ABSTRACT
Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement.
Subject(s)
Autism Spectrum Disorder/genetics , Gene Deletion , Gene Duplication , Alleles , Amino Acid Sequence , Base Sequence , Case-Control Studies , Child , DNA Copy Number Variations , Female , Gene Frequency , Gene Rearrangement , Genetic Loci , Genome, Human , Genotyping Techniques , Humans , INDEL Mutation , Male , Microarray Analysis , Molecular Sequence Data , Pedigree , Reproducibility of Results , Sensitivity and SpecificityABSTRACT
A protocol was devised to select for DNA molecules that efficiently form circles from a library of 126 base pair DNAs containing 90 randomized base pairs. After six rounds of selection, individual molecules from the library showed 20- to 100-fold greater j-factors compared with the starting library, validating the selection protocol. High-throughput sequencing revealed a sinusoidal pattern of enrichment and de-enrichment of A/T dinucleotides in the random region with a 10.4 base pair period associated with the helicity of DNA. A similar, but more moderate pattern of C/G dinucleotides was offset by precisely half a helical turn. While C/G dinucleotide enrichments were evenly distributed, A/T dinucleotide enrichments displayed a preference to cluster in individual DNA molecules. The most highly enriched 10 base pair sequences in the random region contained adjacent blocks of A/T and C/G trinucleotides present in some, but not all, rapidly cyclizing molecules. The phased dinucleotide enrichments closely match those present in accurately mapped yeast nucleosomes, confirming the importance of DNA bending in nucleosome formation. However, at certain sites the nucleosomal DNAs show dinucleotide enrichments that differ substantially from the cyclization data. These discrepancies can often be correlated with sequence specific contacts that form between histones and DNA.
