Genomic changes detected by array CGH in human embryos with developmental defects

Abstract

Developmental abnormalities of human embryos can be visualized in utero using embryoscopy. Our previous embryoscopic and genetic evaluations detected developmental abnormalities in the majority of both euploid (74%) and aneuploid or polyploid (90%) miscarriages. Since we found the pattern of morphological changes to be similar in euploid and non-euploid embryos, we proposed that lethal submicroscopic changes, not detected by standard chromosome testing, may be responsible for miscarriage of euploid embryos. Whole genome oligo and bacterial artificial chromosome array comparative genome hybridization (CGH) was used to screen for submicroscopic chromosomal changes (DNA copy number variants or CNVs) in 17 euploid embryonic miscarriages, with a range of developmental abnormalities documented by embryoscopy. The CNV breakpoints were refined using a custom array (Agilent) with high resolution coverage of the CNVs. Six unique CNVs, previously not reported, were identified in 5 of the 17 embryos (29% of all cases or 50% of cases studied with higher resolution arrays). All six unique CNVs were <250 kb in size. On the basis of parental array CGH analysis, a de novo origin of a CNV was determined for one embryo (at 13q32.1) and suspected for another (at 10p15.3). Three CNVs, at Xq28, 1q25.3 and 7p14.3, were inherited and a CNV at 17p13.1 was of unknown origin. The genes contained within these unique CNVs will be discussed, with specific reference to rearrangements of syntaxin and tryptophan-aspartic acid (WD) repeat genes. Our report describes for the first time, de novo and inherited unique CNVs in euploid human embryos with specific developmental defects.

Improved assay performance of single nucleotide polymorphism array over conventional karyotyping in analyzing products of conception

“…6e10, 18 Recently, two studies showed that potentially pathogenic CNVs were present in 6e15% of POC samples by analyzing the content and function of certain genes within CNVs. 5,15 Another study using SNP array to investigate a large-scale cohort of POC samples revealed potentially pathogenic CNVs in 1.6% of cases. 12 However, at present, because data about clinical significance of most CNVs were determined through genotypeephenotype correlation of individuals with clinical features, it was difficult to define whether or not CNVs were pathogenic in most POC specimens without any recognizable phenotypes.…”

“…Unique CNVs were defined as those that showed no or incomplete overlap with CNVs in the DGV, or that are presented in the DGV, but with < 100 cases studied and/or a frequency of < 1%. 5,15 The building of the human genome assembly was based on GRCH37/hg19. Unique CNVs were assessed by searching for similar cases in DECIPHER and PubMed, and also by searching for gene information in Entrez Gene and OMIM.…”

Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics

“…For the validation of two maternally inherited abnormalities (duplications of 1p34.1 and 20q13.12), for which FISH testing was not possible, custom arrays were designed using eArray (Agilent technologies) and the ADM-2 algorithm as described previously (Rajcan-Separovic et al 2010). …”

Meiotic Nondisjunction: Insights into the Origin and Significance of Aneuploidy in Human Spermatozoa

“…Despite the clear association of abnormal karyotypes and embryogenesis, it is noteworthy that a signifi cant proportion of early failed pregnancies with developmental defects are karyotypically normal. Studies suggest that up to ~20 % of morphologically abnormal embryos possess a normal karyotype (Philipp et al 2003 ;Rajcan-Separovic et al 2010 ). It seems plausible that many of these seemingly euploid developmentally abnormal embryos may be the result of submicroscopic perturbations that are not detectable by routine karyotyping.…”

“…However, the consequence of these submicroscopic aberrations on fertilization, embryogenesis, and fetal development remains poorly understood. To date, a handful of studies have reported that between 4 and 13 % of miscarriages may possess submicroscopic chromosome aberrations that would not be detectable by routine karyotyping (Rajcan-Separovic et al 2010 ;Shaffer et al 2008 ;Shimokawa et al 2006 ). It is important to note that the majority of studies did not determine whether these submicroscopic alterations were de novo, benign, or potentially pathogenic.…”