Methods for haplotyping and DNA copynumber 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.
Materials and methods
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.
Our approach proved accurate on 55 embryos from 12 couples carrying either autosomal dominant, recessive or X-linked Mendelian disorders, or simple or complex translocations. The method allowed diagnosing an embryo for multiple monogenic disorders at once, and, in contrast to current PGD for translocation cases, it enabled distinguishing embryos that inherited normal chromosomes from embryos that inherited a balanced configuration of the rearranged derivative chromosomes.
We demonstrate that the method can be applied as a generic method for preimplantation genetic diagnosis (PGD) 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. The method, therefore, facilitates genetic selection of embryos, and broadens the range of classic PGD.