Box Fig. 1

Technical improvements to the detection of de novo mutations (DNMs). a Trio-based sequencing allows the identification of de novo mutations in an individual. b Increased sequencing coverage benefits the detection of de novo mutations (in blue). Low coverage (upper) reduces the probability that a de novo mutation will be sequenced and called, compared with high sequencing coverage (lower). c Using random tags or unique molecular identifiers (UMIs) decreases the number of false positives (in red) by making consensus calls from all reads with the same UMI. Furthermore, UMIs can be used to remove PCR-derived duplicate reads to determine accurately the allelic ratio. d Long sequencing reads improve mappability, even across difficult genomic regions such as those containing repeats (gray boxes). Additionally, long reads can be used to phase mutations (shown in blue and in green) and generate haplotypes, to help identify the parent of origin of a mutation. IV inherited variant.