Fig. 1

Exome sequencing (ES) coverage, growth parameters, and genetic evaluations of 62 patients with microcephaly. (a) Average coverages of targeted regions (left) and 20-fold average coverages (right) of ES data for all or mitochondrial genes. On average, ES yielded an average coverage of 222-fold (range: 92–419 fold) and covered about 96% of the targeted bases with ≥20 sequence reads and achieved an average off-target mitochondrial read depth of 43.6-fold (range: 3.9–163.9 fold) with a 20× average coverage of 64.4% (range: 1.9–99.4%). Distribution of average sequencing depth and 20× coverage of the targeted region was indistinguishable among patients with P/LP variants (red dots), high-level candidate variants (yellow dots), or others (VUS, [suspected] candidate, no candidate) (black dots). Mitochondrial genes exhibited significantly lower average coverages and 20-fold average coverages (Welch t test) with a higher variability in the 20-fold average coverages. P/LP pathogenic or likely pathogenic, VUS variant of uncertain significance. (b) SD distributions of growth parameters measured at birth and at the time of last investigation (variable ages). Connected lines represent individual cases. SDs below –2 (dotted line) were considered microcephaly. Dark green dots: primary microcephaly (PM, 36 [58.1%] patients); light green dots: secondary microcephaly (SM, 17 [27.4%] patients); gray dots: unknown onset (9 [14.5%] patients). Note that the distributions for OFC consistently show SD reductions at the last follow-up, suggesting progressiveness of microcephaly with a statistically significantly higher OFC reduction in PM compared with that in SM patients (p < 0.001, Wilcoxon rank-sum test). However, 61.3% of PM and 70.6% of SM patients did not show a decline in length or height similar to that in OFC, indicating a disproportionate microcephaly in the majority of our patients. OFC occipitofrontal head circumference, SD standard deviation (given as standard deviation score). (c) Distribution of (potentially) relevant genetic findings in the total cohort. Inner circle shows percentages of diagnostic and uncertain findings in established disease genes, as well as likely deleterious findings in candidate genes. Middle and outer circles show the distribution of CNVs and SVs, and the inheritance pattern in the respective categories of the inner circle, respectively. P/LP variants were identified in almost 50% of the patients. Most of these variants are SVs with comparable amounts of de novo (DN) occurrence and recessive inheritance. CNV copy-number variant, SV sequence variant. (d) Genetic findings in PM and SM. Diagnostic yields between PM (n = 36) and SM (n = 17) were comparable (left panel). Predominantly recessive inheritance was identified in diagnosed PM patients (~69%) and dominant de novo variants in all diagnosed SM patients (middle panel). Likely gene-disrupting (LGD) variants represented the most common disease alleles (~80%) among the diagnosed PM patients, while LGD and missense variants were equally observed among the diagnosed SM patients (right panel). CH compound heterozygous. Numbers on graphs were given as percentage.