The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies

Abstract

Down syndrome (DS), or trisomy 21, is a common disorder associated with several complex clinical phenotypes. Although several hypotheses have been put forward, it is unclear as to whether particular gene loci on chromosome 21 (HSA21) are sufficient to cause DS and its associated features. Here we present a high-resolution genetic map of DS phenotypes based on an analysis of 30 subjects carrying rare segmental trisomies of various regions of HSA21. By using state-of-the-art genomics technologies we mapped segmental trisomies at exon-level resolution and identified discrete regions of 1.8-16.3 Mb likely to be involved in the development of 8 DS phenotypes, 4 of which are congenital malformations, including acute megakaryocytic leukemia, transient myeloproliferative disorder, Hirschsprung disease, duodenal stenosis, imperforate anus, severe mental retardation, DS-Alzheimer Disease, and DS-specific congenital heart disease (DSCHD). Our DS-phenotypic maps located DSCHD to a <2-Mb interval. Furthermore, the map enabled us to present evidence against the necessary involvement of other loci as well as specific hypotheses that have been put forward in relation to the etiology of DS-i.e., the presence of a single DS consensus region and the sufficiency of DSCR1 and DYRK1A, or APP, in causing several severe DS phenotypes. Our study demonstrates the value of combining advanced genomics with cohorts of rare patients for studying DS, a prototype for the role of copy-number variation in complex disease.

Fig. 1.

High-resolution analysis of subject Dup21WB. (A) Photograph (age, 4 mos). (B) BAC-FISH analysis indicates duplication of D21S55 (blue) but not MX1/2 (fuchsia). 21, normal HSA21; DER21, rearranged chromosome. The orientation of nonduplicated segments is indicated in red (SOD1) and blue (CD18/ITBG2). (C) Summary of duplication and orientation of segments detected by using 19 FISH and 24 molecular markers. (D) HR-CGH analysis. Displayed are log₂-ratios measured for Dup21WB relative to the control pool along HSA21.

Fig. 2.

Segmental 21 trisomy map for 30 individuals. Patient-IDs are displayed at the top and bottom. Columns to the right, or the only column indicated, represent FISH/Southern results (Table S6 in the SI Appendix, karyotypic features summarized in Table S7 in the SI Appendix). Copy-numbers are indicated by color-coding: orange, 1:2; blue, 2:2; Yellow, 3:2; Dark gray, 3:2. Dark gray with black lines, 1:2. The left columns depict oligonucleotide microarray results (see also Table S1 and Fig. S4 in the SI Appendix). Light gray, 3:2. Medium gray, 4:2. Light gray with black lines, 1:2.

Fig. 3.

Metaanalysis of DS phenotypes. A panel of 30 patients with segmental trisomy 21 defines DS phenotype candidate regions. Purple boxes, presence of phenotype; yellow boxes, no phenotype; solid boxes, increased copy-number; open boxes, 1:2 (monosomies). (A) DSCHD region. Red box, DSCHD candidate region. Twenty-three subjects have duplications including the DSCHD region, 14 thereof have DSCHD. No subject lacking a segmental trisomy involving the DSCHD critical regions was diagnosed with DSCHD. Corresponding regions for 6 mouse models are indicated to the left (, , –41). TOF, tetralogy of Fallot; PS, pulmonic stenosis; PDA, patent ductus arteriosus; VSD, ventricular septal defect; ASD, atrial septal defect; MI, mitral insufficiency. (B) Proposed DSCHD critical region (red box) determined by combining human and mouse data from A. MMU16 indicates the extent of the duplication in the mouse model Dp (16)1Yu with DSCHD. (C) Gut region. Red box, DST candidate region; purple box, IA; orange box, HSCR. (D) AMKL and TMD. Red box, AMKL/TMD candidate region. (E) IQ in segmental trisomy 21. Vertical black bars at the right indicate the regions of segmental trisomy in individuals with IQs indicated above (thicker bars indicate regions of 4 copies). (F) Bayesian probability map of DS phenotype. The probabilities plotted are per gene or partial gene and therefore each data point is the posterior probability that 3 copies of the given gene cause the relevant phenotype. Thus, the posterior probability that a gene influencing a trait is within a larger chromosomal interval is the area under the curve for that interval. For example, for the DSCHD trait, the area under the curve from 41 Mb to 43.35 Mb is 0.9878, which is calculated by adding the values in Table S4C in the SI Appendix for each gene or partial gene located within the interval (see Table S3 in the SI Appendix for further examples). For AMKL/TMD, the first high-probability interval (30.9–31.4 Mb) corresponds to KRTAP genes and the 3′-end of TIAM1 and is thus unlikely to be relevant to the phenotype.