Human cleavage stage embryos are chromosomally unstable

Embryonic chromosome aberrations cause birth defects and reduce human fertility. However, neither their nature nor incidence are known. Here, we develop a method to assess genome-wide copy number variation and loss of heterozygosity in single cells and apply it to screen blastomeres from in vitro fertilized preimplantation embryos. Complex patterns of chromosome-arm imbalances or segmental deletions, duplications or amplifications that were reciprocal in sister blastomeres were detected in a large proportion of the embryos. In addition, aneuploidies and uniparental isodisomies were frequently observed. Since these embryos were derived from young fertile couples, the data indicate that chromosomal instability is common to human embryogenesis. Keywords: comparative genomic hybridisation In total 180 amplified single cell DNA samples were analyzed by BAC array CGH and 101 of these amplified single cell DNA samples were further analyzed on 250K Nsp I SNP arrays. 19 amplified single cell DNA samples derived from the Epstein Barr virus transformed lymphoblastoid cell lines (EBV-line) were analyzed by BAC array CGH (platform GEO accession number GPL6597). 3 single cell amplified DNA samples from EBV-line [47,XY,+21], 1 single cell amplified DNA sample from EBV-line [46,XY,der(20),t(18;20)(p11.21;p13)], 1 single cell amplified DNA sample from EBV-line [46,X,der(X),t(X;14)(q21.1;q12.2)], 4 single cell amplified DNA samples from EBV-line [46,XX,del(18)(p11.21->pter)], 3 single cell amplified DNA samples from EBV-line [46,XX,del(4)(p16.1->pter)] and 7 single cell amplified DNA samples from EBV-line [47,XXX]. For these single cell BAC array CGH analyses: non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY) was used as a reference sample. 1 single cell amplified DNA sample from EBV-line [47,XY,+21] was re-analyzed by BAC array CGH (platform GPL6597) using non-amplified genomic DNA from a male (46,XY). 7 of these 19 amplified single cell DNA samples derived from the Epstein Barr virus transformed lymphoblastoid cell lines (EBV-line) were further analyzed on 250K Nsp I SNP arrays (GEO accession number GPL3718). One single cell amplified DNA sample from EBV-line [47,XY,+21], one single cell amplified DNA sample from EBV-line [46,XY,der(20),t(18;20)(p11.21;p13)], one single cell amplified DNA sample from EBV-line [46,X,der(X),t(X;14)(q21.1;q12.2)] and four single cell amplified DNA samples from EBV-line [46,XX,del(18)(p11.21->pter)]. 146 amplified single blastomere DNA samples derived from 3-day-old and 4-day-old human embryos were analyzed by BAC array CGH (144 single blastomeres on platform GPL6597 and 2 on a custom-made platform 4K3). Non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY) was used as a reference sample. 86 of these 146 amplified single blastomere DNA samples were further analyzed on 250K Nsp I SNP arrays (platform GPL3718). 15 human fertilized oocytes in the pronuclear stage were analyzed by BAC array CGH (platform GPL6597). Non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY) was used as a reference sample. 8 of these 15 were further analyzed on 250K Nsp I SNP arrays (platform GPL3718). Apart from these 180 single cell amplified DNA samples, also 4 non-amplified genomic DNA samples, respectively from EBV-lines [47,XY,+21], [46,XY,der(20),t(18;20)(p11.21;p13)], [46,X,der(X),t(X;14)(q21.1;q12.2)] and [46,XX,del(18)(p11.21->pter)], were analyzed by BAC array CGH and 250K Nsp I SNP arrays. Non-amplified genomic DNA extracted from the blood of a Klinefelter patient (XXY) was used as a reference sample for BAC array CGH.