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SNP genotyping of cryptic complexity in structural chromosome abnormalities previously detected by cytogenetic analysis

ABSTRACT: Purpose: The purpose of this study was to evaluate SNP genotyping methodology as a means to detect chromosomal abnormalities previously diagnosed by G-band karyotype or fluorescence in situ hybridization (FISH) analysis and to determine the frequency of sub-microscopic (cryptic) chromosomal alterations in these subjects. Methods: We used the Illumina HumanHap Beadchip platform to genotype 40 individuals having previously detected chromosomal anomalies (by G-banded and/or FISH analysis). The resulting data were analyzed for signal intensity (log R ratio) and allelic composition (B allele frequency). Results: SNP array analysis detected 100% of previously identified cytogenetic abnormalities. Changes or clarifications of the ISCN karyotype designation assigned by conventional cytogenetic and/or FISH analysis were made in 82 % of the cases (32 of 39). Nine of the 39 cases (23%) involved a reassignment of an abnormal band while an additional 9 of the 39 (23%) resulted in a clarification of a sub-band assignment. In 8 more of the 39 cases (21%) the previously reported alterations were confirmed, however the SNP analysis also identified related cryptic alterations. SNP analysis not only confirmed FISH-detected abnormalities but also more precisely mapped the breakpoints of 6/6 patients. Investigations into the origin of de novo abnormalities in 15 trio families established that 12 /15 occurred on the paternal chromosome. Conclusions: SNP genotyping array analysis, confirmed all previously detected structural chromosomal abnormalities and provided additional, clinically-relevant genomic information in 82% of these alterations.

ORGANISM(S): Homo sapiens

PROVIDER: GSE20623 | GEO | 2011/02/22

SECONDARY ACCESSION(S): PRJNA124811

REPOSITORIES: GEO

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Project description:Preimplantation genetic diagnosis (PGD) of aneuploidy by fluorescence in situ hybridisation (FISH) has not delivered the expected clinical benefit. Many previous re-analysis studies of embryos deemed aneuploid by FISH on day 3 have found a high degree of chromosomal normalcy at the blastocyst stage. While most have interpreted this as âself correction,â there remains a lack of evidence for such a phenomenon. A more comprehensive technique for 24 chromosome aneuploidy screening was utilised here to re-evaluate blastocysts previously diagnosed as abnormal by FISH and investigate possible self correction mechanisms, including extrusion or duplication of aneuploid chromosomes resulting in uniparental isodisomy (UPID), and preferential segregation of aneuploidy to the trophectoderm (TE). Embryos that developed to a morphologically normal blastocyst after an aneuploidy diagnosis by cleavage stage FISH were biopsed into 4 sections, 3 TE and 1 inner cell mass (ICM), and randomised for evaluation by single nucleotide polymorphism (SNP) microarray based 24 chromosome aneuploidy screening (MA-PGD). Fifty-eight percent of blastocysts were euploid for all 24 chromosomes despite an aneuploid FISH result on day 3. Only 18% were consistent with the original FISH diagnosis, while the remaining 24% identified abnormalities that were different from the original FISH diagnosis. Abnormalities did not preferentially segregate to the TE and aneuploid chromosome extrusion or duplication resulting in UPID did not occur. Cleavage stage FISH is poorly predictive of aneuploidy in an embryo that develops into a morphologically normal blastocyst. Clinicians should consider re-evaluating embryos diagnosed as aneuploid by FISH that form morphologically normal blastocysts using a validated comprehensive 24 chromosome aneuploidy screening method. Affymetrix SNP arrays were processed according to the manufacturer's directions on DNA extracted from 50 cryopreserved blastocysts that were biopsied into 3 sections of trophectoderm and 1 inner cell mass section. Affymetrix SNP array analysis was successfully completed on 145 trophectoderm samples and 47 ICM samples from embryos, 8 lymphocyte samples from cell lines and 6 mixed male and female samples.

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SNP genotyping of cryptic complexity in structural chromosome abnormalities previously detected by cytogenetic analysis

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