Clan genomics: From OMIM phenotypic traits to genes and biology

Abstract

Clinical characterization of a patient phenotype has been the quintessential approach for elucidating a differential diagnosis and a hypothesis to explore a potential clinical diagnosis. This has resulted in a language of medicine and a semantic ontology, with both specialty- and subspecialty-specific lexicons, that can be challenging to translate and interpret. There is no 'Rosetta Stone' of clinical medicine such as the genetic code that can assist translation and interpretation of the language of genetics. Nevertheless, the information content embodied within a clinical diagnosis can guide management, therapeutic intervention, and potentially prognostic outlook of disease enabling anticipatory guidance for patients and families. Clinical genomics is now established firmly in medical practice. The granularity and informative content of a personal genome is immense. Yet, we are limited in our utility of much of that personal genome information by the lack of functional characterization of the overwhelming majority of computationally annotated genes in the haploid human reference genome sequence. Whereas DNA and the genetic code have provided a 'Rosetta Stone' to translate genetic variant information, clinical medicine, and clinical genomics provide the context to understand human biology and disease. A path forward will integrate deep phenotyping, such as available in a clinical synopsis in the Online Mendelian Inheritance in Man (OMIM) entries, with personal genome analyses.

Keywords: HPO; SV mutagenesis; family-based genomics; new mutation; quantitative clinical phenotyping; rare variants.

FIGURE 1

Clan genomics and family based rare variant genomic analyses. Different genetic mechanisms for homozygous biallelic variation aggregating at a locus. (a) Family based genomics. Illustrated is a typical pedigree; standard symbols are used with females as circles and males as squares, double horizontal line demarcating consanguinity and filled symbols designating those individuals manifesting trait. Proband only (orange shade background) and quad and trio approach illustrated with background yellow. In accordance with Mendelian expectations for an AR trait, carrier parents with variant alleles at a locus can independently segregate these and in a child at each genetic locus the alleles may become homozygous by aggregating in the personal genome of an affected child. Note if parental consanguinity then homozygosity more likely to occur. New mutations in distant ancestors can be brought to homozygosity through identity-by-descent, IBD (green shade). wt, wildtype or reference allele; DUP, duplication; − / −, mutation with two LoF alleles. (b) Uniparental disomy, UPD, can result in homozygosity for multiple AR trait loci of genes mapping on the same chromosome. It can result in homozygous marker genotypes at a locus when only one parent is a carrier for a variant allele; thus, distorting segregation and Mendelian expectations at loci mapping to the involved chromosome. UPD usually occurs by trisomy to disomy rescue and thus may increase in frequency with maternal age. (c) New mutation deletion CNV at a locus can uncover or ‘unmask’ a recessive trait variant allele: d*, a carrier variant allele inherited from the mother becomes ‘unmasked’ by a de novo deletion CNV mutation at the locus; lightning bolt, new mutation CNV

FIGURE 2

CMT, chromosomal syndromes, genomic disorders, Mendelizing disease traits: contributing genomic variation. A heuristic illustration of the multiple genetic and genomic variant ways a patient may have a CMT distal symmetric polyneuropathy (a) Chromosome 17 (Ch17) karyogram is shown with the dosage sensitive PMP22 gene designated by an asterisk. Specific chromosome abnormalities that have been reported with a CMT phenotype of distal symmetric polyneuropathy (DSP) include: direct duplications, inverted duplication, inherited translocation and de novo translocation. All result in three copies of wild type PMP22. (b) CMT is most often due to inherited or de novo submicroscopic genomic duplication (CMT1A; MIM# 118220), but has also been reported with exon deletion CNV, point mutation (Roa, Garcia, Suter, et al., 1993), biallelic PMP22 T118M allele (Roa, Garcia, Pentao, et al., 1993; Shy et al., 2006), Yuan-Harel-Lupski duplication (YUHAL; MIM# 616652) (Yuan et al., 2015), and Multiple de novo CNV (MdnCNV) (Liu et al., 2017); the latter two mutational mechanisms not illustrated here. (c) Studies in CMT genes including PMP22 (Roa, Garcia, Pentao, et al., 1993; Shy et al., 2006) and EGR2 (Warner et al., 1998) revealed both biallelic and monoallelic variants at the locus associated with AR and AD neuropathy traits, respectively. The PMP22 gene (horizontal rectangle) on two chromosome 17 homologues (horizontal lines); PMP22 T118M recessive DSP trait alleles and combinations of alleles at the CMT1A/HNPP locus.

