cell type: trophectoderm cells karyotype of patient donor: 45,XY,t(13;14)(q10;q10) karyotype classification: reciprocal translocation analysis result: 46,XX result classification: normal female
Treatment protocol
Blastocyst cultivation and biopsy reference to clinical standard procedure. The normal/balance embryos detected by SNP-array would have been transferred to patients as clinical stantard ptocedure.
Extracted molecule
genomic DNA
Extraction protocol
Whole genome amplification of the biopsied trophectoderm cells was performed using a WGA4 GenomePlex Single Cell Whole Genome Amplification kit (Sigma-Aldrich, MO, USA) according to the manufacturer's instructions.
Label
Biotin
Label protocol
DNA was restriction digested, PCR amplified, fragmented, and labeled according to the manufacturer's instructions.
Hybridization protocol
DNA was hybridized to each array according to the manufacturer's instructions. The arrays were then washed using Affymetrix Fluidics Stations.
Scan protocol
The arrays were scanned using the GeneChip Scanner 7G.
Description
Hybridized to 250K_Nsp Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
Data processing
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using the DNAcopy package for R Bioconductor on raw data.
