[The Role of Molecular Karyotyping in the Genetic Etiology of Autism]. / Otizmli Olgularda Moleküler Karyotipleme Yöntemi ile Genetik Etiyolojinin Aydinlatilmasi.

OBJECTIVE: The aim of this study was to investigate the deletions and duplications with a molecular karyotyping technique and to elucidate the etiology of autism. METHOD: A total of 31 patients (20 boys and 11 girls) between 4 to 18 years old with normal chromosomal analysis and no Fragile X mutation were diagnosed in the Ege University Child and Adolescent Psychiatry Clinic with autism (according to DSM-IV-TR criteria) and were enrolled in the study. Symptom severity of the patients was evaluated with a Childhood Autism Rating Scale. Blood samples (EDTA collected) were obtained in order to extract DNA. Whole genome molecular karyotyping analyses were performed with Illumina IScan system by chips, which can scan 330.000 Single Nucleotid Polymorphisms (SNPs) to detect structural anomalies with a 10-kb resolution. RESULTS: All patients had copy number variations (CNV) that sized between 20-kb and 3-Mb. All detected CNVs were analyzed by the help of KaryoStudio software and DGV database. The ones which might be causal and pathogenic were selected. Pathogenic CNVs (7 deletions, 2 duplications) were detected in 9 patients (29%). CONCLUSION: As a result, this is the first study whereby a molecular karyotyping technique was successfully used in autism patients in Turkey. Moreover, an intermediate resolution of 330.000 SNP chips were proven to be efficient for molecular karyotyping analysis.

The genomic architecture of NLRP7 is Alu rich and predisposes to disease-associated large deletions.

NLRP7 is a major gene responsible for recurrent hydatidiform moles. Here, we report 11 novel NLRP7 protein truncating variants, of which five deletions of more than 1-kb. We analyzed the transcriptional consequences of four variants. We demonstrate that one large homozygous deletion removes NLRP7 transcription start site and results in the complete absence of its transcripts in a patient in good health besides her reproductive problem. This observation strengthens existing data on the requirement of NLRP7 only for female reproduction. We show that two other variants affecting the splice acceptor of exon 6 lead to its in-frame skipping while another variant affecting the splice donor site of exon 9 leads to an in-frame insertion of 54 amino acids. Our characterization of the deletion breakpoints demonstrated that most of the breakpoints occurred within Alu repeats and the deletions were most likely mediated by microhomology events. Our data define a hotspot of Alu instability and deletions in intron 5 with six different breakpoints and rearrangements. Analysis of NLRP7 genomic sequences for repetitive elements demonstrated that Alu repeats represent 48% of its intronic sequences and these repeats seem to have been inserted into the common NLRP2/7 primate ancestor before its duplication into two genes.