Balkan Journal of Medical Genetics

COPY NUMBER VARIATIONS IN FEMALE INFERTILITY IN CHINA
Huang W*, Wang J, Pang M, Zhao Q, Kong L, Mao Y, Li W, Liang B
*Corresponding Author: Professor Weidong Huang, Reproductive Medicine Center, XinJiang JiaYin Hospital, 48 Nanhu North Road, Shuimogou District, Urumchi, Xinjiang Province, 830000, People’s Republic of China. Tel: +86-2363631402. Fax: +86-9914887187. E-mail: hwd@jynk.com
page: 5

MATERIAL AND METHODS

Sample Collection and DNA Extraction. The study was approved by the Clinical Research Ethics Committee of the Xinjiang JiaYin Clinical Laboratory Center, Urumchi, Xinjiang Province, People’s Republic of China (PRC). All patients signed written informed consent before participation. A total of 324 blood samples of female infertility patients (305 unexplained infertility, and 19 females with spontaneous abortions, including spontaneous abortion and recurrent spontaneous abortion) were collected from the Xinjiang JiaYin Clinical Laboratory Center in 2017. Two milliliters of peripheral blood samples were collected in vacutainers containing EDTA as anticoagulant, and DNA was extracted using a TIANamp Genomic DNA Kit (Item no: DP304; Tiangen Biochemical Reagent Co., Beijing, PRC). DNA quality was evaluated by Qubit®2.0 (ThermoFisher Scientific, Waltham, MA, USA) and Qubit™ ds DNA HS Assay kit (Catalog no. Q32854; ThermoFisher Scientific). Library Construction and Sequencing. We enzymatically fragmented 300 ng genomic DNA with an average size of 150 bp, followed by library construction according to the Life Technology Ion Xpress Plus Fragment Library preparation guide (Life Technologies, Carlsbad, CA, USA). The constructed library was quantified using Qubit® 2.0 (ThermoFisher Scientific). The libraries were mixed in proportion, and pooled P1 chip to ensure an average sequencing depth of ~0.1 × for each sample. Data Analysis. All sequencing reads were aligned to the reference human genome National Center for Biotechnology Information (NCBI) Build37/hg19 by TMAP software (www.tmap.net). Meanwhile, duplicate sequences were removed by using Picard software (https://broad institute.github.io/picard/). Each chromosome was divided into 40 kb non overlapped bins, and the number of reads mapped to each bin was calculated. We normalized the GC percentages in each bin by LOWESS regression. Circular binary segmentation (CBS), a reliable algorithm that is widely used in the analysis of comparative genomic hybridization arrays, allowed us to precisely define changed points by partitioning chromosomes into regions of equal copy numbers. The CNVs obtained by analysis were compared to the Database of Genomic Variants (DGV), International Standards for Cytogenomic Arrays (ISCA), DECIPHER databases (DEC), and the normal polymorphism CNVs were filtered out.

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