Prioritization of neurodevelopmental disease genes by discovery of new mutations

Abstract

Advances in genome sequencing technologies have begun to revolutionize neurogenetics, allowing the full spectrum of genetic variation to be better understood in relation to disease. Exome sequencing of hundreds to thousands of samples from patients with autism spectrum disorder, intellectual disability, epilepsy and schizophrenia provides strong evidence of the importance of de novo and gene-disruptive events. There are now several hundred new candidate genes and targeted resequencing technologies that allow screening of dozens of genes in tens of thousands of individuals with high specificity and sensitivity. The decision of which genes to pursue depends on many factors, including recurrence, previous evidence of overlap with pathogenic copy number variants, the position of the mutation in the protein, the mutational burden among healthy individuals and membership of the candidate gene in disease-implicated protein networks. We discuss these emerging criteria for gene prioritization and the potential impact on the field of neuroscience.

Figure 1. Genes with recurrent de novo mutations in four neurodevelopmental disorders

(A) We estimate the number of fully penetrant disease genes based on a de novo model using the “Unseen Species Problem”. We consider all recurrent missense or loss-of-function de novo mutations pathogenic, as well as a defined fraction of mutations in genes observed just once (because all de novo mutations are unlikely to be pathogenic). The ratio between genes mutated recurrently and the rate of “singleton” mutations suggests an estimate for the “true” number of pathogenic genes. Including more singleton mutations increases the fraction of each disorder explained by single de novo SNVs at the “cost” of including more pathogenic genes. Initial exome sequencing studies of epilepsy and ID focused on specific pediatric subtypes or the most severe cases; thus, the number of generalized epilepsy or ID genes is likely to be much higher. (B) Expected hit rate (or sensitivity) of true positive genes discovered using trio sequencing studies (under a family-wise error rate of 5%, i.e. each gene passes exome-wide significance of 2.6e–6). We estimate the power of trio sequencing to detect statistically significant associations for disease genes, under the assumption that 10% or 20% of singleton mutations could be fully penetrant genes (vertical black bar in (A)). We assume the distribution of these genes is uniform within each disorder and that they do not differ significantly from all genes in terms of length and mutability, although these are taken into account when determining significance.

Figure 2. CNV and exome intersections define candidate genes

Deletion (red) and duplication (blue) burden for DD/ID cases and controls for two genes (A) DYRK1A and (B) MBD5 as compared to sporadic LoF mutations based on exome sequencing of 209 autism simplex trios. DYRK1A is a strong candidate gene for cognitive deficits associated with Down syndrome; LoF mutations are associated with minibrain phenotype in Drosophila, autism-like behavior in mouse, and deletion syndrome in humans^,. MBD5 has been implicated as the causal gene for the 2q23.1 deletion syndrome associated with epilepsy, autism, and ID^,.

Figure 3. Phenotypic similarity of two patients with identical PACS1 de novo mutations and two patients with similar ADNP mutations

(A and B) These two unrelated patients show identical de novo point mutations (c.607C>T; p.(Arg203Trp)) mutation in PACS1 (RefSeq NM_018026.2). The striking similarity in clinical phenotype include low anterior hairline, highly arched eyebrows, synophrys, hypertelorism with downslanted palpebral fissures, long eyelashes, a bulbous nasal tip, a flat philtrum with a thin upper lip, downturned corners of the mouth, and low-set ears. (C and D) These two unrelated patients both show LoF mutations in ADNP (c.2496_2499delTAAA; p.(Asp832Lysfs*80) and c.2157C>G; p.(Tyr719*)) resulting in a new SWI-SNF related autism syndrome. Patients present with clinical similarities, including a prominent forehead, a thin upper lip and a broad nasal bridge.

Figure 4. Coincidental de novo mutations in cancer and neurodevelopmental disorders

Examples: SETBP1 (Figure 2A), ARID1B (Figure 2B) and PTEN (Figure 2C). (A) Mutation spectrum of SETBP1. sAML & CMML = secondary acute myeloid leukemia & chronic myelomonocytic leukemia [1× p.Asp868Tyr, 28× p.Asp868Asn, 1× p.Ser869Asn, 15× p.Gly870Ser, 5× p.Ile871Thr]; aCML = atypical chronic myeloid leukemia [7× p.Asp868Asn, 1× p.Ser869Gly, 5× p.Gly870Ser, 2× p.Ile871Thr]; SGS = Schinzel-Giedion syndrome [Hoischen et al. unpublished: 1× p.Asp868Ala, 7× p.Asp868Asn, 1× p.Ser869Arg, 1× p.Ser869Asn, 4× p.GGly870Ser, 2× p.Gly870Asn, 10× p.Ile871Thr]; ID+ = intellectual disability with other features^, [p.Leu592* & p. 906fs]. (B) Mutation spectrum of ARID1B. Somatic mutations retrieve from COSMIC database. Only ‘somatic validated’ and ‘previously described’ somatic mutations with PubMed entry were considered. CSS = Coffin-Siris syndrome^, [p.Gln408Profs*127, p.Ser413Valfs*122, p.Asn420Lysfs*115, p.Pro449Argfs*53, p.Tyr867Thrfs*47, p.Met935Asnfs*7, p.Ser959Argfs*9, p.Ala1000Argfs*5, p.Arg1075*, p.Gly1283Trpfs*38, p.Arg1337*, p.Tyr1366*, p.Pro1489Leufs*10, p.Tyr1540*, p.Gln1541Argfs*35, p.Trp1637Cysfs*6, p.Lys1777*, p.Phe1798Leufs*52, p.Asp1879Thrfs*95, p.Arg1990*, p.Arg1990*, p.Arg1990*, p.Trp2013*, p.Pro2078Leufs*21]; ID = intellectual disability [p.Arg372Profs*163, p.Arg1102*, p.Lys1108Argfs*9, p.Gln1307*, p.Tyr1346*, p.Arg1338Argfs*76, p.Ser2155Leufs*33]; ASD = autism spectrum disorder [p.Phe1798Leufs*52]; splice site mutations not considered. (C) Mutation spectrum of PTEN. Somatic mutations retrieved from COSMIC database. Only ‘somatic validated’ and ‘previously described’ somatic mutations with at least five independent entries are displayed. CS = Cowden syndrome; ASD & MS = autism spectrum disorder and macrocephaly syndrome; BRBS = Bannayan-Riley-Ruvalcana syndrome [based on OMIM entries]; splice site mutations not considered.