FIGURE 3

Variant alleles, biallelic AR disease trait genes, triallelic inheritance and mutational burden models. (a) Depicts alleles at a gene locus and a typical biallelic AR trait locus - Stargardt macular dystrophy (STGD1; MIM #248200). Note duplication CNV can result in a triallelic locus and if fully informative may show three distinguishable marker genotypes. Digenic inheritance can have one variant allele at each of two loci OR alternatively be triallelic as described for Bardet Biedl ciliopathy. Note this terminology of ‘triallelic inheritance’ does NOT distinguish which gene/locus has two alleles and which is monoallelic – perhaps a limitation of the nomenclature ‘digenic triallelic’. Moreover, the term is perhaps agnostic to an interpretation of a ‘biallelic AR trait locus and dominant modifier’ (b) Modeling triallelic inheritance in BBS. Note three variant (i.e. mutant) alleles at two BBS loci may be required for BBS manifestations, i.e. penetrance, in some families. (c) A family with BBS. Pedigree analysis and Sanger sequencing of BBS loci documented the mutational burden required in some families for trait manifestation. Evidence for such a potential model has been confirmed with the elucidation and study of additional ‘BBS associated genes’ and variant allele mutation types (Lupski, 2003).

FIGURE 4

Complex Genomic Rearrangements: DUP-TRP-DUP a mutational signature of constitutional and cancer genomes. (a) Patterns observed for duplication – triplication/inversion - duplication, DUP-TRP/INV-DUP on ChX. Array Comparative Genomic Hybridization (aCGH) pattern showing a structural variant copy number pattern DUP-TRP-DUP complex genomic rearrangement (CGR) with multiple copy number transition states, but only two recombinant junctions reflecting two template switches (TS). Red dots represent gain at that specific interrogating oligonucleotide with the extent of the deflection (log ratio of signal) reflecting the copy number gain at the locus: DUP, duplication; TRP, triplication. Black normal diploid copy number. Red horizontal line duplicated genomic interval; blue horizontal line triplicated genomic interval. Below, interpretation of array data and the idealized interpretation of the copy number changes followed by the actual arrangement of the DNA sequence structure (note a, a’ and c, c’ duplicated whilst segment b, b’ triplicated) in DUP-TRP-DUP with two recombinant junctions, jct1 and jct2, shown. (b) Example autosomal genes triplicated by DUP-TRP-DUP; three different chromosome loci and genes triplicated by DUP-TRP-DUP are shown. Right column shows disease trait observed. (c) Disease traits associated with gene triplication. Note the triplication of the alpha synuclein locus SCNA and that of the gene PMP22 in adult-onset Parkinson disease and Charcot-Marie-Tooth disease, respectively. LIS1 (PAFAH1B1) is the gene deleted in 17p13.3 in association with isolated lissencephaly (MIM #607432) (d) The genomic sequence (GS) interpretation of the DUP-TRP-DUP mutational signature in cancer genomes. DUP-TRP-DUP as a mutational signature of SV mutagenesis in the cancer genome was described in 2020 (Li et al., 2020). Interpretive key with relative dosage versus ‘diploid state’ of autosomes. Note duplication of one chromosome, but three copies of locus due to the presence of the other ‘non-rearranged’ autosomal chromosome (Riccardi & Lupski, 2013). Note general CGR structure of DUP-TRP-DUP and the multiple possible orientations of genomic segments that can be derived from just ‘two jumps’; i,e, two TS, multiple possibilities. Right column phenotype observed with somatic mutagenesis; DUP-TRP-DUP is a frequent mutational signature of SV mutagenesis in cancer genomes.

