title: Concurrent whole-genome haplotyping and copy-number profiling of single cells.
abstract: 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.
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Masoud
authors.initials: M
authors.lastname: Zamani Esteki
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Eftychia
authors.initials: E
authors.lastname: Dimitriadou
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Ligia
authors.initials: L
authors.lastname: Mateiu
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Cindy
authors.initials: C
authors.lastname: Melotte
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Niels
authors.initials: N
authors.lastname: Van der Aa
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Parveen
authors.initials: P
authors.lastname: Kumar
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Rakhi
authors.initials: R
authors.lastname: Das
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Koen
authors.initials: K
authors.lastname: Theunis
authors.affiliation: 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.
authors.forename: Jiqiu
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Eric
authors.initials: E
authors.lastname: Legius
authors.affiliation: Department of Electrical Engineering, ESAT-STADIUS, KU Leuven, 3000 Leuven, Belgium.
authors.forename: Yves
authors.initials: Y
authors.lastname: Moreau
authors.affiliation: Leuven University Fertility Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium.
authors.forename: Sophie
authors.initials: S
authors.lastname: Debrock
authors.affiliation: Leuven University Fertility Center, University Hospital Gasthuisberg, Herestraat 49, 3000 Leuven, Belgium.
authors.forename: Thomas
authors.initials: T
authors.lastname: D'Hooghe
authors.affiliation: Centre for Medical Genetics, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium.
authors.forename: Pieter
authors.initials: P
authors.lastname: Verdyck
authors.affiliation: Centre for Medical Genetics, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium; Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB) Laarbeeklaan 101, 1090 Brussels, Belgium.
authors.forename: Martine
authors.initials: M
authors.lastname: De Rycke
authors.affiliation: Research group Reproduction and Genetics (REGE), Vrije Universiteit Brussel (VUB) Laarbeeklaan 101, 1090 Brussels, Belgium.
authors.forename: Karen
authors.initials: K
authors.lastname: Sermon
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium. Electronic address: joris.vermeesch@med.kuleuven.be.
authors.forename: Joris R
authors.initials: JR
authors.lastname: Vermeesch
authors.affiliation: Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium; Single-cell Genomics Centre, Welcome Trust Sanger Institute, Hinxton CB10 1SA, UK. Electronic address: thierry.voet@med.kuleuven.be.
authors.forename: Thierry
authors.initials: T
authors.lastname: Voet
mesh_terms: D000465:Algorithms; D002869:Chromosome Aberrations; D017931:DNA Primers / Q000235:genetics; D018628:Gene Dosage / Q000235:genetics*; D015894:Genome, Human / Q000235:genetics*; D005838:Genotype; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008957:Models, Genetic; D021141:Nucleic Acid Amplification Techniques; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D019836:Preimplantation Diagnosis / Q000379:methods*; D059010:Single-Cell Analysis / Q000379:methods*; D018709:Statistics, Nonparametric
chemical_list: D017931:DNA Primers