Beneath the surface – the role of small inherited CNVs in autism

Grey zone. Structural genomic variants or copy number variations (CNV) can be reliably assessed using array comparative genomic hybridization (array CGH) or Single Nucleotide Polymorphism (SNP) arrays.  However, for deletions or duplications smaller than 50-100 kB, these technologies have a poor detection rate with many false positive and false negative findings unless platforms are used that target specific candidate regions. Exome analysis, on the other hand, is capable of assessing genetic variation reliably on the single base-pair level. Between both technologies, there is a grey zone of structural genomic variants that are difficult to detect; CNVs smaller than 50 kB are often difficult to assess, and the extent and pathogenic role of these small CNVs is unclear. Now, a recent paper in the American Journal of Human Genetics manages to detect small CNVs through exome data. Their analysis in patients with autism, parents, and unaffected siblings suggests a contribution of small inherited CNVs to the overall autism risk. Continue reading

Exploring samtools – Green Eggs and Ham (*.bam)

That Sam I Am.  The entire field of high-throughput genomics appears to be inspired by the American children’s book author Dr. Seuss. Given that we are currently reading through the original books almost on a daily basis due to the presence of a toddler in our home, mentioning *.sam files, *.bam files or sam2bam routines always makes me smile. However, this is not a post about children’s books; it’s about a likely 2013 trend in genomic research, the redefinition of the boundary between genome center and end user and the laptopification of life sciences. Continue reading