FIGURE 5

Copy number and orientation in Complex Genomic Rearrangements. (a) the proposed model for derivation of DUP-NML-DUP; array CGH as shown in Figure 4. Duplicated genomic segments shown depicted by red horizontal bars. Alu element orientation and direction depicted by arrowheads; filled arrowhead color shows Alu family member according to KEY. Note ‘directionality’ of replicative repair due to TS. (b) Derivation of DUP-TRP/INV-DUP. Note only two TS, but multiple possibilities, Moreover, whether a resultant DUP-NML-DUP or DUP-TRP-DUP there are only two TS postulated and only two breakpoint junctions found. CGR structure also influenced by whether TS occurs between chromatids or chromosome homologues (Carvalho & Lupski, 2016; Carvalho et al., 2015). The orientation of the TS can result in genomic inversion. Whether the TS occurs before or after the migrating replication fork can affect ultimate rearrangement end product outcome and even potentially lead to a rolling circle mechanism and resultant genomic segment amplification (Hastings, Ira, & Lupski, 2009).

FIGURE 6

Birth defects and the compound inheritance gene dosage model. (a) An AD trait may result from a monoallelic null variant allele at a locus resulting in haploinsufficiency. Biallelic null variants may result in lethality due to complete LoF at the locus. Some birth defects may result from gene action below haploinsufficiency, but not complete loss of gene function. (b) Illustrates function and thresholds for phenotypic expression. Note homozygosity for the hypomorphic allele results in no abnormal phenotype. (c) In the compound inheritance gene dosage (CIGD) model, a rare variant null allele at a locus is paired with a common variant noncoding allele; to result in gene action/expression below haploinsufficiency; TBX6 associated congenital scoliosis (TACS) results from hemivertebrae usually involving the lumbar spine (J. Liu et al., 2019). Interestingly, when a non-coding ‘up-expression’ allele, i.e. a hypermorph, is paired with a null allele the vertebral anomalies localize to the cervical spine (Ren et al., 2020). (d) Penetrance of CAKUT, congenital anomalies of the kidney and urinary tract and unilateral renal agenesis, can be related to gene action and gene dosage/expression at the TBX6 locus.

FIGURE 7

Aggregation of multilocus pathogenic variation in a personal genome. (a): interphase FISH molecular diagnostics of BAB1006 (Potocki et al., 1999) revealing a loss of the PMP22 gene (red) on chromosome 17 due to HNPP deletion with a gain of the RAI1 gene (two green dots) on the other chromosome 17 homologue due to PTLS duplication. (b) Horizontal karyogram of Chr17. Note cytogenetic map position of PMP22 (red) in 17p12 and RAI1 (green) in 17p11.2. (c) Southern analysis of three generations of family HOU365. Note the HNPP deletion, as evidenced by the Southern blot visualized HNPP rearrangement junction fragment (HNPP del jct; orange), that is inherited for at least three generations in individuals with operative AD carpal tunnel syndrome. (d) The PTLS duplication (PTLS dup) occurs de novo as evidenced by the appearance of the pulsed field gel electrophoresis (PFGE) junction fragment (jct; orange).

FIGURE 8

Contiguous gene syndromes, CNV, genes and multigenic disease traits. (a) Three physically linked genes: DMD, CGDX, and MCLD and a cytogenetically visible deletion of Xp21.1 in patient BB (Francke, 2013). Below and horizontally is chromosome X karyogram with an expansion of the Xp21.1 locus and physically linked genes for the condition mapped within the deletion interval. (b) The Yuan-Harel-Lupski syndrome (Yuan et al., 2015) (YUHAL; MIM #616652) is caused by, at least, a blended phenotype consisting of two triplosensitive genes, PMP22 and RAI1, linked on one nonrecurrent duplication rearrangement involving chromosome 17, dup17p11.2p12 (red horizontal line); thus, YUHAL could be considered as a multigenic trait. Above chromosome 17 karyogram with physical ‘genomic’ map of 17p12p11.2. Note the green (HNPP del), white, red (PTLS dup) for the personal genome (boxed purple) of BAB#1006; family HOU365 in figure 6. (c) Four physically linked genes, STXBP1, SPTAN1, ENG and TOR1A may be individually or combinatorically deleted in chromosome del9q34.11 syndrome (Campbell et al., 2012).