Zamani Esteki Masoud, Dimitriadou Eftychia, Mateiu Ligia, Melotte Cindy, Van der Aa Niels, Kumar Parveen, Das Rakhi, Theunis Koen, Cheng Jiqiu, Legius Eric, Moreau Yves, Debrock Sophie, D'Hooghe Thomas, Verdyck Pieter, De Rycke Martine, Sermon Karen, Vermeesch Joris R, Voet Thierry
Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; Department of Electrical Engineering, ESAT-STADIUS, KU Leuven, 3000 Leuven, Belgium.
Am J Hum Genet. 2015 Jun 4;96(6):894-912. doi: 10.1016/j.ajhg.2015.04.011. Epub 2015 May 14.
Methods for haplotyping and DNA copy-number typing of single cells are paramount for studying genomic heterogeneity and enabling genetic diagnosis. Before analyzing the DNA of a single cell by microarray or next-generation sequencing, a whole-genome amplification (WGA) process is required, but it substantially distorts the frequency and composition of the cell's alleles. As a consequence, haplotyping methods suffer from error-prone discrete SNP genotypes (AA, AB, BB) and DNA copy-number profiling remains difficult because true DNA copy-number aberrations have to be discriminated from WGA artifacts. Here, we developed a single-cell genome analysis method that reconstructs genome-wide haplotype architectures as well as the copy-number and segregational origin of those haplotypes by employing phased parental genotypes and deciphering WGA-distorted SNP B-allele fractions via a process we coin haplarithmisis. We demonstrate that the method can be applied as a generic method for preimplantation genetic diagnosis on single cells biopsied from human embryos, enabling diagnosis of disease alleles genome wide as well as numerical and structural chromosomal anomalies. Moreover, meiotic segregation errors can be distinguished from mitotic ones.
单细胞的单倍型分型和DNA拷贝数分型方法对于研究基因组异质性和进行基因诊断至关重要。在通过微阵列或下一代测序分析单细胞的DNA之前，需要进行全基因组扩增（WGA）过程，但这会严重扭曲细胞等位基因的频率和组成。因此，单倍型分型方法存在易出错的离散SNP基因型（AA、AB、BB）问题，并且DNA拷贝数分析仍然困难，因为必须将真正的DNA拷贝数畸变与WGA假象区分开来。在这里，我们开发了一种单细胞基因组分析方法，该方法通过采用分阶段的亲本基因型并通过我们称为单倍型计数法的过程来解读WGA扭曲的SNP B等位基因分数，从而重建全基因组的单倍型结构以及这些单倍型的拷贝数和分离起源。我们证明该方法可作为一种通用方法应用于从人类胚胎活检的单细胞的植入前基因诊断，能够在全基因组范围内诊断疾病等位基因以及染色体数目和结构异常。此外，减数分裂分离错误可以与有丝分裂错误区分开来。
