrated that SNP array had certain advantages over G-banded karyotyping, including a higher success rate, additional detection of copy number variations and uniparental disomy, and improved sensitivity to mosaicism. Therefore, it would be an alternative method to karyotyping in clinical genetic practice.
authors.affiliation: Fetal Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
authors.forename: Shao-Bin
authors.initials: SB
authors.lastname: Lin
authors.affiliation: Fetal Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
authors.forename: Ying-Jun
authors.initials: YJ
authors.lastname: Xie
authors.affiliation: Department of Medical Genetics, Zhongshan Medical College, Sun Yat-Sen University, Guangzhou, China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Chen
authors.affiliation: Fetal Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Fetal Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
authors.forename: Jian-Zhu
authors.initials: JZ
authors.lastname: Wu
authors.affiliation: Fetal Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
authors.forename: Zhi-Qiang
authors.initials: ZQ
authors.lastname: Zhang
authors.affiliation: Department of Fetal Medicine Center, First Affiliated Hospital of Jinan University, Guangzhou, China.
authors.forename: Shan-Shan
authors.initials: SS
authors.lastname: Shi
authors.affiliation: Fetal Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
authors.forename: Bao-Jiang
authors.initials: BJ
authors.lastname: Chen
authors.affiliation: Fetal Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China. Electronic address: fang_qun@163.com.
authors.forename: Qun
authors.initials: Q
authors.lastname: Fang
mesh_terms: D000022:Abortion, Spontaneous; D056915:DNA Copy Number Variations; D005260:Female; D006801:Humans; D007621:Karyotyping; D020641:Polymorphism, Single Nucleotide; D011247:Pregnancy; D024182:Uniparental Disomy / Q000235:genetics
keywords: copy number variation; karyotyping; products of conception; single nucleotide polymorphism array; uniparental disomy