title: Identification of PKD2 mutations in human preimplantation embryos in vitro using a combination of targeted next-generation sequencing and targeted haplotyping.
abstract: Here, we evaluate the applicability of a new method that combines targeted next-generation sequencing (NGS) with targeted haplotyping in identifying PKD2 gene mutations in human preimplantation embryos in vitro. To achieve this goal, a proband family with a heterozygous deletion of c.595_595 + 14delGGTAAGAGCGCGCGA in exon 1 of the PKD2 gene was studied. A total of 10 samples were analyzed, including 7 embryos. An array-based gene chip was designed to capture all of the exons of 21 disease-related genes, including PKD2. We performed Sanger sequencing combined with targeted haplotyping to evaluate the feasibility of this new method. A total of 7.09 G of data were obtained from 10 samples by NGS. In addition, 24,142 informative single-nucleotide polymorphisms (SNPs) were identified. Haplotyping analysis of several informative SNPs of PKD2 that we selected revealed that embryos 3, 5, and 6 did not inherit the mutation haplotypes of the PKD2 gene, a finding that was 100% accurate and was consistent with Sanger sequencing. Our results demonstrate that targeted NGS combined with targeted haplotyping can be used to identify PKD2 gene mutations in human preimplantation embryos in vitro with high sensitivity, fidelity, throughput and speed.
authors.affiliation: Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.|International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.
authors.forename: Song-Chang
authors.initials: SC
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, P.R. China.|Hangzhou Genomics Institute, 478 Wensan Road, Hangzhou 310012, P.R. China.
authors.forename: Xiao-Li
authors.initials: XL
authors.lastname: Xu
authors.affiliation: Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.|International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.
authors.forename: Jun-Yu
authors.initials: JY
authors.lastname: Zhang
authors.affiliation: Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.|International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.
authors.forename: Guo-Lian
authors.initials: GL
authors.lastname: Ding
authors.affiliation: Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.|International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.
authors.forename: Li
authors.initials: L
authors.lastname: Jin
authors.affiliation: Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1 Xueshi Road, Hangzhou 310006, P.R. China.
authors.forename: Bei
authors.initials: B
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, P.R. China.|Hangzhou Genomics Institute, 478 Wensan Road, Hangzhou 310012, P.R. China.
authors.forename: Dong-Mei
authors.initials: DM
authors.lastname: Sun
authors.affiliation: Division of Nephrology, Kidney Institute of CPLA, Changzheng Hospital, Second Military Medical University, Shanghai,200003, P.R.China.
authors.forename: Chang-Lin
authors.initials: CL
authors.lastname: Mei
authors.affiliation: BGI-Shenzhen, Shenzhen, 518083, P.R. China.|Hangzhou Genomics Institute, 478 Wensan Road, Hangzhou 310012, P.R. China.
authors.forename: Xiao-Nan
authors.initials: XN
authors.lastname: Yang
authors.affiliation: Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.|International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.|Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1 Xueshi Road, Hangzhou 310006, P.R. China.
authors.forename: He-Feng
authors.initials: HF
authors.lastname: Huang
authors.affiliation: Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.|International Peace Maternity and Child Health Hospital, Shanghai Jiao Tong University School of Medicine, 910 Hengshan Road, Shanghai 200030, P.R. China.|Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, 1 Xueshi Road, Hangzhou 310006, P.R. China.
authors.forename: Chen-Ming
authors.initials: CM
authors.lastname: Xu
mesh_terms: D001755:Blastocyst; D005820:Genetic Testing / Q000379:methods*; D060005:Genotyping Techniques; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009154:Mutation; D020641:Polymorphism, Single Nucleotide; D050396:TRPP Cation Channels / Q000235:genetics*
chemical_list: D050396:TRPP Cation Channels